Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes

Metal complexes featuring a quinazoline schiff base ligand and glycine: synthesis, characterization, DFT and molecular docking analyses revealing their potent antibacterial, anti-helicobacter pylori, and Anti-COVID-19 activities

Mixed ligand complexes of manganese(II), cobalt(II), copper(II), and cadmium(II)with an innovative Schiff base ligand denoted as (L1), 4-(2-((1E,2E)-1-(2-(p-tolyl)hydrazineylidene)propan-2-ylidene)hydrazineyl), served as the principal ligand, while glycine (L2) was employed as secondary ligand were successfully effectively characterized through a comprehensive set of analyses, including Elemental analysis, UV-Visible, FT-IR, Mass spectra, and conductometric measurements. Density functional theory (DFT) computations were executed to discern the enduring electronic arrangement, the energy gap, dipole moment and chemical hardness of the hybrid ligand assemblies. The proposed geometry for the complexes is a distorted octahedral structure. The antimicrobial efficacy of these compounds was assessed against a range of bacterial and fungal strains. Notably, these complexes exhibited promising antimicrobial activities, with the cadmium (II) complex demonstrating superior efficacy towards all tested organisms. These compounds were also examined for their antibiotic properties against H. pylori to explore their broader medical potential. The Schiff base ligand and its corresponding metal complexes displayed substantial potential as an antibiotic against H. pylori. Additionally, the antitumor potential of the synthesized complexes was assessed against MCF-7 (Breast carcinoma) cells-the Cu (II) complex demonstrated superior activity with the lowest IC50 value compared to cisplatin. Moreover, it exhibited reduced cytotoxicity towards normal cells (VERO cells) compared to cisplatin, establishing it as the most potent compound in the study. Furthermore, molecular docking was explored of the Schiff base ligand and its corresponding cadmium(II) complex. The analysis of the docking study yielded valuable structural insights that can be effectively utilized in conducting inhibition studies for example against COVID-19. This comprehensive study highlights these synthesized compounds' multifaceted applications and promising bioactive properties.

Density functional theory methods applied to homogeneous and heterogeneous catalysis: a short review and a practical user guide

The application of density functional theory (DFT) methods in catalysis has been growing fast in the last few decades thanks to both the availability of more powerful high computing resources and the development of new efficient approximations and approaches. DFT calculations allow for the understanding of crucial catalytic aspects that are difficult or even impossible to access by experiments, thus contributing to faster development of more efficient and selective catalysts. Depending on the catalytic system and properties under investigation, different approaches should be used. Moreover, the reliability of the obtained results deeply depends on the approximations involved in both the selected method and model. This review addresses chemists, physicists and materials scientists whose interest deals with the application of DFT-based computational tools in both homogeneous catalysis and heterogeneous catalysis. First, a brief introduction to DFT is presented. Then, the main approaches based on atomic centered basis sets and plane waves are discussed, underlining the main differences, advantages and limitations. Eventually, guidance towards the selection of the catalytic model is given, with a final focus on the evaluation of the energy barriers, which represents a crucial step in all catalytic processes. Overall, the review represents a rational and practical guide for both beginners and more experienced users involved in the wide field of catalysis.

High-entropy halide perovskite single crystals stabilized by mild chemistry

Although high-entropy materials are excellent candidates for a range of functional materials, their formation traditionally requires high-temperature synthetic procedures of over 1,000 °C and complex processing techniques such as hot rolling1-5. One route to address the extreme synthetic requirements for high-entropy materials should involve the design of crystal structures with ionic bonding networks and low cohesive energies. Here we develop room-temperature-solution (20 °C) and low-temperature-solution (80 °C) synthesis procedures for a new class of metal halide perovskite high-entropy semiconductor (HES) single crystals. Due to the soft, ionic lattice nature of metal halide perovskites, these HES single crystals are designed on the cubic Cs2MCl6 (M=Zr4+, Sn4+, Te4+, Hf4+, Re4+, Os4+, Ir4+ or Pt4+) vacancy-ordered double-perovskite structure from the self-assembly of stabilized complexes in multi-element inks, namely free Cs+ cations and five or six different isolated [MCl6]2- anionic octahedral molecules well-mixed in strong hydrochloric acid. The resulting single-phase single crystals span two HES families of five and six elements occupying the M-site as a random alloy in near-equimolar ratios, with the overall Cs2MCl6 crystal structure and stoichiometry maintained. The incorporation of various [MCl6]2- octahedral molecular orbitals disordered across high-entropy five- and six-element Cs2MCl6 single crystals produces complex vibrational and electronic structures with energy transfer interactions between the confined exciton states of the five or six different isolated octahedral molecules.

Reliability of computed molecular structures

When the structures of 1342 molecules are optimized by 30 methods and 7 basis sets, there appear 289 (21.54%) problematic molecules and 112 (8.35%) failed ones. When 278 problematic molecules are compared, the best methods are BHandH and LC-wPBE, while B97D, BP86, HFS, VSXC, and HCTH are very unreliable. When 179 problematic molecules are computed with larger basis sets, the smallest mean absolute deviation (MAD) of bond angle (2.3°) is shown by QCISD(T)/cc-pVTZ, while the smallest MAD of bond length (0.021 Å), the best SUM1 (4.9 unit), and the best SUM2 (2.4 unit) are shown by DSDPBEP86(Full), DSDPBEP86, PBE1PBE-D3, MP2, and MP2(Full) in combination with aug-cc-pVQZ, cc-pVQZ, Def2QZVP, Def2TZVPP, and/or 6-311++G(3df,3pd). Very large basis sets, for example, larger than cc-pVTZ usually have to be used to obtain very good structures and the performances of many density-functional theory methods are encouraging. The best results may be the limit of modern computational chemistry.

A comparison of computational methodologies for the structural modelling of biologically relevant zinc complexes

The impact of a variety of modern computational methods on the structure of biologically relevant zinc complexes is studied. Different density functionals and a Hartree-Fock-based method, scalar-relativistic effects, and basis set integration grid choices, among others, are assessed for set of high-resolution crystallographic structures. While a previous study recommends incorporating relativistic effects into density functional theory calculations in order to improve the accuracy of obtained geometries for small Zn(II) coordination compounds, we show that, for the set in study, relativistic effects do not affect the geometries to a significant extent. The PBEh-3c composite method emerges as good alternative for the treatment of Zn(II) complexes, while the HF-3c method can be employed when computational efficiency is important. Graphical Abstract Which methods are best suited for the computation of Zn(II) bioligand complexes?

A benchmark for the size of the QM system required for accurate hybrid QM/MM calculations on the metal site of the protein copper, zinc superoxide dismutase

The protein superoxide dismutase 1 (SOD1) is a copper and zinc-binding protein that has been implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS). The Zn(II) binding to SOD1 is critical for the stability of the protein, and has been by itself implicated in ALS pathogenesis. Hence, the quantum mechanical (QM) study of the Zn(II)-site of SOD1 is relevant for understanding ALS. The hybrid QM-molecular mechanics (QM/MM) approach commonly employed for the QM study of proteins is highly dependent on the size of the sub-system treated quantum-mechanically. The size of the QM system also determines the computational feasibility of a given method. In the present work, we compare optimized geometries for the metal site and Zn(II) dissociation energies obtained with a QM/MM methodology employing different sizes for the QM sub-system. We find that geometries converge rapidly to RMSDs of around 0.3 Å, and fails to converge further, while a QM system of 480 atoms was required for converging the Zn(II) interaction energy of SOD1 to within 5 kcal*mol^-1, and a 611-atoms QM system for a 1 kcal*mol^-1 convergence with respect to our reference, 1280 QM-atoms system. Graphical Abstract The size of the QM system is critical for both the accuracy and the computational cost of a QM/MM calculation. We have identified a optimum balance for the study of the active site of the coppper, zinc superoxide dismutase.

An efficient protocol for computing the pKa of Zn-bound water

We present an efficient and accurate method for computing absolute pK_w values in Zn²⁺ complexes.

[(H2O)Zn(Imidazole)n]2+: the vital roles of coordination number and geometry in Zn–OH2 acidity and catalytic hydrolysis

The Zn(ii)–(Imidazole(ate))_n coordination motif occurs in numerous biochemical systems, including carbonic anhydrase and the matrix metalloproteinases (MMPs).

Modeling σ-Bond Activations by Nickel(0) Beyond Common Approximations: How Accurately Can We Describe Closed-Shell Oxidative Addition Reactions Mediated by Low-Valent Late 3d Transition Metal?

Accurate modelings of reactions involving 3d transition metals (TMs) are very challenging to both ab initio and DFT approaches. To gain more knowledge in this field, we herein explored typical σ-bond activations of H-H, C-H, C-Cl, and C-C bonds promoted by nickel(0), a low-valent late 3d TM. For the key parameters of activation energy (ΔE^‡) and reaction energy (ΔE_R) for these reactions, various issues related to the computational accuracy were systematically investigated. From the scrutiny of convergence issue with one-electron basis set, augmented (A) basis functions are found to be important, and the CCSD(T)/CBS level with complete basis set (CBS) limit extrapolation based on augmented double-ζ and triple-ζ basis pair (ADZ and ATZ), which produces deviations below 1 kcal/mol from the reference, is recommended for larger systems. As an alternative, the explicitly correlated F12 method can accelerate the basis set convergence further, especially after its CBS extrapolations. Thus, the CCSD(T)-F12/CBS(ADZ-ATZ) level with computational cost comparable to the conventional CCSD(T)/CBS(ADZ-ATZ) level, is found to reach the accuracy of the conventional CCSD(T)/A5Z level, which produces deviations below 0.5 kcal/mol from the reference, and is also highly recommendable. Scalar relativistic effects and 3s3p core-valence correlation are non-negligible for achieving chemical accuracy of around 1 kcal/mol. From the scrutiny of convergence issue with the N-electron basis set, in comparison with the reference CCSDTQ result, CCSD(T) is found to be able to calculate ΔE^‡ quite accurately, which is not true for the ΔE_R calculations. Using highest-level CCSD(T) results of ΔE^‡ in this work as references, we tested 18 DFT methods and found that PBE0 and CAM-B3LYP are among the three best performing functionals, irrespective of DFT empirical dispersion correction. With empirical dispersion correction included, ωB97XD is also recommendable due to its improved performance.

Density Functional Theory Study of Atomic Layer Deposition of Zinc Oxide on Graphene

The dissociation of zinc ions (Zn(2+)) from vapor-phase zinc acetylacetonate, Zn(C5H7O2)2, or Zn(acac)2 and its adsorption onto graphene oxide via atomic layer deposition (ALD) were studied using a quantum mechanics approach. Density functional theory (DFT) was used to obtain an approximate solution to the Schrödinger equation. The graphene oxide cluster model was used to represent the surface of the graphene film after pre-oxidation. In this study, the geometries of reactants, transition states, and products were optimized using the B3LYB/6-31G** level of theory or higher. Furthermore, the relative energies of the various intermediates and products in the gas-phase radical mechanism were calculated at the B3LYP/6-311++G** and MP2/6-311 + G(2df,2p) levels of theory. Additionally, a molecular orbital (MO) analysis was performed for the products of the decomposition of the Zn(acac)2 complex to investigate the dissociation of Zn(2+) and the subsequent adsorption of H atoms on the C5H7O2 cluster to form acetylacetonate enol. The reaction energies were calculated, and the reaction mechanism was accordingly proposed. A simulation of infrared (IR) properties was performed using the same approach to support the proposed mechanism via a complete explanation of bond forming and breaking during each reaction step.

Evolution of Zinc Oxide Nanostructures Grown on Graphene by Ultrasonic Spray Pyrolysis and Its Statistical Growth Modelling

The evolution of zinc oxide nanostructures grown on graphene by alcohol-assisted ultrasonic spray pyrolysis was investigated. The evolution of structures is strongly depended on pyrolysis parameters, i.e., precursor molarity, precursor flow rate, precursor injection/deposition time, and substrate temperature. Field-effect scanning electron microscope analysis, energy dispersive X-ray spectroscopy, X-ray diffraction, and transmission electron microscopy were used to investigate the properties of the synthesized nanostructures and to provide evidence for the structural changes according to the changes in the pyrolysis parameters. The optimum parameters to achieve maximum density and well-defined hexagonally shaped nanorods were a precursor molarity of 0.2 M, an injection flow rate of 6 ml/min, an injection time of 10 min, and a substrate temperature of 250-355 °C. Based on the experimental results, the response surface methodology (RSM) was used to model and optimize the independent pyrolysis parameters using the Box-Behnken design. Here, the responses, i.e., the nanostructure density, size, and shape factor, are evaluated. All of the computations were performed using the Design-Expert software package. Analysis of variance (ANOVA) was used to evaluate the results of the model and to determine the significant values for the independent pyrolysis parameters. The evolution of zinc oxide (ZnO) structures are well explained by the developed modelling which confirms that RSM is a reliable tool for the modelling and optimization of the pyrolysis parameters and prediction of nanostructure sizes and shapes.

The influence of zinc(ii) on thioredoxin/glutathione disulfide exchange: QM/MM studies to explore how zinc(ii) accelerates exchange in higher dielectric environments

QM/MM calculations on thiolate disulfide exchange reveal that a polar, 4-centered, cyclic transition state is formed when Zn(ii) is present, helping to explain faster exchange rates in higher dielectric solvents for metal-assisted exchange.

Theoretical study on the chemical mechanism of enoyl-CoA hydratase and the form of inhibitor binding

Enoyl-CoA hydratase (ECH) catalyzes the second step in the vital β-oxidation pathway of fatty acid metabolism. This enzyme catalyzes the syn-addition of a water molecule across the double bond of 4-(N,N-dimethylamino) cinnamoyl-CoA (DAC-CoA). In this work, the reaction mechanisms of ECH were investigated using the density functional theory (DFT) methods. The different protonation states in which the important residues Glu164 and Glu144 are either neutral or ionized were considered. Four models of the active site were designed based on the X-ray crystal structure of the enzyme. The calculations gave strong support to the proposed mechanism and confirmed that both Glu164 and Glu144 are in a deprotonated state in the reaction mechanism of ECH. In addition, we constructed a model of the active site with the inhibitor acetoacetyl-CoA based on the crystal structure. Caomparison of the calculated energy barriers showed that binding of the keto-enol form of the inhibitor is more reasonable than that of the di-keto form in the inhibition process. Moreover, acetoacetyl-CoA was found to exhibit a keto-enol tautomerism when it acts as an inhibitor in the reaction. The present theoretical results indicated that both residues Glu164 and Glu144 are unprotonated in ECH with the substrate bound, while only Glu164 is unprotonated when the inhibitor binds ECH.

Novel (cyanamide)ZnIIcomplexes and zinc(ii)-mediated hydration of the cyanamide ligands

The Zn^II-mediated hydration of cyanamides does not require any co-catalyst.

COMPARATIVE INVESTIGATION OF THE EFFECT OF TYPE OF DENSITY FUNCTIONAL IN THE DETERMINATION OF GEOMETRICAL PARAMETERS IN A Cu COMPLEX

The effects of short-range electron correlation, long-range electron exchange, local and nonlocal parts of density, higher order gradients of density, and adding some percentage of Hartree–Fock exchange to the functional on the prediction of geometrical parameters were investigated. A copper complex namely 1,2-bis(1,4,7-triaza-1-cyclononyl) ethane copper (II) with Jahn–Teller distortion in octahedral geometry was used to evaluate the performance of 50 commonly available density functionals. The standard 3-21G basis set was used for all light elements, while pseudo potential LANL2DZ was used for the copper atom. The best bond lengths and bond angles were obtained using M05-2x and OP functionals respectively. Also in order to more accurate survey the performance of B3LYP, we used this functional with two all-electron basis sets (6-31G and 3-21G) and three basis sets involving effective core potentials (LANL2DZ/3-21G, LANL2DZ, and LACVP).

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes

In this study, a set of 50 transition-metal complexes of Cu(I) and Cu(II), were used in the evaluation of 18 density functionals in geometry determination. In addition, 14 different basis sets were considered, including four commonly used Pople's all-electron basis sets; four basis sets including popular types of effective-core potentials: Los Alamos, Steven-Basch-Krauss, and Stuttgart-Dresden; and six triple-ζ basis sets. The results illustrate the performance of different methodological alternatives for the treatment of geometrical properties in relevant copper complexes, pointing out Double-Hybrid (DH) and Long-range Correction (LC) Generalized Gradient Approximation (GGA) methods as better descriptors of the geometry of the evaluated systems. These however, are associated with a computational cost several times higher than some of the other methods employed, such as the M06 functional, which has also demonstrated a comparable performance. Regarding the basis sets, 6-31+G(d) and 6-31+G(d,p) were the best performing approaches. In addition, the results show that the use of effective-core potentials has a limited impact, in terms of the accuracy in the determination of metal-ligand bond-lengths and angles in our dataset of copper complexes. Hence, these could become a good alternative for the geometrical description of these systems, particularly CEP-121G and SDD basis sets, if one is considering larger copper complexes where the computational cost could be an issue.

COMPARATIVE QUANTUM STUDY ON TERT-BUTYL RADICAL AND CATION

Detailed comparative analysis of properties of the tert-butyl radical and cation is performed using 14 density functional (DFT) methods combined with double-zeta and triple-zeta quality Gaussian basis sets with polarization and diffuse functions. Stability of different conformers is discussed. Structural parameters, dipole moment, adiabatic ionization potential (IP), inversion barrier and isotropic hyperfine coupling constants are examined and compared to values obtained at the standard MP2 level and to experimental data available. All methods indicate that that the CC bond in the radical is longer than in the cation by about 0.033 Å. The IP values are found to be very sensitive to the method used and range from 612 to 709 kJ/mol, but majority oscillate around 646÷656 kJ/mol. Calculated inversion barrier for the radical is higher than the experimental estimate of 2.68 kJ/mol; with the 6-311++G** basis set and most DFT methods it is predicted in the range 3.86÷4.82 kJ/mol. All DFT methods predict for the out-of-plane CC3 bending mode of the radical the frequency around 260 cm-1, while in the cation the corresponding frequency is higher by about 180 cm-1.

Synthesis, structure, and physical properties for a series of trigonal bipyramidal M(II)-Cl complexes with intramolecular hydrogen bonds

A series of transition metal chloro complexes with the tetradentate tripodal tris(2-amino-oxazoline)amine ligand (TAO) have been synthesized and characterized. X-Ray structural analyses of these compounds demonstrate the formation of the mononuclear complexes [M(II)(TAO)(Cl)](+), where M(II) = Cr, Mn, Fe, Co, Ni, Cu and Zn. These complexes exhibit distorted trigonal-bipyramidal geometry, coordinating the metal through an apical tertiary amine, three equatorial imino nitrogen atoms, and an axial chloride anion. All the complexes possess an intramolecular hydrogen-bonding (H-bonding) network within the cavity occupied by the metal-bound chloride ion. The metal-chloride bond distances are atypically long, which is attributed to the effects of the H-bonding network. Nuclear magnetic resonance (NMR) spectroscopy of the Zn complex suggests that the solid-state structures are representative of that observed in solution, and that the H-bonding interactions persist as well. Additionally, density functional theory (DFT) calculations were carried out to probe the electronic structures of the complexes.

Phosphate mono- and diesterase activities of the trinuclear zinc enzyme nuclease P1--insights from quantum chemical calculations

Nuclease P1 is a trinuclear zinc enzyme that catalyzes the hydrolysis of single-stranded DNA and RNA. Density functional calculations are used to elucidate the reaction mechanism of this enzyme with a model of the active site designed on the basis of the X-ray crystal structure. 2-Tetrahydrofuranyl phosphate and methyl 2-tetrahydrofuranyl phosphate substrates are used to explore the phosphomonoesterase and phosphodiesterase activities of this enzyme, respectively. The calculations reveal that for both activities, a bridging hydroxide performs an in-line attack on the phosphorus center, resulting in inversion of the configuration. Simultaneously, the P-O bond is cleaved, and Zn2 stabilizes the negative charge of the leaving alkoxide anion and assists its departure. All three zinc ions, together with Arg48, provide electrostatic stabilization to the penta-coordinated transition state, thereby lowering the reaction barrier.

ALD growth characteristics of ZnS films deposited from organozinc and hydrogen sulfide precursors

Growth characteristics of zinc sulfide thin films deposited from dialkylzinc and H(2)S reactants by the atomic layer deposition technique have been investigated by quantum chemical methods. The steady-state growth of the films was simulated by studying the reaction of the Zn precursor with the hydrogenated sulfur-terminated (111) surface of zincblende ZnS and then by investigating the chemisorption of hydrogen sulfide on the surface formed by the metal exposure. The behavior of the dissociatively chemisorbed Zn precursors on the growth surface is of particular significance for the film deposition process, since the film growth is limited by the Zn deposition step. Hydrogen sulfide exposure results in the replacement of the surface alkyl groups by SH surface species, whose vibrational features are useful in the experimental verification of the developed growth mechanisms.