A comparative study of semiempirical, ab initio, and DFT methods in evaluating metal-ligand bond strength, proton affinity, and interactions between first and second shell ligands in Zn-biomimetic complexes

An Update in Computational Methods for Environmental Monitoring: Theoretical Evaluation of the Molecular and Electronic Structures of Natural Pigment-Metal Complexes

Metals are beneficial to life, but the presence of these elements in excessive amounts can harm both organisms and the environment; therefore, detecting the presence of metals is essential. Currently, metal detection methods employ powerful instrumental techniques that require a lot of time and money. Hence, the development of efficient and effective metal indicators is essential. Several synthetic metal detectors have been made, but due to their risk of harm, the use of natural pigments is considered a potential alternative. Experiments are needed for their development, but they are expensive and time-consuming. This review explores various computational methods and approaches that can be used to investigate metal-pigment interactions because choosing the right methods and approaches will affect the reliability of the results. The results show that quantum mechanical methods (ab initio, density functional theory, and semiempirical approaches) and molecular dynamics simulations have been used. Among the available methods, the density functional theory approach with the B3LYP functional and the LANL2DZ ECP and basis set is the most promising combination due to its good accuracy and cost-effectiveness. Various experimental studies were also in good agreement with the results of computational methods. However, deeper analysis still needs to be carried out to find the best combination of functions and basis sets.

GPDOCK: highly accurate docking strategy for metalloproteins based on geometric probability

Accurately predicting the interaction modes for metalloproteins remains extremely challenging in structure-based drug design and mechanism analysis of enzymatic catalysis due to the complexity of metal coordination in metalloproteins. Here, we report a docking method for metalloproteins based on geometric probability (GPDOCK) with unprecedented accuracy. The docking tests of 10 common metal ions with 9360 metalloprotein-ligand complexes demonstrate that GPDOCK has an accuracy of 94.3% in predicting binding pose. What is more, it can accurately realize the docking of metalloproteins with ligand when one or two water molecules are engaged in the metal ion coordination. Since GPDOCK only depends on the three-dimensional structure of metalloprotein and ligand, structure-based machine learning model is employed for the scoring of binding poses, which significantly improves computational efficiency. The proposed docking strategy can be an effective and efficient tool for drug design and further study of binding mechanism of metalloproteins. The manual of GPDOCK and the code for the logistical regression model used to re-rank the docking results are available at https://github.com/wangkai-zhku/GPDOCK.git.

Copper(II) and Zinc(II) Complexes with the Clinically Used Fluconazole: Comparison of Antifungal Activity and Therapeutic Potential

Copper(II) and zinc(II) complexes with clinically used antifungal drug fluconazole (fcz), {[CuCl2(fcz)2].5H2O}n, 1, and {[ZnCl2(fcz)2]·2C2H5OH}n, 2, were prepared and characterized by spectroscopic and crystallographic methods. The polymeric structure of the complexes comprises four fluconazole molecules monodentately coordinated via the triazole nitrogen and two chlorido ligands. With respect to fluconazole, complex 2 showed significantly higher antifungal activity against Candida krusei and Candida parapsilosis. All tested compounds reduced the total amount of ergosterol at subinhibitory concentrations, indicating that the mode of activity of fluconazole was retained within the complexes, which was corroborated via molecular docking with cytochrome P450 sterol 14α-demethylase (CYP51) as a target. Electrostatic, steric and internal energy interactions between the complexes and enzyme showed that 2 has higher binding potency to this target. Both complexes showed strong inhibition of C. albicans filamentation and biofilm formation at subinhibitory concentrations, with 2 being able to reduce the adherence of C. albicans to A549 cells in vitro. Complex 2 was able to reduce pyocyanin production in Pseudomonas aeruginosa between 10% and 25% and to inhibit its biofilm formation by 20% in comparison to the untreated control. These results suggest that complex 2 may be further examined in the mixed Candida-P. aeruginosa infections.

Formation and stability of the mixed-chelator complexes of Sr2+, Mg2+, Ca2+, Ba2+, and Y3+ in solution with bio-relevant chelators

The formation and equilibria of Sr²⁺, Mg²⁺, Ca²⁺, Ba²⁺, and Y³⁺ (M) complexes with a mixed-chelator comprising two biodegradable chelators (GLDA, L_G, 2-[bis(carboxymethyl)amino] pentanedioic acid; HIDS, L_H, 2-(1,2-dicarboxyethylamino)-3-hydroxy-butanedioic acid) in an aqueous matrix was evaluated. The potentiometric measurement results (ionic strength, 0.10 M; temperature, 25 ± 0.1 °C) confirmed the formation of 1:1:1 (M:L_G:L_H) complexes and the experimental data sets were further used to derive the equilibrium constants for the ternary complexes. The [MHL_GL_H]^5- complex was the dominant ternary complex with Sr²⁺, Mg²⁺, Ca²⁺, and Ba²⁺, while Y³⁺ formed [M(OH)₂L_GL_H]^7- as the principal ternary species. The trend in the overall formation constants of the ML_mix (L_mix, L_G:L_H = 1:1) complexes was in the order: Y³⁺ > Ca²⁺ > Mg²⁺ > Sr²⁺ > Ba²⁺. The ternary complexation trend was interpreted using the corresponding atomic radii and solution-phase electronegativities of the elements. The modes of interaction between the chelators and cations in the ML_mix systems were subsequently deduced, and evaluated by using Gaussian 16W program. The relative stabilities of the ternary complexes (ΔlogK) were interpreted by comparison with the stabilities of the corresponding binaries, with negative ΔlogK values observed for all the ML_mix complexes.

Toxin ζ Reduces the ATP and Modulates the Uridine Diphosphate-N-acetylglucosamine Pool

Toxin ζ expression triggers a reversible state of dormancy, diminishes the pool of purine nucleotides, promotes (p)ppGpp synthesis, phosphorylates a fraction of the peptidoglycan precursor uridine diphosphate-N-acetylglucosamine (UNAG), leading to unreactive UNAG-P, induces persistence in a reduced subpopulation, and sensitizes cells to different antibiotics. Here, we combined computational analyses with biochemical experiments to examine the mechanism of toxin ζ action. Free ζ toxin showed low affinity for UNAG. Toxin ζ bound to UNAG hydrolyzed ATP·Mg2+, with the accumulation of ADP, Pi, and produced low levels of phosphorylated UNAG (UNAG-P). Toxin ζ, which has a large ATP binding pocket, may temporally favor ATP binding in a position that is distant from UNAG, hindering UNAG phosphorylation upon ATP hydrolysis. The residues D67, E116, R158 and R171, involved in the interaction with metal, ATP, and UNAG, were essential for the toxic and ATPase activities of toxin ζ; whereas the E100 and T128 residues were partially dispensable. The results indicate that ζ bound to UNAG reduces the ATP concentration, which indirectly induces a reversible dormant state, and modulates the pool of UNAG.

Mononuclear gold(iii) complexes with l-histidine-containing dipeptides: tuning the structural and biological properties by variation of the N-terminal amino acid and counter anion

Gold(iii) complexes with different l-histidine-containing dipeptides, [Au(Gly-l-His-N_A,N_P,N3)Cl]Cl·3H₂O (1a), [Au(Gly-l-His-N_A,N_P,N3)Cl]NO₃·1.25H₂O (1b), [Au(l-Ala-l-His-N_A,N_P,N3)Cl][AuCl₄]·H₂O (2a), [Au(l-Ala-l-His-N_A,N_P,N3)Cl]NO₃·2.5H₂O (2b), [Au(l-Val-l-His-N_A,N_P,N3)Cl]Cl·2H₂O (3), [Au(l-Leu-l-His-N_A,N_P,N3)Cl]Cl (4a) and [Au(l-Leu-l-His-N_A,N_P,N3)Cl][AuCl₄]·H₂O (4b), have been synthesized and structurally characterized by spectroscopic (¹H NMR, IR and UV-vis) and single-crystal X-ray diffraction techniques. The antimicrobial efficiency of these gold(iii) complexes, along with K[AuCl₄] and the corresponding dipeptides, was evaluated against the broad panel of Gram-positive and Gram-negative bacteria and fungi, displaying their moderate inhibiting activity. Moreover, the cytotoxic properties of the investigated complexes were assessed against the normal human lung fibroblast cell line (MRC5) and two human cancer, cervix (HeLa) and lung (A549) cell lines. None of the complexes exerted significant cytotoxic activity; nevertheless complexes that did show selectivity in terms of cancer vs. normal cell lines (2a/b and 4a/b) have been evaluated using zebrafish (Danio rerio) embryos for toxicity and antiangiogenic potential. Although the gold(iii) complexes achieved an antiangiogenic effect comparable to the known angiogenic inhibitors auranofin and sunitinib malate at 30-fold higher concentrations, they had no cardiovascular side effects, which commonly accompany auranofin and sunitinib malate treatment. Finally, binding of the gold(iii) complexes to the active sites of both human and bacterial (Escherichia coli) thioredoxin reductases (TrxRs) was demonstrated by conducting a molecular docking study, suggesting that the mechanism of biological action of these complexes can be associated with their interaction with the TrxR active site.

A new class of platinum(ii) complexes with the phosphine ligand pta which show potent anticancer activity

A series of 16 Pt(ii) complexes with 8-hydroxyquinolines and sulfoxide/phosphine ligands were synthetized, characterized and evaluated for cytotoxic and embryotoxic activity.

The interaction strengths and spectroscopy parameters of the C2H2∙∙∙HX and HCN∙∙∙HX complexes (X = F, Cl, CN, and CCH) and related ternary systems valued by fluxes of charge densities: QTAIM, CCFO, and NBO calculations

This theoretical work exhibits a new systematic study of structural parameters, electronic properties, infrared vibration modes, and molecular topography of hydrogen complexes, namely linear-type HCN⋯HX and T-type C₂H₂⋯HX (X = F, Cl, CN, and CCH). Ideally, the knowledge of the ternary systems of C₂H₂⋯HCN⋯HF and HCN⋯HCN⋯HF whose subparts integrate the linear and T-shaped complexes were used to give support in this current research. By means of computational calculations carried out in both levels B3LYP and MP2, the variations of the HX bond lengths are clearly overestimated in the HCN⋯HX linear complexes. In agreement with the analyses of the electrostatic potentials, the higher intermolecular energies of these complexes agree with the larger red-shifts in the stretch frequencies in HX. Also, the QTAIM descriptors and NBO calculations were used to inspect the interaction strength as well as to confirm the π cloud as a proton accepting center. By taking into account the absorption intensity ratio as a standard parameter to predict the interaction strength and intermolecular characterization, the formalism of the charge-charge flux-overlap modified (CCFO) was applied.

Host-Guest Inclusion Complexes between Amlodipine Enantiomers in the Biphasic Recognition Chiral Extraction System using Tartaric Acid and β-Cyclodextrin Derivatives as Positive Confirmation by using their Enantioselective Extraction

The current work reports an extended theoretical study from our previous experimental work for the enantioselective extraction of amlodipine enantiomers in a biphasic recognition chiral extraction system (BRCES) consisting of hydrophobic D-diisopropyl tartrate dissolved in organic phase (n-decanol) and hydrophilic hydroxypropyl-β-cyclodextrin (HP-β-CD) in aqueous phase (acetate buffer) which preferentially recognize the R-enantiomer and S-enantiomer, respectively. The calculations were simulated using a semi-empirical PM3 method as a part of the Gaussian09 software package and were used to optimize the structures of the hosts, guests, and host-guest complexes in the gas phase without any restrictions. It was found that HP-β-CD has the strongest recognition ability among the three β-CD derivatives studied, namely HP-β-CD, hydroxyethyl-β-cyclodextrin (HE-β-CD), and methylated-β-cyclodextrin (Me-β-CD), due to the large interaction energies (E_comp = −14.3025 kcal/ mol), while D-diisopropyl tartrate has the strongest ability among the four tartaric acid derivatives studied namely; L-diisopropyl tartrate, D-diisopropyl tartrate, L-diethyl tartrate, and D-diethyl tartrate (E_comp = −5.9964 kcal/ mol). The computational calculations for the enantioselective partitioning of amlodipine enantiomers rationalized the reasons for the different behaviors for this extraction. The present theoretical results may be informative to scientists who are devoting themselves to developing models for their experimental parts or for enhancing the hydrophobic drug solubility in drug delivery systems.

Silver(I) complexes with phthalazine and quinazoline as effective agents against pathogenic Pseudomonas aeruginosa strains

Five silver(I) complexes with aromatic nitrogen-containing heterocycles, phthalazine (phtz) and quinazoline (qz), were synthesized, characterized and analyzed by single-crystal X-ray diffraction analysis. Although different AgX salts reacted with phtz, only dinuclear silver(I) complexes of the general formula {[Ag(X-O)(phtz-N)]2(μ-phtz-N,N')2} were formed, X=NO3(-) (1), CF3SO3(-) (2) and ClO4(-) (3). However, reactions of qz with an equimolar amount of AgCF3SO3 and AgBF4 resulted in the formation of polynuclear complexes, {[Ag(CF3SO3-O)(qz-N)]2}n (4) and {[Ag(qz-N)][BF4]}n (5). Complexes 1-5 were evaluated by in vitro antimicrobial studies against a panel of microbial strains that lead to many skin and soft tissue, respiratory, wound and nosocomial infections. The obtained results indicate that all tested silver(I) complexes have good antibacterial activity with MIC (minimum inhibitory concentration) values in the range from 2.9 to 48.0μM against the investigated strains. Among the investigated strains, these complexes were particularly efficient against pathogenic Pseudomonas aeruginosa (MIC=2.9-29μM) and had a marked ability to disrupt clinically relevant biofilms of strains with high inherent resistance to antibiotics. On the other hand, their activity against the fungus Candida albicans was moderate. In order to determine the therapeutic potential of silver(I) complexes 1-5, their antiproliferative effect on the human lung fibroblastic cell line MRC5, has been also evaluated. The binding of complexes 1-5 to the genomic DNA of P. aeruginosa was demonstrated by gel electrophoresis techniques and well supported by molecular docking into the DNA minor groove. All investigated complexes showed an improved cytotoxicity profile in comparison to the clinically used AgNO3.

Monoligand Zn(II) Complexes: Ab Initio Benchmark Calculations and Comparison with Density Functional Theory Methodologies

A systematic theoretical study on several models of Zn(II) complexes has been carried out employing both ab initio correlated wave function and density functional methods. The performance of five different functionals namely PW91, PBE, B3LYP, MPWLYP1M, and TPSS in the prediction of metal-ligand bond distances, binding energies, and proton affinities has been assessed comparing the results to those obtained with the MP2 and CCSD(T) wave function methodologies. Several basis sets ranging from double-ζ up to quintuple-ζ quality have been used, including the recently developed all-electron correlation consistent basis sets for zinc. It is shown that all the tested functionals overestimate both the metal-ligand bond distances and the binding energies, being that the B3LYP and TPSS functionals are the ones that perform the best. An analysis of the metal-ligand interaction energy shows that induction and charge-transfer effects play a prominent role in the bonding of these systems, even for those complexes with the less polarizable ligands. This finding highlights the importance of a correct description of the polarization of the monomers' charge densities by any theoretical method which aims to be applied to the study of Zn(II) complexes.

Synthesis and evaluation of series of diazine-bridged dinuclear platinum(II) complexes through in vitro toxicity and molecular modeling: correlation between structure and activity of Pt(II) complexes

Polynuclear Pt(II) complexes are a novel class of promising anticancer agents with potential clinical significance. A series of pyrazine (pz) bridged dinuclear Pt(II) complexes with general formulas {[Pt(L)Cl]2(μ-pz)}(2+) (L, ethylenediamine, en; (±)-1,2-propylenediamine, 1,2-pn; isobutylenediamine, ibn; trans-(±)-1,2-diaminocyclohexane, dach; 1,3-propylenediamine, 1,3-pd; 2,2-dimethyl-1,3-propylenediamine, 2,2-diMe-1,3-pd) and one pyridazine (pydz) bridged {[Pt(en)Cl]2(μ-pydz)}(2+) complex were prepared. The anticancer potential of these complexes were determined through in vitro cytotoxicity assay in human fibroblasts (MRC5) and two carcinoma cell lines (A375 and HCT116), interaction with double stranded DNA through in vitro assay, and molecular docking study. All complexes inhibited cell proliferation with inhibitory concentrations in the 0.5-120 μM range. While {[Pt(1,3-pd)Cl]2(μ-pz)}(2+) showed improved activity and {[Pt(en)Cl]2(μ-pydz)}(2+) showed comparable activity to that of clinically relevant cisplatin, {[Pt(en)Cl]2(μ-pydz)}(2+) was less toxic in an assay with zebrafish (Danio rerio) embryos, causing no adverse developmental effects. The in vitro cytotoxicity of all diazine-bridged dinuclear Pt(II) complexes is discussed in correlation to their structural characteristics.

Study of the chelating properties of Ge(OH)2 functionality as metal binding group for Zn2+ cation in simplified protease-like environments: a DFT analysis

The development of protease's inhibitors is an active field of research in the pharmaceutical industry. As concerns the design of new inhibitors, the theoretical study of the binding patterns and energies of known metal binding groups (MBGs) toward Zn(2+) using quantum-chemical calculations may offer a better understanding of their interaction models and may be useful for the improvement and design of novel ZBGs. Here the properties of gem-Ge(OH)(2)-based compounds as ZBG were assessed theoretically using DFT calculations. [Zn(Imdz)(2) R - OH(2)](2+) complexes (Imdz =imidazole rings; R = imidazole ring, acetic acid molecule or acetate anion) were used to partially reproduce the coordination sphere in metalloproteases (ACE, amgiotensin converting enzyme, and TLN, thermolysine) being inhibited by related compounds (i.e., silanediols). The MBG- Zn(2+) interaction was analyzed through the energy of the reaction: [Zn(Imdz)(2) R - OH(2)](2+) + L → [Zn(Imdz)(2) R - L](2+) + H(2)O using DFT (M06L/cc-pVDZ) in gas-phase and in solution (IEF-PCM). Although the functional used (M06L) has proven its efficiency to study systems containing transition metal governed by non-covalent interactions, dispersion effects were implemented by the correction of the computed energies using the DFT-D3 program. Accounting for dispersion effects produced a systematic increase of c.a. 13 kJ mol(-1) on the energies, whereas the effect of solvent goes in the opposite direction (i.e., BE under the IEF-PCM model are on average 125 kJ mol(-1) lower). The Ge(OH)(2) - Zn(2+) interaction seems to be similar (or even stronger) than the Si(OH)(2) -Zn(2+). Their better performance as ZBG is explained by the combined NBO-AIM analysis. The results of this work may encourage the preparation, isolation, and experimental assay of the chelating properties of these compounds, which may propose a new family of protease's inhibitors.

Catalytic zinc complexes for phosphate diester hydrolysis

Creating efficient artificial catalysts that can compete with biocatalysis has been an enduring challenge which has yet to be met. Reported herein is the synthesis and characterization of a series of zinc complexes designed to catalyze the hydrolysis of phosphate diesters. By introducing a hydrated aldehyde into the ligand we achieve turnover for DNA-like substrates which, combined with ligand methylation, increases reactivity by two orders of magnitude. In contrast to current orthodoxy and mechanistic explanations, we propose a mechanism where the nucleophile is not coordinated to the metal ion, but involves a tautomer with a more effective Lewis acid and more reactive nucleophile. This data suggests a new strategy for creating more efficient metal ion based catalysts, and highlights a possible mode of action for metalloenzymes.

Spectroscopic, colorimetric and theoretical investigation of salicylidene hydrazine based reduced Schiff base and its application towards biologically important anions

A reduced Schiff base anionic receptor 1 [N,N'-bis-(2-hydroxy-5-nitro-benzyl)hydrazine] has been synthesized, characterized and reported as a selective chromogenic receptor for fluoride, acetate and phosphate anions over the other tested anions such as chloride, bromide, iodide and hydrogensulphite. Colorimetric naked-eye detection and UV-vis absorption spectroscopic techniques were used to distinguish the recognition behaviours towards various anions. The receptor-anion complexation mainly occurs via hydrogen bonding interactions which facile to generate the charge transfer band in the UV-vis spectra and cause large bathochromic shift as well as naked-eye colour change. Complexation stoichiometry, binding constant and free energy change due to complex formation were determined from Benesi-Hildebrand plot. The binding constant and the free energy change values are well interactive for spontaneous complexation. The experimental results have been correlated with the theoretical calculations using B3LYP hybrid functional and 6-311++G(d,p) basis set for both the receptor and complex by Density Functional Theory (DFT) method.

Tuning the photophysical properties of pyrene-based systems: a theoretical study

Recently new molecular systems based on the pyrene moiety were developed for photovoltaic applications. Here we present the results of a quantum chemical study focused on the effects induced by some different substituents on the electronic properties of pyrene, to obtain general hints for the molecular design of new pyrene-based systems. In particular, a series of electron-donating (hydroxy, amino, acetylamino) and electron-withdrawing (cyano, carbamoyl, formyl, ethynyl, ethenyl) groups were considered. Furthermore, in addition to the single pyrene molecule, two pyrene units linked by ethenylene, ethynylene, 2,5-thienylene, and ethynylene-p-phenylene containing chains of different lengths were taken into account. For all of the model structures presented, the ground state geometries have been optimized using the density functional approach, while the vertical transition energies were calculated using the time-dependent density functional theory. We will show that the tuning of the lowest electronic excitation energy (i.e., the HOMO-LUMO energy gap) as well as the localization of the spatial distributions of the frontier molecular orbitals (i.e., the nature of the electron-hole pair, generated by photon absorption) can be obtained through the analysis of the pyrene frontier molecular orbitals. This approach allows to evaluate the most suitable position of the substituents on the pyrene moiety giving rise to enhanced electronic effects also in function of their electronic nature. In this way, pyrene-structures with tailored electronic properties could be modeled. Our screening shows that promising candidates for photovoltaic applications could be molecular structures formed by two pyrene units joined/linked by a short conjugated bridge containing double or triple bonds (henceforth pyrene-linked dimers). As far as the single pyrene units are considered, the most significant reduction of the transition energy of the lowest optical electronic excitation is obtained with disubstituted pyrenes with push-pull character.

Energies, Geometries, and Charge Distributions of Zn Molecules, Clusters, and Biocenters from Coupled Cluster, Density Functional, and Neglect of Diatomic Differential Overlap Models

We present benchmark databases of Zn-ligand bond distances, bond angles, dipole moments, and bond dissociation energies for Zn-containing small molecules and Zn coordination compounds with H, CH3, C2H5, NH3, O, OH, H2O, F, Cl, S, and SCH3 ligands. The test set also includes clusters with Zn-Zn bonds. In addition, we calculated dipole moments and binding energies for Zn centers in coordination environments taken from zinc metalloenzyme X-ray structures, representing both structural and catalytic zinc centers. The benchmark values are based on relativistic-core coupled cluster calculations. These benchmark calculations are used to test the predictions of four density functionals, namely B3LYP and the more recently developed M05-2X, M06, and M06-2X levels of theory, and six semiempirical methods, including neglect of diatomic differential overlap (NDDO) calculations incorporating the new PM3 parameter set for Zn called ZnB, developed by Brothers and co-workers, and the recent PM6 parametrization of Stewart. We found that the best DFT method to reproduce dipole moments and dissociation energies of our Zn compound database is M05-2X, which is consistent with a previous study employing a much smaller and less diverse database and a much larger set of density functionals. Here we show that M05-2X geometries and single-point coupled cluster calculations with M05-2X geometries can also be used as benchmarks for larger compounds, where coupled cluster optimization is impractical, and in particular we use this strategy to extend the geometry, binding energy, and dipole moment databases to additional molecules, and we extend the tests involving crystal-site coordination compounds to two additional proteins. We find that the most predictive NDDO methods for our training set are PM3 and MNDO/d. Notably, we also find large errors in B3LYP for the coordination compounds based on experimental X-ray geometries.