Evaluation of DFT methods for predicting geometries and NMR spectra of Bi(III) dithiocarbamate complexes with antitumor properties

CONTEXT

Bismuth complexes with dithiocarbamate ligands have attracted attention because of their biological applications, such as antimicrobial, antileishmanial, and anticancer properties. These complexes have high cytotoxic activity against cancer cells, being more active than the standard drugs cisplatin, doxorubicin, and tamoxifen. In the present study, we investigated the ability of some DFT methods to reproduce the geometries and NMR spectra of the Bi(III) dithiocarbamate complexes, selected based on their proven antitumor activity. Our investigation revealed that the M06-L/def2-TZVP/ECP/CPCM method presented good accuracy in predicting geometries, while the TPSSh/def2-SVP/ECP/CPCM method proved effective in analyzing the 13C NMR spectra of these molecules. In general, all examined methods exhibited comparable performance in predicting 1H NMR signals.

METHODS

Calculations were performed with the Gaussian 09 program using the def2-SVP and def2-TZVP basis sets, employing relativistic effective core potential (ECP) for Bi and using the CPCM solvent model. The exchange-correlation functionals BP86, PBE, OLYP, M06-L, B3LYP, B3LYP-D3, M06-2X, TPSSh, CAM-B3LYP, and ωB97XD were used in the study. Geometry optimizations were started from crystallographic structures available at the Cambridge Structural Database. The theoretical results were compared with experimental data using the mean root-mean-square deviation (RMSD), mean absolute deviations (MAD), and linear correlation coefficient (R2).

Combined Machine Learning, Computational, and Experimental Analysis of the Iridium(III) Complexes with Red to Near-Infrared Emission

Various coordination complexes have been the subject of experimental and theoretical studies in recent decades because of their fascinating photophysical properties. In this work, a combined experimental and computational approach was applied to investigate the optical properties of monocationic Ir(III) complexes. An interpretative machine learning-based quantitative structure-property relationship (ML/QSPR) model was successfully developed that could reliably predict the emission wavelength of the Ir(III) complexes and provide a foundation for the theoretical evaluation of the optical properties of Ir(III) complexes. A hypothesis was proposed to explain the differences in the emission wavelengths between structurally different individual Ir(III) complexes. The efficacy of the developed model was demonstrated by high R2 values of 0.84 and 0.87 for the training and test sets, respectively. It is worth noting that a relationship between the N-N distance in the diimine ligands of the Ir(III) complexes and emission wavelengths is detected. This effect is most probably associated with a degree of distortion in the octahedral geometry of the complexes, resulting in a perturbed ligand field. This combined experimental and computational approach shows great potential for the rational design of new Ir(III) complexes with the desired optical properties. Moreover, the developed methodology could be extended to other transition-metal complexes.

Molecular docking and simulation studies of some pyrazolone-based bioactive ligands targeting the NF-κB signaling pathways

NF-κB has become a predominant regulator responsible for multiple physiological and pathological processes. NF-κB signaling pathway has canonical and non-canonical components which strategize the cancer-related metabolic processes. Non-canonical NF-κB pathways are known to contribute towards the chemoresistance of cancer cells. Consequently, NF-κB can be utilized as a potential therapeutic target for modifying the behaviour of tumor cells. In view of this, we herein report a series of pyrazolone-based bioactive ligands that potentially target NF- κB and, thereby, unveil their anticancer properties. The pharmacological screening of the synthesized compounds were carried out using various virtual screening techniques. The anticancer studies of synthesized pyrazolones showed that APAU exhibited the most potent effect against the MCF-7 cells with an IC₅₀ value of 30 μg/ml. Molecular docking studies revealed that the pyrazolones inhibited cell proliferation by targeting the NFκB signaling pathway. The molecular dynamics simulation studies predicted the stability and flexibility of pyrazolone-based bioactive ligands.

Antiproliferative studies of transition metal chelates of a pyrazolone based hydrazone derivative

Pyrazolone derivatives play a significant role in the treatment of cancer. The synergic effect which emerges from the combination of pyrazolone moiety with hydrazone functionality was investigated. The objective of this study was to explore the antiproliferative potential of copper(II), cobalt(II), nickel(II) and zinc(II) metal chelates synthesized from pyrazolone based hydrazone derivative. The ligand and the metal chelates were characterized by various spectroscopic and analytical studies. The ligand was characterized by single crystal X-ray diffraction analysis.The results were in line with the spectroscopic methods. The geometry optimization of ligand and metal chelates were performed using density functional theory (DFT). The invitro cytotoxicity of ligand and metal chelates against different cancer cell lines was investigated by MTT assay. The cell-viability experiments showed that copper(II) complex is an efficient cytotoxic agent against HeLa cell line. Moreover, possible inhibition mechanism of synthesized compounds was evaluated in silico against HPV16-E6 receptor.Communicated by Ramaswamy H. Sarma.

Water-soluble dinuclear iridium(III) and ruthenium(II) bis-terdentate complexes: photophysics and electrochemiluminescence

The synthesis, photophysics, and electrochemiluminescence (ECL) of four water-soluble dinuclear Ir(III) and Ru(II) complexes (1-4) terminally-capped by 4'-phenyl-2,2':6',2''-terpyridine (tpy) or 1,3-di(pyrid-2-yl)-4,6-dimethylbenzene (N^C^N) ligands and linked by a 2,7-bis(2,2':6',2''-terpyridyl)fluorene with oligoether chains on C9 are reported. The impact of the tpy or N^C^N ligands and metal centers on the photophysical properties of 1-4 was assessed by spectroscopic methods including UV-vis absorption, emission, and transient absorption, and by time-dependent density functional theory (TDDFT) calculations. These complexes exhibited distinct singlet and triplet excited-state properties upon variation of the terminal-capping terdentate ligands and the metal centers. The ECL properties of complexes 1-3 with better water solubility were investigated in neutral phosphate buffer solutions (PBS) by adding tripropylamine (TPA) as a co-reactant, and the observed ECL intensity followed the descending order of 3 > 1 > 2. Complex 3 bearing the [Ru(tpy)₂]²⁺ units displayed more pronounced ECL signals, giving its analogues great potential for further ECL study.

Metal Complexes as DNA Synthesis and/or Repair Inhibitors: Anticancer and Antimicrobial Agents

Medicinal inorganic chemistry involving the utilization of metal-based compounds as therapeutics has become a field showing distinct promise. DNA and RNA are ideal drug targets for therapeutic intervention in the case of various diseases, such as cancer and microbial infection. Metals play a vital role in medicine, with at least 10 metals known to be essential for human life and a further 46 nonessential metals having been involved in drug therapies and diagnosis. These metal-based complexes interact with DNA in various ways, and are often delivered as prodrugs which undergo activation in vivo. Metal complexes cause DNA crosslinking, leading to the inhibition of DNA synthesis and repair. In this review, the various interactions of metal complexes with DNA nucleic acids, as well as the underlying mechanism of action, were highlighted. Furthermore, we also discussed various tools used to investigate the interaction between metal complexes and the DNA. The tools included in vitro techniques such as spectroscopy and electrophoresis, and in silico studies such as protein docking and density-functional theory that are highlighted for preclinical development.

Zirconium (IV)-3-hydroxy-2-tolyl-4H-chromen-4-one complex-the analytical and DFT studies

Trace determination of Zr(IV) was carried out by its complexation with a newly synthesized chromone derivative, 3-hydroxy-2-tolyl-4H-chromen-4-one (HToC) for the formation of a 1:4 (M:L) yellow-colored complex from the bicarbonate medium maintained at pH 7.90-8.13. The complex was extractable into the non-aqueous organic solvents showing maximum and stable color intensity in dichloromethane in the wavelength range 414-430 nm. The complex obeyed Beer's law showing linearity of calibration curve in the range 0.0-1.1 µg Zr(IV) ml^-1 with an optimum range of determination as 0.44-1.0 ppm Zr(IV) detected from the Ringbom plot. Molar absorptivity, specific absorptivity, and Sandell's sensitivity of thus prepared complex were ascertained, respectively as 4.1971 × 10⁴ l mol^-1 cm^-1, 0.4601 ml g^-1 cm^-1, and 0.0022 µg Zr(IV) cm^-2 at 420 nm. The linear regression equation being [Formula: see text] (Y = absorbance, X = µg Zr(IV) ml^-1) with the correlation coefficient of 0.9977 and detection limit of the procedure as 0.0729 µg ml^-1. Theoretical calculations were used to determine and compare structural and bonding properties of the Zr(IV)-HToC complex along with justification of the donor sites provided by ligand for complexation with respect to the metal. The consequences obtained were highly cogent with standard deviation of ± 0.0021 absorbance unit. The procedure was applied to various synthetic (some analogous to cooperate and nickel zirconium) and technical (reverberatory flue dust and water) samples with satisfactory results.

Computational determination of the mechanism of the Pd-catalyzed formation of isatoic anhydrides from o-haloanilines, CO, and CO2

The palladium-catalyzed annulation of o-haloanilines with carbon monoxide (CO) and carbon dioxide (CO₂), discovered by Wen-Zhen Zhang and co-workers, provides a convenient method to synthesize isatoic anhydrides. We explored the mechanism of this reaction, particularly the order of the reaction of CO and CO₂ and the effect of the base, using density functional theory (DFT) calculations (ωB97X-D and M06). It was found that the base-assisted N-H bond activation through a concerted metalation-deprotonation (CMD) mechanism is a requisite for carboxylation, and the carboxylation proceeds via the nucleophilic attack of the (Pd)NH nitrogen on CO₂. The results show that carbonylation occurs prior to carboxylation, because the facile and exergonic carbonylation greatly decreases the energies of the following intermediates and transition states. The mechanistic exploration of the alternative pathways (e.g., mono-carbonylation and carboxylation) and the comparison with the annulation mechanism of the o-iodobenzylamine substrate further demonstrate the perfect cooperation of CO and CO₂ in constructing an anhydride moiety for o-haloanilines.

The Se-S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study

The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of Mpro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se-S covalent bond mediated by EBS and EBS-OH on Mpro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of Mpro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies.

Benchmarking of Density Functionals for Z-Azoarene Half-Lives via Automated Transition State Search

Molecular photoswitches use light to interconvert from a thermodynamically stable isomer into a metastable isomer. Photoswitches have been used in photopharmacology, catalysis, and molecular solar thermal (MOST) materials because of their spatiotemporal activation. Visible-light-absorbing photoswitches are especially attractive because low-energy light minimizes undesired photochemical reactions and enables biological applications. Ideal photoswitches require well-separated absorption spectra for both isomers and long-lived metastable states. However, predicting thermal half-lives with density functional theory is difficult because it requires locating transition structures and chosing an accurate model chemistry. We now report EZ-TS; by automatically calculating activation energies for the thermal Z → E isomerization. We used 28 density functionals [local spin density approximation, generalized gradient approximation, meta-GGA, hybrid GGA, and hybrid meta-GGA] and five basis sets [6-31G(d), 6-31+G(d,p), 6-311+G(d,p), cc-pVDZ, and aug-cc-pVDZ]. The hybrid GGA functionals performed the best among all tested functionals. We demonstrate that the mean absolute errors of 14 model chemistries approach chemical accuracy.

Understanding Plant Biomass via Computational Modeling

Plant biomass, especially wood, has been used for structural materials since ancient times. It is also showing great potential for new structural materials and it is the major feedstock for the emerging biorefineries for building a sustainable society. The plant cell wall is a hierarchical matrix of mainly cellulose, hemicellulose, and lignin. Herein, the structure, properties, and reactions of cellulose, lignin, and wood cell walls, studied using density functional theory (DFT) and molecular dynamics (MD), which are the widely used computational modeling approaches, are reviewed. Computational modeling, which has played a crucial role in understanding the structure and properties of plant biomass and its nanomaterials, may serve a leading role on developing new hierarchical materials from biomass in the future.

Luminescent gold-thallium derivatives with a pyridine-containing 12-membered aza-thioether macrocycle

The coordination modes of the ligand 2,5,8-trithia[9](2,6)pyridinophane (L) to thallium(i), gold(iii) and gold(i) have been studied. Thallium(i) is coordinated by the macrocyclic ligand in [Tl(L)](PF6) (1) through all the sulfur and nitrogen atoms, in a distorted square-pyramidal geometry with the thallium(i) ion in the apical position and with the presence of an inert lone pair. Gold(iii) is bonded by the ligand only through the nitrogen of the pyridine group in [AuCl3(L)] (2), whereas two AuI-C6F5 fragments coordinate the sulfur atoms next to the pyridine moiety of the ligand in [{Au(C6F5)}2(μ-L)] (3), which form a linear polymer through intermolecular aurophilic contacts. The heterometallic TlI/AuI complex {[Au(C6F5)2Tl]2(L)}n (4) features a polymeric structural nature with a metallic pseudo-rhombic Au2Tl2 core, which repeats itself forming a zig-zag polymer. In each Au2Tl2 unit only one thallium atom is bonded by the NS3 donor set of the macrocyclic ligand and also forms two unsupported Au-Tl bonds with two [Au(C6F5)2]- units in an overall pseudo-octahedral geometry. The other thallium atom similarly bridges the same [Au(C6F5)2]- units and links a neighbouring Au2Tl2 moiety, thus exhibiting a distorted trigonal planar geometry being bonded only to three gold atoms with unsupported Au-Tl interactions. This complex displays an interesting thermochromic behaviour showing emissions mainly resulting from MM'CT transitions at room temperature. At 77 K a dual emission appears, probably arising from the two different thallium environments. DFT calculations have been carried out in the attempt to investigate the origin of the emissions of complex 4.

Composition- and Condition-Dependent Kinetics of Homogeneous Ester Hydrogenation by a Mn-Based Catalyst

The reaction medium and conditions are the key parameters defining the efficiency and performance of a homogeneous catalyst. In the state-of-the-art molecular descriptions of catalytic systems by density functional theory (DFT) calculations, the reaction medium is commonly reduced to an infinitely diluted ideal solution model. In this work, we carry out a detailed operando computational modeling analysis of the condition dependencies and nonideal solution effects on the mechanism and kinetics of a model ester hydrogenation reaction by a homogeneous Mn(I)-P,N catalyst. By combining DFT calculations, COSMO-RS solvent model, and the microkinetic modeling approach, the kinetic behavior of the multicomponent homogeneous catalyst system under realistic reaction conditions was investigated in detail. The effects of the reaction medium and its dynamic evolution in the course of the reaction were analyzed by comparing the results obtained for the model methyl acetate hydrogenation reaction in a THF solution and under solvent-free neat reaction conditions. The dynamic representations of the reaction medium give rise to strongly nonlinear effects in the kinetic models. The nonideal representation of the reaction medium results in pronounced condition dependencies of the computed energetics of the elementary reaction steps and the computed kinetic profiles but affects only slightly such experimentally accessible kinetic descriptors as the apparent activation energy and the degree of rate control.

Multinuclear 2-(Quinolin-2-yl)quinoxaline-Coordinated Iridium(III) Complexes Tethered by Carbazole Derivatives: Synthesis and Photophysics

Five mono/di/trinuclear iridium(III) complexes (1-5) bearing the carbazole-derivative-tethered 2-(quinolin-2-yl)quinoxaline (quqo) diimine (N^N) ligand were synthesized and characterized. The photophysical properties of these complexes and their corresponding diimine ligands were systematically studied via UV-vis absorption, emission, and transient absorption (TA) spectroscopy and simulated by time-dependent density functional theory. All complexes possessed strong well-resolved absorption bands at <400 nm that have predominant ligand-based ¹π,π* transitions and broad structureless charge-transfer (¹CT) absorption bands at 400-700 nm. The energies or intensities of these ¹CT bands varied pronouncedly when the number of tethered Ir(quqo)(piq)₂⁺ (piq refers to 1-phenylisoquinoline) units, π conjugation of the carbazole derivative linker, or attachment positions on the carbazole linker were altered. All complexes were emissive at room temperature, with 1-3 showing near-IR (NIR) ³MLCT (metal-to-ligand charge-transfer)/³LLCT (ligand-to-ligand charge-transfer) emission at ∼710 nm and 4 and 5 exhibiting red or NIR ³ILCT (intraligand charge-transfer)/³LMCT (ligand-to-metal charge-transfer) emission in CH₂Cl₂. In CH₃CN, 1-3 displayed an additional emission band at ca. 590 nm (³ILCT/³LMCT/³MLCT/³π,π* in nature) in addition to the 710 nm band. The different natures of the emitting states of 1-3 versus those of 4 and 5 also gave rise to different spectral features in their triplet TA spectra. It appears that the parentage and characteristics of the lowest triplet excited states in these complexes are mainly impacted by the π systems of the bridging carbazole derivatives and essentially no interactions among the Ir(quqo)(piq)₂⁺ units. In addition, all of the diimine ligands tethered by the carbazole derivatives displayed a dramatic solvatochromic effect in their emission due to the predominant intramolecular charge-transfer nature of their emitting states. Aggregation-enhanced emission was also observed from the mixed CH₂Cl₂/ethyl acetate or CH₂Cl₂/hexane solutions of these ligands.

Antimony-Oxo Porphyrins as Photocatalysts for Redox-Neutral C-H to C-C Bond Conversion

The use of high-valent antimony-oxo porphyrins as visible-light photocatalysts operating via direct hydrogen atom transfer has been demonstrated. Computational analysis indicates that the triplet excited state of these complexes shows an oxyl radical behavior, while the Sb^V center remains in a high-valent oxidation state, serving uniquely to carry the oxo moiety and activate the coordinated ligands. This porphyrin-based system has been exploited upon irradiation to catalyze C-H to C-C bond conversion via the addition of hydrogen donors (ethers and aldehydes) onto Michael acceptors in a redox-neutral fashion without the need of any external oxidant. Laser flash photolysis experiments confirmed that the triplet excited state of the photocatalyst triggers the desired C-H cleavage.

Hierarchy of Commonly Used DFT Methods for Predicting the Thermochemistry of Rh-Mediated Chemical Transformations

The accuracy and reliability of 17 commonly used density functionals in conjunction with Poisson-Boltzmann finite solvation model were gauged for predicting the free energy of Rh(I)- and Rh(III)-mediated chemical transformations such as ligand exchange, hydride elimination, dihydrogen elimination, chloride affinity, and silyl hydride bond activation reactions. In total, six Rh-mediated reactions were examined, and the computed density functional theory results were then subjected to comparison with the experimentally reported values. For reaction A, involving replacement of N₂ with η²-H₂ over Rh(I), MPWB1K-D3, B3PW91, B3LYP, and BHandHYLP emerged to be the best functionals of all the tested methods in terms of their deviations ≤2 kcal mol^-1 from experimental data. For reaction B, in which exchange of η²-C₂H₄ with N₂ over Rh(I) takes place, MPWB1K-D3 and M06-2X-D3 functionals performed the best, while as for reaction C (hydride elimination reaction in Rh(III) complex), it is PBE functional that showed impressive performance. Similarly, for reaction D (H₂ elimination reaction in Rh(III) complex), PBE0-D3 and PBE-D3 showed exceptional results compared to other functionals. For reaction E (H₂O/Cl^- exchange), the PBE0 again shows impressive performance as compared to other functionals. For reaction F (Si-H activation), M06-2X-D3, PBE0-D3, and MPWB1K-D3 functionals are undoubtedly the best functionals. Overall, PBE0-D3 and MPWB1K-D3 functionals were impressive in all cases with lowest mean unsigned errors (3.2 and 3.4 kcal mol^-1, respectively) with respect to experimental Gibbs free energies. Thus, these two functionals are recommended for studying Rh-mediated chemical transformations.

Reactivity of Gold(I) Monocarbene Complexes with Protein Targets: A Theoretical Study

Neutral N–heterocyclic carbene gold(I) compounds such as IMeAuCl are widely used both in homogeneous catalysis and, more recently, in medicinal chemistry as promising antitumor agents. In order to shed light on their reactivity with protein side chains, we have carried out density functional theory (DFT) calculations on the thermodynamics and kinetics of their reactions with water and various nucleophiles as a model of plausible protein binding sites such as arginine, aspartic acid, asparagine, cysteine, glutamic acid, glutamine, histidine, lysine, methionine, selenocysteine, and the N-terminal group. In agreement with recent experimental data, our results suggest that IMeAuCl easily interacts with all considered biological targets before being hydrated—unless sterically prevented—and allows the establishment of an order of thermodynamic stability and of kinetic reactivity for its binding to protein residues.

Magnetic Exchange Interaction in Nitronyl Nitroxide Radical-Based Single Crystals of 3d Metal Complexes: A Combined Experimental and Theoretical Study

Two stable nitronyl nitroxide free radicals {R ¹ = 4'-methoxy-phenyl-4,4,5,5,-tetramethylimidazoline-1-oxyl-3-oxide (NNPhOMe) and R ² = 2-(2'-thienyl)-4,4,5,5-tetramethylimidazoline 3-oxide 1-oxyl (NNT)} are successfully synthesized using Ullmann condensation. The reactions of these two radicals with 3d transition metal ions, in the form of M(hfac)₂ (where M = Co or Mn, hfac: hexafluoroacetylacetone), result in four metal-organic complexes Co(hfac)₂(NNPhOMe)₂, 1; Co(hfac)₂(NNT)₂·(H₂O), 2; Mn(hfac)₂(NNPhOMe)·x(C₇H₁₆), 3; and Mn(hfac)₂(NNT)₂, 4. The crystal structure and magnetic properties of these complexes are investigated by single-crystal X-ray diffraction, dc magnetization, infrared, and electron paramagnetic resonance spectroscopies. The compounds 1 and 4 crystallize in the triclinic, P1̅, space group, whereas complex 3 crystallizes in the monoclinic structure with the C2/c space group and forms chain-like structure along the c direction. The complex 2 crystallizes in the monoclinic symmetry with the P2₁/c space group in which the N-O unit of the radical coordinates with the Co ion through hydrogen bonding of a water molecule. All compounds exhibit antiferromagnetic interactions between the transition metal ions and nitronyl nitroxide radicals. The magnetic exchange interactions (J/K _B) are derived using isotropic spin Hamiltonian H = -2J∑(S _metal S _radical) for the model fitting to the magnetic susceptibility data for 1, 2, 3, and 4. The exchange interaction strengths are found to be -328, -1.25, -248, and -256 K, for the 1, 2, 3, and 4 metal-organic complexes, respectively. Quantum chemical density functional theory (DFT) computations are carried out on several models of the metal-radical complexes to elucidate the magnetic interactions at the molecular level. The calculations show that a small part of the inorganic spins are delocalized over the oxygens from hfac {∼0.03 for Co(II) and ∼0.015 for Mn(II)}, whereas a more significant fraction {∼0.24 for Mn(II) and ∼0.13 for Co(II)} of delocalized spins from the metal ion is transferred to the coordinated oxygen atom(s) of nitronyl nitroxide.

Probing the geometry of copper and silver adatoms on magnetite: quantitative experiment versus theory

Accurately modelling the structure of a catalyst is a fundamental prerequisite for correctly predicting reaction pathways, but a lack of clear experimental benchmarks makes it difficult to determine the optimal theoretical approach. Here, we utilize the normal incidence X-ray standing wave (NIXSW) technique to precisely determine the three dimensional geometry of Ag1 and Cu1 adatoms on Fe3O4(001). Both adatoms occupy bulk-continuation cation sites, but with a markedly different height above the surface (0.43 ± 0.03 Å (Cu1) and 0.96 ± 0.03 Å (Ag1)). HSE-based calculations accurately predict the experimental geometry, but the more common PBE + U and PBEsol + U approaches perform poorly.