A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

A general molecular mechanics (MM) model for treating aqueous Cu²⁺ and Zn²⁺ ions was developed based on valence bond (VB) theory and incorporated into the atomic multipole optimized energetics for biomolecular applications (AMOEBA) polarizable force field. Parameters were obtained by fitting MM energies to that computed by ab initio methods for gas‐phase tetra‐ and hexa‐aqua metal complexes. Molecular dynamics (MD) simulations using the proposed AMOEBA‐VB model were performed for each transition metal ion in aqueous solution, and solvent coordination was evaluated. Results show that the AMOEBA‐VB model generates the correct square‐planar geometry for gas‐phase tetra‐aqua Cu²⁺ complex and improves the accuracy of MM model energetics for a number of ligation geometries when compared to quantum mechanical (QM) computations. On the other hand, both AMOEBA and AMOEBA‐VB generate results for Zn²⁺–water complexes in good agreement with QM calculations. Analyses of the MD trajectories revealed a six‐coordination first solvation shell for both Cu²⁺ and Zn²⁺ ions in aqueous solution, with ligation geometries falling in the range reported by previous studies. © 2012 Wiley Periodicals, Inc.     

The structures of the isomorphous potassium and rubidium salts of 4‐nitrobenzoic acid and an overview of the metal complex stereochemistries of the alkali metal salt series with this ligand

4‐Nitrobenzoic acid (PNBA) has proved to be a useful ligand for the preparation of metal complexes but the known structures of the alkali metal salts of PNBA do not include the rubidium salt. The structures of the isomorphous potassium and rubidium polymeric coordination complexes with PNBA, namely poly[μ₂‐aqua‐aqua‐μ₃‐(4‐nitrobenzoato)‐potassium], [K(C₇H₄N₂O₂)(H₂O)₂]_n, (I), and poly[μ₃‐aqua‐aqua‐μ₅‐(4‐nitrobenzoato)‐rubidium], [Rb(C₇H₄N₂O₂)(H₂O)₂]_n, (II), have been determined. In (I), the very distorted KO₆ coordination sphere about the K⁺ centres in the repeat unit comprise two bridging nitro O‐atom donors, a single bridging carboxylate O‐atom donor and two water molecules, one of which is bridging. In Rb complex (II), the same basic MO₆ coordination is found in the repeat unit, but it is expanded to RbO₉ through a slight increase in the accepted Rb—O bond‐length range and includes an additional Rb—O_carboxylate bond, completing a bidentate O,O′‐chelate interaction, and additional bridging Rb—O_nitro and Rb—O_water bonds. The comparative K—O and Rb—O bond‐length ranges are 2.7352 (14)–3.0051 (14) and 2.884 (2)–3.182 (2) Å, respectively. The structure of (II) is also isomorphous, as well as isostructural, with the known structure of the nine‐coordinate caesium 4‐nitrobenzoate analogue, (III), in which the Cs—O bond‐length range is 3.047 (4)–3.338 (4) Å. In all three complexes, common basic polymeric extensions are found, including two different centrosymmetric bridging interactions through both water and nitro groups, as well as extensions along c through the para‐related carboxylate group, giving a two‐dimensional structure in (I). In (II) and (III), three‐dimensional structures are generated through additional bridges involving the nitro and water O atoms. In all three structures, the two water molecules are involved in similar intra‐polymer O—H...O hydrogen‐bonding interactions to both carboxylate and water O‐atom acceptors. A comparison of the varied coordination behaviour of the full set of Li–Cs salts with 4‐nitrobenzoic acid is also made.     

Generating and Trapping Metalla‐N‐Heterocyclic Carbenes

By means of a combined experimental and theoretical approach, the electronic features and chemical behavior of metalla‐N‐heterocyclic carbenes (MNHCs, N‐heterocyclic carbenes containing a metal atom within the heterocyclic skeleton) have been established and compared with those of classical NHCs. MNHCs are strongly basic (proton affinity and pK_a values around 290 kcal mol^?1 and 36, respectively) with a narrow singlet–triplet gap (around 23 kcal mol^?1). MNHCs can be generated from the corresponding metalla‐imidazolium salts and trapped by addition of transition‐metal complexes affording the corresponding heterodimetallic dicarbene derivatives, which can serve as carbene transfer agents.     

pKA in proteins solving the Poisson–Boltzmann equation with finite elements

Knowledge on pK_A values is an eminent factor to understand the function of proteins in living systems. We present a novel approach demonstrating that the finite element (FE) method of solving the linearized Poisson–Boltzmann equation (lPBE) can successfully be used to compute pK_A values in proteins with high accuracy as a possible replacement to finite difference (FD) method. For this purpose, we implemented the software molecular Finite Element Solver (mFES) in the framework of the Karlsberg+ program to compute pK_A values. This work focuses on a comparison between pK_A computations obtained with the well‐established FD method and with the new developed FE method mFES, solving the lPBE using protein crystal structures without conformational changes. Accurate and coarse model systems are set up with mFES using a similar number of unknowns compared with the FD method. Our FE method delivers results for computations of pK_A values and interaction energies of titratable groups, which are comparable in accuracy. We introduce different thermodynamic cycles to evaluate pK_A values and we show for the FE method how different parameters influence the accuracy of computed pK_A values. © 2015 Wiley Periodicals, Inc.     

An embedded QM/MM study for different SiO2/Al2O3 ratios of the HZSM‐5 zeolite and for their interaction with n‐heptane

We carried out a theoretical study of the HZSM‐5 zeolite, for different SiO₂/Al₂O₃ ratios, that interacts with the n‐heptane molecule. The study was performed using a QM/MM (quantum mechanics/molecular mechanics) methodology. For the QM part, we have chosen a hybrid Hartree‐Fock density functional theory (DFT). The hybrid ACM/DZP approach, as implemented in Turbomole, was used for the treatment of the QM cluster containing 84 atoms that represents a ring structure model of the zeolite‐n‐heptane interacting system. The MM part was represented by means of an electrostatic forcefield (ESFF), which assesses the electronic embedding. The chosen QM/MM silicalite base model contains 3862 atoms. The studied SiO₂/Al₂O₃ ratios were 2300, 573.5, 287.7, and 189.83, containing 1, 4, 8, and 12 Al atoms, respectively. For the first ratio, the site for the substitution of Al for Si was that of minimum QM total energy value, because this replacement was done in the QM region. For the other SiO₂/Al₂O₃ ratios, the Al atoms were randomly spread through the MM region in accordance with the Lowenstein substitution rule. These results show the importance of the environment on the electronic properties in the QM region, where the active site lies, and their effects on the earlier steps on the activation experienced by the n‐heptane moiety. A minimal content of 12 Al atoms produces significant effects of the environment on the electronic structure of the QM region. Moreover, the carbocationic character of n‐heptane increases with the aluminum content. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Transition metal complexes of 6‐mercaptopurine: Characterization,Theoretical calculation,DNA‐Binding,molecular docking,and anticancer activity

6‐mercaptopurine (6‐MP) is used for treating various cancers and autoimmune disorders. A few examples of transition metal complexes of 6‐MP have been shown to enhance its anticancer activity, but many remain untested. We isolated five highly stable and colored metal complexes of 6‐MP and confirmed their structures by elemental analysis, spectral, and thermal techniques. Infrared (IR) spectra revealed that 6‐MP is a bidentate ligand that interacts through sulfur and pyrimidine nitrogen in a 1:2 (M:L) molar ratio. The magnetic susceptibility and electron paramagnetic resonance (EPR) spectra for the Cu(II) complex revealed an octahedral arrangement around the metal ion with strong covalent bonding. The fully optimized geometries of the metal structures obtained using density function theory (DFT)/B3LYP calculations were used to verify the structural and biological features. DNA titration revealed that the octahedral Cu(II) complex has a critical binding constant value of K_b = 8 × 105. Docking studies using three different cancer protein receptors were used to predict the biological applications of the synthesized drug‐metal complexes. Finally, cytotoxicity assays against a myeloma cancer cell line (MM) and a colon cancer cell line (Caco‐2) revealed favorable anticancer activity for the copper complex, exceeding that of the gold‐standard chemotherapeutic cisplatin.     

CPMD/GULP QM/MM interface for modeling periodic solids: Implementation and its application in the study of Y‐zeolite supported Rhn clusters

We report here the development of hybrid quantum mechanics/molecular mechanics (QM/MM) interface between the plane‐wave density functional theory based CPMD code and the empirical force‐field based GULP code for modeling periodic solids and surfaces. The hybrid QM/MM interface is based on the electrostatic coupling between QM and MM regions. The interface is designed for carrying out full relaxation of all the QM and MM atoms during geometry optimizations and molecular dynamics simulations, including the boundary atoms. Both Born–Oppenheimer and Car–Parrinello molecular dynamics schemes are enabled for the QM part during the QM/MM calculations. This interface has the advantage of parallelization of both the programs such that the QM and MM force evaluations can be carried out in parallel to model large systems. The interface program is first validated for total energy conservation and parallel scaling performance is benchmarked. Oxygen vacancy in α‐cristobalite is then studied in detail and the results are compared with a fully QM calculation and experimental data. Subsequently, we use our implementation to investigate the structure of rhodium cluster (Rh_n; n = 2 to 6) formed from Rh(C₂H₄)₂ complex adsorbed within a cavity of Y‐zeolite in a reducible atmosphere of H₂ gas. © 2016 Wiley Periodicals, Inc.     

Mn(III) mixed‐ligand complexes with bis‐pyrazolones and ciprofloxacin drug: synthesis,characterization and antibacterial activities

The fluoroquinolone family member ciprofloxacin is well known for its drug design and coordinating ability towards metal ions. The coordination chemistry of this drug with metal ions of biological and pharmaceutical importance is of considerable interest. Novel Mn(III) mixed‐ligand complexes of ciprofloxacin with various bis‐pyrazolone‐based dinegative bidentate ligands were synthesized and characterized on the basis of their physical properties, magnetic susceptibility measurements, (FT‐IR and electronic) spectral studies. The FAB‐mass spectrum of [Mn(A⁹)(L)(H₂O)₂]·H₂O [where H₂A⁹ = 4,4′‐(p‐tolylmethylene)bis(3‐methyl‐1‐phenyl‐4,5‐dihydro‐1H‐pyrazol‐5‐ol) and HL = 1‐cyclopropyl‐6‐fluoro‐4‐oxo‐7‐(piperazin‐1‐yl)‐1,4‐dihydroquinoline‐3‐carboxylic acid] was determined. All the synthesized compounds were screened for their bioactivity. The mixed‐ligand complexes exhibited comparable activities against two Gram‐negative (Escherichia coli and Serratia marcescens) and two Gram‐positive (Staphylococcus aureus and Bacillus subtilis) microorganisms. Copyright © 2011 John Wiley & Sons, Ltd.     

Bridge‐Splitting Reactions of Platinum(II) Complexes with Parametalated Pyridine Spacer Groups: A Kinetic and Mechanistic Study

Substitution reactions of three dinuclear Pt(II) complexes connected by a pyridine‐bridging ligand of variable length, namely [ cis‐{PtOH₂(NH₃)₂}₂–μ–L]⁴⁺, where L = 4,4′‐bis(pyridine)sulfide ( Pt1 ), 4,4′‐bis(pyridine)disulfide ( Pt2 ), and 1,2‐bis(4‐pyridyl)ethane ( Pt3 ) with S‐donor nucleophiles (thiourea, 1,3‐dimethyl‐2‐thiourea, and 1,1,3,3‐tetramethyl‐2‐thiourea) and anionic nucleophiles (SCN^?, I^?, and Br^?) were investigated. The substitutions were followed under pseudo–first‐order conditions as a function of the nucleophile concentration and temperature, using stopped‐flow and UV–visible spectrophotometric methods. The observed pK_a values were, respectively, Pt1 (pK_a1: 4.86; pK_a2: 5.53), Pt2 (pK_a1: 5.19; pK_a2: 6.42), and Pt3 (pK_a1: 5.04; pK_a2: 5.45). The second‐order rate constants for the lability of aqua ligands in the first step decreased in the order Pt2 > Pt3 > Pt1 , whereas for the second step it is Pt1 > Pt2 > Pt3 . The obtained results indicate that introduction of a spacer atom(s) on the structure of the bridging ligand influences the substitution reactivity as well as acidity of the investigated dinuclear Pt(II) complexes. Also nonplanarity of the bridging ligand of Pt1 complex significantly slows down the rate of substitution due to steric hindrance, whereas release of the strain enhances the dissociation of the bridging ligand. The release of the bridging ligand in the second step was confirmed by the ¹H NMR of Pt1‐Cl with thiourea in DMF‐d₇. The temperature dependence of the second–order rate constants and the negative values of entropies of activation (ΔS^#) support an associative mode of the substitution mechanism.     

Influence of electronic effect on catalytic activity of salicylaldiminato nickel(II) complexes

A means of correlation between the activity and the net charge, the metal atom net charge correlation (MANCC), which was successful in the activity prediction of the early‐transition metal catalysts, has been used to study the catalytic activities of salicylaldiminato Ni(II) complexes, the late‐transition metal catalysts, in olefin polymerization or oligomerization. A comparison with the available quantum mechanics/molecular mechanics (QM/MM) calculation data suggests that even without a detailed mechanism, MANCC results mostly agree with QM/MM calculation data regarding insertion barrier data and enthalpy change. Eight experimental complexes were further built up by modeling; their catalytic activities predominantly increased in line with the net charges on the metal atoms. The same results were obtained for the other four complexes synthesized in the present work. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 4765–4774, 2004     

Prediction of pKas of Late Transition-Metal Hydrides via a QM/QM Approach

Three implicit solvation models, the conductor-like polarizable continuum model (C-PCM), the conductor-like screening model (COSMO), and universal implicit solvent model (SMD), combined with a hybrid two layer QM/QM approach (ONIOM), were utilized to calculate the pK_a values, using a direct thermodynamic scheme, of a set of Group 10 transition metal (TM) hydrides in acetonitrile. To obtain the optimal combination of quantum methods for ONIOM calculations with implicit solvation models, the influence of factors, such as the choice of density functional and basis set, the atomic radii used to build a cavity in the solvent, and the size of the model system in an ONIOM scheme, was examined. Additionally, the impact of Grimme's empirical dispersion correction and exact exchange was also investigated. The results were calibrated by experimental data. This investigation provides insight about effective models for the prediction of thermodynamic properties of TM-containing complexes with bulky ligands. © 2019 Wiley Periodicals, Inc.     

Stepwise Versus Concerted Mechanisms in General‐Base Catalysis by Serine Proteases

General‐base catalysis in serine proteases still poses mechanistic challenges despite decades of research. Whether proton transfer from the catalytic Ser to His and nucleophilic attack on the substrate are concerted or stepwise is still under debate, even for the classical Asp‐His‐Ser catalytic triad. To address these key catalytic steps, the transformation of the Michaelis complex to tetrahedral complex in the covalent inhibition of two prototype serine proteases was studied: chymotrypsin (with the catalytic triad) inhibition by a peptidyl trifluoromethane and GlpG rhomboid (with Ser‐His dyad) inhibition by an isocoumarin derivative. The sampled MD trajectories of averaged pK_a values of catalytic residues were QM calculated by the MD‐QM/SCRF(VS) method on molecular clusters simulating the active site. Differences between concerted and stepwise mechanisms are controlled by the dynamically changing pK_a values of the catalytic residues as a function of their progressively reduced water exposure, caused by the incoming ligand.     

Dependence of reactivity of propagation centers of oxide catalysts for ethylene polymerization on catalyst composition and activation conditions

The propagation rate constant K_p was used as a measure of reactivity of propagation centers in ethylene polymerization with oxide catalysts. This constant was determined by a radiotracer quenching technique for oxide catalysts of different compositions and activation conditions. For catalysts based on various transition metal oxides, an increase of K_p was observed in the series W < Mo < Cr and V < Cr. In the case of chromium oxide catalyst it was shown that K_p value does not depend on the content of the transition metal in a catalyst. A change of propagation center reactivity was found when oxides of different composition (SiO₂, Al₂O₃, ZrO₂, TiO₂) were used as supports. An increase of the vacuum activation temperature of a catalyst results in increasing K_p. Pretreatment of catalyst with different reducing agents (SO₂, CO₂, NH₃, HCN) results in the change of K_p value in comparison in comparison with the catalyst activated by the vacuum treatment only. The data obtained on the variation of the reactivity of the propagation centers permit one to draw a conclusion about the composition of surface compounds as acitve centers of the oxide polymerization catalysts.     

Spectroscopic investigation,DFT, fluorescence,molecular docking and biological studies of divalent and trivalent binuclear complexes prepared from benzoyl thiosemicarbazide derivative of 2‐benzylmalonohydrazide

The binuclear Cr (III), Mn (II) and Fe (III) complexes of N,N′‐(2,2′‐(2‐benzylmalonyl)bis (hydrazine‐1‐carbonothioyl))dibenzamide (H₄BPCD), which derived from the combination of 2‐benzylmalonohydrazide suspension with benzoyl‐isothiocyanate, have been isolated and investigated by the necessary analytical and spectroscopic techniques. The IR studies show that H₄BPCD dispose as a mono‐negative hexadentate ligand (NOS)₂ towards Mn (II) ion and tetra‐negative hexadentate (NOS)₂ towards both Cr (III) and Fe (III) ions. The values of molar conductance in DMSO suggested the non‐electrolytic nature for all complexes. The magnetic measurements and the electronic transitions data confirmed the hexa‐coordinate geometry of complexes. The DFT geometry optimization of all compounds and IR comparative study of both theoretical and experimental of H₄BPCD were carried out. Moreover, the H₄BPCD and its Cr (III) complex displayed intra ligand (π → π*) fluorescence emission spectra which corroborate their photoactive nature. The coordinated and crystalline water molecules have been investigated by (TG/DTG) studies. The kinetic and thermodynamic parameters were computed using Horowitz‐ Metzger, Coats‐Redfern and Broido methods. Biological studies of DNA binding, minimum inhibitory concentration, in vitro determination of SOD‐like activity and MTT‐cytotoxicity assay as well as molecular docking studies were tested for the ligand and its complexes.     

Selective retention of basic compounds by metal aquo‐ion affinity chromatography

A novel metal aquo‐ion affinity chromatography has been developed for the analysis of basic compounds using heat‐treated silica gel containing hydrated metal cations (metal aquo‐ions) as the packing material. The packing materials of the metal aquo‐ion affinity chromatography were prepared by the immobilization of a single metal component such as Fe(III), Al(III), Ag(I), and Ni(II) on silica gel followed by extensive heat treatment. The immobilized metals form aquo‐ions to present cation‐exchange ability for basic analytes and the cation‐exchange ability for basic analytes depends on pK_a of the immobilized metal species. In the present study, to evaluate the retention characteristics of metal aquo‐ion affinity chromatography, the on‐line solid‐phase extraction of drugs was investigated. Obtained data clearly evidence the selective retention capability of metal aquo‐ion affinity chromatography for basic analytes with sufficient capacity.     

Physicochemical characterization of nanobidentate ferrocene‐based Schiff base ligand and its coordination complexes: Antimicrobial,anticancer, density functional theory,and molecular operating environment studies

A novel bidentate Schiff base ligand (HL, Nanobidentate Ferrocene based Schiff base ligand L (has one replaceable proton H)) was prepared via the condensation of 2‐amino phenol with 2‐acetyl ferrocene. The ligand was characterized using elemental analysis, mass spectrometry, infrared (IR) spectroscopy, ¹proton nuclear magnetic resonance (H‐NMR) spectroscopy, scanning electron microscopy (SEM), and thermal analysis. The corresponding 1:1 metal complexes with some transition‐metal ions were additionally characterized by their elemental analysis, molar conductance, SEM, and thermogravimetric ana1ysis (TGA). The complexes had the general formula [M(L)(Cl)(H₂O)₃]xCl·nH₂O (M = Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II), and Cd(II)), (x = 0 for Mn(II), Co(II), Ni(II), Cu(II), Zn(II), and Cd(II), x = 1 for Cr(III) and Fe(III)), (n = 1 for Cr(III), n = 3 for Mn(II) and Co(II), n = 4 for Fe(III), Ni(II), Cu(II), Zn(II), and Cd(II)). Density functional theory calculations on the HL ligand were also carried out in order to clarify molecular structures by the B31YP exchange‐correlation function. The results were subjected to molecular orbital diagram, highest occupied mo1ecu1ar orbital–lowest occupied molecular orbital, and molecular electrostatic potential calculations. The parent Schiff base and its eight metal complexes were assayed against four bacterial species (two Gram‐negative and two‐Gram positive) and four different antifungal species. The HL ligand was docked using molecular operating environment 2008 with crystal structures of oxidoreductase (1CX2), protein phosphatase of the fungus Candida albicans (5JPE), Gram(?) bacteria Escherichia coli (3T88), Gram(+) bacteria Staphylococcus aureus (3Q8U), and an androgen‐independent receptor of prostate cancer (1GS4). In order to assess cytotoxic nature of the prepared HL ligand and its complexes, the compounds were screened against the Michigan cancer foundation (MCF)‐7 breast cancer cell line, and the IC₅₀ values of compounds were calculated.     

Theoretical study of the electronic spectrum of binuclear gold(I) complexes

The electronic structure and the spectroscopic properties of [Au₂(CS₃)₂]^?2, [Au₂(pym‐2‐S)₂] (pym = pyrimidethiolate), [Au₂(dpm)₂]⁺² (dpm = bis(diphosphino)methane) were studied using density functional theory (DFT) at the B3LYP level. The absorption spectrum of these binuclear gold(I) complexes was calculated by single excitation time‐dependent (TD) method. All complexes showed a ¹(5dσ* → 6pσ) transition associated with a metal–metal charge transfer, which is strongly interrelated with the gold–gold distance. Furthermore, we have calculated the frequency of the gold–gold vibration (ν_Au2) on the above complexes. The values obtained are theoretically in agreement with experimental range. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

pH‐Dependent Self‐Assembly of Complexes with Tripodal Amino Acid Ligand

Three new metal complexes were synthesized by reactions of [bis(2‐amino‐ethyl)‐amino]‐acetic acid (HL) and different metal salts at different pH values. Their structures were characterized by X‐ray crystallography. Interestingly, under acidic conditions, the dinuclear structure {Cu₂[H(L)]₂Cl₂}(ClO₄)₂ ( 1 ) was obtained, whereas under alkaline conditions, the complexes {[Cu(L)](ClO₄)}_n ( 2 ) and [Cd(L)Cl]_n ( 3 ), which exhibit distinct one‐dimensional (1D) structures, were obtained. The results indicate that the pH value, metal ions, and anions have remarkable influence on the formation and structure of the complexes.     

Structural studies and quantum chemical calculations of Cr(III), Fe(III) and Ru(III) bromazepam complexes

The reaction of bromazepam (7‐bromo‐1,3‐dihydro‐5‐(2‐pyridyl)‐2H ‐1,4‐benzodiazepin‐2‐one, BZM) with Cr(III) ( 1 ), Fe(III) ( 2 ) and Ru(III) ( 3 ) salts gives complexes of the type [M(BZM)₃]⋅3X (X = Cl or NO₃). Structural characterization was extensively carried out using various analytical and spectral tools such as infrared, ¹H NMR and UV–visible spectroscopies and magnetic, conductance, elemental and thermal analyses. BZM is a bidentate ligand and interacts with the metal ions via the pyridine and benzodiazepin‐2‐one nitrogen atoms. The magnetic and electronic properties of 2 and 3 are consistent with low‐spin octahedral complexes. The three BZM molecules are non‐isoenergetically coordinated to the metal ions and this is reflected in the values of the second‐order interaction energy. The antibacterial activity was studied using Staphylococcus aureus and Escherichia coli . Coordination of BZM to Cr(III) or Ru(III) ions leads to a marked increase in toxicity with respect to the inactive Fe(III) complex 2 .