A quantum chemistry evaluation of the stereochemical activity of the lone pair in Pb<Superscript>II</Superscript> complexes with sequestering ligands

The stereochemical activity of the lone pair on Pb^II complexes is assessed using several theoretical methods, including structural analyses, computations of Fukui functions, natural bond orbitals, electron localization function, investigation of the electron density and of its laplacian. The attention is focused on four octadentate N-carbamoylmethyl-substituted tetraazamacrocycles of various ring sizes ranging from 8 to 14 atoms associated with the Pb^II cation. The theoretical study illustrates the geometrical constraints imposed by the ring structure which limits the spatial development of the lone pair but without fully preventing it. For a given coordination number, the lone pair activity is strongly correlated to the geometry of the ligand and in particular to the size of the cage that the ligand forms around the Pb^II cation. Some limitations of the theoretical tools used are also evidenced, among them the necessity to sample around a critical point instead of just analyzing its nature. In the case of the laplacian of the electron density, a visualization method is introduced to moderate the results based only on the nature of a critical point. These limitations should also be related to the difficulty to extend the lone pair concept for the heaviest atoms of the classification.     

Synthesis, characterization and crystal structure of zirconium complex containing amidinate, guanidinate and amide ligand sets

A new zirconium complex containing amidinate, guanidinate and amide ligand sets with formula Zr[(CyN)₂CMe][(CyN)₂CNMe₂](NMe₂)₂ (1) (Cy = cyclohexyl) was synthesized by the insertion of the 1,3-dicyclohexylcarbodiimide moiety into the bond of zirconium and dimethylamido group. Characterization of the complex 1 was achieved using elemental analysis, ¹H and ¹³C NMR spectra and single crystal X-ray diffraction. The molecular structure of the complex 1 revealed that the coordination geometry around the zirconium is a distorted pseudo-octahedron. The metal center is surrounded by the four nitrogen atoms of two bidentate amidinate and guanidinate ligands positioned cis to each other and two cis-NMe₂ groups.     

Bis(2-methyltetrazole)dichlorocopper(II) is a layered coordination polymer built from dinuclear chloro-bridged Cu units linked by bridging tetrazoles. The first structurally and magnetically characterized complex of 2-monosubstituted tetrazoles

The data on synthesis, crystal structure, magnetic susceptibility and thermal properties of coordination compound of copper(II) chloride with 2-methyltetrazole (2mtet) of Cu(2mtet)₂Cl₂ composition are reported. The Cu atom environment forms an elongated octahedron, with two 2-methyltetrazole ligands (N4 bound) and two Cl atoms in the equatorial positions. Symmetry related 2-methyltetrazole ligand and Cl atom are in the axial positions. One of the two 2-methyltetrazole molecules of the asymmetric unit exhibits bridging properties being linked to two Cu atoms through two N atoms (i.e., N4 and N1) of the tetrazole ring, while the other ligand molecule is coordinated in monodentate fashion via one tetrazole N4 atom. The Cu-octahedra form dinuclear building bricks by sharing edges with equatorial and axial Cl atoms. These dinuclear units are linked together via bridging 2-methyltetrazole ligands to form infinite layers parallel to the plane. Magnetic properties of Cu(2mtet)₂Cl₂ and the data of quantum-chemical calculations of molecular electrostatic potential and energies of hydronation of nitrogen atoms for 2mtet using B3LYP/6-31G^* level of theory are in agreement with the structural data obtained.     

New dinuclear arene ruthenium complexes with P,S- or P,O-chelating ligands

Two equivalents of 2-diphenylphosphinobenzoic acid react with 1,2-ethanedithiol and 1,8-diaminonaphthalene under peptidic coupling conditions to give the new ligands 1,2-bis-S-[2^′-(diphenylphosphino)benzoyl]dithioethane (dppte) (1) and 1,2-bis-N-[2^′-(diphenylphosphino)benzoyl]diaminonaphthalene (dppan) (2), respectively. 1 and 2 have been characterised by mass spectrometry, elemental analysis, NMR, IR spectroscopy, and by single-crystal X-ray structure analysis. 2 is easily oxidised by air to give the monophosphine oxide derivatives (3). Single-crystal X-ray structure analysis of 3 shows an intramolecular hydrogen bond between an amido and the phosphoryl oxygen atom. Compounds 1 and 2 react with [RuCl₂(η⁶-p-cymene)]₂ to give the dinuclear complexes [RuCl(η⁶-p-cymene)(dppte)RuCl(η⁶-p-cymene)]²⁺ (4) and [RuCl(η⁶-p-cymene)(dppan)RuCl(η⁶-p-cymene)]²⁺ (5). As determined by single-crystal X-ray structure analysis, 4 and 5 adopt different coordination modes to the ruthenium atoms. In 4 the symmetric dppte ligand is P,S coordinated to the ruthenium atom, whereas in 5 the dppan ligand prefers a P,O coordination mode.     

Synthesis, characterization and crystal structure of dicesium bis(1,2-dithiole-3,5-dithiolato-4-yl)disulfide

Dicesium bis(1,2-dithiole-3,5-dithiolato-4-yl)disulfide, 3, was obtained by aerial oxidation of dicesium 1,3-dithiole-3-thione-4,5-dithiolate in aqueous ethanol. The dianion in 3, in the 4e special positions of the space group Pbcn, lies on a crystallographic twofold axis and has, therefore, C2 molecular symmetry. As a consequence the asymmetric unit consists of, in addition to one cesium atom, precisely one half of the anion. The negative charges of the dianion are sustained by 1,3-dithiolate groups. The cesium atom has 11 nearest sulfur atoms with CsS distances in the range 3.5762(11)-4.1383(11) Å, from five different anions and as a result provides complete three-dimensional connectivity throughout the structure. The vibrational spectra of 3 and related compounds, including dicesium 1,3-dithiole-3-thione-4,5-dithiolate are presented as are RHF calculations on [dmt]²⁻ and [dmt-dmt]²⁻ species.     

Mercury(II) complex formation with glutathione in alkaline aqueous solution

The structure and speciation of the complexes formed between mercury(II) ions and glutathione (GSH = L-glutamyl-L-cysteinyl-glycine) have been studied for a series of alkaline aqueous solutions (\( C_{{{\text{Hg}}^{{2 + }}}}\,{\sim18\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}}\) and C _GSH = 40–200 mmol dm^?3 at pH ～10.5) by means of extended X-ray absorption fine structure (EXAFS) and ¹⁹⁹Hg NMR spectroscopy at ambient temperature. The dominant complexes are [Hg(GS)₂]^4? and [Hg(GS)₃]^7?, with mean Hg–S bond distances of 2.32(1) and 2.42(2) Å observed in digonal and trigonal Hg–S coordination, respectively. The proportions of the Hg²⁺–glutathione complexes were evaluated by fitting linear combinations of model EXAFS oscillations representing each species to the experimental EXAFS spectra. The [Hg(GS)₄]^10? complex, with four sulfur atoms coordinated at a mean Hg–S bond distance of 2.52(2) Å, is present in minor amounts (<30%) in solutions containing a large excess of glutathione (C _GSH ≥ 160 mmol dm^?3). Comparable alkaline mercury(II) cysteine (H₂Cys) solutions were also investigated and a reduced tendency to form higher complexes was observed, because the deprotonated amino group of Cys^2? allows the stable [Hg(S,N-Cys)₂]^2? chelate to form. The effect of temperature on the distribution of the Hg²⁺–glutathione complexes was studied by comparing the EXAFS spectra at ambient temperature and at 25 K of a series of glycerol/water (33/67, v/v) frozen glasses with \( C_{{{\text{Hg}}^{{2 + }} }} \,{\sim7\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}} \) and C _GSH = 16–81 mmol dm^?3. Complexes with high Hg–S coordination numbers, [Hg(GS)₃]^7? and [Hg(GS)₄]^10?, became strongly favored when just a moderate excess of glutathione (C _GSH ≥28 mmol dm^?3) was used in the glassy samples, as expected for a stepwise exothermic bond formation. Addition of glycerol had no effect on the Hg(II)–glutathione speciation, as shown by the similarity of the EXAFS spectra obtained at room temperature for two parallel series of Hg(II)-glutathione solutions with \( C_{{{\text{Hg}}^{{2 + }} }} \,{\sim7\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}},\) with and without 33% glycerol. Also, the ¹⁹⁹Hg NMR chemical shifts of a series of ～18 mmol dm^?3 mercury(II) glutathione solutions with 33% glycerol were not significantly different from those of the corresponding series in aqueous solution.     

The investigation of the G-quadruplex aptamer selectivity to Pb2+ ion: a joint molecular dynamics simulation and density functional theory study

Abstract

The aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb²⁺ in comparison with some ions. The Free Energy Landscape (FEL) analysis indicates that Pb²⁺ has remained inside the aptamer during the MD simulation, while the other ions have left it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energies prove that the conformational stability of the aptamer is the highest in the presence of Pb²⁺. According to the compaction parameters, the greatest compressed ion-aptamer complex, and hence, the highest ion-aptamer interaction have been induced in the presence of Pb²⁺. The contact maps clarify the closer contacts between the nucleotides of the aptamer in the presence of Pb²⁺. The density functional theory (DFT) results show that Pb²⁺ forms the most stable complex with the aptamer, which is consistent with the MD results. The QM calculations reveal that the N-H bonds and the O…H distances are the longest and the shortest, respectively, in the presence of Pb²⁺. The obtained results verify that the strongest hydrogen bonds (HBs), and hence, the most compressed aptamer structure are induced by Pb²⁺. Besides, atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm the results.

Communicated by Ramaswamy H. Sarma     

Active site modeling in copper azurin molecular dynamics simulations

Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the polypeptide chain, using for the ligand residues a set of charges that is modified with respect to the apo form of the protein by the presence of the copper ion.The results show that the different charge values do not lead to relevant effects on the geometry of the active site of the protein, as long as bond distance constraints are used for all the five ligand atoms. The distance constraint on the O atom of Gly45 can be removed without altering the active site geometry. The coordination between Cu and the other axial ligand Met121 is outlined as being flexible. Differences are found between the bonds of the copper ion with the two apparently equivalent N¹ atoms of His46 and His117.The overall findings are discussed in connection with the issue of determining a model for the active site of azurin suitable to be used in molecular dynamics simulations under unfolding conditions. Figure Model of azurin active site. Copper ligand residues are cut off at C position except Gly45, for which the portion of backbone connecting it to His46 is shown. Only polar H atoms are shown. All atoms are in standard colors (Cu in violet), and the five ligands are labeled     

Synthesis, crystalline structure and photoluminescence investigations of the new trivalent rare earth complexes (Sm, Eu and Tb) containing 2-thiophenecarboxylate as sensitizer

New complexes with the general formula [RE(TPC)₃ · (H₂O)₂], where RE=Eu³⁺, Sm³⁺, Gd³⁺, Tb³⁺ and TPC=2-thiophenecarboxylate, have been prepared and investigated by photoluminescence spectroscopy. These compounds were characterized by complexometric titration, elemental analyses and infrared spectroscopy. The X-ray crystal structure has been determined for the [Eu(TPC)₃ · (H₂O)₂] compound, indicating that this complex is in dimeric form bridged by two carboxylate ions with monoclinic crystal system and space group P2₁/n. The coordination polyhedron can be described as a distorted square antiprism, where six oxygen atoms belong to the TPC ligand and two oxygen atoms belong to the water molecules, with site symmetry close to C_2v. The theoretical value of the intensity parameter , which is in agreement with the experimental one, indicates that the Eu³⁺ ion is in a highly polarizable chemical environment. Based on the luminescence spectra, the energy transfer from the ligand triplet state (T) of TPC to the excited levels of the Eu³⁺ ion is discussed. The emission quantum efficiency of the ⁵D₀ emitting level of the Eu³⁺ ion was also determined. In the case of the Tb³⁺ ion, the photoluminescence data show the high emission intensity of the characteristic transitions ⁵D₄ → ⁷F_J (J=0-6), indicating that the TPC ligand is a good sensitizer. It is also noticed that the complexes with the Eu³⁺ and Tb³⁺ ions are more luminescent than the complex with the Sm³⁺ ion.     

Structural preferences and thermal stability of complexes with the exo-bidentate ligand 1,2-bis(2-methylimidazol-1-ylmethyl)benzene

We describe a series of new coordination polymers of Cd(II), Co(II) and Ag(I) with 1,2-bis(2-methylimidazol-1-ylmethyl)benzene. All complexes were characterized by single crystal X-ray diffraction which reveals polymeric bridging of metal centers by the ligand in all cases. The cadmium center in complex 1 has a slightly irregular octahedral geometry involving two Cl⁻ ions and four N atoms from individual ligands, resulting in the formation of undulated (4,4) layers. In complex 2 the cobalt(II) ion is coordinated by two Cl⁻ ions and two N atoms from separate ligands. This yields a slightly irregular tetrahedral coordination environment around the metal center and the formation of a 1D zigzag-chain structure. Each of the three Ag(I) complexes (3-5) forms an infinite 1D chain. These three complexes are similar both in conformation and packing mode despite modification of the counterions. The size of the counterion appears to affect the thermal stabilities of the resulting networks.     

Further study of the effect of macrocyclic pendant groups on the supramolecular architecture: Synthesis and structures of macrocyclic nickel (II) complexes with trans-butene dicarboxylate

Two nickel (II) complexes with the formula [NiL(H₂O)₂] · 6H₂O (1 · 6H₂O) and [NiH₂L(BDC)]_n (2), where L = 3,10-bis(3-propylcarboxyl)-1,3,5,8,10,12-hexaazacyclo-tetradecane, BDC = trans-butene dicarboxylate, have been synthesized and characterized by elemental analyses, IR spectra and single-crystal X-ray analyses. In 1, the Ni(II) ion is six-coordinated with four nitrogen atoms from the macrocyclic ligand in the equatorial plane and two water molecules in axial position. In 2, the structure is made up of one-dimensional chain of [NiH₂L]²⁺ units with BDC²⁻ anions, in which the Ni(II) ion is also six-coordinated with four nitrogen atoms from the macrocyclic ligand in the equatorial plane and two carboxylate oxygen atoms from the BDC²⁻ group in axial position. In 2, the 1D chains are aligned in a parallel mode.     

Iron-iron interaction through an ethanedithiolate ligand: a magnetic and theoretical study

The compound ([CpFe(dppe)]₂[μ-SCH₂CH₂SS,S′])(PF₆)₂ ([1][PF₆]₂) has been synthesized and its magnetic properties have been investigated by susceptometer quantum interface device (SQUID) measurements in the temperature range 5-300 K. The d⁵-d⁵1²⁺ complex exhibits intramolecular antiferromagnetic behavior, with a magnetic coupling constant of −6.4 cm⁻¹. Density functional theory (DFT) calculations on a model of 1²⁺ (as well as on models of 1⁺ and 1) allow to determine its molecular structure and analyse its bonding and magnetic properties. The computed spin density exhibits significant localization on both the Fe and S centers. Replacing the heteroatoms of the bridging ligand by CH₂ groups leads to a relocalization of the spin density on the metal atoms and favors ferromagnetic coupling.     

A double helical dicopper(II) complex with biacetyl bis(benzoylhydrazone)

A dinuclear double helicate of copper(II) with the Schiff base biacetyl bis(benzoylhydrazone) (H₂babh) is reported. The solid state physical properties of the dicopper(II) species are compared with that of its mononuclear precursor. The O,N,N,O-donor babh²⁻ shows an unusual bridging coordination mode in [Cu₂(μ-babh)₂]. Each metal center in the complex is in very similar tetrahedrally distorted square-planar N₂O₂ coordination sphere assembled by the two halves of the two babh²⁻. To accommodate the metal centers, two halves of each ligand are twisted along the (CH₃)C-C(CH₃) bond.     

Ferromagnetic coupling by the spin-polarization mechanism in a trinuclear V triplesalen complex

The first trinuclear vanadium complex [(talen^t-Bu₂)(V^IVO)₃] (1) of a triple tetradentate triplesalen ligand has been synthesized and characterized. The triplesalen ligand (talen^t-Bu₂)^6- provides three salen-like coordination environments bridged in a meta-phenylene arrangement by a phloroglucinol backbone. In the electronic absorption spectrum of 1 all four ligand field transitions are detected below 21 400 cm⁻¹. The region above 23 000 cm⁻¹ is dominated by strong absorption from imine π → π^∗ and ligand-to-ligand CT transitions. The latter may also be described by a combined phenolate-to-vanadium LMCT and vanadium-to-imine MLCT through the empty metal d orbitals in a push-pull type interaction. The temperature-dependent magnetic susceptibility measurements reveal a ferromagnetic coupling of the three V^IVO units in the triplesalen complex with J = +0.44 cm⁻¹. The correlation of the electronic structure to the weakness of the ferromagnetic coupling by the spin-polarization mechanism in the trinuclear VO system is discussed.     

Synthesis and characterisation of [[μ-(1,7,11,17-tetraaza-2,6,12,16-tetraoxacycloeicosane)][(μ-(aquo)]bis[(acac)(ethanol)nickel(II)]] [BPh4]2

The pale blue title compound, 4, was obtained from the reaction between 1,7,11,17-tetraaza-2,6,12,16-tetraoxacycloeicosane, Ni(acac)₂ and NaBPh₄ in aqueous acetone. X-ray structure determination at 120 K revealed that the dication of the ionic complex, 4, contains two independent octahedral Ni^II centres with trans-Ni₂N₂O₄ chromophores. The macrocyclic ligand and an aqua ligand act as bridges to the two nickel centres: the Ni-O(aquo)-N bond angle is 137.65(17)°. Each Ni centre is bonded to two nitrogens of the macrocycle, to a chelating acac unit, to an ethanol molecule as well as the bridging oxygen of the aqua group. The two nickel atoms sit outside the macrocycle cavity, such that the macrocyclic ligand acts as a canopy for the remainder of the dication. While none of the macrocycle oxygens are involved in the coordination to Ni, they are involved in internal hydrogen bonding with the aqua and ethanol ligands. Magnetic measurements show a paramagnetic behaviour down to 2 K, with an effective moment of 2.8 Bohr magnetons at room temperature.     

Density functional theory studies on a designed photoactive {FeNO} nitrosyl and the corresponding photoinactive {FeNO} species: Insight into the origin of NO photolability

Density functional theory (DFT) and time-dependent DFT (TDDFT) studies on a photoactive {FeNO}⁶ nitrosyl [(PaPy₃)Fe(NO)](ClO₄)₂ (1) and the corresponding light-insensitive {FeNO}⁷ species [(PaPy₃)Fe(NO)](ClO₄) (2) have been carried out to determine the origin of NO photolability of 1. The iron center in these two nitrosyls formally exists in 2+ oxidation state and the difference in π-accepting ability of NO⁺ in 1 versus NO in 2 greatly affects the extent of NO photolability of these two nitrosyls. Low energy transitions from the carboxamido/π(FeNO) to the FeNO antibonding molecular orbitals lead to release of NO from 1 upon exposure to visible light. The decreased π-accepting ability of the NO moiety in 2 does not favor such transitions; instead transitions from orbitals centered at the FeNO unit to the π_py orbitals of the ligand frame become more favorable and the photolability of NO is lost in 2.     

Oxo-rhenium(V) complexes containing bis(diphenylphosphino)ethane and catecholate ligands

Bis(diphenylphosphino)ethane (dppe) complexes of the type ReOCl(dppe)(O-O), where O-O = catecholate or tetrachlorocatecholate dianion, were prepared by reacting ReOCl₃(dppe) with the catechol ligand in the presence of NEt₃. X-ray diffraction on the tetrachlorocatecholate compound showed that the molecule adopts a distorted octahedral structure, in which the dppe ligand and the bidentate catecholate lie in the equatorial plane, perpendicular to the ORe-Cl unit. In contrast, for ReOCl(PPh₃)₂(O-O), the position trans to the ReO bond is occupied by a catecholate oxygen, whereas the two PPh₃ ligands are trans to one another in the equatorial plane. The UV-Vis absorption spectrum of ReO(OMe)(dppe)(oxalate) is similar to those of ReO(OR)X₂(dppe) compounds, showing two weak bands for the spin-allowed d-d transitions from the filled interaxial d orbital in the xy plane into the inequivalent metal d_xz and d_yz orbitals, respectively. For the catecholate complexes, the spectra are dominated by charge-transfer transitions from the HOMO π orbital of the catecholate ligand into the d_xz and d_yz orbitals. Both the singlet-singlet and the singlet-triplet transitions are generally observed. No information could be obtained on the weaker d-d transitions for the catecholate compounds.     

Synthesis, crystal structure, hydrogen bonding and spectroscopy of Co, Mn and Ni oxalate complexes with the ligand (N,N′-bis(2-pyridylmethyl)-1,3-propanediamine)

Three new compounds are reported with the tetradentate ligand (N,N′-bis(2-Pyridylmethyl)-1,3-propanediamine) (abbreviated as pypn), two mononuclear compounds i.e. [Co(pypn)(C₂O₄)](ClO₄) (1), [Mn(pypn)(C₂O₄)](ClO₄) (2) and one dinuclear compound [Ni₂(pypn)₂(C₂O₄)](ClO₄)₂(C₂H₆O)_1/4(H₂O) (3). In the Co(III) and Mn(II) complexes the oxalate behaves as bidentate ligand, chelating the metal in the O,O′ mode, whereas in the Ni(II) compound the oxalate behaves as tetradentate ligand binding each Ni(II) ion by two oxygen atoms and bridging the two metallic centers.The synthesis, X-ray crystal structure of all three compounds and their spectroscopic properties are presented in detail. The geometry around the Co³⁺, Mn³⁺, Ni²⁺ ions is essentially octahedrally based, while the stabilization of the crystal lattice in all cases is maintained by interesting hydrogen bond systems.     

Synthesis and characterization of two new triazolate-aliphatic dicarboxylate bridged Zn(II) coordination polymers based on 2D layer motifs with different crystal packing

Two new zinc(II)-triazole-aliphatic dicarboxylate coordination polymers, [Zn(trz)(Hsuc)]_n (1), [Zn₂(trz)₂(tar)]_n (2), have been hydrothermally synthesized by reaction of Zn salt, Htrz with H₂suc and H₂tar, respectively (Htrz = 1,2,4-triazole, H₂suc = succinic acid, H₂tar = tartaric acid).Their structures were determined by single-crystal X-ray diffraction analyses and further characterized by X-ray powder diffraction, elemental analyses, IR spectra and TG analyses. Compound 1 displays a 2D layer structure containing {[Zn₄(trz)₄]⁴⁺}_n layers decorated by the suc ligand. Compound 2 is in a 3D structure formed by the interconnection of 2D {[Zn₄(trz)₄]⁴⁺}_n layers with tar ligand, resulting a 3,4-connected topological network. Due to the different coordination mode and conformation of aliphatic carboxylate ligand, the similar 2D {[Zn₄(trz)₄]⁴⁺}_n layers stack in the -AAA- fashion in 1, while the {[Zn₄(trz)₄]⁴⁺}_n layers hold together in the -ABAB- stacking sequence in 2. Additionally, the two compounds show strong fluorescence in the solid state at room temperature.