Home – Home – Jornals – Journal of Structural Chemistry 2014 number Приложение 2

Octahedral cluster complexes of transition metals are associated with halogen or chalcogen inner ligands to form edge-bridged {M₆(μ₂X)₁₂} or face-capped {M₆(μ₃-X)₈} cluster cores. The partial exchange of X atoms leading to mixed inner ligand environment invokes a distortion of metallic cluster, reduction of symmetry as well as an isomerism of the cluster cores. This review summarizes preparation methods of mixed ligand cluster complexes with the general formulas [{M₆(μ₂-X)₁₂}L₆]ⁿ or [{M₆(μ₃-X)₈}L₆]ⁿ and their structural features.

The crystal structure of previously unknown ammonium succinate peroxosolvate is studied. It is shown that it represents a rare example of the structure where H₂O₂ molecule forms two donor hydrogen bonds and does participate in any acceptor hydrogen bonds, despite the presence of substantial quantity of non-peroxide active hydrogen atoms.

A two-dimensional Cd(II) complex {[Cd(BTE)(PBEA)(H₂O)]×3H₂O}_n (1) (BTE = 2,2'-bis(1H-1,2,4-triazolyl)ether, H₂PBEA = benzene-1,4-diacetic acid) has been synthesised and characterised using single crystal X-ray diffraction, IR and elemental analysis. Single-crystal X-ray diffraction analysis revealed that complex 1 is a two-dimensional polymer based on the 24-membered rhomboid subunit [Cd₂(BTE)₂] with a Cd–Cd separation of 5.354 Å. More interestingly, there is a T4(2)6(2) water tape in complex 1. The thermal stability and luminescent properties of the title complex have been briefly investigated.

The crystallization products from the liquid phase of DClO₄×2D₂O (99 at.% D) on a silver chloride substrate were investigated by IR absorption spectroscopy. The conditions of crystallization and heat treatment of the resulting crystal film of D₅O₂⁺ClO₄^– (I) were varied to detect signs of polymorphism. The results of the study indicate the existence of four metastable crystalline phases for I. It is shown that the chain of transformations of the metastable phases initiated by heat treatment is accompanied by disturbances of the symmetry of the symmetry of the D₅O₂⁺ cation. The detected phase transformations are irreversible. The most stable metastable phase is isostructural with the well-known orthorhombic phase of D₅O₂⁺ClO₄^– The metastable nature of the orthorhombic phase is confirmed by the presence of a monotropic transition, which dramatically reduces the symmetry of the D₅O₂⁺ cation. The polymorphism typical of I disappears with the addition of more than 10 at.% of protium. Instead of the four metastable phases found for the deutertaed sample, only one orthorhombic phase crystallizes. Extraordinary stabilization by the addition of the protium isotope prevents polymorphic transition.

Optimized structures and vibration frequencies of H-bonded complexes formed by one or two molecules of CF₃COOH (or CF₃COO^– ion) with water molecules and the monomers and dimers of formic, acetic, trifluoroacetic, and tribromoacetic acids were calculated using density functional theory (B3LYP/6-31++G(d,p)). The results were compared with available experimental data on the vibrational spectra and equilibrium composition of the CF₃COOH—H₂O system and the acids listed above. The structure of the hydrated forms of CF₃COOH molecules and CF₃COO^– anions which are present in aqueous solutions of trifluoroacetic acid was determined. In these solutions at concentrations 100 % > [CF₃COOH] > 35 %, (CF₃COOH)₂×(H₂O)₂ cyclic tetramers form in which the acid and water molecules are arranged pairwise side-by-side, and starting at 75 % CF₃COOH, CF₃COO^–×(H₂O)₂ cyclic dihydrates of the anion are formed. The average strength of the hydrogen bonds in these heteroassociates is ~9–10 kcal/mol, and the properties and mutual position of their constituent molecules almost completely determine their vibrational spectra in solution. This approach provides a good reproduction of the IR and Raman spectra of molecular complexes, that have a cyclic structure and an average H–bond energy not less than 7 kcal/mole, in solution.

The compound Cs₂[Mo₂O₂S₂(C₃H₂O₄)₂(H₂O)₂]×2H₂O has been synthetized and isolated as single crystals. It crystallizes in the Pnma space group and the structural analysis reveals that all the components are held together to build a 3D compact layered network, evidencing that {Mo₂O₂S₂}–based molecular complexes can be used as building units for the elaboration of metal organic frameworks materials.

Trigonal pyramidal oxyanions, EO₃^2– (E = S, Se, Te), were utilized as a template in the formation of Ag₁₆ clusters, which dimerize via intermolecular Ag-S bonds to form a Ag₃₂ cluster stabilized by 1,1-dithiolate ligands. Structural elucidations on [Ag₁₆(EO₃){S₂P(OEt)₂}₁₂]²⁺ in comparison with tetrahedral oxyanion-centered Ag₁₆ clusters previously characterized from this group clearly suggest that the lone-pair electrons on chalcogen center has a structure-directing effect.

Reaction of [Cp*IrCl₂]₂ with (Me₃Si)₂S in the presence of moisture leads to the formation of a triangular cluster [Cp₃*Ir₃S₂]²⁺, which was isolated and characterized as supramolecular adduct [Cp₃*Ir₃S₂]Cl{(H₂O)(HSO₄)(H₂SO₄)}·CHCl₃ (1).

The structures of [Yb₅(dbm)₁₀(OH)₅]×2CH₂Cl₂ and [Er₅(dbm)₁₀(OH)₅]×6CH₂Cl₂ (dbm = dibenzoylmethanate) were established. The compounds are crystallized in different space groups P4/n and P2₁/n correspondingly. Ytterbium complex is isostructural to known [Ln₅(dbm)₁₀(OH)₅]×2C₇H₈ (Ln = Er, Yb). Structural type of erbium complex prepared in this work has no analogues amongst similar pentanuclear dibenzoylmethanate complexes. The cavities types of the structures filled by CH₂Cl₂ molecules are different.

Two double-chain chiral coordination polymers [Cu₂^I(bpy)₂(phlac)](NO₃)×H ₂O (1) and [Cu₂^I(bpy)₂(clman)](NO₃)×H₂O (2) were obtained by heating a DMF/H₂O solution of copper(II) nitrate, 4,4'–bipyridyl (bpy), S–3–phenyllactic (Hphlac) or R–3–chloromandelic (Hclman) acid. The compounds were structurally characterized by X–ray crystallography.

A supramolecular adduct [Mg(H₂O)₆](bdc)CB[6]·14H₂O (1) and the inclusion compound [dmf@CB[6]]·3HCOOH·4H₂O (2) were obtained from a mixture of magnesium chlorid (for compound 1) or magnesium sulfate (for compound 2), and cucurbit[6]uryl (CB[6]) in the presence of terephthalic or 4,4'-biphenildiarbonic acid in water. X-ray diffraction studies showed that magnesium cation in compound 1 form hydrogen bonds with oxygen atoms of the CB[6] molecule. When 4,4'-biphenildiarbonic acid was used instead of terephthalic acid under similar conditions of synthesis, no supramolecular adduct took place, rather an inclusion compound of DMF into the macrocyclic cavitand was formed. Compounds 1 and 2 were characterized by X-ray diffraction data, IR spectroscopy, and elemental analysis. Supramolecular adduct of hexaaqua magnesium cation with cucurbit[6]uril was isolated to the solid phase and structurally characterized for the first time.

Two new polyoxovanadoborates based crystalline lattices are being reported: K₅(H₃O)₂(1,3–diapH₂) ₂[V₁₂B₁₈O₆₀H₆]×10.80H₂O (1), and K₂(H₃O)₇(enH₂)[V₁₂B₁₈O₆₀H₆]×9H₂O (2). These structures are characterized by presenting multiple hydrogen bonds between the diprotonated diamines (enH₂ and 1,3–diapH₂) and hydronium ions, and the oxygen atoms of the [V₁₂B₁₈O₆₀H₆] cluster. The crystalline packing and stability of these new polyoxovanadoborates is dominated by the different types of hydrogen interactions present in the lattices ranging from unidirectional to trifurcated ones. The crystallographic data, together with the BVS method, permit to assign a mixed valence ratios for the [V₁₂B₁₈O₆₀H₆] anionic cluster for (1) and (2) being 11/1 (V^IV/V^V) ratio.

New coordination compounds based on 1,3,5–benzenetricarboxylate (btc^3–) and complex cations of copper(II) and nickel(II) with monodentate ligands {{[Cu(py)₃]₃(btc)₂}×4,5H₂O}_n (1) and {[Ni(py)₃(H₂O)]₃(btc)₂}_n (2) were obtained. The molecular and crystal structures of these compounds and their isomorphism were determined by X–ray diffraction analysis. Crystals of 1 and 2 are characterized by a layered structure due to the stacking of two-dimensional coordination-polymer layers interacting with each other through С–H···π non-covalent interactions and С–H···О weak hydrogen bonds. It is shown that these compounds are potentially highly porous materials with coordinatively unsaturated metal ions (Lewis acid sites).

Unusual pentanuclear copper cluster based on 1,2–diphosphacyclopentadienide ligand was first synthesized and characterized by X-ray diffraction analysis.

The preparation of a copper(I) iodide complex with a N-donor ligand 3–methyl–2–phenylpyridine of formula [CuI(3–methyl–2–phenylpyridine)₂] is described. The isolated complex was characterized by elemental analyses, IR spectroscopy and crystallographic studies. Single crystal X-Ray diffraction analysis of the complex reveal their monomeric tri-coordinated nature. The coordination polyhedron around the copper center may be described as a distorted trigonal planar geometry. The Cu–N distances for this compound are 1.984(7) and 1.982(7) Å, while the Cu-I distance is 2.5507(9) Å.

X-Ray structure determinations of three crystal forms of a 18–crown–6–containing styryl dye of the pyridine series in iodide form ( 1), containing various solvate molecules, namely water (1a), 2,6-dihydroxyoaphthalene (1b), 1,4–hydroquinone (1c), and analysis of crystal packings of these crystals, together with the previously investigated non-solvated form (crystal 1) and the solvates with benzene and water (crystal 1d) has been carried out. Crystal packing in 1a, 1b, 1c, and 1d involves a stacking leading to dimers of the dye cations, structurally preorganized for the [2+2]–photocycloaddition (PCA) reaction. On irradiation of with visible light, the PCA reaction with the centrosymmetric rctt isomer leads to the cyclobutane derivative formation. In the case of 1a and 1b the PCA proceeds with the retention of crystallinity, while with other solvates crystals are transformed into a glass. The glasses keep the form and the shine of the initial crystals, nevertheless. In the cases of the non–solvated crystal form (1), translation-related stacks form, with the geometry inconsistent with that of the preorganized dimer. These crystals are stable in visible light.

The molecular and crystal structure of 2–amino–1,1,4,5,6,7–hexafluoroindene–3–carbonitrile, its complex, and two polymorphic modifications of the complex of 2–amino–1,1,4,5,6,7–hexafluoro–3–trifluoroacetylindene with 1,4–dioxane were determined with X-ray diffraction analysis. The supramolecular architecture of the crystals was analyzed based on the interaction energies of molecular pairs calculated by the DFT (M06–2X/TZV) method using experimental crystal atomic coordinates.

The equimolar complexation behavior of urea or thiourea with 2–alcoxybenzamides has been studied by theoretical calculations. Structural models for the calculation were constructed from the X-ray crystallographic structures of 2–methoxybenzamide (MB) crystal and 2–ethoxybenzamide (EB)–thiourea, MB–thiourea, and MB–urea equimolar cocrystals. Structural optimization for EB–urea equimolar cocrystal was performed by the density functional theory (DFT) method (B3LYP/6–31G** level) and the complexation energy was determined using the DFT with higher order basis set (6–31+G**). Energetic stabilization by the equimolar complexation was observed in the three equimolar complexes. The reason why the amide group of MB is out–of–plane in unprocessed MB crystals is well explained by the calculations. It was suggested that intermolecular hydrogen bonding increases in the out–of–plane structure of MB and that subsequently leads to stabilization in the crystal. The amide group of MB or EB was in–plane by the complex formation with urea or thiourea. Finally, we predict the possibility of EB–urea equimolar complex formation in terms of the complexation energy.

The crystal structures of 12–hydroxynorfluorocurarine (vincanidine) isolated from the plant Vinca erecta, its hydrochloride monohydrate, quaternary salts — chloromethylate and iodomethylate, and the quaternary base (zwitterionic betaine) have been studied. The asymmetric centers of the molecules have the 3S, 7R, 15S configuration. In all cases, the carbonyl group is in a twisted orientation with respect to the N1H group and participates in the intramolecular H–bond with this group. In crystals, the 12–hydroxy group is involved in intermolecular interactions. The quaternary base of 12–hydroxynorfluorocurarine contains a zwitterionic form of the alkaloid due to deprotonation of the 12–hydroxyl group. The packing in the crystal structure of 12–hydroxynorfluorocurarine and the quaternary base contains voids (19.8 % and 21.8 % of the total volume of the crystal cell, respectively) of the channel type along the c crystallographic axis .

Synthesis of 5R*–(3–methoxy–phenyl)–3,7–dimethyl–5H–thiazolo[3,2–a]pyrimidine–2,6–dicarboxylic acid diethyl ester (2a) and 3,7–dimethyl–5S*–thiophen–2–yl–5H–thiazolo[3,2–a]pyrimidine–2,6–dicarboxylic acid diethyl ester (2b) are achieved by the cyclocondensation of 3,4–dihydropyrimidine–2–thione derivative with a-haloester. Preliminary analysis was done spectroscopically by means of ¹H NMR spectra, mass spectra and elemental analyses. Further the structures were confirmed by X-ray crystal structure analysis. The two molecules are not identical in configuration. In both the compounds the central pyrimidine ring adopts a conformation which is best described as an intermediate between a boat and screw boat form. The crystal structure is stabilized by intermolecular C–H…O and C–H…π weak interactions.

The crystal structure has been solved for a 1:1 molecular complex of 5–aminoisophthalic acid and 1,2–bis(4–pyridyl)ethane. Crystal data: C₂₀H₁₉N₃O₄, M = 365.38, orthorhombic, P2₁/n space group; unit cell parameters: a = 10.7521(6) Å, b = 11.9151(6) Å, c = 13.7645(8) Å, V = 1763.40(17) ų, Z = 4, d_x = 1.376 g/cm³, R₁ = 0.0514, T = 110 K. The 5–aminoisophthalic acid molecule is linked by O–H···N hydrogen bond to 1,2–bis(4–pyridyl)ethane, forming a linear hydrogen bonded chain running parallel to [0 3 0]. In the crystal, the intermolecular interactions link 5–aminoisophthalic acid molecules with head–to–head N–H···O hydrogen bonds generating R₂²(14) centrosymmetric dimers, which are extended head–to–tail via amine and carboxyl group N–H···O=C hydrogen bond. The supramolecular structure is consolidated by C–H···O hydrogen bonds and π···π interactions.

Quantum chemical and molecular dynamics simulation of a fragment of a sulfonated cation exchanger in the form of valinium salt has been performed. Contact ionic pair formation has been found.

The aggregation properties of supramolecular systems based on polyethyleneimines and cationic surfactants with a bicyclic head group — mono– and diquaternized derivatives of 1,4–diazabicyclo[2.2.2]octane are studied by surface tension measurements, potentiometry, conductivity measurement, and dynamic light scattering. The critical aggregation concentrations of individual and mixed systems based on them, as well as the size of the ensembles they form are determined. The relationship between the aggregation behavior and hydrophobicity of the polymer and the structure of the cationic surfactant is established.

Supramolecular systems based on tetracationic pyrimidine–containing surfactants of acyclic and macrocyclic structures with varying nature of the spacer were studied. The critical micelle concentrations (CMC) and the hydrodynamic diameter of aggregates were determined, and the packing of molecules in the surface layer was analyzed. Insignificant differences in the CMC with variation in the nature of the spacer and in the transition from acyclic to macrocyclic surfactants suggest elimination of the structural factor in the self-organization of the investigated compounds. The molecular packing is shown to change greatly in the transition from monomeric pyrimidinophane to oligomeric tetracationic amphiphiles.

The structure and properties of supramolecular complexes of α–chymotrypsin with hydroxyl-containing alkyl ammonium gemini surfactants (GSs) — α,ω–alkanedyl–bis(hydroxyethylmethylcetyl ammonium dibromides), with a polymethylene spacer of varying length have been studied. IR spectroscopy and tryptophan fluorescence data show that the interaction of GSs with α–chymotrypsin leads to changes of different intensity in the structural state of proteins. The most probable complexation mode of enzyme with GSs have been proposed by the molecular docking method. A correlation is found between the activity of α–chymotrypsin and the length of the GS spacer moiety. The enzyme activity correlates with the change in the substrate concentration in the aqueous phase of the surfactant micellar solution.

The structure of supramolecular complexes of poly–γ–benzyl–L–glutamate (PBG) with water and dioxane molecules during sorption from pure liquids and their binary mixtures is studied by IR spectroscopy and quantum chemical calculations. It is shown that the sorption sites of water and dioxane in PBG are different in nature. Water molecules are bound in the monomeric form to the carbonyl groups of the ester moieties of the side chains and the helical backbone of the peptide to form complexes with two hydrogen bonds. Dioxane molecules are sorbed in a large amount in the region of the side chains of PBG, causing their repacking with preservation of the helicity of the polypeptide backbone. Under simultaneous sorption of water and dioxane vapors, the binding of the latter increases the number of water molecules bound to the carbonyl groups of PBG. In this case, there is also an additional absorption of water molecules on the oxygen atoms of dioxane molecules. Calculations have shown that in the most probable configuration of the complexes, the water molecule simultaneously forms hydrogen bonds with the carbonyl groups of the side chain and the peptide backbone. Dioxane molecules do not penetrate to the peptide groups of helical backbone of PBG due to steric hindrance and are localized in the region of the benzyl moieties of the side chains; such complexes are stabilized by weak CH...O interactions.

The complex between carbonic anhydrase enzyme center (CA) and a derivative of fullerene as a nanoscale inhibitor (C60–Inh) has been investigated, based on, B3LYP level, using 6–31G* basis set. The results of calculations indicate that this special fullerene derivative could be deprotonated from three different positions and interacts with CA active site to form three CA–C60–Inh complexes. The calculated results indicate that deprotonated inhibitor is coordinated to the Zn²⁺ ion and all the complexes have tetrahedral geometry. The calculated binding energy (BD) and complexation energy clearly show the complex between C60–Inh and CA active site from N13 position is more favorable than the other position. Also thermodynamic functions such as standard enthalpy of complexation (ΔH⁰_com), standard entropy of complexation (ΔS⁰_com) and standard Gibbs free energy of complexation (ΔG⁰_com) for three CA–inhibitor complexes are evaluated. In order to approach the ideal geometry and provide further insight into the different complexation properties, the single point calculation at the B3LYP/6–311G** level have been used for all three different complexes to confirm the results of B3LYP/6–31G*. Thus, fullerene derivatives show a new class of nano scale carbonic anhydrase inhibitors that might find applications for targeting physiologically relevant isoforms of different forms of CA.