The molecular and electronic structure features of silatranes, germatranes, and their carbon analogs

Molecular geometries of fifty-six metallatranes N(CH₂CH₂Y)₃M-X and fifty-six carbon analogs HC(CH₂CH₂Y)₃M-X (M = Si, Ge; X = H, Me, OH, F; Y = CH₂, O, NH, NMe, NSiMe₃, PH, S) were optimized by the DFT method. Correlations between changes in the bond orbital populations, electron density ρ(r), electron density laplacian ∇²ρ(r), |λ₁|/λ₃ ratio, electronic energy density E(r), bond lengths, and displacement of the central atom from the plane of three equatorial substituents and the nature of substituents X and Y were studied. As the number of electronegative substituents at the central atom increases, the M←N, M-X, and M-Y bond lengths decrease, while the M←N bond strength and the electron density at critical points of the M←N, M-X, and M-Y bonds increase. An increase in electronegativity of a substituent (X or Y) is accompanied by a decrease in the ionicities of the other bonds (M-X, M-Y, and M←N) formed by the central atom (Si, Ge). A new molecular orbital diagram for bond formation is proposed, which takes into account the interaction of all five substituents at the central atom (M = Si, Ge) in atrane molecules. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 448–460, March, 2006.     

Hydroxid-halogenid-verbindungen des di-t-butyl-substituierten zinns

The di-t-butyltin hydroxide halides t-Bu₂Sn(OH)X (X = F, Cl or Br) have been prepared starting from the dihalides t-Bu₂SnX₂ or the oxide (t-Bu₂SnO)₃. X-Ray analysis of the three compounds shows dimeric molecules: two 5-coordinated tin atoms and the oxygen atoms of the hydroxyl groups are linked to a four-membered ring. As confirmed by the IR spectra, the molecules in the crystal are held together by OH?X hydrogen bonds. These are strong in the hydroxide fluoride but are weak in the analogous chloride and bromide.     

Nickel(II) and copper(II) complexes of 2,5-dimethyl-1,3,4-thiadiazole

Summary Nickel(II) and copper(II) complexes of 2,5-dimethyl-1,3,4-thiadiazole Ni(DTZ)X₂ (X = Cl or Br) and M(DTZ)₂X₂ (M = Ni, X = 1 or N03; M = Cu, X = Cl, Br or NO₃) have been prepared. The i.r. spectra show that in all the complexes the ligand is N,N- or N-bonded to the metal while the sulfur atom does not participate in coordination, and that the halide ions are coordinated forming terminal M-X bonds. The NO ₃ ^- group is coordinated in both the nitrato complexes. Magnetic moments of 3.07–3.29 B.M. for the nickel(II) and 1.86–1.92 B.M. for the copper(II) complexes were observed. The Ni(DTZ)X₂ complexes have a pseudo-tetrahedral [N₂X₂] coordination with N,N-bridging ligand molecules. The Ni(DTZ)₂X₂ and Cu(DTZ)₂X₂ complexes, with predominantly monodentate ligand, involve six-coordinate metal atoms with strong equatorial [N₂X₂] bonds and weaker axial bonds.Author to whom all correspondence should be directed.     

Concomitant polymorphism and conformational isomerism in 4‐acetylresorcinol

Two polymorphs of the title compound [systematic name: 1‐(2,4‐dihydroxyphenyl)ethanone], C₈H₈O₃, were investigated. The known structure [designated (I‐M); P2₁/c, Z = 4; previously investigated at room temperature by Robert, Moore, Eichhorn & Rillema (2007). Acta Cryst. E 63 , o4252] was redetermined at low temperature, and a new form [(I‐O); P2₁2₁2₁, Z = 12] was discovered in the same sample. In both forms, the molecules are planar (apart from the methyl H atoms) and they contain intramolecular O—H...O=C hydrogen bonds. In polymorph (I‐M), molecules are linked into chains by a single intermolecular O—H...O hydrogen bond, and the chains are linked into sheets by two C—H...O hydrogen bonds. Three O—H...O hydrogen bonds link the molecules of polymorph (I‐O) into chains and neighbouring chains are connected by one C—H...O interaction to form an offset layer structure. Two weak methyl C—H...O interactions link the layers.     

Bis[diaquabis(2,2‐bipyridine N,N′‐dioxide‐κ2O,O′)cobalt(II)] ξ‐octamolybdate dihydrate

The title organic–inorganic hybrid compound, [Co(C₁₀H₈N₂O₂)₂(H₂O)₂]₂[Mo₈O₂₆]·2H₂O, consists of [Co(bpdo)₂(H₂O)₂]²⁺ (bpdo is 2,2‐bipyridine N,N′‐dioxide) and ξ‐[Mo₈O₂₆]⁴⁻ groups in a 2:1 ratio, plus two water solvent molecules. The independent Co atom in the cation is coordinated by four O atoms from two bpdo ligands and two water molecules, in a distorted octahedral geometry. The counter‐anions, built up around a symmetry center, are linked by solvent water molecules through O—H...O hydrogen bonds to generate two‐dimensional layers, which are in turn linked by coordinated water molecules from the cationic units through further O—H...O hydrogen bonds, forming a three‐dimensional supramolecular structure.     

Zoledronic acid: monoclinic and triclinic polymorphs from powder diffraction data

The crystal structures of the monoclinic and triclinic polymorphs of zoledronic acid, C₅H₁₀N₂O₇P₂, have been established from laboratory powder X‐ray diffraction data. The molecules in both polymorphs are described as zwitterions, namely 1‐(2‐hydroxy‐2‐phosphonato‐2‐phosphonoethyl)‐1H‐imidazol‐3‐ium. Strong intermolecular hydrogen bonds (with donor–acceptor distances of 2.60 Å or less) link the molecules into layers, parallel to the (100) plane in the monoclinic polymorph and to the (10) plane in the triclinic polymorph. The phosphonic acid groups form the inner side of each layer, while the imidazolium groups lie to the outside of the layer, protruding in opposite directions. In both polymorphs, layers related by translation along [100] interact through weak hydrogen bonds (with donor–acceptor distances greater than 2.70 Å), forming three‐dimensional layered structures. In the monoclinic polymorph, there are hydrogen‐bonded centrosymmetric dimers linked by four strong O—H...O hydrogen bonds, which are not present in the triclinic polymorph.     

Evaluation of N—H…S and N—H…π interactions in O,O′‐diethyl N‐(2,4,6‐trimethylphenyl)thiophosphate: a combination of X‐ray crystallographic and theoretical studies

In the crystal structure of O,O′‐diethyl N‐(2,4,6‐trimethylphenyl)thiophosphate, C₁₃H₂₂NO₂PS, two symmetrically independent thiophosphoramide molecules are linked through N—H…S and N—H…π hydrogen bonds to form a noncentrosymmetric dimer, with Z′ = 2. The strengths of the hydrogen bonds were evaluated using density functional theory (DFT) at the M06‐2X level within the 6‐311++G(d,p) basis set, and by considering the quantum theory of atoms in molecules (QTAIM). It was found that the N—H…S hydrogen bond is slightly stronger than the N—H…π hydrogen bond. This is reflected in differences between the calculated N—H stretching frequencies of the isolated molecules and the frequencies of the same N—H units involved in the different hydrogen bonds of the hydrogen‐bonded dimer. For these hydrogen bonds, the corresponding charge transfers, i.e. lp (or π)→σ*, were studied, according to the second‐order perturbation theory in natural bond orbital (NBO) methodology. Hirshfeld surface analysis was applied for a detailed investigation of all the contacts participating in the crystal packing.     

A new type of benzotriazole coordination in carbonyl complexes of molybdenum

We report the synthesis of new complexes of molybdenum carbonyl with benzotriazole and 1-methylbenzotriazole in which heterocycles containing the NH or NCH₃ group still act as bidentate ligands.Crystals of the benzotriazole derivative were subjected to an X-ray study. Its structure is built of complex molecules (BtH)₃Mo₂(CO)₆ linked with THF molecules via hydrogen bonds. The molecule has the crystallographic symmetry C_s with the Mo atoms, two CO groups and one benzotriazole ligand in the symmetry plane.     

The PtX n Coordination Polyhedra (X = S,Se, Te) in Crystal Structures

Using the Voronoi–Dirichlet partition procedure and the method of intersecting spheres, it is demonstrated that in the crystal structures of chalcogen-containing compounds, Pt(IV) atoms form only PtX₆ octahedra (X = S, Se, Te), whereas in the case of Pt(III) and Pt(II), square coordination by X atoms is typical. The Pt(II) atoms can also form PtX₅ square pyramids (X = S, Se), PtS₆ octahedra, and PtTe₃Pt₃ quasi-octahedra in which a platinum atom is located in the trans-position to each coordinated tellurium atom. It was found that Pt(II) atoms in the PtX₄ squares (X = S, Se), unlike square-coordinated Pt(III) atoms, can form one or two Pt–M bonds (M is a d metal) and 1 to 4 secondary Pt–Q bonds, where Q is an s metal or hydrogen. The main features of platinum stereochemistry depending on the metal valence state and coordination number (CN) and on the nature of the chalcogen atom were quantitatively characterized in terms of the Voronoi–Dirichlet polyhedra.     

2‐Ethyl‐6‐methylpyridin‐3‐ol and its salt bis(2‐ethyl‐3‐hydroxy‐6‐methylpyridinium) succinate

The title compounds, C₈H₁₁NO, (I), and 2C₈H₁₂NO⁺·C₄H₄O₄²⁻, (II), both crystallize in the monoclinic space group P2₁/c. In the crystal structure of (I), intermolecular O—H...N hydrogen bonds combine the molecules into polymeric chains extending along the c axis. The chains are linked by C—H...π interactions between the methylene H atoms and the pyridine rings into polymeric layers parallel to the ac plane. In the crystal structure of (II), the succinate anion lies on an inversion centre. Its carboxylate groups interact with the 2‐ethyl‐3‐hydroxy‐6‐methylpyridinium cations via intermolecular N—H...O hydrogen bonds with the pyridine ring H atoms and O—H...O hydrogen bonds with the hydroxy H atoms to form polymeric chains, which extend along the [01] direction and comprise R₄⁴(18) hydrogen‐bonded ring motifs. These chains are linked to form a three‐dimensional network through nonclassical C—H...O hydrogen bonds between the pyridine ring H atoms and the hydroxy‐group O atoms of neighbouring cations. π–π interactions between the pyridine rings and C—H...π interactions between the methylene H atoms of the succinate anion and the pyridine rings are also present in this network.     

Sur les carbonates basiques de fer (III): II. Préparation,radiocristallographie et spectres IR. du (NH4)2Fe2(OH)4(CO3)2 · H2O

The obtention of the crystalline basic carbonate of iron (III) and ammonium, (NH₄)₂Fe₂(OH)₄(CO₃)₂ · H₂O, is described and its formula is established by chemical analysis and infrared spectroscopy. The powder X-ray diagram could be indexed tetragonally leading to a body centred elementary cell with a = 12,04 ± 0,02 Å and c = 6,62 ± 0,01 Å. The infrared spectra show that in the CO groups either one oxygen atom is linked to one iron atom or, rather, two oxygen atoms are linked to two iron atoms. The symmetry of the NH groups is lower than C_3v. The OH-groups are linked by hydrogen bonds of 2,75 Å. Two sorts of OH-groups can be distinguished, with a radius of approximately 1,34 Å and 1, 48 Å, respectively. The iron atoms are octahedrally coordinated by oxygen atoms, but either the octahedra are deformed or the iron atoms are in part coordinated tetrahedrally.     

Two two‐dimensional hydrogen‐bonded coordination networks: bis(3‐carboxybenzoato‐κO)bis(4‐methyl‐1H‐imidazole‐κN3)copper(II) and bis(3‐methylbenzoato‐κN)bis(4‐methyl‐1H‐imidazole‐κN3)copper(II) monohydrate

The title two‐dimensional hydrogen‐bonded coordination compounds, [Cu(C₈H₅O₄)₂(C₄H₆N₂)₂], (I), and [Cu(C₈H₇O₂)₂(C₄H₆N₂)₂]·H₂O, (II), have been synthesized and structurally characterized. The molecule of complex (I) lies across an inversion centre, and the Cu²⁺ ion is coordinated by two N atoms from two 4‐methyl‐1H‐imidazole (4‐MeIM) molecules and two O atoms from two 3‐carboxybenzoate (HBDC⁻) anions in a square‐planar geometry. Adjacent molecules are linked through intermolecular N—H...O and O—H...O hydrogen bonds into a two‐dimensional sheet with (4,4) topology. In the asymmetric part of the unit cell of (II) there are two symmetry‐independent molecules, in which each Cu²⁺ ion is also coordinated by two N atoms from two 4‐MeIM molecules and two O atoms from two 3‐methylbenzoate (3‐MeBC⁻) anions in a square‐planar coordination. Two neutral complex molecules are held together via N—H...O(carboxylate) hydrogen bonds to generate a dimeric pair, which is further linked via discrete water molecules into a two‐dimensional network with the Schläfli symbol (4³)₂(4⁶,6⁶,8³). In both compounds, as well as the strong intermolecular hydrogen bonds, π–π interactions also stabilize the crystal stacking.     

Hydrogen‐bonding patterns in two aroylthiocarbamates and two aroylimidothiocarbonates

In O‐ethyl N‐benzoylthiocarbamate, C₁₀H₁₁NO₂S, the molecules are linked into sheets by a combination of two‐centre N—H...O and C—H...S hydrogen bonds and a three‐centre C—H...(O,S) hydrogen bond. A combination of two‐centre N—H...O and C—H...O hydrogen bonds links the molecules of O‐ethyl N‐(4‐methylbenzoyl)thiocarbamate, C₁₁H₁₃NO₂S, into chains of rings, which are linked into sheets by an aromatic π–π stacking interaction. In O,S‐diethyl N‐(4‐methylbenzoyl)imidothiocarbonate, C₁₃H₁₇NO₂S, pairs of molecules are linked into centrosymmetric dimers by pairs of symmetry‐related C—H...π(arene) hydrogen bonds, while the molecules of O,S‐diethyl N‐(4‐chlorobenzoyl)imidothiocarbonate, C₁₂H₁₄ClNO₂S, are linked by a single C—H...O hydrogen bond into simple chains, pairs of which are linked by an aromatic π–π stacking interaction to form a ladder‐type structure.     

Trinitratobis{N′‐[1‐(2‐pyridyl)ethylidene]isonicotinohydrazide}cerium(III): a three‐dimensional cerium–organic supramolecular structure

The Ce^III ion in the title complex, [Ce(NO₃)₃(C₁₃H₁₂N₄O)₂], is 12‐coordinated by six chelating nitrate O atoms and six donors (2 O and 4 N atoms) of two N′‐[1‐(2‐pyridyl)ethylidene]isonicotinohydrazide ligands, exhibiting a bicapped pentagonal‐antiprism‐type coordination geometry. The title complex possesses C₂ point symmetry and is located on a twofold crystallographic axis. Each molecule is linked with four surrounding molecules by four N—H...N hydrogen bonds, resulting in an extended two‐dimensional layer parallel to the ab plane, while π–π interactions between pyridine rings from neighboring complex molecules connect the two‐dimensional layers into a three‐dimensional cerium–organic supramolecular structure.     

2,12‐Dichloro‐10,20‐diphenyl‐5,7,15,17‐tetrahydro‐6H,16H‐dibenzo[d,l][1,9,2,6,10,14]dioxotetraazacyclohexadecine‐6,16‐dione dioxane solvate as a potential macrocyclic hexadentate ligand

The macrocyclic title compound crystallizes as a dioxane solvate, C₃₀H₂₂Cl₂N₄O₄·C₄H₈O₂, with two independent formula units in the unit cell. The observed syn conformation is controlled by both intramolecular N—H...O hydrogen bonds and intermolecular C—H...π interactions. The relative macrocyclic inner bore is estimated to be 4.19 Å. In the crystal structure, molecules form dimers via intermolecular C—H...π interactions, and these dimers are, in turn, linked to form columns along the a axis by intermolecular C—H...O hydrogen bonds. Both X‐ray diffraction analysis and density functional theory (DFT) calculations reveal that the macrocycle possesses very high flexibility. This property, as well as the presence of six donor atoms accessible for coordination, makes the title macrocycle a very promising ligand for complexation with the majority of transition metals.     

Replacing the hydrogen in the intermolecular hydrogen bond of the cyanuric acid-bipyridyl adduct by Ag(I)

A complex between cyanuric acid (CA), 4,4′-bipyridyl (BP) and Ag(I), with the composition, [Ag₂(C₃H₂N₃O₃-κN)₂ (C₁₀H₈N₂-κN)] has been prepared. Crystal structure analysis shows that it has a chain structure in which the CA molecules are linked to the BP units through silver atoms by the formation of N-Ag-N bonds, wherein one of the hydrogens of CA is replaced by Ag(I), showing thereby the chains connected to one another by N-H...O hydrogen bonds formed between the CA molecules. This intermolecular chain structure resembles the chain structure of the CA.BP adduct where CA-BP-CA chains formed by N-H...N hydrogen bonds are linked to one another by N-H...O hydrogen bonds between the CA molecules.     

4,6‐Diaminopyrimidine‐2(1H)‐thione hemihydrate: a three‐dimensional hydrogen‐bonded framework

In the title compound, C₄H₆N₄S·0.5H₂O, there are two independent pyrimidinethione units, both of which lie across mirror planes in the space group Cmca. Hence, the H atoms bonded to the ring N atoms in each molecule are disordered over two symmetry‐related sites, each having an occupancy of 0.5. The water molecule lies across a twofold rotation axis parallel to [010]. The molecular components of (I) are linked by seven independent hydrogen bonds, of N—H...N, N—H...S, N—H...O and O—H...S types. A combination of disordered N—H...N hydrogen bonds and ordered N—H...S hydrogen bonds links the pyrimidinethione units into a continuous tubular structure. The water molecule acts as both a double donor of hydrogen bonds and a double acceptor, forming hydrogen bonds with components of four distinct pyrimidinethione tubes, thus linking these tubes into a three‐dimensional structure.     

Two polymorphs of N‐(2‐methoxyphenyl)‐4‐oxo‐4H‐chromone‐3‐carboxamide

The title compound, C₁₇H₁₃NO₄, crystallizes in two polymorphic forms, each with two molecules in the asymmetric unit and in the monoclinic space group P2₁/c. All of the molecules have intramolecular hydrogen bonds involving the amide group. The amide N atoms act as donors to the carbonyl group of the pyrone and also to the methoxy group of the benzene ring. The carbonyl O atom of the amide group acts as an acceptor of the β and β′ C atoms belonging to the aromatic rings. These intramolecular hydrogen bonds have a profound effect on the molecular conformation. In one polymorph, the molecules in the asymmetric unit are linked to form dimers by weak C—H...O interactions. In the other, the molecules in the asymmetric unit are linked by a single weak C—H...O hydrogen bond. Two of these units are linked to form centrosymmetric tetramers by a second weak C—H...O interaction. Further interactions of this type link the molecules into chains, so forming a three‐dimensional network. These interactions in both polymorphs are supplemented by π–π interactions between the chromone rings and between the chromone and methoxyphenyl rings.     

1,3‐Bis(ethylamino)‐2‐nitrobenzene, 1,3‐bis(n‐octylamino)‐2‐nitrobenzene and 4‐ethylamino‐2‐methyl‐1H‐benzimidazole

1,3‐Bis(ethylamino)‐2‐nitrobenzene, C₁₀H₁₅N₃O₂, (I), and 1,3‐bis(n‐octylamino)‐2‐nitrobenzene, C₂₂H₃₉N₃O₂, (II), are the first structurally characterized 1,3‐bis(n‐alkylamino)‐2‐nitrobenzenes. Both molecules are bisected though the nitro N atom and the 2‐C and 5‐C atoms of the ring by twofold rotation axes. Both display intramolecular N—H...O hydrogen bonds between the amine and nitro groups, but no intermolecular hydrogen bonding. The nearly planar molecules pack into flat layers ca 3.4 Å apart that interact by hydrophobic interactions involving the n‐alkyl groups rather than by π–π interactions between the rings. The intra‐ and intermolecular interactions in these molecules are of interest in understanding the physical properties of polymers made from them. Upon heating in the presence of anhydrous potassium carbonate in dimethylacetamide, (I) and (II) cyclize with formal loss of hydrogen peroxide to form substituted benzimidazoles. Thus, 4‐ethylamino‐2‐methyl‐1H‐benzimidazole, C₁₀H₁₃N₃, (III), was obtained from (I) under these reaction conditions. Compound (III) contains two independent molecules with no imposed internal symmetry. The molecules are linked into chains via N—H...N hydrogen bonds involving the imidazole rings, while the ethylamino groups do not participate in any hydrogen bonding. This is the first reported structure of a benzimidazole derivative with 4‐amino and 2‐alkyl substituents.     

catena‐Poly­[[di­aqua­cobalt(II)]‐μ‐oxalato]

Single crystals of the title compound, [Co(C₂O₄)(H₂O)₂]_n, have been prepared by hydro­thermal methods and characterized by X‐ray diffraction analysis. The crystal structure consists of infinite one‐dimensional chains of di­aqua­cobalt(II) units bridged by oxalate groups. These chains lie on twofold symmetry axes parallel to the b axis, and the [Co(C₂O₄)]_n system is nearly planar within experimental error. The cobalt(II) coordination polyhedra are irregular octahedra, with oxalate O atoms at the equatorial positions and water mol­ecules at the axial positions. The chains are linked by hydrogen bonds via the water mol­ecules.