Formation Of Centrosymmetric Dimers Research Articles

Syntheses, Characterizations and Crystal Structures of Two New Racemic Amidophosphoesters: rac-(C6H5O)(cyclo-C6H11NH)P(O)N(C4H8)NP(O)(NH-cyclo-C6H11)(OC6H5) and rac-(p-CH3-C6H4NH)P(O)(OC6H4-p-CH3)(OC6H5)

The new racemic compounds, rac-diphenyl bis(cyclo-hexylamido)(piperazine)-1,4-diyldiphosphinate, C28H42N4O4P2 (I), and rac-phenyl(p-methylphenyl)(p-tolylamido)-phosphonate, C20H20NO3P (II), were synthesized and characterized by elemental analysis, 31P, 13C, 1H nuclear magnetic resonance, infrared spectroscopy and single-crystal X-ray diffraction analysis. The phosphorus atoms exhibit distorted tetrahedral environment [O]P=O[N][N] in I and [N]P=O[O][O] in II. In compound I, two (C6H5O)P(O)(NH-cyclo-C6H11) fragments are bridged via a NC4H8N linker that accepts chair conformation. In structure II, the environment of the P atom is a result of the linking of one amido and two different phenoxy groups bonded to the P atom. In crystal structure I, adjacent molecules are linked to each other through hydrogen bonds N–H⋅⋅⋅OP in a two-dimensional network along the ab plane, including $$R_{4}^{4}$$ (26) ring motifs, while in structure II, pairs of intermolecular hydrogen bonds N–H⋅⋅⋅OP lead to the formation of centrosymmetric dimers with the $$R_{2}^{2}$$ (8) graph-set motif.

Bromination of bis-(pyridin-2-yl) diselenide in methyl-ene chloride: the reaction mechanism and crystal structures of 1H-pyridine-2-selenenyl dibromide and its cyclo-adduct with cyclo-pentene (3aSR,9aRS)-2,3,3a,9a-tetra-hydro-1H-cyclo-penta-[4,5][1,3]selenazolo[3,2-a]pyridinium bromide.

1H-Pyridine-2-selenenyl dibromide, C5H5NSeBr2, 1, is a product of the bromination of bis-(pyridin-2-yl) diselenide in methyl-ene chloride recrystallization from methanol. Compound 1 is essentially zwitterionic: the negative charge resides on the SeBr2 moiety and the positive charge is delocalized over the pyridinium fragment. The C-Se distance of 1.927 (3) Å is typical of a single bond. The virtually linear Br-Se-Br moiety of 178.428 (15)° has symmetrical geometry, with Se-Br bonds of 2.5761 (4) and 2.5920 (4) Å, and is twisted by 63.79 (8)° relative to the pyridinium plane. The Se atom forms an inter-molecular Se⋯Br contact of 3.4326 (4) Å, adopting a distorted square-planar coordination. In the crystal, mol-ecules of 1 are linked by inter-molecular N-H⋯Br and C-H⋯Br hydrogen bonds, as well as by non-covalent Se⋯Br inter-actions, into a three-dimensional framework. (3aSR,(9aRS)-2,3,3a,9a-Tetra-hydro-1H-cyclo-penta[4,5][1,3]selenazolo[3,2-a]pyridinium-9 bromide, C10H12NSe+·Br-, 2, is a product of the cyclo-addition reaction of 1 with cyclo-pentene. Compound 2 is a salt containing a selenazolopyridinium cation and a bromide anion. Both five-membered rings of the cation adopt envelope conformations. The dihedral angle between the basal planes of these rings is 62.45 (11)°. The Se atom of the cation forms two additional non-covalent inter-actions with the bromide anions at distances of 3.2715 (4) and 3.5683 (3) Å, attaining a distorted square-planar coordination. In the crystal, the cations and anions of 2 form centrosymmetric dimers by non-covalent Se⋯Br inter-actions. The dimers are linked by weak C-H⋯Br hydrogen bonds into double layers parallel to (001).

Expanding the Family of Pyclen-Based Ligands Bearing Pendant Picolinate Arms for Lanthanide Complexation.

We report a detailed characterization of lanthanide complexes with two azaligands based on the pyclen macrocycle containing two picolinate and one acetate pendant arms. The two picolinate arms are attached to either opposite (L3) or adjacent (L4) amine nitrogen atoms of the macrocyclic platform. The X-ray structures of the Yb3+ complexes show nine coordination of the ligand to the metal ion, a situation that is also observed for EuL4 in the solid state. The EuL3 complex forms centrosymmetric dimers in the solid state joined by μ2-η1:η1 carboxylate groups, which results in 10-coordinate Eu3+ ions. The emission spectra of EuL3 measured in H2O and D2O solution reveal the presence of a hydration equilibrium involving a nine-coordinate species lacking inner-sphere water molecules and a monohydrated 10-coordinate species. The Eu3+ complexes present modest emission quantum yields in buffered aqueous solution (Φ = 16 and 22% for EuL3 and EuL4, 0.1 M tris buffer, pH 7.4), while the corresponding Tb3+ complexes present very high emission quantum yields under the same conditions (∼90%). 1H NMR studies show that the complexes of L3 present a fluxional behavior in D2O solution, while those of L4 are more rigid. The analysis of the Yb3+-induced NMR shifts of YbL4 indicates that the complex presents a structure in solution similar to that observed in the solid state. The Gd3+ complexes present very high thermodynamic stability constants (log KGdL = 23.56(2) and 23.44(2) for GdL3 and GdL4, respectively). The corresponding pGd values (pGd = -log[Gd3+]free with cL = 1 × 10-5 M and cGd = 1 × 10-6 at pH 7.4) of 20.69 (GdL3) and 21.83 (GdL4) are higher than that of Gd(dota)- (pGd = 19.21). The Gd3+ complexes also show remarkable inertness with respect to their proton-assisted dissociation, with dissociation half-life times of 50 min (GdL3) and 20 h (GdL4) in 1 M HCl.

Crystal structure of bis-(benzoato-κO)di-butyl-tin(IV), nBu2Sn(bzo)2.

The title compound, [Sn(C4H9)2(C6H5COO)2], was synthesized in order to study the inter-action between di-n-butyl-tin(IV) oxide and some carb-oxy-lic acids. Di-n-butyl-tin(IV) dibenzoate, nBu2Sn(obz)2, exhibits the same structural features as other diorganotin(IV) dibenzoates characterized by an unsymmetrical bidentate bonding mode [Δ(Sn-O) ≃ 0.4 Å] of the two benzoate groups to tin. In a first approximation, the coordination sphere at tin resulting from the two stronger bonded O atoms [2.1227 (17) and 2.1405 (16) Å] and the two α-C atoms of the n-butyl groups [2.125 (3) and 2.129 (2) Å] is compressed to a tetra-gonal disphenoid [〈(C-Sn-C) = 148.2 (1)° and 〈(O-Sn-O) = 82.01 (6)°]. This coordination sphere is expanded by the less strongly bonded two O atoms [2.507 (2) and 2.485 (2) Å] to a substanti-ally distorted octa-hedron and by a weak inter-molecular Sn⋯O inter-action [2.943 (2) Å] to a penta-gonal bipyramid with the formation of centrosymmetric dimers. The unbranched butyl groups adopt two different conformations: anti-gauche [torsion angles: 166.0 (2)-63.9 (4)°] and gauche-gauche [65.0 (3)-56.3 (3)°]. Inter-molecular inter-actions between the dimers are restricted to O⋯H-C contacts (2.64 Å) and van der Waals inter-actions.

Crystal structures of 3-(2H-1,3-benzodioxol-5-ylmethyl)-2-(m- and p-nitrophenyl)-1,3-thiazolidin-4-ones: different roles of the oxygen atoms

Abstract The crystal structures of two isomeric 3-(2H-1,3-benzodioxol-5-ylmethyl)-2-(aryl)-1,3-thiazolidin-4-one compounds (1: aryl=4-O2NC6H4; 2: aryl=3-O2NC6H4) are reported. In both these nonplanar, compounds, the carbonyl oxygen is involved in intramolecular C–H···O hydrogen bonds. However, there are significant differences in the sets of intermolecular interactions, in particular the roles of the oxygen atoms, exhibited by the two compounds. Thus in 1, a dioxolyl oxygen and the two nitro group oxygen atoms are each involved in different chain forming C–H···O intermolecular hydrogen bonds, while the carbonyl oxygen atom is not involved in any intermolecular interaction. In 2, the dioxolyl oxygen atom is involved in the formation of centrosymmetric dimers, the carbonyl oxygen in three different C–H···O hydrogen bonds and the nitro group oxygens in two N–O···π(aryl) interactions. Compound 2 exhibits also C–H···π(phenyl), π(phenyl)···π(phenyl) and π(benzodioxolyl)···π(benzodioxolyl) interactions, while in 1 only the latter interaction is present. Compound 1 crystallizes in the monoclinic space group, P21/a with Z=4, while compound 2 crystallizes in the triclinic space group, P1̅, with Z=2.

Synthesis, crystal and molecular structure of [Co(L)3](OH)Cl · H3Ssal) · H2O, where L is benzhydrazide and H3Ssal is 5-sulfosalycilic acid

The coordination compound [Co(L)3](OH)Cl(H3Ssal) · H2O (I) (L is benzhydrazide, and H3Ssal is 5-sulfosalycilic acid) has been synthesized and studied by IR spectroscopy and X-ray diffraction. Orange crystals are triclinic: a = 9.948(2) A, b = 12.288(3) A, c = 14.710(3) A, α = 109.39(3)°, β = 95.60(3)°, γ = 110.38(3)°, V = 1668.7(6) A3, Z = 2, space group \(P\bar 1\) Structural units of compound I are complex CoL32+ cations, OH− and Cl− anions, sulfosalycilic acid molecules, and an H2O molecule disordered over two positions and linked to each other by hydrogen bonds. Phenyl rings participate in π-π-stacking interaction with the formation of centrosymmetric dimers.

The fac diastereoisomer of tris(2-pyridinealdoximato)cobalt(III) and a cationic cobalt(III) complex containing both the neutral and anionic forms of the ligand: Synthetic, structural and spectroscopic studies

The study of the general reaction system Co(NO3)2·6H2O/Ln(NO3)3·6H2O (Ln=Tb, Dy, Ho, Er)/2-pyridinealdoxime (paoH)/Bun4NOH in MeCN under aerobic conditions provided access to fac-[CoIII(pao)3] (4). Starting from Co(II) sources, i.e. in the absence of LnIII ions, the known [Polyhedron 28 (2009) 1638] mer diastereoisomer, mer-[CoIII(pao)3] (3), could only be isolated. The crystallization of 4 is probably due to the formation of a mixed CoIII/LnIII species in solution, which already possesses the fac-{CoIII(pao)3} unit. The fac isomer 4 is converted readily to the mer-isomer 3, while the opposite transformation was not achieved under the reaction conditions employed. Complex [CoIII(pao)2(paoH)](ClO4) (5) was prepared in good yield from the aerobic reaction of Co(ClO4)2·6H2O and excess of paoH in MeOH. Treatment of 5 in MeCN/MeOH with one equivalent of base gives 3. The structures of the new complexes 4·MeCN and 5 have been determined by single-crystal X-ray crystallography. The distorted octahedral CoIII ion in 4 is coordinated by three N,N′-bidentate chelating ligands; the molecule is the facial diastereoisomer. The distorted octahedral CoIII center in the cation of 5 is coordinated by four nitrogen atoms of two pao− ligands and two nitrogen atoms of one neutral paoH molecule; the disposition of the donor atoms around the metal center is meridional. The cations [CoIII(pao)2(paoH)]+ form centrosymmetric dimers in the crystal lattice as a consequence of O(oxime)–H⋯O− (oximate) H bonds; the dimers form tetramers through weak C(oxime)–H⋯O(oxime) H-bonding interactions. Metric parameters show that the deprotonated oximato group of the pao− ligands in 4·MeCN and 5 is better described as ▪. Solid-state UV–Vis and IR data are discussed in terms of the low-spin octahedral stereochemistry of CoIII and the nature of bonding, respectively. The 1NMR spectrum of 4·MeCN in CDCl3 provides strong evidence of the fac→mer transformation in solution.

Molecular and crystal structures of p-heptyloxyphenyl p-hexyloxybenzoate and p-butyloxyphenyl p-heptyloxybenzoate: Mesophase design

Two aromatic esters with the formulas C6H13-O-C6H4-C(O)O-C6H4-O-C7H15 (1) and C7H15-O-C6H4-C(O)O-C6H4-O-C4H9 (2) belonging to nematic liquid-crystal compounds were studied by X-ray diffraction. Compound 1 crystallizes in two modifications: monoclinic (1-m) and triclinic (1-tr). The crystal packing of 1 and 2 is built from alternating loosely packed aliphatic regions and closely packed aromatic regions. In crystal structures 1-m and 2, the aromatic regions are linked into chains by hydrogen bonds with the participation of the carbonyl oxygen atom of the ester group and the C-H fragment of the benzene ring, but these hydrogen bonds in 1-m are much weaker than in 2. In 1-m there are π-stacking interactions between the molecules, resulting in the formation of centrosymmetric dimers with an interplanar distance of 3.45 A. In 1-tr, the aromatic fragments form a herringbone packing motif favorable for a two-dimensional network of directional C-H...π-system interactions.

6-(3-Chlorophenyl)imidazo[2,1-b][1,3,4]thiadiazole

In the title compound, C10H8ClN3S, the dihedral angle between the mean planes of the benzene and imidazo[2,1-b][1,3,4]thia­diazole rings is 6.0 (9)°. In the crystal, mol­ecules are assembled by the formation of centrosymmetric dimers by π-stacking of the thia­diazole and benzene rings of neighboring mol­ecules [centroid–centroid distance = 3.6938 (11) Å] along [010].

Structures of nitrato-(2-hydroxybenzaldehydo) (2,2′-bipyridyl)copper and nitrato-(2-hydroxy-5-nitrobenzaldehydo)(2,2′-bipyridyl)copper

Nitrato-(2-hydroxy-5-nitrobenzaldehydo)(2,2′-bipyridyl)copper (I) and nitrato-(2-hydroxybenzaldehydo)(2,2′-bipyridyl)copper (II) were synthesized and characterized by X-ray diffraction. The coordination polyhedron of the central copper atom in complex I can be described as a distorted tetragonal pyramid whose base is formed by the phenol and carbonyl oxygen atoms of the monodeprotonated 2-hydroxy-5nitrobenzaldehyde molecule and the nitrogen atoms of the 2,2′-bipyridyl ligand and whose apex is occupied by the oxygen atom of the nitrato group. In the crystal structure, complexes I are linked by the acido ligands and the NO2 groups of the aldehyde molecule into infinite chains. In complex II, the central copper atom is coordinated by 2-hydroxybenzaldehyde, 2,2′-bipyridyl, and the nitrato group, resulting in the formation of centrosymmetric dimers. The coordination polyhedron of the central copper atom can be described as a bipyramid (4 + 1 + 1) with the same base as in complex I. The axial vertices of the bipyramid are occupied by the oxygen atom of the nitrato group and the bridging phenol oxygen atom of the adjacent complex related to the initial complex by a center of symmetry. In the crystal structure, complexes II are hydrogen bonded into infinite chains.

N-(3-Methylphenyl)pyrimidin-2-amine

Two independent mol­ecules comprise the asymmetric unit in the title compound, C11H11N3. These differ in terms of the relative orientations of the aromatic rings: the first is somewhat twisted, while the second is approximately planar [dihedral angles between the pyrimidine and phenyl rings = 39.00 (8) and 4.59 (11)°]. The mol­ecules also form distinct patterns in their hydrogen bonding. The first independent mol­ecule forms centrosymmetric dimers featuring an eight-membered {HNCN}2 synthon. The second independent mol­ecule forms an N—H⋯N hydrogen bond with the other pyrimidine N atom of the first mol­ecule. Thereby, tetra­meric aggregates are formed. These associate via C—H⋯N and C—H⋯π inter­actions, consolidating the crystal packing.

Molecular conformation of the racemic indan derivative (±)-1-trans-3-(3,4-dichlorophenyl)-2,3-dihydro-1H-indene-1-carboxamide

This paper presents the structural characterization of the indan derivative (±)-1-trans-3-(3,4-dichlorophenyl)-2,3-dihydro-1H-indene-1-carboxamide, which was unambiguously determined by X-ray diffraction (XRD) to be a racemate (R/S: 50/50) crystallizing in an achiral crystal structure (P21/c, a = 9.3180(1) A, b = 7.9070(2) A, c = 19.7550(4) A, β = 103.250(1)°, V = 1416.75(5) A3 and Z = 4). The diastereomers are related by the inversion symmetry and linked by H bond forming a dimer. The crystal packing is stabilized by hydrogen bonds, including the classical one responsible for the formation of centrosymmetric dimers, and non-classical ones involving C–H···O and C–H···π-aryl interactions. The intra and intermolecular geometry of the title compound is compared to the (±)-1-trans-3-(3,4-dichlorophenyl)-2,3-dihydro-1H-indene-1-carboxylic acid one, which also present an achiral crystal structure from racemates (R/S: 50/50). The two indan derivatives crystallize in a very similar unit cell.

2-(2,4-Diphenyl-3-azabicyclo[3.3.1]nonan-9-ylidenehydrazono)-1,3-thiazolidin-4-one

In the title compound, C23H24N4OS, the piperidine and cyclo­hexane rings adopt twin chair conformations and the phenyl groups occupy equatorial positions. The dihedral angle between the two benzene rings is 10.25 (12)°. The crystal structure is stabilized by intermolecular N—H⋯O hydrogen bonds with the formation of centrosymmetric dimers.

A solution thermodynamic study of the Cu(II) and Zn(II) complexes of EBTA: X-ray crystal structure of the dimeric complex [Cu 2(EBTA)(H 2O) 3] 2

The copper(II) complex of the acyclic EBTA ligand (H 4EBTA = 1,2-bis(2-aminoethoxy)benzene- N, N, N′, N′-tetraacetic acid) has been prepared and characterized by X-ray analysis. The two copper ions of the dinuclear unit present the same distorted octahedral coordination polyhedra. The EBTA ligand is shared between two copper coordination centres, with the formation of centrosymmetric dimers, which are linked in a supramolecular tridimensional structure via additional interactions through the coordinated waters molecules with adjacent carboxylic oxygen atoms. The stability and protonation constants of EBTA with Cu(II) and Zn(II) ions indicate a higher stability of these complexes with respect to the corresponding complexes with the more flexible EGTA ligand (H 4EGTA = ethyleneglycol-bis(2-aminoethylether)- N, N, N′, N′-tetraacetic acid). On the other hand, the lower stability of [Gd(EBTA)] − than [Gd(EGTA)] − results in a decreased overall selectivity (lower K sel) of EBTA towards Gd(III) and suggests that this complex may undergoes transmetallation reactions under physiological conditions.

Crystal structures of copper(II) chloride, copper(II) bromide, and copper(II) nitrate complexes with pyridine-2-carbaldehyde thiosemicarbazone

The crystal structures of chloro-(2-formylpyridinethiosemicarbazono)copper dimethyl sulfoxide solvate (I), bromo-(2-formylpyridinethiosemicarbazono)copper (II), and (2-formylpyridinethiosemicarbazono)copper(II) nitrate dimethyl sulfoxide solvate (III) are determined using X-ray diffraction. In the crystals, complexes I and II form centrosymmetric dimers in which the thiosemicarbazone sulfur atom serves as a bridge and occupies the fifth coordination site of the copper atom of the neighboring complex related to the initial complex through the center of symmetry. In both cases, the coordination polyhedron of the complexing ion is a distorted tetragonal bipyramid. Complex III in the crystal structure forms polymer chains in which the copper atom of one complex forms the coordination bond with the thicarbamide nitrogen atom of the neighboring complex. In this structure, the coordination polyhedron of the central atom is an elongated tetragonal bipyramid. It is established that complexes I–III at a concentration of 10−5 mol/l selectively inhibit the growth of 60 to 90 percent of the cancer tumor cells of the human myeloid leukemia (HL-60).

α-Indolyl-β-nitroacrylates. Synthesis and structure

A one-pot procedure has been developed for the synthesis of α-indolyl-β-nitroacrylates by reaction of β-bromo-β-nitroacrilates with indole and substituted indoles. All indolylnitroacrilates thus obtained have Z configuration of the double bond. According to the X-ray diffraction data, ethyl 2-(1-methyl-1H-indol-3-yl)-3-nitroacrylate is characterized by s-trans conformation of the double C=C bond and indole ring; its crystal packing involves intermolecular hydrogen bonds C-H…O and C-H…π with formation of centrosymmetric dimers which give rise to bilayer supramolecular structures.

Low-temperature study of a new nevirapine pseudopolymorph

The title compound (systematic name: 11-cyclo­propyl-4-methyl-5,11-dihydro-6H-dipyrido[3,2-b:2′,3′-e][1,4]diazepin-6-one butanol 0.3-solvate), C15H14N4O·0.3C4H9OH, was crystallized in a new triclinic pseudopolymorphic form, a butanol solvate, and the crystal structure determined at 150 K. The mol­ecular conformation of this new form differs from that reported previously, although the main inter­molecular hydrogen-bond pattern remains the same. N—H⋯O hydrogen bonds [N⋯O = 2.957 (3) Å] form centrosymmetric dimers and the crystal packing of this new pseudopolymorph generates infinite channels along the b axis.

{1-[1-(3-Carboxypropanamido)ethyl]-1′,2-bis(diphenylphosphino)ferrocene-κ2P,P′}dichloridoplatinum(II) dichloromethane 1.25-solvate

The dinuclear title compound, [FePtCl2(C17H14P)(C23H23NO3P)]·1.25CH2Cl2, has a slightly distorted cis-PtCl2P2 square-planar geometry around the Pt atom, and the ferrocenylphosphine ligands are staggered at an angle of 29.4 (2)° about Pt. In the crystal structure, the complex forms centrosymmetric dimers via two strong inter­molecular O—H⋯O bonds resulting in R 2 2(8) rings. A weak intra­molecular N—H⋯Cl bond leads to an S(8) motif. The solvent is highly disordered and has not been modelled with discrete atoms.

5-(3,4-Dimethylphenylsulfonyl)-8-methoxy-2-methyl-2,3,5,6-tetrahydro-4H-2,6-methano-1,3-benzoxazocin-4-one

Mol­ecules of the title mol­ecule, C21H23NO5S, form centrosymmetric dimers via inter­molecular N—H⋯O bonds. In addition, there are inter­molecular C—H⋯O bonds. The eight-membered ring and both six-membered rings belonging to the tricycic ring system adopt a conformation which is intermediate between a sofa and a half-chair.

The conformation cis of N-acetyl-N-methyl-α,β-dehydroalanine N′-methylamide and saturated analogues

A series of three homologous amino acids derivatives: N-acetyl-N-methyl-α,β–dehydroalanine N′-methylamide (1), N-acetyl-N-methyl-L-alanine N′-methylamide (2), and N-acetyl-N-methyl-DL-alanine N′-methylamide have been synthesised. The racemic species undergoes spontaneous separation into L and D-enantiomers. From these two chiral forms, the structure of L-enantiomer (3) was analysed. The molecules of 1 – 3 adopt the cis arrangement of the N-terminal amide bond. The molecular conformations are similar for 1 (φ, ψ = 94.6(1)°, −1.7(1)°) and 3 (φ, ψ = 111.5(1)°, −23.8(1)°), and also 2 (φ, ψ = −114.8(2)°, 29.5(2)°), if inversion through the chiral C2 carbon is considered. They are stabilised by intramolecular N—H…N hydrogen bond. In the case of 1, the π—electron conjugation resulting from the planar arrangement of the C2—C21 double bond and C-terminal amide group is another stabilising force of this conformation. Thus, the N-methyldehydroalanine residue should promotes trans-cis isomerisation to a greater extend than the saturated analogue. The compounds 1 – 3 reveal similar associative pattern and form centrosymmetric dimers linked by the intermolecular N—H…O hydrogen bonds.