Synthese und Röntgenkristallstruktur eines (15E)-Dihydrobilatrien-abc-Derivats

The crystal structure of the (15E)-configurated 2,3-dihydrobilatriene-abc2, representing a model compound for the active form of the phytochrome chromophore, was determined at room temperature and at 97 K. Compared to the crystal structure of the corresponding (15Z)-derivative1, the molecule of2 shows a similar helix conformation, but with considerably larger helix pitch. The azide hydrogen atoms are localized at the nitrogen atoms of rings A, C and D. The distribution of bond lengths and bond angles is compatible with previous crystal structures and with the canonical formula. Tautomeric form, conformation and crystal packing are understandable on the basis of the observed intra- and intermolecular hydrogen bonds.

     

Crystal and moleclar structures of 5-allyl-25-methoxy-26,27,28-tribenzoylcalix[4]arene

The crystal and molecular structures of 5-allyl-25-methoxy-26,27,28-tribenzoylcalix[4]arene, an unsymmetrically substituted macrocycle, are reported. The space group is orthorhombic,P2₁2₁2₁, witha=13.4181(6),b=16.6652(10) andc=18.9936(14) Å andZ=4. Refinement by least-squares calculations converged with aR=0.060 for 4018 observed reflections. The molecule assumes a 1,3 alternate conformation with 2 benzoate rings and the disordered allyl side chain on one side and the third benzoate ring and the methoxy group on the opposite side of the mean plane of the methylene bridging groups. The four phenyl rings that comprise the macrocycle are approximately parallel in pairs; the members of a pair are 5.6 Å apart. The carbonyl oxygen atoms of the 3 benzoate groups are oriented away from the center of the cavity while the ester oxygen atoms and the methoxy oxygen atom are oriented toward the cavity center. Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82033 (26 pages).     

Molecular structures and spectroscopic characterization of cobalt(III) and nickel(II) complexes of <Emphasis Type="Italic">N</Emphasis>-(2-hydroxyethyl)-2-(thiophene-2-ylmethylene)-hydrazinecarbothioamide

Two complexes of a thiosemicarbazone ligand, namely N-(2-hydroxyethyl)-2-(thiophene-2-ylmethylene)-hydrazinecarbothioamide (HL), have been synthesized. The complexes have been characterized by physico-chemical and spectroscopic methods. The crystal and molecular structures of [CoL₃]·2MeOH (1) and [NiL₂] (2) have been determined by X-ray diffraction studies. For both complexes, the metal is coordinated through the sulfur and azomethine nitrogen atoms of the thiosemicarbazone. The ligand exists in its thiolate tautomeric form, and the central Co(III) and Ni(II) atoms have distorted octahedral and square planar geometries, respectively, with five-membered chelate rings formed by the ligand. The lattice of 1 shows infinite oxygen donor/acceptor hydrogen bonds in the ab plane and weak interactions between rings along the c axis, respectively, giving a supramolecular network. The molecular units in 2 are linked together by hydrogen bonds between the hydroxyl oxygen and hydrazone N proton, giving rise to an infinite ribbon extended along the c-axis. These chains are connected by N3–H3···O1 interactions that form a sheet within the ac plane.     

Synthesis,crystal structure,and spectra of the trichloromethane solvate of nickel(II) 9(E)-phenanthrene-9,10-dione[(1Z)-3,3-dimethyl-3,4-dihydroisoquinolin-1(2H)-ylidene]hydrazonate

The complex [Ni(L-H)₂] · CHCl₃ (I), where L-H is the (9E)-phenanthrene-9,10-dione[(1Z)-3,3-dimethyl-3,4-dihydroisoquinolin-1(2H)-ylidene]hydrazone anion (L), was synthesized for the first time. The crystal structure of I was solved. The L-H and L-H′ anions exist as cis- and trans-isomers and are linked to the central Ni²⁺ atom in a tridentate chelating mode giving rise to two conjugated five-membered metal rings of different composition (NiN₃C and NiONC₂) at each anion. The Ni²⁺ coordination polyhedron is a highly distorted octahedron whose axial positions are occupied by N(3) and N(3)′ atoms. The vertices of the tetrahedrally distorted equatorial base of the octahedron are occupied by the N(1) and N(1)′ atoms of the dihydroisoquinoline fragment (A) and the O(1) and O(1)′ atoms of the phenanthrenequinone fragment (B). Complex I occurs as the cis-isomer. The conformations of the L-H anions in I and the L molecules in L · H₂O do not differ much. The randomly disordered CHCl₃ solvent molecules in I occupy crystal voids between the centrosymmetric dimeric associates. Spectroscopic (IR and UV-Vis) characteristics of I were obtained.     

Syntheses and structures of three new coordination polymers with the flexible 1,2-bis(1,2,4-triazol-1-yl)ethane ligand

Three new coordination polymers {[Ni(bte)₂(NCO)₂](H₂O)} _n (1), {[Ni(bte)₂(N₃)₂](H₂O)} _n (2) and {[Ag(bte)₂](NO₃)} _n (3) (bte?=?1,2-bis(1,2,4-triazol-1-yl)ethane) were synthesized and characterized by X-ray crystallography, IR and thermogravimetric analysis. The coordination geometry of the Ni(II) atom is distorted octahedral, coordinated equatorially by four nitrogen atoms from four triazole rings of four symmetry-related bte ligands, and axially by two nitrogen atoms from two isocyanate anions in 1 and azide anions in 2, respectively. The structures of 1 and 2 are both polymeric, with 18-membered spiro-fused rings and each 18-membered ring involving two inversion-related bte molecules. The coordination geometry of the Ag(I) atom in 3 is distorted tetrahedral, formed by four nitrogen atoms from four triazole rings of four symmetry-related bte ligands. Each bte ligand links two Ag(I) atoms and forms a two-dimensional undulated (4,4) network in 3.     

Structures and magnetic properties of two new heterospin complexes involving nitroxide radicals and oxamido-bridged copper(II)

Two new binuclear copper(II) complexes containing four spin carriers with pyridyl-substituted nitroxide radicals have been synthesized and characterized structurally and magnetically. These complexes are formulated as [Cu₂(oxap)(IM4py)₂](ClO₄)₂ (1) and [Cu₂(oxap)(NIT4py)₂](ClO₄)₂ (2), respectively, in which oxap stands for N,N′-bis(2-aminopropyl). IM4py stands for 2-(4′-pyridyl)-4,4,5,5-tetramethylimidazoline-1-oxyl and NIT4py for 2-(4′-pyridyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide. The structures of the complexes consist of centro-symmetric trans oxamido-bridged copper(II) binuclear units and nitroxide radicals. In 1 and 2 the copper atoms are in a distorted square plane and radicals (IM4py and NIT4py) coordinate to copper via nitrogen atoms from pyridine rings. Magnetic analysis indicates that 1 and 2 exhibit strong metal-metal antiferromagnetic coupling through oxamido-bridged and antiferromagnetic exchange interactions between copper(II) ion and radicals, respectively. The magnetic behaviors are discussed with reference to their crystal structures.     

The Crystal Structure of YPdSi,the Isotypic Compounds LnPdSi (Ln = Gd–Lu), and their Structural Relation to some other Equiatomic Compounds of the Rare Earth and Transition Metals with Main Group Elements

The nine title compounds were prepared from the elements by arc-melting and subsequent heat treatment in resistance and high-frequency furnaces. The crystal structure of these isotypic compounds was determined for YPdSi from single-crystal X-ray diffractometer data: Pmmn, a = 430.8(1) pm, b = 1391.2(1) pm, c = 743.1(1) pm, Z = 8, R = 0.024 for 417 structure factors and 40 variable parameters. The crystal structures of the isotypic compounds GdPdSi and ErPdSi were also refined from single-crystal data. The structure is of a new type. It consists of condensed, six-membered rings of alternating palladium and silicon atoms with Pd–Si bond distances varying between 249.6 and 258.8 pm. These two-dimensionally infinite nets are connected to each other via weak Pd–Si and Si–Si bonds with bond distances of 276.3 and 259.5 pm. The rare earth atoms are situated above and below the six-membered palladium-silicon rings in a manner as it is known for the aluminum atoms in the AlB₂ type structure. The crystal-chemical similarities and topologies of several structures derived from the aristotype AlB₂ (including those of BaPtSb, EuAuGe, KHg₂, ZrBeSi, and TiNiSi) are described, emphasizing their group-subgroup relationships. The previously reported compound ”︁Er₂Pd₂Si”︁”︁ has the same structure as has been found here for ErPdSi.     

THE CRYSTAL STRUCTURES OF 10,10′-BIS(PHENOXARSINE) OXIDE AND SELENIDE

Abstract

The reaction between 10,10′-bis(phenoxarsine) oxide (I) and HI gives 10-iodophenoxarsine. The latter, on treatment with H₂Se give 10,10′-bis(phenoxarsine) selenide (II). The crystal structures of I and II have been determined from single crystal X-ray data. The unit cell for I is monoclinic, P2₁/c (No. 14) with a = 15.976(3) Å, b = 10.582(2) Å, c = 12.581(2) Å, β = 111.70(1)° V = 2018.6 ų; d(calc.) = 1.65Mg/m³ at 23°C for four molecules per unit cell. From 3279 reflections for which I>0.5σ(I), F>σ(F), R = 0.041 with anisotropic thermal parameters for all non-hydrogen atoms and with fixed positions and thermal parameters for hydrogens. One of the phenoxarsina rings deviates from planarity by approximately 5° while the other deviates by more than 24°. The (As[sbnd]O) distances are 1.810(3) and 1.821(3) Å for the flat and bent ring and the (As[sbnd]O[sbnd]As) angle is 122.3(1)°. The bond distances to As and O from C are nearly the same for both rings, but the bond angles with As and the ring O as the apex are systematically larger for the flat ring. For II the unit cell is triclinic, P1 (No. 2) with a = 9.368(1) Å, b = 14.089 Å, c = 9.269(2) Å, α = 111.37(2), β = 113.11(2), γ = 74.76(1); V = 1037.5 ų, d(calc) = 1.81 Mg/m³ for two molecules per unit cell at 23°C. From 2945 reflections for which I > 0.5σ(I), F > σ(F), R = 0.055 with anisotropic thermal parameters for all non-hydrogen atoms and with fixed positions and thermal parameters for hydrogen. One of the phenoxarsina rings deviates by 3° from planarity and the other by 8°. The (As[sbnd]Se) bond distances are 2.416(1) and 2.406(1) Å. The (As[sbnd]Se[sbnd]As) bond angle is 96.66(4)° and the corresponding (As[sbnd]C) and (C[sbnd]C) distances in the two rings are nearly the same. In comparison with I, the angles with As or O as the central atoms are about the same in both rings of II.     

Synthesis and Crystal Structure of a Polymeric Benzimidazole Complex of Mn(II) Bridged by Succinate

The title complex has been prepared and its crystal structure determined by X-ray diffraction methods. The Mn (II) complex is seven coordinate with two benzimidazole (bimid)ligands in axial positions and two succinate and one bimid ligands in the equatorial plane. The succinate bridges Mn (II) atoms to form polymeric chains, linked by intermolecular H-bonding. Free bimid molecules occur in the crystal structure; they link Mn (II) complexes with H-bonds involving N atoms. Aromatic stacking between bimid rings is observed, resulting in a gauche confirmation of succinate in the structure. The IR spectrum is assigned based on the crystal structure. The difference of 139cm^-1 between symmetric and asymmetric stretching vibrations of carboxyl groups is in line with seven coordination at the Mn (II) atom.     

On the Macrolactonization of β-Hydroxy Acids. Crystal structures of the pentolide and the hexolide from (R)-3-hydroxybutanoic acid. Molecular modeling studies of the tetrolide

The temperature and concentration dependence of the previously reported formation of oligolides from (R)- or (S)-3-hydroxybutanoic acid under Yamaguchi's macrolactonization conditions (2,4,6-trichlorobenzoyl chloride/base) was studied. While the content of hexolide 2 in the product mixture is almost invariably ca. 35%, the amounts of pentolide 1 and of the larger rings strongly depend upon the temperature employed (Fig.1). Cyclic oligomers ( 5,6 ) are also obtained from 3-hydroxypentanoic acid. Enantiomerically pure β-butyrolactone can be used for the preparation of pento-, hexo-, and heptolide under Shanzer's macrolactonization conditions (tetra-oxadistannacyclodecane ‘template’). The X-ray crystal structures of the pentolide 1 and of two modifications (space groups C 2 and P 2₁) of the hexolide 2 were determined (Figs. 2–6 and Tables 1 and 5). No close contacts between substituent atoms and atoms in the rings or between ring atoms are observed in these structures. The hexolide C 2 modification is ‘just a large ring’, while the crystals of the P 2₁ modification contain folded rings the backbones of which resemble the seam of a tennis ball. A comparison of the torsion angles in the folded hexolide ring of the P 2₁ modification with those in the helical poly-(R)-3-hydroxybutanoate ( PHB ) suggests (Table 2) that the same interactions might be responsible for folding in the first and helix formation in the second case. Molecular modeling with force-field energy minimization of the tetrolide from four homochiral β-hydroxybutanoic acid units was undertaken, in order to find possible reasons for the fact that we failed to detect the tetrolide in the reaction mixtures. The calculated conformational energies (per monomer) for some of the tetrolide models (Figs. 7–9 and Tables 3 and 4) are not significantly higher than for the pentolide and hexolide crystal structures. We conclude that thermodynamic instability is an unlikely reason for the lack of tetrolide isolation. This result and failure to observe equilibration of pentolide 1 to a mixture of oligomers under the reaction conditions suggest that product distribution is governed by kinetic control.     

Crystal structures and photoreactivity of trans- and cis-valerophenone diperoxides

Abstract  

The crystal structures of valerophenone diperoxides trans-1 and cis-1 were elucidated by X-ray crystallographic analysis. The 1,2,4,5-tetraoxane rings of both compounds adopt chair conformations. Intermolecular CH···O hydrogen bond, π–π, and CH/π interactions exist in cis-1, whereas only CH/π interactions exist in trans-1. In the asymmetric unit of the crystal, a half molecule exists for trans-1, while one molecule for cis-1 which shows whole-molecule disorder. Solid-state photolysis (at 254 nm) or solution-state thermolysis (at 150 °C) of trans-1 and cis-1 produced valerophenone (2) and butyl benzoate (3). Rationalization of the solid-state photoreactivity of the diperoxides by their crystal structures was attempted.     

MH4P6N12 (M=Mg,Ca): New Imidonitridophosphates with an Unprecedented Layered Network Structure Type

Isotypic imidonitridophosphates MH₄P₆N₁₂ (M=Mg, Ca) have been synthesized by high‐pressure/high‐temperature reactions at 8 GPa and 1000 °C starting from stoichiometric amounts of the respective alkaline‐earth metal nitrides, P₃N₅, and amorphous HPN₂. Both compounds form colorless transparent platelet crystals. The crystal structures have been solved and refined from single‐crystal X‐ray diffraction data. Rietveld refinement confirmed the accuracy of the structure determination. In order to quantify the amounts of H atoms in the respective compounds, quantitative solid‐state ¹H NMR measurements were carried out. EDX spectroscopy confirmed the chemical compositions. FTIR spectra confirmed the presence of NH groups in both structures. The crystal structures reveal an unprecedented layered tetrahedral arrangement, built up from all‐side vertex‐sharing PN₄ tetrahedra with condensed dreier and sechser rings. The resulting layers are separated by metal atoms.     

Synthesis and structural studies of C-5 aryl- and C-6 alkyl-substituted pyrimidine derivatives

C-5 and C-6 disubstituted pyrimidine derivatives 2–7 were synthesized. Introduction of the aryl rings at C-5 of pyrimidine moiety in 5 and 6 was performed using palladium-catalyzed Stille cross-coupling reaction. The novel C-6 fluorophenylalkylated 5-phenylpyrimidine derivative (7) was prepared by lithiation of 5-phenylpyrimidine (6) and subsequent reaction of thus obtained organolithium intermediate with p-fluoroacetophenone. The structures of 3, 4 and 6 were determined by X-ray crystal structure analysis. Both methoxy groups in these structures adopt a synperiplanar conformation with respect to the N1 and N3 atoms of the pyrimidine ring. The molecules of 3 and 4 are linked through weak Br···Br interactions into zig-zag chains. The molecules of 6 are assembled into layers by one C–H···O hydrogen bond, C–H···π and aromatic π···π stacking interactions.     

Structural diversity in pseudohalide complexes of cadmium(II) with N-methylthiourea (Metu): Polymeric [Cd(Metu)2(NCS)2]n versus monomeric [Cd(Metu)2(CN)2]

Cadmium(II) complexes, catena-poly[bis(thiocyanato-κN)bis(N-methylthiourea)cadmium(II)], [Cd(Metu)₂(NCS)₂]_n (1) and dicyanidobis(N-methylthiourea)cadmium(II), [Cd(Metu)₂(CN)₂] (2) were prepared and their structures were determined by single crystal X-ray analysis. In 1, the cadmium(II) ion is bound to four sulfur atoms of bridging Metu ligands and two nitrogen atoms of thiocyanate adopting a distorted octahedral environment. In 2, the geometry around cadmium is distorted tetrahedral attained by two cyanide ions and two methylthiourea molecules bound through the sulfur atoms. The crystal structures of both complexes show intra and intermolecular hydrogen bonding interactions. The complexes were also characterized by IR and NMR spectroscopy and the spectroscopic data were discussed in terms of the nature of bonding.     

Investigation of the crystal structure of two amphiphilic diols

Abstract

The crystal and molecular structures of (R)-4′-(2,3-dihydroxypropyloxy)-4-cyanobiphenyl, 1 and 4′-(cis-cis-3,5-dihydroxycyclohexyloxy)-4-cyanobiphenyl, 5 have been determined. The packing of compound 1 occurs in sheets, with a dense hydrogen bonding network within the layer of one sheet and to the next sheet, whereby the cyano groups are incorporated into the hydrogen bonding network. The hydrogen bonding scheme of compound 5 involves a water molecule; there is some disorder with regard to the hydrogen atoms bound to the water molecules.     

Crystal Structures of Mono-, Di-, and Tri(p-tert-butyl)-thiacalix[4]arenes: Dimeric Self-inclusion Behavior

X-Ray crystal structures of the mono-, di-, and tri(p-tert-butyl)-substituted thiacalix[4]arenes (TC4As; 1, 2, and 3, respectively) have beendetermined. TC4As 1–3 adopt a cone conformation and form dimeric self-inclusion units in such a manner that phenol moieties are inserted into the cavity of each molecule. In all the crystal structures of 1–3, lateralface-to-face interactions exist between the phenol rings that do not bear a tert-butyl substituent, and seemingly, this molecular assembly stabilizes the formation of self-inclusion. TC4As 1 and 2 adopt a cone conformation with C₂ symmetry, leading to the formation of rim-to-rim intermolecular hydrogenbonds so as to link the dimeric units up and down. On the other hand, 3 adopts a regular cone conformation with C₄ symmetry to form cyclic hydrogen bonds withinthe rim part of TC4A.     

Overcrowded naphthologs of mono-bridged tetraarylethylenes: analogs of bistricyclic aromatic enes

The naphthalogous mono-bridged tetraarylethylenes 9,9′-di-(1-naphthylmethylene)-9H-fluorene (5) and 9,9′-di-(1-naphthylmethylene)-9H-xanthene (6), analogs of bifluorenylidene (1) and bixanthenylidene (2), have been synthesized and their molecular and crystal structures have been determined. Ene 5 has been prepared by two alternative synthetic routes. The molecular structures of 5 and 6 show that each of these enes has very small twist around the central double bond, but the two naphthalene rings in both 5 and 6 are highly twisted. According to the NMR study, 5 and 6 in solution adopt conformations which are similar to those found by X-ray crystal structure analysis. The notable upfield shifts of H¹ and H⁸ (6.11 and 6.83 ppm, respectively) and H² and H⁷ (6.70 and 6.44 ppm, respectively) in 5 and 6 are due to the shielding caused by the nearly orthogonally twisted naphthalene rings. The B3LYP/6-31G(d) calculations of 5, 6, and their 2-naphthyl and phenyl analogs have been performed. In the 1-naphthyl series, the more efficient conjugation between the naphthyl substituents and the central C=C and the overcrowding due to the peri-hydrogen atoms lead to higher twists of the naphthyl groups and to lower twists of the central C=C. In the 2-naphthyl series, the opposite effects are noted. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

Structure and Spectroscopic Studies of 4,8-bis(2-Hydroxybenzyl)-cis-octahydro[1,4]-oxazino [3,2-b]-1,4-oxazine

The title compound 4,8-bis(2-Hydroxybenzyl)-cis-octahydro [1,4]-oxazino [3,2-b]-1,4-oxazine (1) has been synthesized by the reaction of N-(2-hydroxybenzyl)-2-amino-1-ethanol with glyoxal. This novel compound was characterized by elemental analysis, IR, and ¹H NMR. The structure was also confirmed by a single crystal X-ray study. The compound crystallizes in monoclinic C2/C space group with unit cell dimensions: a = 18.318(4), b = 8.6110(17), c = 13.267(3) Å, = 119.90(3), V = 1814.1(6) ų, Z = 4. The two fused six-membered rings in 1 adopt chairlike conformations slightly flattened around the nitrogen atoms. In the central fusion bond, the geometry is a staggered conformation, with the two angular hydrogen atoms in the cis positions with respect to the rings, the nitrogen atoms antiperiplanar to each other, while the oxygen atoms remain gauche to each other and antiperiplanar to the hydrogen atoms. The ring conformations in 1 have been discussed on the basis of the anomeric effects and the presence of two strong intramolecular hydrogen bonds between the phenolic hydrogens and the amino groups.     

Crystal structures of [Hg(<Emphasis Type="Italic">N</Emphasis>-ethylthiourea)<Subscript>2</Subscript>(CN)<Subscript>2</Subscript>] and [Hg(<Emphasis Type="Italic">N</Emphasis>-propylthiourea)<Subscript>2</Subscript>(CN)<Subscript>2</Subscript>]

Two mercury(II) cyanide complexes of N-ethylthiourea (Ettu) and N-propylthiourea (Prtu) ligands, [Hg(Ettu)₂(CN)₂] (1) and [Hg(Prtu)₂(CN)₂] (2), were prepared and their crystal structures were determined by X-ray crystallography. In both structures, the mercury atom is coordinated to two sulfur atoms of thioureas and two cyanide carbon atoms in a pseudo-tetrahedral mode with the bond angles in the range of 90.52(11)–162.2(3)°. The structures are stabilized by N-H—S, N-H—N, and C-H—N intramolecular and intermolecular hydrogen bonds.     

ReviewInverse coordination. Organic nitrogen heterocycles as coordination centers. A survey of molecular topologies and systematization. Part 1. Five-membered and smaller rings

Abstract

This review continues the previous articles (I. Haiduc, J. Coord. Chem., 71, 3139 (2018) and J. Coord. Chem., 72, 35 (2019)), which discussed the structures with nitrogen-donor species (atoms and molecules) acting as centers in inverse coordination complexes. i.e. metal compounds which display an arrangement of acceptor and donor sites opposite to that occurring in conventional coordination complexes. This review is Part 1 of a work which introduces the topology of inverse coordination complexes with organic nitrogen heterocycles, and presents a panorama of five-membered rings and covers pyrazole, imidazole, triazoles, tetrazole, pyrrole, oxadiazole, thiadiazole, azaphospholes, and smaller rings.