Three modulation patterns in four related [M(H2O)2(15-crown-5)](NO3)2 structures

2005 ◽  
Vol 61 (6) ◽  
pp. 675-688 ◽  
Author(s):  
Xiang Hao ◽  
Sean Parkin ◽  
Carolyn Pratt Brock
Keyword(s):  
Hydrogen Bond ◽  
Three Dimensional ◽  
Basic Structure ◽  
Water Ligand ◽  
Nitrate Anion ◽  
Cell Axis ◽  
Hydrogen Bond Pattern ◽  
Diffraction Patterns ◽  
Water Ligands ◽  
Hydrogen Bonded

The structures of [M(H2O)2(15-crown-5)](NO3)2, M = Cu, Zn, Mg and Co, and 15-crown-5 = 1,4,7,10,13-pentaoxacyclopentadecane, have been redetermined at 294 and 90 K. The four structures, and a second form of the Cu structure, have been reported in the literature, but are all incorrect in some significant way. The structures, which all have at least two independent formula units (i.e. Z′ ≥ 2), are related; each water ligand is hydrogen-bonded to two nitrate anions, while each nitrate anion is hydrogen bonded to the water ligands of two cations. In the tetragonal Co structure the hydrogen-bond pattern is three-dimensional; in the monoclinic Cu, Zn and Mg structures the hydrogen-bond patterns are two-dimensional. In the isostructural Zn and Mg structures Z′ = 3, while in the Cu structure Z′ = 5. The Cu, Zn and Mg structures are modulated variants of a basic structure, which was reported for Cu but which probably does not exist. The conformations of the 11 independent cations are remarkably similar; they all have approximate twofold symmetry and so exist as conformational enantiomers. The most important modulation is imperfect enantiomeric alternation of the cations along the longest cell axis; the independent cations are related by very good pseudotranslation and pseudoinversion operations. The diffraction patterns for all four structures have classes of weak, even very weak, reflections.

The heterobifunctional ligand 5-[4-(1,2,4-triazol-4-yl)phenyl]-1H-tetrazole and its role in the construction of a CdIImetal–organic chain structure

2012 ◽  
Vol 68 (10) ◽  
pp. m291-m294
Author(s):  
Andrey B. Lysenko
Keyword(s):  
Hydrogen Bond ◽  
Three Dimensional ◽  
Organic Ligand ◽  
Chain Structure ◽  
Polar Space ◽  
Hydrogen Bond Donor ◽  
Donor Acceptor ◽  
A Chain ◽  
Water Ligands ◽  
Hydrogen Bonded

5-[4-(1,2,4-Triazol-4-yl)phenyl]-1H-tetrazole, C9H7N7, (I), an asymmetric heterobifunctional organic ligand containing triazole (tr) and tetrazole (tz) termini linked directly through a 1,4-phenylene spacer, crystallizes in the polar space groupPc. The heterocyclic functions, serving as single hydrogen-bond donor (tz) or acceptor (tr) units, afford hydrogen-bonded zigzag chains with no crystallographic centre of inversion. In the structure ofcatena-poly[[diaquacadmium(II)]bis{μ2-5-[4-(1,2,4-triazol-4-yl)phenyl]tetrazol-1-ido-κ2N1:N1′}], [Cd(C9H6N7)2(H2O)2]n, (II), the CdIIdication resides on a centre of inversion in an octahedral {N4O2} environment. In the equatorial plane, the CdIIpolyhedron is built up from four N atoms of two kinds, namely oftrans-coordinating tr and tz fragments [Cd—N = 2.2926 (17) and 2.3603 (18) Å], and the coordinating aqua ligands occupy the two apical sites. The metal centres are separated at a distance of 11.1006 (7) Å by means of the double-bridging tetrazolate anion,L−, forming a chain structure. The water ligands and tz fragments interact with one another, like a double hydrogen-bond donor–acceptor synthon, leading to a hydrogen-bonded three-dimensional array.

scholarly journals Polymeric coordination complex of lithium(I) with aqua and cyanurate ligands

2021 ◽  
Vol 77 (10) ◽  
Author(s):  
Anjapuli Ponnuvel ◽  
Arumugam Pillai Kala ◽  
Karachalacherevu Seetharamiah Nagaraja ◽  
Chandran Karnan
Keyword(s):  
Three Dimensional ◽  
Water Ligand ◽  
Water Molecules ◽  
Equatorial Position ◽  
Tetrahedral Geometry ◽  
Trigonal Bipyramidal ◽  
Dimensional Network ◽  
Vis Spectroscopy ◽  
Dta Analysis ◽  
Water Ligands

The polymeric title complex, poly[hexa-μ-aqua-diaquatetra-μ-cyanurato-tetralithium] [Li4(C3H2N3O3)4(H2O)7] n , synthesized at room temperature from an aqueous solution of lithium hydroxide and cyanuric chloride, crystallizes in the triclinic space group P\overline{1}. There are two distinct Li+ cations in the asymmetric unit, one of which, Li1, has distorted trigonal–bipyramidal geometry and is coordinated via oxygen to two cyanurate anions occupying equatorial positions, and three water molecules, two in the axial positions and the third in an equatorial position. One of the axial water ligands and the equatorial water ligand are involved in bridging to a crystallographically equivalent Li1 cation. A centre of inversion lies between the two Li1 cations and the Li1...Li1 distance is 3.037 (5) Å. The remaining axial water ligand bridges to the second Li cation, Li2, which is disordered over two crystallographic sites with approximately equal occupancy, and has an Li1...Li2 distance of 3.438 (7) Å. The terminal Li2 cation is coordinated to three water molecules and an oxygen atom from a cyanuric anion and has a distorted tetrahedral geometry. A three-dimensional network of intermolecular hydrogen bonds involving N—H...O, O—H...O and O—H...N interactions serves to hold the structure together, as confirmed by a Hirshfeld surface analysis. The title compound was further characterized using IR and UV–vis spectroscopy and TG–DTA analysis.

Sulfur as hydrogen-bond acceptor in cocrystals of 2-thio-modified thymine

2018 ◽  
Vol 74 (1) ◽  
pp. 21-30 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Crystal Engineering ◽  
Rational Design ◽  
Three Dimensional ◽  
Good Reliability ◽  
Hydrogen Bond Acceptor ◽  
Hydrogen Bonding Interactions ◽  
Hydrogen Bonding Site ◽  
Hydrogen Bonded

Doubly and triply hydrogen-bonded supramolecular synthons are of particular interest for the rational design of crystal and cocrystal structures in crystal engineering since they show a high robustness due to their high stability and good reliability. The compound 5-methyl-2-thiouracil (2-thiothymine) contains an ADA hydrogen-bonding site (A = acceptor and D = donor) if the S atom is considered as an acceptor. We report herein the results of cocrystallization experiments with the coformers 2,4-diaminopyrimidine, 2,4-diamino-6-phenyl-1,3,5-triazine, 6-amino-3H-isocytosine and melamine, which contain complementary DAD hydrogen-bonding sites and, therefore, should be capable of forming a mixed ADA–DAD N—H...S/N—H...N/N—H...O synthon (denoted synthon 3s N·S;N·N;N·O), consisting of three different hydrogen bonds with 5-methyl-2-thiouracil. The experiments yielded one cocrystal and five solvated cocrystals, namely 5-methyl-2-thiouracil–2,4-diaminopyrimidine (1/2), C5H6N2OS·2C4H6N4, (I), 5-methyl-2-thiouracil–2,4-diaminopyrimidine–N,N-dimethylformamide (2/2/1), 2C5H6N2OS·2C4H6N4·C3H7NO, (II), 5-methyl-2-thiouracil–2,4-diamino-6-phenyl-1,3,5-triazine–N,N-dimethylformamide (2/2/1), 2C5H6N2OS·2C9H9N5·C3H7NO, (III), 5-methyl-2-thiouracil–6-amino-3H-isocytosine–N,N-dimethylformamide (2/2/1), (IV), 2C5H6N2OS·2C4H6N4O·C3H7NO, (IV), 5-methyl-2-thiouracil–6-amino-3H-isocytosine–N,N-dimethylacetamide (2/2/1), 2C5H6N2OS·2C4H6N4O·C4H9NO, (V), and 5-methyl-2-thiouracil–melamine (3/2), 3C5H6N2OS·2C3H6N6, (VI). Synthon 3s N·S;N·N;N·O was formed in three structures in which two-dimensional hydrogen-bonded networks are observed, while doubly hydrogen-bonded interactions were formed instead in the remaining three cocrystals whereby three-dimensional networks are preferred. As desired, the S atoms are involved in hydrogen-bonding interactions in all six structures, thus illustrating the ability of sulfur to act as a hydrogen-bond acceptor and, therefore, its value for application in crystal engineering.

Channel- and layer-type anionic host structures in inclusion compounds of urea, tetraalkylammonium terephthalate/trimesate and water

2000 ◽  
Vol 56 (1) ◽  
pp. 142-154 ◽  
Author(s):  
Feng Xue ◽  
Thomas C. W. Mak
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Directed Assembly ◽  
Water Molecules ◽  
Triclinic Space Group ◽  
Dimensional Network ◽  
Graph Set ◽  
Host Lattices ◽  
Hydrogen Bonded

New crystalline adducts of tetraalkylammonium terephthalate/trimesate with urea and water molecules result from hydrogen-bond directed assembly of complementary acceptors and donors, and the anionic host lattices are described using the graph-set notation to identify distinct hydrogen-bonding motifs and patterns. Tetra-n-butylammonium terephthalate–urea–water (1/6/2), C46H104N14O12 (1), triclinic, space group P1¯, a = 8.390 (2), b = 9.894 (2), c = 18.908 (3) Å, α = 105.06 (2), β = 94.91 (1), γ = 93.82 (2)°, Z = 1, is composed of hydrogen-bonded terephthalate–urea layers, which are intersected by urea layers to generate a three-dimensional network containing large channels for accommodation of the cations. Tetraethylammonium terephthalate–urea–water (1/1/5), C25H58N4O10 (2), triclinic, P1¯, a = 9.432 (1), b = 12.601 (1), c = 14.804 (1) Å, α = 79.98 (1), β = 79.20 (1), γ = 84.18 (1)°, Z = 2, has cations sandwiched between hydrogen-bonded anionic layers. Tetraethylammonium trimesate–urea–water (1/2/7.5), C35H86N7O15.5 (3), triclinic, P1¯, a = 13.250 (1), b = 14.034 (1), c = 15.260 (1) Å, α = 72.46 (1), β = 78.32 (1), γ = 66.95 (1)°, Z = 2, manifests a layer-type structure analogous to that of (2). Tetra-n-propylammonium hydrogen trimesate–urea–water (1/2/5), C35H78N6O13 (4), orthorhombic, Pna21, a = 16.467 (3), b = 33.109 (6), c = 8.344 (1) Å, Z = 4, features hydrogen trimesate helices in a three-dimensional host architecture containing nanoscale channels each filled by a double column of cations.

A complex pseudo-decagonal quasicrystal approximant, Al37(Co,Ni)15.5, solved by rotation electron diffraction

2014 ◽  
Vol 47 (1) ◽  
pp. 215-221 ◽  
Author(s):  
Devinder Singh ◽  
Yifeng Yun ◽  
Wei Wan ◽  
Benjamin Grushko ◽  
Xiaodong Zou ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Single Crystal ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Basic Structure ◽  
Electron Diffraction Data ◽  
Dimensional Electron ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Patterns

Electron diffraction is a complementary technique to single-crystal X-ray diffraction and powder X-ray diffraction for structure solution of unknown crystals. Crystals too small to be studied by single-crystal X-ray diffraction or too complex to be solved by powder X-ray diffraction can be studied by electron diffraction. The main drawbacks of electron diffraction have been the difficulties in collecting complete three-dimensional electron diffraction data by conventional electron diffraction methods and the very time-consuming data collection. In addition, the intensities of electron diffraction suffer from dynamical scattering. Recently, a new electron diffraction method, rotation electron diffraction (RED), was developed, which can overcome the drawbacks and reduce dynamical effects. A complete three-dimensional electron diffraction data set can be collected from a sub-micrometre-sized single crystal in less than 2 h. Here the RED method is applied forab initiostructure determination of an unknown complex intermetallic phase, the pseudo-decagonal (PD) quasicrystal approximant Al37.0(Co,Ni)15.5, denoted as PD2. RED shows that the crystal is F-centered, witha= 46.4,b= 64.6,c= 8.2 Å. However, as with other approximants in the PD series, the reflections with oddlindices are much weaker than those withleven, so it was decided to first solve the PD2 structure in the smaller, primitive unit cell. The basic structure of PD2 with unit-cell parametersa= 23.2,b= 32.3,c= 4.1 Å and space groupPnmmhas been solved in the present study. The structure withc= 8.2 Å will be taken up in the near future. The basic structure contains 55 unique atoms (17 Co/Ni and 38 Al) and is one of the most complex structures solved by electron diffraction. PD2 is built of characteristic 2 nm wheel clusters with fivefold rotational symmetry, which agrees with results from high-resolution electron microscopy images. Simulated electron diffraction patterns for the structure model are in good agreement with the experimental electron diffraction patterns obtained by RED.

Two closely related, and unexpected, quinolinone derivatives: a three-dimensional hydrogen-bonded framework structure and a hydrogen-bonded molecular ribbon ofR22(18) andR44(24) rings

2012 ◽  
Vol 68 (6) ◽  
pp. o220-o225
Author(s):  
Daniel Insuasty ◽  
Rodrigo Abonía ◽  
Justo Cobo ◽  
Christopher Glidewell
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Unit Cell ◽  
Isomeric Form ◽  
Framework Structure ◽  
Space Group ◽  
Solvent Molecules ◽  
Hydrogen Bonded

1,5-Bis(4-chlorophenyl)-3-(2-oxo-1,2-dihydroquinolin-3-yl)pentane-1,5-dione, (Ia), and 1,5-bis(2-chlorophenyl)-3-(2-oxo-1,2-dihydroquinolin-3-yl)pentane-1,5-dione, (Ib), crystallize as an 84:16 mixture, 0.84C26H19Cl2NO3·0.16C26H19Cl2NO3, in the space groupI41/a, where the molecules of the two isomers occupy very similar sites in the unit cell. A combination of one N—H...O hydrogen bond and one C—H...O hydrogen bond links the molecules, regardless of isomeric form, into a single three-dimensional framework structure. The molecules of (9RS,10RS)-8,9-bis(4-chlorobenzyl)-10-(2-oxo-1,2-dihydroquinolin-3-yl)-5,6,9,10-tetrahydrophenanthridine, C36H22Cl2N2O4, (II), are linked by two hydrogen bonds, one each of the N—H...O and C—H...O types, into a molecular ribbon in which centrosymmetric rings ofR22(18) andR44(24) types alternate. The hydrogen-bonded ribbons enclose channels, which contain highly disordered solvent molecules.

Two tautomers in one crystal: 4(5)-nitro-5(4)-methoxyimidazole

2004 ◽  
Vol 60 (2) ◽  
pp. 191-196 ◽  
Author(s):  
Maciej Kubicki
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Imidazole Derivative ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Dimensional Network ◽  
Hydrogen Bond Pattern ◽  
Annular Tautomerism

The case of prototropic annular tautomerism in an imidazole derivative has been found. The crystal structure contains a 50:50 mixture of two tautomers: 4-nitro-5-methoxyimidazole and 5-nitro-4-methoxyimidazole. The X-ray experiment actually shows the superposition of these compounds; it appears as if the structure is centrosymmetric and the N—H hydrogen atoms are disordered over two ring N atoms. Owing to the hydrogen-bond pattern, the values of their site occupation factors have to be exactly equal to 1/2. The molecules are connected into a three-dimensional network by means of N—H...N and C—H...O hydrogen bonds.

Ambiguities in the structure determination of antimony tellurides arising from almost homometric structure models and stacking disorder

2010 ◽  
Vol 43 (5) ◽  
pp. 1012-1020 ◽  
Author(s):  
Matthias N. Schneider ◽  
Markus Seibald ◽  
Patrick Lagally ◽  
Oliver Oeckler
Keyword(s):  
Powder Diffraction ◽  
Three Dimensional ◽  
Basic Structure ◽  
Initial Structure ◽  
Data Sets ◽  
Layered Chalcogenides ◽  
Potential Applications ◽  
Diffraction Patterns ◽  
Characteristic Layers ◽  
Stacking Disorder

Ambiguities in the interpretation of both single-crystal and powder diffraction data can lead to wrong conclusions concerning the structure analysis of layered chalcogenides with interesting physical properties and potential applications. This is illustrated for binary and Pb-doped phases of the homologous series (Sb2)k(Sb2Te3)m. Almost homometric structure models for 39R-Sb10Te3[R\bar 3m,a = 4.2874 (6),c = 64.300 (16) Å,R1 = 0.0298] have been derived from initial structure solutions and crystal chemical considerations. The variation of the electron density on certain positions may further reduce the differences between the calculated diffraction patterns of non-congruent structure models as exemplified by the new compound 33R-[Sb0.978(3)Pb0.022(3)]8Te3[R\bar 3m,a = 4.2890 (10),c = 75.51 (2) Å,R1 = 0.0615]. Both compounds are long-range ordered, and in either case both `almost homometric' models can be refined equally well on experimental data sets. The models can only be distinguished by chemical analysis, as reasonable atom assignments lead to different compositions for each model. Interestingly, all structure solution attempts led to the wrong models in both cases. In addition, it is shown that stacking disorder of characteristic layers may lead to powder diffraction patterns that can be misinterpreted in terms of three-dimensional randomly disordered almost isotropic structures with a simple α-Hg-type basic structure.

A novel tubular hydrogen-bond pattern in a new diazaphosphole oxide: a combination of X-ray crystallography and theoretical study of hydrogen bonds

2017 ◽  
Vol 73 (7) ◽  
pp. 508-516 ◽  
Author(s):  
Fahimeh Sabbaghi ◽  
Mehrdad Pourayoubi ◽  
Abolghasem Farhadipour ◽  
Nazila Ghorbanian ◽  
Pavel V. Andreev
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Coupling Constant ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Hydrogen Bond Pattern ◽  
Orbital Analysis ◽  
Tubular Array ◽  
Hydrogen Bonded

In the structure of 2-(4-chloroanilino)-1,3,2λ4-diazaphosphol-2-one, C12H11ClN3OP, each molecule is connected with four neighbouring molecules through (N—H)2...O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R 3 3(12) and R 4 3(14) hydrogen-bond ring motifs, combined with a C(4) chain motif. The hole constructed in the tubular architecture includes a 12-atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other. One of the N—H groups of the diazaphosphole ring, not co-operating in classical hydrogen bonding, takes part in an N—H...π interaction. This interaction occurs within the tubular array and does not change the dimension of the hydrogen-bond pattern. The energies of the N—H...O and N—H...π hydrogen bonds were studied by NBO (natural bond orbital) analysis, using the experimental hydrogen-bonded cluster of molecules as the input file for the chemical calculations. In the 1H NMR experiment, the nitrogen-bound proton of the diazaphosphole ring has a high value of 17.2 Hz for the 2 J H–P coupling constant.

Three closely related thienyl-substituted 1,4-epoxynaphtho[1,2-b]azepines: hydrogen-bonded assembly in one, two and three dimensions

2013 ◽  
Vol 69 (3) ◽  
pp. 307-312 ◽  
Author(s):  
Andrés F. Yépes ◽  
Alirio Palma ◽  
Justo Cobo ◽  
Christopher Glidewell
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Geometrical Isomer ◽  
Three Dimensions ◽  
Racemic Mixtures ◽  
Hydrogen Bonded

(2R,4S)-2-(3-Methylthiophen-2-yl)-2,3,4,5-tetrahydro-1,4-epoxynaphtho[1,2-b]azepine, C19H17NOS, (I), crystallizes with a single enantiomer in each crystal, whereas its geometrical isomer (2RS,4SR)-2-(5-methylthiophen-2-yl)-2,3,4,5-tetrahydro-1,4-epoxy-naphtho[1,2-b]azepine, (II), and (2RS,4SR)-2-(5-bromothiophen-2-yl)-2,3,4,5-tetrahydro-1,4-epoxynaphtho[1,2-b]azepine, C18H14BrNOS, (III), both crystallize as racemic mixtures. A combination of one C—H...O hydrogen bond and two C—H...π(arene) hydrogen bonds links the molecules of (I) into a three-dimensional framework; the molecules of (II) are linked into aC(4)C(4)[R22(7)] chain of rings by a combination of C—H...N and C—H...O hydrogen bonds; and in (III), whereZ′ = 2, a combination of four C—H...π(arene) hydrogen bonds and two C—H...π(thienyl) hydrogen bonds links the molecules into complex sheets. Comparisons are made with the assembly patterns in some aryl-substituted 1,4-epoxynaphtho[1,2-b]azepines.

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