Hydrogen-bond networks in the mono- and diprotonated cyclic diamine [9]aneN2S

The hydrogen-bond networks in the mono- and diprotonated cyclic diamine, 1-thia-4,7-diazacyclononane, [9]aneN₂S, have been examined. Crystals of the monoprotonated, form [9]aneN₂S HCl, contain a ribbon-like network of alternating strong and weak intermolecular N H Cl hydrogen bonds and weak intramolecular N H N hydrogen bonds. Crystal data for [9]aneN₂S HCl: monoclinic, a = 6.6640(6) Å, b = 10.3493(9) Å, c = 6.9807(6) Å, = 108.847(1)°, V = 455.63(7) ų, space group P2₁, Z = 2. In the di-protonated form, [9]aneN₂S 2HBr, the ribbon-like network comprises strong intermolecular and weak intramolecular N H Br hydrogen bonds. Crystal data for [9]aneN₂S 2HBr: orthorhombic, a = 12.5918(13) Å, b = 8.0753(9) Å, c = 10.6856(11) Å, V = 1086.5(2) ų, space group Pnma, Z = 4. The chloride anions of [9]aneN₂S HCl align in interlocking columns in the a- and c-direction whereas the bromide anions in [9]aneN₂S 2HBr occupy channels in the b-direction.     

Crystal structure of barbituric acid (1,4)-dioxane solvate at −173°C

The structure of barbituric acid (1,4)-dioxane solvate has been determined by X-ray diffraction at 100 K. The compound crystallizes in the triclinic space group P , with cell dimensions of a = 6.7770(16) Å, b = 9.583(2) Å, c = 9.697(2) Å, = 85.868(5)°, = 82.566(5)°, = 70.675(5)°, V = 589.0(2) ų, and Z = 1. In the solid state, one asymmetric unit consists of C₄H₄N₂O₃ 3/2(C₄H₈O₂), each barbituric acid molecule being involved in two hydrogen bonds. The two nitrogen atoms of the acid act as hydrogen donors to two oxygen atoms, each from a different molecule of (1,4)-dioxane, which serve as the acceptors. Not all of the hydrogen-bonding capacity of the chemical moieties is used, and the principal feature of the supramolecular structure is a sawtooth ribbon composed of alternating barbituric acid and (1,4)-dioxane molecules, connected through hydrogen bonds and C H O interactions.     

Crystal structures and vibrational spectra of racemic and chiral 4-phenyl-1,3-oxazolidine-2-thione

The crystal structures of (rac)- and (R)-4-phenyl-1,3-oxazolidine-2-thione (4-POT) have been determined by X-ray diffraction. The structure of (rac)-4-POT is monoclinic P2₁/n with a = 11.9096(9) Å, b = 5.9523(6) Å, c = 12.3563(8) Å, = 91.054(6)°, V = 875.8(1) ų, and Z = 4. The structure of (R)-4-POT is orthorhombic P2₁2₁2₁ with a = 7.7197(6) Å, b = 21.603(2) Å, c = 5.4613(9) Å, V = 910.8(2) ų, and Z = 4. (rac)-4-POT and (R)-4-POT crystals are shown to have different hydrogen-bonding patterns. In the racemic crystals, the enantiomeric (R)- and (S)-4-POT molecules are connected to form a cyclic dimer via the N–H S hydrogen bond of the cis thioamide moiety [N Sⁱ 3.438(2) Å, N–H Sⁱ 176(2)° symmetry code: (i) 1 – x, 1 – y, 1 – z]. In the chiral (R)-4-POT crystals, the N–H S intermolecular hydrogen bond forms a zigzag chain around the twofold screw axis [N Sⁱⁱ 3.347(3) Å, N–H Sⁱⁱ 161(3)° symmetry code: (ii) 1/2 + x, 1/2 – y, 2 – z]. Observed difference of 46°C in the melting points between the (rac)-4-POT and (R)-4-POT crystals is correlated with difference in the crystal packing. Vibrational spectra of (rac)- and (R)-4-POT crystals are discussed both in the solid state and in solution.     

Unusual nucleotide stability through C–H ⋅ ⋅ ⋅ water interaction in crystal: Recognition of nucleotide-water duplex-helix

The direct and indirect roles of the C2- and C8-bonded water molecules (C–H    O_W) in the stabilization of unusual inosine monophosphate containing nucleotides have been observed in their highly hydrated and amino acid cocrystals, which have been discussed in this work for the first time. The intermolecular H-bonding of W_R (the oxygen of ribose 2- and 3-hydroxyls bonded water molecule, O2    W_R    O3) with the C2–H bonded O_W's (O_W    W_R 2.43–2.78 Å) can influence the ribose and thus the nucleotide stability, whereas the water molecule (O_W) of C8–H    O_W can participate in the base stability by sandwiching the stacked purines through N7    O_W    N7 intermolecular interactions, with N7    O_W 2.63–2.75 Å. However, in some cases the water oxygen (O_W) of C8–H can get intermolecularly H-bonded to water molecular oxygen W_N (with O_W    W_N 2.57–2.85 Å), which has previously stabilized the nucleotide single-strand through intermolecular stacking N7    W_N    N7 interaction (N7    W_N 2.56–2.63 Å). The conjugal survival of the H-bonded nucleotide single-strand with the water-helix thus forming the duplex and its stabilization through the C–H    O_W mediated water molecular (O_W) cooperative H-bonding network, specially with the ribose and the base units, in the crystals could favor the support of single-stranding potentiality and thus the stability of the purine-rich RNAs or the small unusual nucleotides in the aquated environment besides the other interactive factors.     

Rotational disorder in 1,5-dihydroxy xanthone

The crystal structure of 1,5-dihydroxy xanthone obtained from Callophyllum trapezifolium has been determined (C₁₃H₈O₄), Mr = 228.21, a = 5.547(5), b = 5.186(5), c = 16.487(5) Å, = 91.40(1), Z = 2 and V = 474.1(6) ų. The xanthone molecule is planar and exhibits rotational disorder in the crystal. The packing of the molecules in the crystal lattice is due to inter- and intramolecular O–H O hydrogen bonds forming infinite chains.     

A comparison of the crystal structures of (dabcoH2)CuCl4 and (dabcoH2)CuCl4⋅H2O

The crystal structures of the anhydrous and monohydrated (dabcoH₂)CuCl₄nH₂O salts (n = 0,1) have been determined and a comparison of their crystal structures has been reported. The anhydrous salt is monoclinic P2₁/c with a = 9.045(2) Å, b = 6.9270(10) Å, c = 18.767(4) Å and = 90.07(3)° with V = 1175.8(4) ų. The hydrated salt is also monoclinic P2₁/c with a = 9.266(2) Å, b = 9.395(2) Å, c = 14.386(3) Å and = 93.32(3)° with V = 1250.3(5) ų. The structures of the two salts are closely related. Both compounds contain isolated distorted (compressed) tetrahedral CuCl₄ ^2– anions, diprotonated dabco cations, and in the case of the hydrated salt, lattice H₂O molecules. In the anhydrous salt, each of the two N–H⁺ groups of the dabcoH₂ ²⁺ dications form bifurcated hydrogen bonds to chloride ions on adjacent CuCl₄ ^2– anions along the c axis, thus forming chains running parallel to the c axis. In the hydrated salt, a water molecule is inserted into one of the pair of bifurcated hydrogen bonds, forming instead N–H O–H CuCl₄ ^2– linkages. The chains thus formed are cross-linked by O–H Cl hydrogen bonds between the chains. Because of this additional hydrogen bonding, the CuCl₄ ^2– anions in the hydrated salt are distorted further from tetrahedral geometry.     

Crystal structure of 1-phenylamino-2-phenyl-4-p-chlorophenylimidazole, C21H16N3Cl

The condensation of amidrazones with -bromoketones through ring closure affords two isomeric products. The minor product was subjected to X-ray diffractometric analysis and turned-out to be a substituted imidazole. The title compound crystallizes in space group P2₁/c, with a = 11.838(2), b = 13.249(1), c = 11.226(2) Å, = 91.01(1)°. The packing of molecules is determined by a hydrogen bond N–HN (2.908(5)).     

Synthesis and structure of 4-R,5-R-[5-(hydroxy-diphenyl-methyl)-2, 2-dimethyl-[1,3]dioxolan-4-yl]-phenyl-methanone, a chiral ligand building block

A triphenyl analog of taddol, 4-R,5-R-[5-(hydroxy-diphenyl-methyl)-2,2-dimethyl-[1,3]dioxolan-4-yl]-phenyl-methanone, has been synthesized and structurally characterized. This molecule could act as a chiral ligand building block in the creation of tuned taddol analogs. Structural analysis of the title compound reveals that the hydroxyl group is involved in an intramolecular hydrogen bond and does not take part in any intermolecular interaction. Crystal packing is influenced by C–H O hydrogen bonding and phenyl phenyl interactions. Crystal data: Triclinic, P1 (No. 1), a = 5.9343(4) Å, b = 8.2367(17) Å, c = 10.987(2) Å, = 88.290(6), = 75.442(4), = 80.655(6), V = 512.86(15) ų, Z = 1, D _calc = 1.258 mg/m³. Final residual values were R ₁ = 0.0407 for 3022 observed data (I > 2s(I) ) and wR ₂ = 0.0941 for all 3524 unique data.     

Synthesis and crystal structure of Bi(mpo)3 (Hmpo = 2-mercaptopyridine N-oxide)

The synthesis as well as crystal and molecular structure of [Bi(C₅H₄NOS)₃] are reported. The complex crystallizes in the monoclinic system, space group P2₁/n with lattice parameters a = 9.6521(3) Å, b = 10.0659(4) Å, c = 18.4484(7) Å, = 102.13(6)°, and D _calc = 2.227 Mg · m^–3 for Z = 4. It is clear from the packing diagram that the title compound is a dimer via the secondary coordination. Surrounding Bi atom, three five-membered ring planes (Bi,O,N,C,S) make a dihedral angle of 55.91, 54.72, and 26.13° respectively. The whole crystal presents a three-dimensional network structure as each molecule produces four weak C–H O hydrogen bonds and a weak C–H S hydrogen bond.     

Synthesis and X-ray structure analysis of 2-acetylamino-benzoic acid

The title compound crystallizes in the orthorhombic space group Fdd2 with unit cell parameters a = 10.848(1) Å, b = 30.264(1) Å and c = 10.577(1) Å, V = 3472.47(2) ų, and Z = 4. The final reliability index is 0.030 for 700 observed reflections. Nitrogen of the amide group and carbon atom of the acid group deviate significantly below and above the plane of the phenyl ring. The crystal cohesion is accentuated by N—HO and O—HO hydrogen bonds.     

Synthesis and X-ray crystallography of cholest-3,5-diene-7-one-oxime

Cholest-3,5-diene-7-one-oxime (C₂₇H₄₃NO) was prepared using a usual synthetic route and its three-dimensional structure was determined by X-ray diffraction methods. The transparent platelike crystals of this compound crystallized in the monoclinic space group P2₁, with unit cell parameters a = 14.302(2) Å, b = 11.475(2) Å, c = 15.919(4) Å, = 106.04(1)°, (Cu K) = 1.5418 Å, Z = 4. The structure was solved by direct methods and refined to an R-value of 0.075 for 4640 observed reflections. Two crystallographically independent molecules were observed in the asymmetric unit cell. The ring A in both the molecules was found to exist in 1,10 half-chair conformation while ring C in chair conformation. The rings B and D in both the molecules adopted different conformations. Three intermolecular interactions of the type C–H O and C–H N were also observed.     

Crystal structure of di(N-benzyl piperidinium) pentachloroantimonate(III) dihydrate

The salt di(N-benzyl piperidinium) pentachloroantimonate(III) dihydrate crystallizes in the orthorhombic system with space group Cmc2₁, the unit cell dimensions are: a = 29.383(1), b = 10.509(2), c = 9.941(1) Å, with Z = 8. The structure shows a layer arrangement perpendicular to the a axis: planes of SbCl₆ octahedra alternate with planes of [C₁₂H₁₇N]⁺ cations. The SbCl₆ octahedra are connected through a O(W)–HCl hydrogen bonds and a chlorine bridge, so that infinite unidimensional chains of composition [SbCl₅(H₂O)₂]^2n– _n are formed in the structure along the c direction. These chains are connected to [C₁₂H₁₇N]⁺ entities by N–HCl and N–HO(W) hydrogen bonds, forming a three-dimensional network. It was found that lengths of Sb–Cl bonds may differ from each other. The differences shown as a distortion of the SbCl₆ octahedra were attributed to the Sb(III) lone electron pair stereoactivity.     

Synthesis and structural characterization of the bitopic ferrocene-based tris(pyrazolyl)methane ligand Fe[C5H4CH2OCH2C(pz)3]2 (pz = pyrazolyl ring)

The structure of Fe[C₅H₄CH₂OCH₂C(pz)₃]₂ (pz = pyrazolyl ring) contains 1.5 independent molecules in the asymmetric unit. One molecule has no imposed symmetry with the iron atom located on a general position while in the other the iron atom is located on an inversion center. The two independent molecules are arranged into a three-dimensional supramolecular structure by a series of C—H s N and C—H s O weak hydrogen bonding interactions and C—H s interactions. The crystals are triclinic, space group, P , with a = 8.1202(4) Å, b = 16.7209(9) Å, c = 18.6540(10) Å = 85.8270(10), = 85.4740(10), = 81.5910(10), and Z = 3     

Crystal structure analysis of norbornadiene adduct of diphenyl hexamethylenimino phosphiniminocyclotrithiazene

The title compound (C₆H₁₂N)Ph₂P-N S₃N₃ C₇H₈ crystallizes in the monoclinic space group P2₁/n with unit cell dimensions: a = 9.9200(5), b = 16.3316(11), c = 15.7009(17) Å, = 91.99(1)°, and Z = 4. The cyclotrithiazene ring adopts a chair conformation with equal bond distances and the norbornadiene is fused in an exo, exo fashion to the heterocycle. Norbornadiene addition to the cyclotrithiazene influences the bonding pattern in the ring as well as the P N S moiety.     

Crystal and molecular structure of glutaconic acid

Crystals of Glutaconic acid, C₅O₄H₆, are triclinic, space group P , with the cell dimensions (294 K), a = 4.843(1) Å, b = 10.188(1) Å, c = 12.609(1) Å, = 83.46(1)°, = 80.02(1)°, = 78.71(1)°, V = 598.8(3) ų with D _m = 1.47, D _x = 1.443 gcm ^–3. There are two independent molecules in the asymmetric unit. The crystal structure was solved by multi solution techniques with three-dimensional data collected (to the limit of 2_max of 154° for Cu K) on a CAD-4 diffractometer. The crystal structure was refined by full matrix least squares method to a final R value of 0.058 for 1894 reflections (I 2). The two independent molecules are conformationally similar. In both the molecules, the carboxyl ends are trans to each other with respect to the central C=C double bond in the structure. The molecules are self-paired through dimeric type of hydrogen bonding involving the terminal carboxyl groups, characteristic of many dicarboxylic acid structures. The crystal structure is stabilized by a series of O–HO hydrogen bonds of the glutaconic acid dimeric units. Free radicals have been shown to be involved in a number of chemical and biological processes and lipid peroxidation is one such process. Glutaconic acid was chosen as a simple unsaturated model of a fatty acid. When irradiated with X-rays, it was found to form a stable free radical structure. ESR (electron spin resonance) and ENDOR (electron nuclear double resonance) studies were used to characterize the free radical structure and correlate with the X-ray structure. The free radical was found to be HOOC–CH=CH–CH–COOH with the glutaconic acid in the trans conformation. The damage occurs at the -carbon atom (the first carbon of the double bond). The damage consists of a loss of an hydrogen atom. This results in an unpaired electron in the p-orbital delocalized over the three central carbon atoms. The two -proton couplings were resolved in the ENDOR spectrum. ESR spectra show that the two molecules are magnetically similar that is in agreement with the crystal structure that reveals that the two independent molecules are conformationally similar. This is the characteristic type of damage that occurs in lipids when they form free radicals that in turn reacts with oxygen and other compounds and ultimately results in cellular damage.     

Purported “melamine cyanuric acid trihydrochloride” C3H6N6⋅C3H3N3O3⋅3HCl is actually “diprotonated-melamine cyanuric acid dichloride dihydrate” (C3H8N6)2+⋅C3H3N3O3⋅2Cl−⋅2H2O

On the basis of the published results, melamine cyanuric acid trihydrochloride (MCA3HCl) is shown to be better described as diprotonated melamine cyanuric acid dichloride dihydrate (C₃H₈N₆)²⁺C₃H₃N₃O₃2Cl^–2H₂O. Details are given of the revised hydrogen bonding scheme, which requires further elaboration.     

A comparative study on structure and conformation of three hydroxybenzylamine ligands

Structure and conformation of three tridentate ligands are determined. All these three compounds crystallize in different space groups, the details are as follows: Bis[(3,5-dimethyl,2-hydroxy)-2-hydroxy-5-methoxy]benzylcyclohexylamine (DHBC): monoclinic I2/a (a = 17.691(1) Å, b = 9.707(1) Å, c = 24.235(2) Å, = 91.028(1)°); bis[(3,5-dimethyl,2-hydroxy)-2-hydroxy-5-bromo]benzylcyclohexylamine (DHBrBC): tetragonal P4₁2₁2 (a = b = 12.1138(1) Å, c = 28.485(1) Å) and bis[(3,5-dimethyl,2-hydroxy)-2-hydroxy-5-bromo]benzylmethylamine (DHBrBM): triclinic (a = 5.228(1), b = 12.364(1) Å, c = 13.234(1) Å, = 94.04(1)°, = 95.72(1),° = 95.90(1)°). The cyclohexane rings in DHBC and DHBrBC assume chair conformation. Both the phenyl rings are planar in all the molecules and orient at angles of 75.5(1)°, 62.2(1)°, and 53.9(2)°, respectively with each other. The bond angles around N atom show the sp³ character. Inter- and intramolecular O–HN and O–HO types of hydrogen bondings stabilize the molecules in the unit cell in addition to van der Waals forces.     

The crystal structure of 5-amino-2-nitrobenzoic acid

The crystal structure of 5-amino-2-nitrobenzoic acid (5A2NB) was determined by the X-ray diffraction method. The 5-amino-2-nitrobenzoic acid crystallizes in the monoclinic P2₁/c space group with a = 3.898(2) Å, b = 13.531(3) Å, c = 14.301(3) Å, and = 90.83(3)°. The adjacent molecules form a cyclic dimmer by intermolecular hydrogen bonds of type O—HsO with their carboxyl groups. In the crystal structure NH₂ group forms a three-center hydrogen bond with oxygen atoms of NO₂ group. The IR spectrum and thermal properties of acid are discussed.     

Templated assembly of 1,2-bis(chloromercurio) tetrafluorobenzene in the presence of THF

Slow evaporation of a THF solution containing the bidentate Lewis acid 1,2-bis(chloromercurio) tetrafluorobenzene (1) , yields colorless crystals of the complex 1₂-THF (2) as indicated by elemental analysis, thermal gravimetric analysis and ¹³C CPMAS solid-state NMR spectroscopy. As shown by X-ray analysis, the oxygen atom of the THF molecules bridges the two mercury center of the bidentate Lewis acid. Compound 2 forms an extended structure that features channels filled with THF molecules. In this structure, the individual molecules of the organomercurial are held together by - and Hg Cl interactions. Immersion of 2 in water results in THF loss to afford 1,2-bis(chloromercurio) tetrafluorobenzene in a pure form. Exposure to THF vapor results in a stoichiometric uptake and formation of a solid whose composition corresponds to that of 2.     

Structural characterization of Elisabatin B and Elisabatin C

X-ray structures of Elisabatin B (1) and Elisabatin C (2) have been determined. Crystal data for 1: Triclinic, P (No. 2), a = 7.528(2) Å, b = 9.404(2) Å, c = 11.414(2) Å, = 75.363(3)°, = 86.668(4)°, = 89.683(4)°, and Z = 2. Crystal data for 2: Monoclinic, P2₁/c (No. 14), a = 8.242(2) Å, b = 14.870(2) Å, c = 13.060(2) Å, = 101.458(3)°, and Z = 4. Both compounds are highly unsaturated leading to extended aromatic conjugation. They show different intermolecular O–HO hydrogen bonds, via which 1 forms dimers, and 2 zig-zag polymeric chains.