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.     

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 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.     

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.     

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.     

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.     

Structure, thermal behavior, and IR investigations of (C6H9N2)H2PO4

Chemical preparation, X-ray single-crystal, thermal behavior, and IR spectroscopy studies of a new dihydrogenmonophosphate associated to an organic cation, the 3-(ammoniummethyl)pyridine dihydrogenmonophosphate (denoted as AMPP) are described. The AMPP crystallizes in the monoclinic system with P2₁/c space group. The unit cell dimensions are a = 5.8465(2) Å, b = 19.9776(9) Å, c = 7.3103(3) Å, = 90.848(3)° with V = 853.74(4) ų and Z = 4. The structure has been solved using direct method and refined to a reliability R factor of 0.0393. The structure of AMPP includes three types of hydrogen bonds. The first one, O H O, links the H₂PO₄ groups to form infinite inorganic chains [H₂PO₄]n ^n–, parallel to the c axis. The two other types, O H N and N H O assemble inorganic chains so as to build up a three-dimensional arrangement.     

Structure of bis(2-amino-5-methylpyridinium) tetrachlorozincate at 298 and 150 K

Reaction of 2-amino-5-methylpyridine with zinc chloride and HCl in aqueous solution yields bis(2-amino-5-methylpyridinium) tetrachlorozincate. The complex crystallizes in the monoclinic space group P2₁/c, with minimal tetrahedral distortion of the ZnCl₄ ^2– ion at both 298 and 150 K; at 298 K, a = 8.090(2) Å, b = 14.795(6) Å, c = 15.850(4) Å, = 101.93 (2); at 150 K, a = 8.0986(2) Å, b = 14.7190(5) Å, c = 15.7684(7) Å, = 102.862(2). The anisotropic cell contraction results in significant changes in nonbonding Cl Cl contacts.     

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.     

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.     

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.     

Synthesis and structural properties of a 1-D copper(I) coordination polymer

A coordination polymer catena-chloro(4-pyridinecarboxylic acid)copper(I): [Cu(C₆H₅ O₂N)Cl]_n (1) has been prepared directly by reacting Cu^IICl₂ 2H₂O and 4-cyanopyridine in the presence of disodium maleate under hydrothermal conditions at 140°C. Crystal data for 1 are as follows: monoclinic, P2₁/n, a = 16.4623(9) Å, b = 3.7795(2) Å, c = 24.7612(11) Å, = 101.534(1)°, V = 1509.5(1) ų, Z = 4, D _calc. = 1.955 g cm^–3, R1 = 0.0511, wR2 = 0.1060 for all 2666 reflections. In this 1-D stair-polymer, two [Cu–Cl–Cu]_n zigzag chains are held together by weak interchain Cu–Cl bonds. The 4-pyridinecarboxylic acid ligands derived from the 4-CNpy molecules coordinate to the approximately tetrahedral Cu(I) centers through pyridyl-N atoms. The carboxyl ends of 4-pyridinecarboxylic acid participate in interchain hydrogen-bonding interactions to form a 2-D supramolecular network.     

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.     

Crystal structures of two substituted key intermediates of phenothiazine derivatives

The key intermediates, in the synthesis of phenothiazines, 5-hydroxy-5-methyl 3(phenyl) 2,4-N-dimethylcarbamoyl cyclohexanone, C₁₇H₂₂O₄N₂ (I), and 5-hydroxy-5-methyl 3(2-methylphenyl) 2,4-N-dimethylcarbamoyl cyclohexanone, C₁₈H₂₄O₄N₂ (II), contain essentially substituted cyclohexanone rings in chair conformation with approximately perpendicular oriented phenyl rings. The carbamoyl groups are aligned in opposite directions to facilitate the formation of intramolecular C–HO interaction and O–HO hydrogen bonding. The molecules are linked in helical fashion by an N–HO type intermolecular hydrogen bonding framework. Crystal data: [I], orthorhombic, space group Pbca, a = 9.278(1), b = 19.094(2), c = 19.802(2) Å, V = 3508.0(6) ų, Z = 8 and d = 1.206 Mg m^–3, R = 0.074 (wR = 0.137) for 208 parameters and 1190 observed reflections with I 2 (I); [II], monoclinic, space group P2₁/n, a = 10.523(1), b = 9.005(1), c = 19.771(2) Å, = 94.96(6)°, V = 1866.5(3) ų, Z = 4 and d = 1.183 Mg m^–3, R = 0.062 (wR = 0.131) for 217 parameters and 2276 observed reflections with I 2 (I).     

Synthesis and structure of [(nitrito-O,O′) bis(di-2-pyridylamine)copper(II)] nitrite

The synthesis and molecular structure of the title compound, [(nitrito-O,O) (dpa)₂Cu(II)] (NO₂), 1, is reported. Compound 1 crystallized in the orthorhombic space group Pccn with a = 11.397(5) Å, b = 12.256(6) Å, c = 14.876(8) Å, and V = 2077.9(17) ų with Z = 4. The distorted octahedral copper(II) cations are linked through a hydrogen-bonded polymer network. The polymer network is formed through the amine N–H of the cations and hydrogen bonded to the N–HO nitrite anions.     

Hydrogen bonding in labdane diterpenoids, labda-7,12(E),14-triene-17-oic acid and labda-12(Z),14,17-triene-18-oic acid

Two labdane diterpenoids, labda-7,12(E),14-triene-17-oic acid (1) and labda-12(Z),14,17-triene-18-oic acid (2), C₂₀H₃₀O₂, have been isolated from Croton oblongifolius. Both 1 and 2 crystallized in the monoclinic system, space group C2, with cell dimensions of a = 21.912(1) Å, b = 7.4002(4) Å, c = 11.5079(7) Å, = 101.999(1)^o and a = 21.308(2) Å, b = 11.9067(9) Å, c = 7.5606(6) Å, = 100.763(1)^o, respectively. Compound 1, a rare example of carboxylic group bound to a cyclohexene ring, forms an infinite intermolecular hydrogen-bonded polymer [O1 O2(–x + 1/2, y + 1/2, –z + 2) 2.697(2) Å], whereas molecules of compound 2 are linked to form an asymmetric hydrogen-bonded dimer [O1 O2(–x, y, –z) 2.657(3) Å].     

Crystal structure of 6-nitrobenzo(a)pyrene

In 6-nitrobenzo(a)pyrene, an environmental pollutant, the nitro substituent lies at 69.5(1) to the mean plane of the aromatic moiety. The C–C bond distances range from 1.341(3) to 1.443(3) Å. The crystal is in the monoclinic space group, P2₁/c, with a = 8.3239(3) Å, b = 8.9530(3) Å, c = 18.0678(5) Å, = 99.264(2) and Z = 4. Molecules are assembled in sheets in the unit cell through stacking and alternating C–H O interactions.     

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.     

Synthesis and crystal structure of a new two-dimensional chromium(III) network through hydrogen bonds

A new chromium(III) complex, [Cr(ox)(bdmpza)(H₂O)], (ox = oxalate dianion and bdmpza = bis(3,5-dimethylpyrazol-1-yl)acetate, respectively), has been synthesized and characterized by X-ray crystallography. This compound crystallizes in the monoclinic space group P2₁/c, with a = 7.008(3) Å, b = 14.229(5) Å, c = 16.497(7) Å, = 101.588(7)°, V = 1611.5(11) ų, Z = 4. The chromium atom has a distorted octahedral environment with different coordination atoms. Bis(3,5-dimethylpyrazol-1-yl)acetate anion is a tridentate ligand, and the oxalate group acts as a chelating bidentate ligand. This compound also forms an infinite two-dimensional network through O–H O hydrogen bonds. The lengths of the hydrogen bonds are 2.765(5) and 2.733(5) Å, respectively.