Hydrogen bonding in 2-hydroxy((di)thio)benzoates. I. X-ray structures of 2,6-dimethylpiperidinium salts

X-ray structural data are reported for 2,6-dimethyl-piperidinium-2-hydroxybenzoate (C₁₄H₂₁NO₃, orthorhombic,P2₁2₁,2₁, (19);a=7.983(1)Å,b=12.680(2)Å,c=13.838(2)Å;Z=4;R=0.042) and for two polymorphs of 2,6-dimethylpiperidinium-2-hydroxythiobenzoate (C₁₄H₂₁NO₂S), an-form (monoclinic,P2₁/n (14);a=8.005(4)Å,b=22.150(2)Å,c=8.672(4)Å,=101.91(6)°;Z=4;R=0.059) with an intramolecular O-HS hydrogen bond, and a-form (orthorhombic,P2₁2₁2₁ (19);a=8.188(1)Å,b=14.781(2)Å,c=24.163(4)Å;Z=8;R=0.15) with an intramolecular O-HO hydrogen bond. The intra-and intermolecular hydrogen bond patterns are discussed, including the literature data of 2,6-dimethylpiperidinium-2-hydroxydithiobenzoate.     

Molecular structure and some reactivity aspects of 2,6-diamino-4(3H)-pyrimidinone monohydrate

Crystals of C₄H₆N₄O·H₂O are orthorhombic:Pbca,a=16.721(2),b=4.242(1),c=18.293(2)Å,Z=8. The structure has been solved by direct methods and refined by full-matrix least-squares techniques toR=0.046 for 1252 unique reflections. The structure consists of approximately planar molecules of the 3(H)4-one tautomer. Delocalization of the ring and the C=O-electrons, and conjugation of the lone-pair electrons of the amine groups with the pyrimidinone nucleus are observed. The molecules are connected by O-HO, N-HN, and N-HO hydrogen bonds. The molecular structure clarifies the chemical properties of the compound.     

Crystal and molecular structure of 1-amino-1-methylethylphosphonic acid monohydrate

The crystal and molecular structure of 1-amino-1-methylethylphosphonic acid monohydrate (C₃H₁₀NO₃P·H₂O) has been determined by single-crystal X-ray diffraction methods. The crystals are orthorhombic:Pna2₁,a=11.665(2),b=9.415(1),c=6.386(1) Å,Z=4. The structure was solved by the heavy-atom method and refined to a finalR=0.028. The molecule exists as a zwitterion, H ₃ ⁺ N-C-(CH₃)₂-PO₃₄H^–. There are six independent hydrogen bonds in the structure, three of the type N-HO with lengths 2.904(5), 2.745(6), and 2.765(5) Å and three of the type O-HO with lengths 2.754(4), 2.833 (7), and 2.548(5) Å.     

X-ray diffraction and total 1H and 13C NMR assignment of (RS)-5,6-dihydro-7,8-dimethoxy-5-methyl-6-(2-oxopropyl)-(2,3-methylenedioxyphenyl)-[c]-phenanthridine ((RS)-6-acetonyldihydrochelerythrine)

The X-ray diffraction structure of (RS)-5,6-dihydro-7,8-dimethoxy-5-methyl-6-(2-oxopropyl)-(2,3-methylenedioxyphenyl)-[c]-phenanthridine ((RS)-6-acetonyldihydrochelerythrine), isolated as an artifact from Bocconia Arborea, is reported. This compound crystallizes as orthorhombic system, space group Pna2₁, with a = 13.216(2) Å, b = 7.6547(10) Å, c = 20.096(3) Å. The phenanthridine central ring presents a distorted boat conformation, which gives rise to two planes with 21.30° between them. The acetonyl group at the six position forms weak C — H O and C — H -ring interactions. The title compound was completely characterized in solution by ¹H and ¹³C and 2D NMR experiments.     

Crystal and molecular structure of 4-p-hydroxyphenyl-2,2,4-trimethylthiachroman-1,1-dioxide

The title compound1 crystallizes as colorless polyhedra in the monoclinic polar space groupCc, witha=8.107(2),b=21.577(3),c=9.542(2)Å,=103.58(2)°, by contrast with its thioether precursor3, crystals of which have the trigonal space groupR¯3. The structure comprises infinite chains of molecules linked head-to-tail by S=OHO hydrogen bonds of length 2.723(2)Å, with HO contact 1.97(4)Å and O-HO 177(3)°; HÔ=S 146(1)°.     

Crystal and molecular structure of 6-nitro-1,3-benzdioxin: Comparison with the molecular structures of the 2,4-bis(dichloromethyl) and 2,4-bis(trichloromethyl) derivatives

6-Nitro-1,3-benzdioxin is orthorhombic,Pbca,a=7.278(4),b=19.292(3),c=10.978(1) Å,Z=8. The structure was solved by direct methods from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer and refined by least squares to a finalR value of 0.041 using 725 reflections. Some parameters associated with the heterocycle are torsion angle (C_Ar)O-C-O-C(C_Ar) 69.1(4)°; bond lengths C_Ar-O 1.362(3), (C_Ar)O-C 1.434(5), (C_Ar.O)C-O 1.377(5), O-C(C_Ar) 1.431(5), C-C_Ar 1.501(5) Å; bond angles C_Ar-O-C 113.5(3), O-C-O 111.5(3), C-O-C(C_Ar) 110.3(3), O-C-C_Ar 109.9(3)°;H_axH_ax 2.52(5) Å.     

Crystal and molecular structure of (+)-6,7∶8,9∶10,11-tri-O-isopropylidene-2,3-dideoxy-d-arabino-l-allo-undec-2-enono-1,4-lactone,C20H30O9

The crystal structure of the title lactone, C₂₀H₃₀O₉, a potential precursor of uncommon 11-carbon sugar derivatives, has been determined by single-crystal diffraction methods. The compound crystallizes in the orthorhombic space groupP2₁2₁2₁ witha=15.581(3),b=14.047(2),c=9.888(2) Å, andZ=4. The structure was solved by direct methods and refined by full-matrix least-squares toR=0.054. The absolute configuration of the seven stereogenic carbon atoms was deduced as 4R, 5R, 6R, 7R, 8S, 9R, 10R, being (R)-(+)-glyceraldehyde its progenitor. An intramolecular O-HO hydrogen bond is present. Weak interaction C-HO links the molecules in sheets parallel to the (100) plane.     

Interaction of aromatic hydrocarbons with organometallic compounds of the main group elements: VI. Synthesis and crystal structure of cesium diiododimethylaluminatep-xylene solvate,Cs[Al(CH3)2I2]·C6H4(CH3)2

The crystal structure of thep-xylene solvate of cesium diiododimethylaluminate has been determined from counter data, and refined by full-matrix least-squares techniques. The crystals belong to the orthorhombic space groupC222₁ witha = 12.577(4),b = 9.311(3),c = 14.256(4) Å, andD _x = 2.19 g cm^–3 forZ = 4. The finalR value for 481 observed reflections is 0.036. The anion resides on a two-fold axis; the Al-I bond length is 2.647(4) Å, and the Al-C distance, 1.98(2) Å. Important bond angles include I-Al-I, 102.3(2) °; C-Al-C, 115(1) °; I-Al-C, 114(3) °; and I-Al-C, 106(3) °. The cesium ion also lies on the two-fold axis. Throughout the crystal the cesium ions are separated byp-xylene molecules. The Cs C distances average 3.84 Å. In the lattice the iodine atoms reside on thea,b face diagonals (and symmetry-related positions) and are situated almost exactly between the cesium ions. The Cs I contact, 3.925(1) Å, is consistent with a significant bonding interaction.For Part V see Atwood et al. (1978).     

Crystal and molecular structure of tetra-n-butylammoniumbis(stilbenedithiolato)-nickelate(III)

The crystal and molecular structure of the title compound, C₄₄H₅₆NS₄Ni, are reported. Crystals are triclinic, space groupP¯1 (No. 2) withZ=2 in a unit cell of dimensionsa=8.874(2) Å,b=9.549(5) Å,c=26.025(7) Å,=97.22(3)°,=95.06(2)°, and=98.75(3)°. The structure was solved by Patterson and Fourier methods and refined by full-matrix least squares toR=0.062 for 2910 unique diffractometer data. The metal atom of the anion has an approximate square-planar configuration and the nitrogen atom of the cation an approximate tetrahedral configuration. The anions as well as the cations are well separated, the closest NiNi and NN approaches being the lattice repeat of 8.874(2) Å.     

Crystal and molecular structure of cesium isothiocyanatotrimethylaluminate,Cs[Al(CH3)3NCS]

The crystal structure of the title compound has been determined from three-dimensional X-ray diffraction data, and refined by full-matrix least-squares techniques. The crystals belong to the monoclinic space groupP2₁/c, witha = 8.849(4),b = 13.798(5),c = 7.943(4) Å, = 102.98(3) °, andD _x = 1.85g cm^–3 forZ = 4. The finalR factor for 1283 observed reflections is 0.046. The aluminum atom is bonded to the nitrogen atom of the thiocyanate ligand, where the Al-N bond length is 1.94(1) Å. The SCN is linear, and the CN-Al angle is 175(1) °. The cesium ion exhibits four contacts less than 3.60 Å: Cs C(thiocyanate) = 3.39(1) Å, Cs C(methyl) = 3.52(1) Å, Cs C.(methyl) = 3.56(1) Å, and Cs N = 3.575(9) Å. The closest Cs S is 3.772(3) Å.     

Crystal structure of a nucleoside analog: 9-(R)-[6-(R)-hydroxymethyl-1-oxa-4-thiacyclohexan-2-yl] adenine

The title compound (C₁₀H₁₃N₅O₂S,M _r=267.3) crystallizes in the orthorhombic space groupP2₁2₁2₁ witha=7.579(8),b=7.686(2) andc=20.941(4)Å,V=1220(1)ų,D _x=1.456 gm cm^–3,Z=4,=23.6 cm^–1,F(000)=560 andT=293 K. The structure was solved by direct methods and refined to aR value of 0.068 for 776 unique observed reflections. The oxathiane ring adopts a chair conformation. In the crystal structure the molecules are held together by hydrogen bonds and C-HO close contacts.     

Crystal structure of a nucleoside analog: 2′,3′-dideoxy-3′-fluoro-5-bromocytidine

The title compound crystallizes in the orthorhombic space groupP2₁2₁2₁ witha=5.084(1),b=14.322(3),c=16.065(2)Å,Z=4. The structure was solved by the heavy atom method and refined by full-matrix least-squares calculations to a finalR value of 0.033 for 1106 unique observed reflections. The N-glycosidic torsion anglex has a value of –153.7(4)°, in the anti-range. The sugar pucker is²T₃ withP=175(1)° and=30(1)°. The C4-C5 conformation is + sc with =46.7(7)°. The structure is stabilized by N-HN, N-HO and O-HO hydrogen bonds and C-HO close contacts.     

Crystal structure of racemic 5-(p-nitrobenzoylamino)-5-methyl-4-oxo-1,3-dioxane

C₁₂H₁₂N₂O₆ crystallized from methanol in the monoclinic space group P2₁/c (Z=4) witha=13.333(4),b=10.154(3),c=9.597(2) Å and=102.37(2)°.M _r=280.24,V=1269.1(6) ų,D _x=1.466 g cm^–3,(Mo K)=0.71069 Å,=1.29 cm^–1,T=295 K. The structure was solved by direct methods and refined by full-matrix least-squares to a finalR (R _w)=0.049 (0.057) for 916 observed reflections. The molecules are linked by strong N-HO(4) hydrogen bonds with NO distance of 2.995(4) Å. The infinite racemic chains run in [001] direction.     

Crystal structure of the 1:1 complex formed by 4-nitropyridine N-oxide and 4-nitrophenol

The title complex (C₆H₅NO₃·C₅H₄N₂O₃,M _r =279.21) crystallizes in the orthorhombic space groupPna2₁ witha=18.862(2),b=5.876(1),c=10.803(2) Å,V=1197.3(6) ų,D _c =1.549 g cm^–3 forZ=4,F(000)=576, (MoK)=0.71073 Å,=0.84 mm^–1,T=297 K. The structure was solved by direct methods and refined by block matrix least-squares. FinalR=0.032, wR=0.037 for 904 observed reflections. The complex is held together by an intermediate hydrogen bond between the hydroxyl and the N-oxide group with an OO distance equal to 2.618(3) Å. The stacking of thea glide related complex molecules by translation in theb direction results in a herringbone structure with an overlap of the nitrophenol and 4-nitropyridine N-oxide rings and a mean interplanar distance of 3.4(1) Å between those rings.On leave from Universidad del Valle, Departamento de Quimica, Cali, Colombia.     

X-ray diffraction and vibrational spectra of the guanidine:maleic acid (1:1) complex—two crystal forms

From an equimolar mixture of guanidine and maleic acid, two different crystal modifications of guanidinium hydrogen maleate, CH₆N ₃ ⁺ ·C₄H₃O ₄ ^– , were isolated and their crystal structures determined using three-dimensional diffractometer data. Crystals of both forms are orthorhombic:Pca2₁,a=19.012(8)b=3.758(1),c=11.119(5) Å,Z=4 for form I;Fdd2,a=18.505(2),b=20.007(3),c=8.406(2) Å,Z=16 for form II. The structures were solved by direct methods and refined by full-matrix least squares to conventionalR values of 0.064 for form I and 0.043 for form II, with 488 and 605 reflections respectively. The structures consist of planar guanidinium cations C(NH₂) ₃ ⁺ and hydrogen-maleate residues C₄H₃O ₄ ^– . There are no significant differences in distances and angles within the guanidinium and hydrogen-maleate units. However, a substantial difference appears in the length and geometry of the intramolecular hydrogen bond OHO. The packing of cations and anions is also completely different in the two forms. Infrared and Raman spectra of the title compound are presented, and salient differences between them and the spectrum of the symmetrically bonded potassium hydrogen maleate are discussed briefly.     

Polymorphs of nitrofurantoin. 2. Preparation and X-ray crystal structures of two anhydrous forms of nitrofurantoin

The preparation and X-ray crystal structures of two polymorphs of the antibacterial drug nitrofurantoin are reported. The -polymorph is triclinic, space groupP¯1 witha=6.774(1),b=7.795(1),c=9.803(2)Å, =106.68(1),=104.09(2), =92.29(1)°,Z=2. The-polymorph is monoclinic, space groupP2₁/n witha=7.840(5),b=6.486(1),c=18.911(6)Å,=93.17(3)°,Z=4. The nitrofurantoin molecules adopt the same, planar conformation in both polymorphs. Both crystal structures are built up from layers held together by van der Waals forces. In each polymorph, intralayer cohesion is effected by N-HO and C-HO hydrogen bonds, but their arrangements differ in the two crystals. The significance of the C-HO hydrogen bond, now known to occur in four modifications of nitrofurantoin, is discussed.     

Crystal structure of a nucleoside analog: 1-(R)-[6-(R)-hydroxymethyl-1,4-dioxan-2-yl] uracil

The title compound (C₉H₁₂N₂O₅,M _r =228.2) crystallizes in the trigonal space groupP3₁,21 witha=b=9.438(3) andc=19.775(3) Å,V=1525.5 ų,D _x =1.490 gm cm^–3,Z=6,=0.12 mm^–1,F(000)=720.0,T=293 K. The structure was solved by direct methods and refined by full-matrix least-squares calculations to anR value of 0.044 on 843 unique observed reflections. The dioxane ring adopts a chair conformation. The crystal structure is stabilized by N-HO hydrogen bonds and C-HO close contacts.     

Crystal structure of a nucleoside analogue, 2′,3′-dideoxy-3′-fluoro-5-chlorocytidine

The title compound, 1-(2,3-dideoxy-3-fluoro--d-erythro pentofuranos-1-yl)-5-chlorocytosine, crystallises in the orthorhombic space groupP2₁2₁2₁ witha=5.142(1),b=14.177(2),c=15.721(2) Å,Z=4. The crystal structure was solved by the heavy atom method and refined by full-matrix least-squares method to a finalR value of 0.031 for 1629 unique observed reflections. The N-glycosidic torsion angle is –156.1(2)° and the sugar moiety is anti to the cytosine base. The sugar pucker is ₂ ³ T withP=178.2(1)° and=31(1)°. The atom 05 is in a +sc conformation with respect to the furanose ring. The molecular packing in the crystal is stabilized by N-HN, N-HO, O-HO hydrogen bonds and C-HO close contacts.     

Structure of dichloro[(2,4-dimethyl-5-oxo-2,3,4,5-tetrahydro-2-furyl)methyl]-(4-methoxyphenyl)tellurium(IV)

The crystal structure of TeCl₂(C₇H₇O)(C₇H₁₁O₂) has been determined from three dimensional, single crystal X-ray diffraction data. It crystallizes in the monoclinic space group C2/c with the lattice constantsa=24.551(5),b=11.435(2),c=12.368(2)Å,=97.33(1)° andZ=8,D _X=1.67 g cm^–3. Final least-squares refinement based on 3023 independent observed reflections yieldedR=0.026. The Te^iv ion is in a trigonal bipyramidal configuration with its lone pair of electrons at one of the equatorial positions. Distances and angles are: Te-Cl=2.495(1), 2.517(1); Te-C=2.134(3), 2.106(3)(aryl)Å; Cl-Te-Cl=173.45(4), Cl-Te-C=88.11(9), 88.60(9), 88.72(9), 86.06(9); C-Te-C=96.5(1)°. There are two secondary bonds to the tellurium: TeCl=3.824(1) and TeO(2)=3.006(1)Å. The methyl group to the carbonyl oxygen and the aryltelluro moiety exhibit atrans 2,4 relationship.     

Crystal and molecular structure of 3-dimethylaminobenzoic acid

The title compound C₉H₁₁NO₂ is triclinic, space group P¯1, with the cell dimensionsa=7.022(1),b=7.476(2),c=8.957 (1) Å,=87.02(2),=110.88(1),=99.10(1)°,V=433.8(4) ų,Z=2,M _r =165.2,Do=1.27,Dx=1.26 mg/m³,F(000)=176,T=293 K,R=0.057 for 939 observed reflections. The molecules are packed as centrosymmetric hydrogen bonded dimers with an O-HO distance of 2.626(3) Å. The COOH group is rotated by 1.7(1)° about the exocyclic C(1)-C(7) bond out of the benzene ring plane. The molecules lie on (0 2-1) plane for which thed value is found to be 3.378 Å which is very close to the mean separation between the parallel packed benezene rings [3.347(4) Å]. The entire molecule is planar except for the two methyl groups attached to the nitrogen atom. The N atom is free from any binding of either type C-HN or O-HN.N. C. L. Communication No. 4699.