Structure determination and hydrogen bonding of 1-naphthoxyacetic acid, a potential plant growth hormone

1-Napthoxyacetic acid crystallizes in the centrosymmetric space group C2/c (No. 15) with cell dimensions of a=14.273(2)Å, b=5.845(1)Å, c=24.211(1)Å, =105.815(2)°. The structure of the title compound reveals a carboxyl group-naphthalene ring dihedral angle of 4.85(14)°, O—H- - -O hydrogen bonded dimer, hydrogen bond distance of 2.640(2)Å, hydrogen bond angle of 172(2)°, and a cis configuration of O2 (double bond) and O3 relative to the C11—C12 bond all of which indicate that the title compound may be effective as a plant growth hormone.     

Structure, absolute configuration, and conformation of the antimalarial compound, Artemisinin

The crystal and molecular structure of the antimalarial compound Artemisinin (formerly known as Qinghaosu), C₁₅H₂₂O₅ has been determined by direct methods. Crystals are orthorhombic colorless needles, space group P2₁2₁2₁, Z = 4. D _c = 1.299 g cm ^–3, with unit cell parameters a = 6.3543(9), b = 9.439(3), c= 24.066(4) Å. The molecule incorporates a fused ring system containing a six-membered ring C which includes an oxygen bridge and a peroxy-bridge. The ring C has a distorted boat conformation and the C - O - O - C torsion angle is 47.8(2)°. Rings A and D have symmetrical chair and distorted chair conformations, repectively. Ring junctions A/B, A/D, and C/D are cis, junction B/D is trans. All inter-molecular contacts are van der Waals. The absolute configuration of Artemisinin was determined from the refined value of the Flack x parameter. [The atomic coordinates given in a previous structure analysis, Crystal Structure and Absolute Configuration of Qinghaosu, Qinghaosu Research Group, Institute of Biophysics, Academica Sinica, Scientia Sinica, Vol. XXIII No. 3, 380 (1980), do not display the molecule in its absolute configuration.]     

Molecular structure of PhOCH2CH(OH)CH2OPh

The molecular structure of PhOCH₂CH(OH)CH₂OPh has been determined. The C—O—C—C—C—O—C backbone adopts an anti-anti-anti-anti conformation. Inter-molecular O—H ··· O hydrogen-bonding results in dimeric units which stack into zig-zag tapes. Crystal data: orthorhombic, Pbca, a = 10.383(1), b = 8.0532(0), c = 31.295(3) Å, V = 2616.8(3) ų, and Z = 8.     

Silver(I) complexes of 6-methyl-2-pyridinecarboxylic acid: the crystal structure of [Ag(MeC5H3NCOO)(MeC5H3NCOOH)]

Silver(I) complexes of 6-methyl-2-pyridinecarboxylic acid (HL) have been prepared, and the crystal structure of [Ag(L)(LH)] has been determined from X-ray diffraction data. This complex crystallizes in the monoclinic space group P2₁/n, with a = 13.4055(13), b = 7.1012(7), c = 15.588(2) Å, = 112.779(2)°, and Z = 4. Anionic [AgL₂]^– units are linked together by protons in approximately symmetrical linear O—H—O hydrogen bonds involving uncoordinated carboxylate oxygen atoms, to give polymeric chains. The most significant intermolecular interaction between adjacent parallel chains is offset ring stacking of pairs of aromatic rings with a perpendicular distance of 3.27 Å. The Ag coordination geometry is highly distorted tetrahedral, from two pyridine N atoms and two carboxylate O atoms, each ligand forming a five-membered chelate ring.     

Crystal and molecular structure of pyridinium di-μ-oxo-bis(oxodichloroaquomolybdate(V)) monohydrate, (pyh)2[Mo2O4Cl4(H2O)2] · H2O

The crystal and molecular structure of pyridinium di--oxo-bis(oxodichloroaquomolybdate(V)) monohydrate has been determined from MoK diffractometer data. The compound crystallizes in the monoclinic space groupP2 ₁/m witha = 7.544(1),b= 17.046(3),c = 7.894(1) Å, = 106.00(1) ° andZ = 2. The structure was solved by the heavy-atom technique and refined by full-matrix least-squares method toR = 0.046, using 1800 reflections for whichF> 4(F). Molybdenum atoms are linked by the double oxygen bridge with an Mo—O distance of 1.943(4) Å and an Mo—O—Mo angle of 83.4(2) °. The Mo—Mo distance is 2.584(1) Å, indicating direct Mo—Mo bonding. The pyridinium and [Mo₂O₄C1₄(H₂O)₂]^2- ions are hydrogen bonded through N—H ... O bonds. The N ... O contact is 2.656(8) Å.     

Dalspinin, an isoflavone from Dalbergia spinosa roots

The X-ray crystal structure of the plant isoflavone dalspinin from Dalbergia spinosa is determined. The compound, C₁₇H₁₂O₇, is monoclinic in P2₁/n with a = 3.970(1), b = 23.607(5), c = 14.633(3) Å, = 94.46(3)°, V = 1367.2(5) ų, D _calc = 1.595 g cm^–1 and Z = 4. The molecular structure is characterized by a short intramolecular O–H···O=C hydrogen bond, and a large tilt angle of the two rigid ring systems with respect to each other. The intermolecular interactions in the crystal are discussed.     

17α-acetoxy-17β-methyl-16β-phenyl-D-homo-4,6-pregnadiene-3,17a-dione: synthesis and crystal structure determination of a new rearranged pregnane derivative

The title compound is C₂₉H₃₄O₄, tetragonal, P4₃, a = b = 10.310(1), c = 23.871(2)Å. The A, B, C, and D rings adopt envelope, half-chair, chair, and distorted chair conformations, respectively. The phenyl ring is planar. The methyl substituents at the A/B, C/D, and at C(17) are axial; and the –OCOCH₃ group at C(17) and phenyl ring at C(16) are equatorial. The molecules in the crystal are held together by van der Waals forces and several C–H···O hydrogen bond interactions.     

Crystal structure of the charge transfer complex 9-cyclohexyladenine-iodine

The crystal structure of the charge-transfer complex of iodine with 9-cyclohexyladenine, C₁₁H₁₅I₂N₅, has been determined, and refined by three-dimensional least-squares techniques. The crystals are monoclinic:P2₁/c,Z = 4,a = 9·1728(7),b = 12·289(1),c = 13·596(1) Å, = 99·564 °(6). The finalR value for 3629 reflexions is 0·039. The iodine forms a charge-transfer bond with N(1) of the adeninering, with an N—I bond length of 2·520(3) Å. The I—I—N(1) arrangement is approximately linear (bond angle, 177·1 °). The I—I molecule makes an angle of 21·5 ° with the plane of the adenine ring.Supported by N. I. H. Development Award 5-K4-GM-42572.     

Absolute configuration of C27H41NO8Si, the diastereoselective product of the rhodium(II) octanoate catalyzed decomposition of a chiral vinyldiazomethane in the presence of 2-acetylpyrrole: A structural study rendered difficult by disorder of a “heavy” atom

The title compound crystallized in space group P2₁ with a = 12.647(8), b = 14.542(4), c = 17.077(16) Å, = 97.51(6)°, and D _calc = 1.143 mg/m³ for Z = 4. There are two chemically-equivalent C₂₇H₄₁NO₈Si molecules in the crystallographic asymmetric unit. Each contains three chiral centers, one of known absolute configuration based upon the (R)-pantolactone,—CH*—CMe₂—CH₂—O—CO—, moiety. The structural study was greatly complicated by disorder of an —OSiMe₂(t-Bu) group in one molecule.     

Synthesis and structure determination of 3β-hydroxyandrost-5-en-17-one (C19H28O2·CH3OH)

3-Hydroxyandrost-5-en-17-one (C₁₉H₂₈O₂.CH₃OH) has been prepared for undertaking its crystallographic analysis and to investigate the role of intra- and intermolecular interactions in steroids. The title compound crystallizes in the orthorhombic space group C222₁ with unit cell parameters a = 6.7892(17), b = 12.624(2), and c = 41.136(5) Å; V = 3525.7(12) ų and Z = 8. The three-dimensional structure has been solved by direct methods. The final reliability index for the computed structure is 0.050 for 1088 observed reflections. Ring A exist in chair conformation, Ring B in half-chair conformation, and the Ring C assumes a distorted chair conformation. The five-membered Ring D adopts half-chair conformation. The A/B ring junction is quasi-trans while as B/C and C/D are trans-fused. The oxygen atom of the solvent molecule (CH₃OH) is involved in O–H···O intermolecular interaction.     

Crystal and molecular structures of three trimethylamine-boron halide adducts: (CH3)3NBCl3, (CH3)3NBBr3, and (CH3)3NBI3

X-ray diffraction data from single crystals of the trimethylamine complexes of the three boron halides, BCl₃, BBr₃, and BI₃, lead to aP2₁/m monoclinic cell containing two molecules for each complex. The unit cell dimensions area = 6·68(1),b = 10·247(3),c = 6·502(6) Å, =116·2(1)° (chloro);a = 6·86(1),b = 10·612(4),c = 6·737(6) Å, = 115·8(1)° (bromo);a = 6·92(2),b = 10·86(1),c = 7·147(6) Å, = 93·9(1)° (iodo). The structures were solved by three-dimensional sharpened Patterson functions and show only the chloro and bromo compounds to be isomorphous. Refinement of 662,718 and 954 observed reflexions for the chloro, bromo and iodo complexes, respectively, using anisotropic thermal parameters yielded conventionalR factors of 0·045, 0·087 and 0·054.The molecules are shown to possess a B—N dative bond, a staggered conformation, and effective 3m (C _3v) symmetry. Average C—N bond lengths are 1·52(1) Å for all three complexes. Boronhalogen bond lengths average 1·864(4), 2·04(2) and 2·28(2) Å, while B—N bond distances are 1·609(6), 1·60(2) and 1·58(3) Å, respectively, for the chloro through iodo compounds. Bond angles are approximately tetrahedral with the C—N—C angle decreasing by several degrees in the Cl Br I series.Based in part on a dissertation submitted by Patty H. Clippard to the Rackham School of Graduate Studies of the University of Michigan, January 1969 in partial fulfillment of the requirements of the Ph.D. Degree.     

Anticooperative C—C—H···O···H—O hydrogen bonding in 5β-Hydroxy-5α-ethynyl-10β-methyl-Δ1(9)-octalin-2-one

In the x-ray crystal structure of the alkynol 5-hydroxy-5-ethynyl-10-methyl-¹⁽⁹⁾-octalin-2-one [C₁₃H₁₆O₂, Pbca, a = 10.244(7), b = 12.734(2), c = 17.125(2) Å, Z = 8], the hydroxyl and ethynyl groups are involved in a hydrogen bond arrangement C—C—H···O···H—O, which is supposed to be anticooperative, i.e., weaker than the sum of two isolated hydrogen bonds.     

Crystal structure of the keto-enamine form of (+) (1S,2S)-2-(2-hydroxybenzylidene)amine-1-phenyl-1,3-propanediol

The title compound crystallizes in the orthorhombic space group P2₁2₁2₁, withZ=4,a=6.068(1)Å,b=10.922(1)Å, andc=21.713(2)Å. The compound is the chiral ligand of a copper complex used as an enantioselective catalyst. It crystallizes from methanol in the keto-enamine form, though the enol-imine isomer predominates in the solution. Most N-salicylideneamines studied by X-ray are enol-imines. The two tautomeric forms may interchange through anintramolecular hydrogen bond and the distances between non-H atoms in the resulting cyclic –O–H...N=C–C=C- or –C=O...H–N–C=C- fragment may be misleading, so that H atom position is the crucial factor for determination of the proper tautomeric form.     

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.     

The crystal structures of (p-ClPh)3PO and (p-OMePh)3PO, including an analysis of the P-O bond in triarylphosphine oxides

The crystal structures of the compounds tris(para-chlorophenyl)phosphine oxide {(p-ClPh)₃PO} and tris(para-methoxyphenyl)phosphine oxide {(p-OMePh)₃PO} were determined by X-ray diffraction methods. (p-ClPh)₃PO crystallizes in the space group P-1 (no. 2) with a = 11.828(2), b = 12.645(2), c = 14.072(2) Å, = 97.90(1), = 109.45(1), = 115.43(1), V = 1692.3(2) ų and Z = 4. The mean O–P and C–P distances are 1.481(6) and 1.806(2) Å, respectively, and the mean C–P–C angle is 106.5(1.1). (p-OMePh)₃PO crystallizes in the space group P2₁/c (no. 14) with a = 18.8642 (10), b = 10.3999(5), c = 21.3462(16) Å, = 115.414(6)°, V= 3782.6(4) ų, and Z = 8. The mean O–P and C–P distances are 1.484(5) and 1.798(4) Å, respectively, and the mean C–P–C angle is 106.5(1.0). These two structures were analyzed along with the previously determined structures of triphenylphosphine oxide {Ph₃PO} and tri-p-tolylphosphine oxide {(p-MePh)₃PO}, and IR data were collected on all four compounds. Both the observed P–O distances and the IR stretching frequencies for these triarylphosphine oxides support the interpretation of the P–O bond as having substantial multiple-bond character, with a bond order between 1.7 and 1.8. The para-substituents on these triarylphosphines were shown to have a statistically insignificant effect on the P–O bond.     

Synthesis and crystal structures of 2-amino-3-cyano-4-(2-chlorophenyl)-1,4-dihydro-2H-pyrano[3, 2-h]quinoline and 2-amino-3-cyano-4-(2-chlorophenyl)-8-(2-chlorobenzylidene)-1,4,5,6,7,8-hexahydrobenzo[b]pyran

The title compounds 2-amino-3-cyano-4-(2-chlorophenyl)-1,4-dihydro-2H-pyrano[3, 2-h]quinoline 1 (C₁₉H₁₂ClN₃O, M _r = 333.77) and 2-amino-3-cyano-4-(2-chlorophenyl)-8-(2-chlorobenzylidene)-1,4,5,6,7,8-hexahydrobenzo[b]pyran 2 were synthesized and crystallized. The crystals of compound 1 are triclinic, space group P-1, a = 7.488(2), b = 9.127(3), c = 12.252(3) Å, = 73.58(2), = 78.38(2)°, = 75.39(2), Z = 2, V = 769.5(4) ų; The compound 2 crystallizes in space group P2₁/n, with cell parameters a = 13.582(2), b = 8.974(1), c = 16.960(2) Å, = 103.34(1)° and D _calc = 1.352 g/cm^–3 for Z = 4. X-ray analysis reveals that atoms C(1)—C(5) and O form a pyran ring in compound 1, which adopts half-chair conformation. In compound 2 the atoms C(12)—C(16) and O form a pyran ring which adopts boat conformation, another six-membered ring (C(8)—C(13)) adopts a half-chair conformation. In addition, there are intermolecular hydrogen bonds in the crystal structures 1 and 2.     

Crystal structure of triphenylphosphine-(1-(di(trifluoromethyl)-hydroxymethyl)-cyclopentadienyl)-(1,2-di(carboxymethyl) ethylene-1-yl) ruthenium (0)

The structure of triphenylphosphine — (1 — (di(trifluoromethyl) — hydroxymethyl) — cyclopentadienyl) — (1,2 — di(carboxymethyl)ethylene — 1 — yl) — ruthenium (0) has been studied by single-crystal X-ray diffraction techniques. This compound, [C₅ H₄(CF₃)2 COH] Ru(PPh₃)C2(CO₂Me)₂H, crystallizes in the triclinic space groupP¯1 witha =10.131,b= 15.107,c= 10.798 Å, = 102.14, = 107.04, = 89.64° andZ = 2. The structure was refined by block-diagonal least-squares methods to a finalR value of 0.042, including hydrogen atoms. The compound contains a dicarboxymethylethylene ligand coordinated to ruthenium both through a ketonic oxygen and through a metal--carbon -bond. An intramolecular hydrogen bond is observed. Details of the structure are reported, and the structures of several Ru(0) complexes are compared.     

Crystal structure of the cytotoxic marine alkaloid 2-bromoleptoclinidinone

2-Bromoleptoclinidinone methanol solvate, C₁₈H₈BrN₃O·CH₄O, crystallizes in the orthorhombic space group Pbca with a = 15.7013(2), b = 7.3308(1), and c = 26.9326(1) Å. The molecule is essentially planar, with the largest deviations occurring at bromine (–0.21 Å), carbonyl oxygen O(l) (+0.19 Å) and in ring-A (C(9) –0.15 Å, C(10) –0.15 Å). Methanol occupies the 1,10-phenanthroline-like metal binding site of the title compound.     

The synthesis and crystal structure of one novel ternary complex of 2,2′-bipyridine N-salicylidenetyrosinatocopper(II)

The crystal structure of copper(II)—salicylidene-aminoacidate Schiff base—nitrogen-donor chelating ligand, [Cu(sal-tyr)(bipy)] (sal-tyr: N-salicylidenetyrosinato; bipy: 2,2-bipyridine) which is obtained by means of one-step synthesis, is presented. It crystallizes in space group P2₁2₁2₁ with a = 9.0356(18) Å, b = 11.992(2) Å, c = 20.618(4) Å. The Cu^II ion is five coordinated by one oxygen atom of carboxylate, the imine nitrogen atom, and the hydroxyl oxygen atom of the salicylidene in the Schiff base anion as well as two nitrogen atoms of bipy, resulting in a seriously distorted square pyramid coordination polyhedron. The phenol group and the apical coordination bond Cu(1)–N(2) are in the same side of the Schiff base chelating plane which could be attributed to the intramolecular C–H s interaction between the H(17) of the bipy and the benzene ring of the phenol. The hydrogen bond between the hydroxyl hydrogen atom of the phenol group and the coordinated oxygen atom of the carboxylate from neighboring molecule is helpful to stabilize the crystal.     

Complexes with Hg(II) and macrocyclic ligands

The crystal structures of 1,4,7,10,13,16-hexaoxa-cyclooctadecane dicyano mercury(II) monohydrate, C₁₄H₂₄HgN₂O₆·H₂O, 1, and 2,5,8,11,18,21,24,27-octaoxa-tricyclo[26.4.0.0_12,17]-dotriconta-1(28),12,14,16,29,31-hexaene dicyano mercury(II) monohydrate, C₂₆H₃₂HgN₂O₈·H₂O, 2, were determined: 1 crystallizes in the trigonal space group R3¯ with cell dimensions a = 11.7842(1) and c = 12.0316(1) Å. 2 crystallizes in the monoclinic space group P2₁/c with cell dimensions a = 11.156(3) Å, b = 8.417(2), c = 30.901(8) Å, and = 93.279°. In spite of the different cyclic systems, similar complexes are formed where the Hg atom is coordinated by two CN groups and six oxygen atoms of the crown ether. The structure of 1 is isostructural with the crystal structures of 18C6—HgCl₂, 18C6—CdBr₂, 18C6—Sr(BH₄)₂, and 18C6—Ba(BH₄)₂. Furthermore, 1 is very similar to other 18C6—HgX₂ complexes.