Synthesis,spectroscopic studies,and X-ray crystallographic analysis of the organophosphorus carbohydrate: methyl 4,6-O-benzylidene-3-deoxy-3-C-diphenylphosphinyl-α-D-altropyranoside

The synthesis and molecular structure determination of an organophosphorus carbohydrate are reported. In the solid state the molecules of methyl 4,6-O-benzylidene-3-deoxy-3-C-diphenyl-phosphinyl--D-altropyranoside are linked together by intermolecular hydrogen bonding involving the oxygen attached to phosphorus and the hydroxy group. The five-valent phosphorus atom is in a distorted tetrahedral environment. The chiral molecules crystallize in the monoclinic space groupP2₁ withZ+2. Results from¹ H.¹³C and³¹P NMR investigations together with IR data are presented.     

Synthesis,structure, spectroscopic investigations,and computational studies of optically pure β-ketoamide

Chemical preparation, X-ray single crystal diffraction, IR and NMR spectroscopic investigations of a novel nonlinear optical organic compound (C₁₇H₂₂NO₂Cl) are described. The compound crystallizes in the orthorhombic system with the non-centrosymmetric sp. gr. P2₁2₁2₁. In the crystal structure, molecules are interconnected by N–H…O hydrogen bonds forming infinite chains along a axis. The Hirshfeld surface and associated fingerprint plots of the compound are presented to explore the nature of intermolecular interactions and their relative contributions in building the solid-state architecture. The molecular HOMO–LUMO compositions and their respective energy gaps are also drawn to explain the activity of the compound. The first hyperpolarizability β_tot of the title compound is determined using DFT calculations. The optical properties are also investigated by UV–Vis absorption spectrum.     

Synthesis,NMR, and X-ray crystallographic determination of the absolute configuration of 4,6-O-ethylidene-2,3-di-O-methanesulfonyl-α-d-glucopyranosyl chloride

The synthesis, NMR spectra and crystal structure of 4,6-O-ethylidene-2,3-di-O-methanesulfonyl--d-glucopyranosyl chloride are reported. The chloro substituted carbohydrate, C₁₀H₁₇ClO₉S₂, crystallizes in the monoclinic space group.,P2₁, witha=10.124(4),b=9.517(4),c=18.058(8) Å and =105.18(1)°. FinalR=0.0434. There are two independent molecules in the asymmetric unit with conformations that differ around the mesyl (–S(O)₂CH₃) groups.     

Synthesis,spectroscopic studies,and crystal structure of the first monopyridinium salt of 1,1′-bis-(2-naphthol) sulfone,C25H19NO4S

The crystal and molecular structure of 1,1-bis-(2-naphthol) sulfone monopyridine (3) determined by single-crystal X-ray diffraction is reported. C₂₅H₁₉NO₄S crystallizes in the monoclinic space groupC2/c (No. 15) witha=17.095(4),b=14.574(2),c=18.731(2) Å,=116.29(2)°,Z=8,D _x =1.364 Mg m^–3,D _m =1.353(8) Mg m^–3. The phase problem was solved by direct methods and the final reliability factor obtained from full-matrix least-squares refinement of 2306 independent reflections is 0.067. The unit cell contains eight molecules with intramolecular hydrogen bonding and the molecules in the crystal lattice are held together by van der Waals forces. Conoscopic, infrared, and¹H and C¹³ NMR analyses have been performed. Details of the structural content and selected bond lengths and angles are discussed.     

(−)-S-Benzyl-α-hydroxymethylcysteine: Confirmation of its (S)-configuration by x-ray analysis of itsN-benzoyl derivative

LaevorotatoryN-benzoyl-S-benzyl--hydroxymethylcysteine (1) crystallizes in space groupP2₁ with cell parameters:a=8.972(1),b=10.004(1),c=10.302(1)Å,=106.4(1)°,V _c=887.2(5)ų,Z=2. The structure was solved by direct methods and refined toR _w=0.054 with 1324 independent reflections. The absolute configuration of1 was determined asS by the application of Hamilton test and by the estimation of the Bijvoet coefficientB. The-amino acid residue adopts the C₅ ring conformation similar to the fully extended form. The two side chains also adopt an extended conformation around the C atom. X-Ray analysis of1 confirms theS configuration assigned previously for laevorotatoryS-benzyl--hydroxymethylcysteine (2) by chemical correlation.     

X-ray crystal structure of the 1∶2∶2 pentaethyleneglycol dimethyl ether(pentaglyme)∶dichloropicric acid∶water complex. Infrared studies of the 1∶2∶2 complexes with tri-, tetra-, and pentaglyme

The 122 pentaglymedichloropicric acidwater adduct crystallizes in two polymorphic forms. Polymorph I is triclinic, space groupP¯1; at –96°Ca=11.629(6),b=12.566(8),c=12.877(16)Å,=89.19(8),=83.76(8), =85.95(5)°,D _x =1.599 g cm^–3,V=1866(5)ų,Z=2. Refinement on 7729 observed reflections yielded a finalR value of 0.045. Polymorph II is orthorhombic, space groupP2₁2₁2₁; at –87°Ca=13.631(7),b=26.441(8),c=5.182(6)Å,D _x =1.597(3) g cm^–3,V=1868(3)ų,Z=2. Refinement of 1610 observed reflections yielded a finalR of 0.071 for a disordered structure. The hydrogen bonding pattern in I is similar to that found in the analogous 18-crown-6 complex. Two pairs of alternate O atoms in the polyether are hydrogen bonded to two water molecules, each of which is hydrogen bonded to the phenol O atom of a neutral dichloropicric acid molecule. The bond distances and torsion angles in the S shaped polyether are similar to those in the cyclic polyether with C-C-O-C angles near 180° and O-C-C-O near±60°. The complex in II resembles that in I in overall shape and dimensions, also having normal bond distances and angles. The nonhydrogen atoms in water and the dichloropicric acid can be located unambiguously. However, the polyether molecule is disordered, and a satisfactory model for the disorder could not be found. Comparison of the IR spectra of the 122 tri-, tetra-, and pentaglymedichloropicric acidwater complexes suggests that the hydrogen-bonding in the tetraglyme complex is weaker than in the pentaglyme complex, but that in the triglyme complex is as strong or stronger.Deceased, March, 1993.     

Structure ofN,N′-diphenyl-N-(2-pyridmyl)urea hemihydrate: A crystallographic and spectroscopic investigation

N,N-diphenyl-N-(2-pyridinyl)urea hemihydrate (C₁₈H₁₅N₃O·1/2H₂O) has been studied by crystallographic and NMR-spectroscopic methods. The crystals are monoclinic,I2/a with unit-cell parameters at 86K,a=17.820(1),b=14.857(1),c=11.299(1) Å,=99.17(1)° andZ=8. The structure was solved by direct methods which involved the use of seventeenmeasured triplet phases in the starting set. This appears to be the first centrosymmetric structure solution being based extensively on physically acquired X-ray phases. Refinement was by full-matrix least-squares involving 3843F _o and yieldedRR _w=0.042. The shape of the molecules can be described approximately by two, nearly orthogonal planes, one containing pyridine, the urea group and the NH-bonded phenyl ring, the other containing the second phenyl ring. Both the X-ray and the NMR studies show that there is an intramolecular H-bond between the urea N and the pyridine N atoms. When pH is lowered, this H-bond is weakened, and eventually breaks due to protonation of the pyridine ring. The X-ray study indicates that about 20% of the pyridine rings in the crystal are protonated. The structure details of the rings, in particular the valency angles, have been analyzed in relation to the orientation of the rings relative to the main molecular plane, and the electronic effects of the substituants.     

Reactivity of 6α,7α-epoxyhimachal-2-ene and crystal structures of 2α,3α-dibromocyclopropanehimachal-5,7-diene and 2α,3α-dibromocyclopropane-6α,7α-epoxyhimachalane

We report here the reactivity of 6,7-epoxyhimachal-2-ene with dibromocarbene generated in situ by phase-transfer catalysis. The stereochemistry of products resulting from dibromocyclopropanation has been established by X-ray crystallography. Compound 3 is orthorhombic P2₁2₁2₁ with a = 7.549 (1), b = 8.432 (1), c = 24.469 (1) Å, V = 1559.8 (5) ų, Z = 4 and compound 5 is monoclinic P2₁ with a = 8.779 (1), b = 15.684 (1), c = 12.111 (1) Å, = 91.869 (1)°, V = 1666.7 (4) ų and Z = 4.     

Molecular structures of four triterpenoids. X-ray crystallographic analysis of methyl 2α,3β,23α-triacetoxy-19α-hydroxyurs-12-en-28β-oate

A triterpenoid glycoside has been isolated from the roots of a herb used in traditional Chinese medicine. The molecular structure of this compound and its derivatives have been determined by spectroscopic studies and an X-ray analysis of the 2,3,23-triacetoxy-28-methyl ester of the aglycone. This aglycone belongs to the ursene structure series. The hydroxy group on ring E of these triterpenoids is orientated and the side chains at C(2), C(3), C(4) and C(17) are .,, and orientated, respectively. The C ring, which has a double bond at C(12)=C(13), adopts a sofa conformation.     

Structure and spectroscopic properties of the 1∶2 complex of 3,5-dimethylpyridine with 3,5-dinitrobenzoic acid and its deuterated analog

The structure of the nondeuterated and deuterated complexes of 3,5-dimethylpyridine with 3,5-dinitrobenzoic acid in a stoichiometric ratio 12 have been determined by X-ray diffraction methods. The crystals of the nondeuterated complex are triclinic, space groupP¯1 witha=9.409(9),b=10.813(7),c=12.310(7)Å,a=95.75(5),=108.17(7), =91.46(7)° andZ=2. The crystals of the deuterated complex are monoclinic, space groupP2₁/c, witha=11.680(6),b=8.451(4),c=24.382(9)Å,=102.94(4)° andZ=4. Both structures have been solved by direct methods and refined toR=0.035 for 2235 and toR=0.044 for 1938 independent reflections for nondeuterated and deuterated crystal, respectively. The structures consist of 3,5-dimethylpyridinium cations and hydrogen (or deuterium) bis(3,5-dinitrobenzoate) anions. The N(1)⁺-H(N1)O(1)^–, O(7)-H(7)O(2), N(1)⁺-D(1)O(l)^– and O(7)-D(7)O(2) bond lengths are 2.644(4), 2.499(3), 2.739(5), and 2.526(5)Å, respectively. The IR spectra of both complexes within the proton (or deuteron) absorption range have been studied.     

X-ray and NMR studies on the rotational isomerism about the C(5)-C(6) bond of 6-substituted methyl 2,3,4,-tri-O-acetyl-6-X-α-D-glucopyranoside derivatives

The rotamers about the C(5)–C(6) bond of a series of 2,3,4-tri-O-acetyl-6-X--D-glucopyranozide derivatives resulting by substitution at C(6) or O(6) have been studies with¹H-NMR spectroscopy (400 MHz) and X-ray structure analysis. The methyl 2,3,4-tri-O-acetyl-6-O-triphenylmethyl--D-glucopyranoside and the N-(I-O-methyl-2,3,4-tri-O-acetyl--D-glucopyranose-6-yl)-pyridinium nitrate crystallize in the P2₁ space group with =14.940(1),b=11.232(1),c=9.0773(7), and =94.480(7) anda=7.670(1),b=15.384(3),c=9.624(1) and =104.90(1), respectively; the methyl 2,3,4-tri-O-acetyl-6-O-nitro--D-glucopyranoside and methyl 2,3,4-tri-O-acetyl-6-O-deoxy-6-iodo--D-glucopyrano-side crystallize in the P2₁2₁2₁ space group witha=5.630(1),b=14.360(1) andc=22.388(3), anda=5.556(1),b=14.303(6) andc=21.963(6), respectively.     

4-Hydroxy-N′-[(1E)-1-(4-methylphenyl)ethylidene]benzohydrazide: Synthesis, crystal structure, and spectroscopic studies

The titled compound has been synthesized by reaction of 4′-methylacetophenon with 4-hydrox-ybenzohydrazide in presence of catalytic amount of glacial acetic acid. The compound is characterized by elemental analysis, IR, ¹H NMR, ¹³C NMR and UV-visible spectra. The crystal structure was determined by X-ray diffraction method. Both X-ray data and NMR spectra indicate that the molecule exists in a trans configuration with respect to the C=N bond. The observation of strong ν(C=O) peak in IR spectra of the aroylhydrazone compound suggests that it is in keto form in solid state. X-ray diffraction results confirm this suggestion. In the crystal structure, there are N-H...O and O-H...O hydrogen bonds and weak C-H...π interaction.     

Structure of the 1∶1∶1 complex between 1,4,7,10,13,16-hexaoxacyclooctadecane (18-crown-6), 2,3-dichlorophenol,and water

The structure of the title compound, C₁₂H₂₄O₆·C₆H₄OCl₂·H₂O, has been determined by X-ray diffraction methods. The crystals are monoclinic, space groupP2₁ witha=8.628(2),b=13.767(4),c=9.676(2), =96.38(2)°, andD _x =1.295 Mg m^–3 forZ=2; 2355 reflections were recorded on a CAD4 diffractometer using CuK radiation atT=243° K. The structure was solved usingMultan andShelx. The finalR value based on 1901 reflections is 0.071. The 18-crown-6 molecule has approximatelyD _3d symmetry. The host molecule (18-crown-6), the guest molecule (dichlorophenol), and water form a super-molecule. Binding between host and guest is effected by bridging water molecule: the water and dichlorophenol molecule are linked by a very strong hydrogen bond (OO=2.58 Å); weaker interactions exist between water and oxygens of the crown ether (OO distances 2.85 and 2.90 Å).     

Structural and spectroscopic properties of the 1∶1 complex of Δ2, 2′-bis-1,3-dithiole (TTF) and 1,2,4,5-tetracyanobenzene (TCNB)

{2,2-bis-1,3-dithiole-1,2,4,5-tetracyanobenzene}, (TTF-TCNB), C₆H₄S₄-C₁₀H₂N₄,M=382.3, monoclinic,P2₁/a,a=9.194(3),b=12.342(3),c=7.426(2) Å,=95.12(3)°,Z=2,D _x =1.52 Mg m^–3, (MoK)=0.71069 Å,=0.51 mm^–1,F(000)=776,T=293 K, finalR=0.039 for 1480 unique observed [F _o >4(F _o ² )] reflections. The complex represents a member of the series of crystal structures of molecular complexes containing TTF as an electron donor and TCNB as an electron acceptor. The structure was solved by direct methods and has been refined by full matrix least-squares calculations. The constituent molecules are stacked alternatively in infinite columns along thec axis. The mean separation of the molecular planes, which are inclined at the angle of 4.4°, is 3.48 Å. There are no unusually short intermolecular contacts. Bond lengths and angles in the component molecules agree with values for neutral species; also the infrared and Raman spectra indicate a very slight degree of ionicity.     

Anticancer agent development. 5. X-ray structure and1H nmr spectral analysis of (1α,2α,5α,6α)-2,6-bis(3,4-methylenedioxyphenyl)-3,7-dioxabicyclo[3.3.0]octane-4,8-dione

The title compound, C₂₀H₁₄O₈, Mr=382.3, crystallized from chloroform in the centric space group P¯1 witha=6.516(4),b=6.798(3),c=9.545(7) Å,=85.31(5),=73.87(5), =79.59(4)°,V=399.2 ų, and D_calc=1.59 g cm^–3 forZ=1. Least-squares refinement of 1035 observed [F_o5(F_o)] reflections led to the final agreement index ofR=0.074. The molecule resides on a crystallographic center of inversion and is disordered into two different conformations. This manifests itself as a 50/50 disorder at O(4), C(2), and C(3). The observed structure reveals acis relationship between the bridgehead hydrogen atoms and the aryl rings. The 90 MHz¹H nmr spectrum of the title compound exhibits an AAXX spin system with a H(1)C(2) to H(1)C(3) and H(1)C(2) to H(1)C(3) coupling constant of 2.8 Hz. Computer spectral simulation and Karplus equation analysis are utilized to illustrate a relaxation of the torsion angles between H(1)C(2) and H(1)C(3), and H(1)C(2) and H(1)C(3) is solution.     

Co-crystal structures of 2,4-diamino-6-phenyl-1,3,5-triazine – 4-chlorobenzoic acid/4-methoxybenzoic acid: Synthesis,structural and Hirshfeld surface analysis

The co-crystal structure of 2,4-diamino-6-phenyl-1,3,5-triazine with 4-chlorobenzoic acid/4-methoxybenzoic acid molecules are explain the link between the dimension and shape of their hydrogen-bonded assembly. The co-crystal structure of 2,4-diamino-6-phenyl-1,3,5-triazine with 4-chlorobenzoic acid/4-methoxybenzoic acid forming a cyclic R₂²(8) ring motif via N–H?O and O–H?N hydrogen bonding interactions, to form a supramolecular heterosynthon. In both the co-crystal structures, self-association of 2,4-diamino-6-phenyl-1,3,5-triazine moieties are connected via N-H^….N base pairs with cyclic R₂²(8) motif form a supramolecular homosynthon. In co-crystal II, the centrosymmetrically paired methoxy group of 4-methoxy benzoic acid form a supramolecular homosynthon via weak intermolecular C-H^….O hydrogen bonds, generating R₂²(6) ring motif. Both the co-crystal structures are stabilized by weak aromatic π-π and C—Cl???π stacking interactions. Hirshfeld surface and fingerprint plots were used to study the intermolecular interactions both of the crystal structures.     

α-Hydroxymethylaspartic acid: Synthesis and absolute configuration by X-ray analysis of its derivative (+)-4-benzoylamino-4-carboxy-γ-butyrolactone

(+)-4-Benzoylamino-4-carboxy--butyrolactone was synthesized, and its structure solved by direct methods and refined toR=0.033. The molecule adopts a skew conformation with a C7-N1-C8-C12 torsion angle of 59.6(2)°. The lactone ring has an envelope conformation, with the C(8) atom deflected from the ring plane. The absolute configuration of (+)-benzylami-no-4-carboxy--butyrolactone5 was assigned asR by the application of Hamilton's test to the unique diffraction data, and confirmed by the estimation of the Bijvoet coefficientB fromhkl and diffraction data. This result proves theR configuration for (+) enantiomer of the parent-hydroxymethylaspartic acid.     

Synthesis and Crystal Structure of 3β-Acetoxy-5α-bromo-6β-hydroxyandrostan-17-one

Abstract  

The title steroid 3β-acetoxy-5α-bromo-6β-hydroxyandrostan-17-one 1 was synthesized from the reaction of 3β-acetoxy-5-androstene-17-one with N-bromosuccinimide (NBS) and characterized by FT-IR, ¹H-NMR, EI-MS and ESI-HRMS techniques. The structure of the compound was also determined crystallographically. The crystal structure was solved by direct methods and refined by full-matrix least-squares. It crystallized with two molecules in the asymmetric unit in the triclinic space group P1 with a = 7.0518(9), b = 10.1362(16), c = 15.3472(19) ?, α = 100.579(8), β = 99.354(6), γ = 109.267(5)°, V = 988.1(2) ?³, D _x  = 1.436 g cm⁻³, respectively (R ₁ = 0.0262 and wR ₂ = 0.0468 for 5273 reflections [I > 2σ(I)]). Three-six-membered rings A, B and C exist in chair conformation while the five-membered ring D displays an envelope conformation. The intermolecular interactions O–H···O link the molecules into a three dimensional network. The crystal structure was compared with our previously reported similar structures.     

Synthesis of spinacine and spinacine derivatives: crystal and molecular structures of Nπ-hydroxymethyl spinacine and Nα-methyl spinaceamine

The natural amino acid L-Spinacine (4,5,6,7-tetrahydro-1H-imidazo[4,5-c]pyridine-6-carboxylic acid) has been synthesized following a new pathway which gives a chemically and optically pure product with an excellent yield. The crystal structures of a synthetic intermediate, N^π-hydroxymethyl-spinacine, and a spinacine derivative, N^α-methyl-spinaceamine, have been investigated through X-ray diffraction: Spi(πMeOH)·H₂O, monoclinicP2 _i,a=8.571(1),b=6.682(1),c=8.588(1) Å, and β=94.67(1)^o. Spm(αMe)·2HCl·H₂O, triclinicP l,a=7.492(4),b=10.799(3),c=7.040(2) Å, α=91.88(2), β=98.36(3) and γ=73.34(3)^o. Spi(πMeOH) crystallizes with a water molecule and displays a zwitterionic character. The carboxylate group is in equatorial position and forms a short electrostatic interaction of 2.618(2) Å between one of its oxygens and the protonated nitrogen of the tetrahydropyridine ring. The crystal packing is assured by strong O?H???O, O?H???N, N?H???N intermolecular hydrogen bonds and C?H???O close contacts. The biprotonated compounds Spm(αMe) crystallizes with two Cl^? anions and a water molecule. The positive charge on the imidazole ring is delocalized on the conjugated moiety N=C?N. The crystal is built up by clusters formed by two biprotonated Spm(αMe) molecules, four Cl^? anions and two water molecules linked together by hydrogen bonds.