Home Crystal structure of 3,5–di-O-benzoyl-1,2-O-isopropylidene-α–D-ribose, C22H22O7
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Crystal structure of 3,5–di-O-benzoyl-1,2-O-isopropylidene-α–D-ribose, C22H22O7

  • Binbin Wu ORCID logo , Guangying Chen ORCID logo EMAIL logo and Haixin Ding ORCID logo EMAIL logo
Published/Copyright: May 23, 2023
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 238 Issue 4

Abstract

C22H22O7, orthorhombic, C2221 (no. 20), a = 8.891(2) Å, b = 17.938(5) Å, c = 25.996(6) Å, V = 4146.0(18) Å3, Z = 8, R gt (F) = 0.0461, wR ref (F 2) = 0.1189, T = 296 K.

CCDC no.: 2248486

The molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Block
Size: 0.30 × 0.28 × 0.22 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.10 mm−1
Diffractometer, scan mode: φ and ω
θ max, completeness: 27.6°, >99 %
N(hkl)measured, N(hkl)unique, R int: 16,702, 4539, 0.039
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 3164
N(param)refined: 262
Programs: CrysAlisPRO [1], SHELX [2, 3], Diamond [4]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y z U iso*/U eq
C1 0.1626 (5) 0.0859 (2) 0.38010 (14) 0.0652 (10)
H1A 0.116402 0.043860 0.396622 0.098*
H1B 0.087305 0.114108 0.362154 0.098*
H1C 0.236943 0.068727 0.356095 0.098*
C2 0.3521 (5) 0.0935 (2) 0.45118 (17) 0.0773 (12)
H2A 0.306689 0.050838 0.467146 0.116*
H2B 0.432646 0.077580 0.429196 0.116*
H2C 0.390962 0.126199 0.477237 0.116*
C3 0.2360 (3) 0.13426 (15) 0.41978 (11) 0.0449 (7)
C4 0.2015 (3) 0.25657 (16) 0.39634 (10) 0.0412 (7)
H4A 0.155877 0.264618 0.362469 0.049*
C5 0.2739 (3) 0.32682 (15) 0.41806 (10) 0.0364 (6)
H5A 0.218325 0.370889 0.406401 0.044*
C6 0.2528 (3) 0.31661 (15) 0.47597 (10) 0.0389 (6)
H6A 0.324881 0.279962 0.489135 0.047*
C7 0.0852 (4) 0.23637 (16) 0.43776 (11) 0.0439 (7)
H7A −0.017381 0.237567 0.423974 0.053*
C8 0.4671 (3) 0.35846 (15) 0.36009 (11) 0.0385 (7)
C9 0.6304 (3) 0.37551 (16) 0.35571 (11) 0.0412 (7)
C10 0.7246 (3) 0.37604 (16) 0.39792 (12) 0.0491 (8)
H10A 0.687503 0.363802 0.430283 0.059*
C11 0.8743 (4) 0.3948 (2) 0.39188 (16) 0.0634 (10)
H11A 0.937685 0.395709 0.420315 0.076*
C12 0.9296 (5) 0.4122 (2) 0.34423 (17) 0.0788 (13)
H12A 1.030490 0.424649 0.340360 0.095*
C13 0.8372 (5) 0.4113 (3) 0.30249 (17) 0.0803 (13)
H13A 0.875577 0.422604 0.270146 0.096*
C14 0.6865 (4) 0.3936 (2) 0.30784 (13) 0.0604 (9)
H14A 0.623356 0.394020 0.279316 0.073*
C15 0.2631 (4) 0.38726 (15) 0.50629 (10) 0.0456 (7)
H15A 0.358821 0.411607 0.500152 0.055*
H15B 0.182983 0.421154 0.496545 0.055*
C16 0.2560 (4) 0.42233 (16) 0.59383 (11) 0.0487 (7)
C17 0.2418 (4) 0.39580 (16) 0.64724 (11) 0.0499 (8)
C18 0.2857 (5) 0.44208 (19) 0.68670 (13) 0.0673 (11)
H18A 0.321579 0.489607 0.679348 0.081*
C19 0.2770 (7) 0.4187 (2) 0.73654 (13) 0.0937 (16)
H19A 0.310966 0.449345 0.762933 0.112*
C20 0.2182 (10) 0.3498 (2) 0.74772 (16) 0.137 (3)
H20A 0.209099 0.334167 0.781687 0.165*
C21 0.1737 (11) 0.3048 (3) 0.70877 (16) 0.163 (4)
H21A 0.134819 0.257896 0.716242 0.196*
C22 0.1848 (7) 0.3272 (2) 0.65851 (14) 0.1032 (19)
H22A 0.153551 0.295724 0.632184 0.124*
O1 0.1254 (3) 0.16429 (12) 0.45359 (9) 0.0612 (7)
O2 0.3056 (2) 0.19714 (11) 0.39654 (8) 0.0507 (6)
O3 0.1028 (2) 0.28716 (11) 0.47855 (7) 0.0469 (5)
O4 0.4308 (2) 0.33617 (10) 0.40787 (7) 0.0404 (5)
O5 0.3767 (3) 0.36370 (14) 0.32595 (8) 0.0577 (6)
O6 0.2492 (2) 0.36672 (10) 0.55980 (7) 0.0467 (5)
O7 0.2735 (4) 0.48615 (12) 0.58175 (9) 0.0806 (9)

1 Source of materials

The title compound was synthesized according to the previous reports [5], [6], [7]. 1,2-O-isopropylidene-α–D-ribose (1.9 g, 10.0 mmol) and triethylamine (6.9 mL, 50.0 mmol) were dissolved in anhydrous dichloromethane (30 mL). After it was cooled to 0 °C, benzoyl chloride (3.5 mL, 30.0 mmol) was added dropwise. After addition, the reaction mixture was stirred at room temperature for 3 h until TLC showed the reaction was finished. Then, the reaction was quenched with ice water. Another dichloromethane (30 mL) was added and the obtained reaction mixture was washed with 5 % aqueous HCl (30 mL × 2), water (30 mL × 2), and brine (30 mL × 2). After dried over anhydrous Na2SO4 and filtration, the solvent was evaporated under vacuum. The residue was purified to afford 3,5–di-O-benzoyl-1,2-O-isopropylidene-α–D-ribose (3.9 g, 98 %) by column chromatography, which was further recrystallized with ethanol. Crystals were acquired by slow evaporation from the solution at 268–270 K.

2 Experimental details

Fixed U iso at 1.2 times for all C(H) groups, all C(H,H) groups and at 1.5 times for all C(H,H,H) groups; Ternary CH were refined with riding coordinates: C4(H4A), C5(H5A), C6(H6A), C7(H7A); Secondary CH2 were refined with riding coordinates: C15(H15A,H15B); Me were refined with riding coordinates: C1(H1A,H1B,H1C), C2(H2A,H2B,H2C); Aromatic/amide H were refined with riding coordinates: C10(H10A), C11(H11A), C12(H12A), C13(H13A), C14(H14A), C18(H18A), C19(H19A), C20(H20A), C21(H21A), C22(H22A).

3 Comment

Nucleosides, the basic building blocks of nucleic acids such as RNA and DNA, play crucial roles in many biological processes [8]. Modified nucleosides have demonstrated great therapeutic promise for antiviral and anticancer chemotherapies [9, 10]. Among them, sugar-modified nucleosides are a type of modified nucleoside with alterations to the ribose component at the 2′, 3′, or 5′ positions, affecting the conformation, stability, and reactivity of the nucleoside [11]. For instance, 2′-deoxy-2-fluoro-β–D-arabinoadenine (Fludarabine) is an FDA approved drug for the treatment of chronic lymphocytic leukemia (CLL) [12]. During our ongoing work to synthesize novel nucleoside analogues, 3,5-di-O-benzoyl-1,2-O-isopropylidene-α–D-ribose has been identified as a highly desirable key intermediate [13, 14]. Using this intermediate, we can synthesize a series of novel nucleosides and test them for antiviral activity. Recently, our group has developed an improved synthetic approach using tetra-O-acetyl-β–D-ribose as the starting material in three steps, with an overall yield of 86 %. The crystal structure of this intermediate has not been reported previously, which is crucial for analysing its conformation.

The title structure (see Figure) consists of a furanosy D-ribose with four OH groups protected by two benzoyl groups at O4 and O6 and a bridged isopropylidene at O1 and O2, where a large dihedral angle (116.1°) between O3–C7–C4–C5 and O1–C7–C4–O2 was observed. The orientation between C6–C15 bond and C7–O1 bond is a trans-form (that is, α-configuration). Summarily, the bond lengths and angles are in the expected ranges.

Corresponding authors: Guangying Chen, Key Laboratory of Tropical Medicinal Resource Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Hainan Normal University, Haikou 571158, People’s Republic of China, and Key Laboratory of Tropical Medicinal Plant Chemistry of Hainan Province, Haikou 571158, People’s Republic of China, E-mail: ; and Haixin Ding, Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science & Technology Normal University, Nanchang, 330013, People’s Republic of China, E-mail:

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This project was supported by the National Natural Science Foundation of China (22177023, 41866005); the Key Science and Technology Program of Hainan Province (No. ZDKJ202008); Hainan Provincial Natural Science Foundation of China (221RC1054); the specific reseach fund of The Innovation Platform for Academicians of Hainan Province (YSPTZX202030).

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

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Received: 2023-03-24
Accepted: 2023-05-01
Published Online: 2023-05-23
Published in Print: 2023-08-28

© 2023 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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https://doi.org/10.1515/ncrs-2023-0140
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of a polymorph of potassium picrate, C6H2KN3O7
  4. The crystal structure of (1E,2E)-1,2-bis(quinolin-2-ylmethylene)hydrazine, C20H14N4
  5. 5-Amino-2-chloro-4-fluoro-N-(N-isopropyl-N-methylsulfamoyl) benzamide, C11H15O3ClFN3S
  6. Crystal structure of trans-N 1,N 8-bis(2-cyanoethyl)-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane, C22H42N6
  7. The crystal structure of [N-{[2-(oxy)-4-methoxyphenyl](phenyl)methylidene}alaninato]-diphenyl-silicon(IV) – chloroform (1/1), C29H25NO4Si·CHCl3
  8. Crystal structure of tetracarbonyl-{μ-[N-(diphenylphosphanyl)-N,P,P-triphenylphosphinous amide]}-bis[μ-(phenylmethanethiolato)]diiron (Fe–Fe), C48H39Fe2NO4P2S2
  9. Crystal structure of baryte from Mine du Pradet (France)
  10. The crystal structure of [(2,2′-bipyridine-6-carboxylato-κ3 N,N,O)-(6-phenylpyridine-2-carboxylate-κ2 N,O)copper(II)] monohydrate, C23H17N3O5Cu
  11. Crystal structure of bis(μ-benzeneselenolato)-(μ-[N-benzyl-N-(diphenylphosphanyl)-P,P-diphenylphosphinous amide])-tetracarbonyl diiron (Fe–Fe), C47H37Fe2NO4P2Se2
  12. The crystal structure of diaqua-methanol-κ1 O- (3-thiophenecarboxylato-κO)-(2,2′-dipyridyl-κ2 N,N′)manganese(II) 3-thiophenecarboxylate, C21H22N2O7S2Mn
  13. Crystal structure of catena-poly[tetrakis(butyl)-μ2-2-((oxido(phenyl)methylene)hydrazineylidene)propanoato-κ4 O:O,O′,N-μ2-2-((oxido(phenyl)methylene)hydrazineylidene)propanoato-κ4 O,N,O′:N′-ditin(IV)], C34H50N6O6Sn2
  14. Crystal structure of 4-chloro-N′-[(1E)-(2-nitrophenyl)methylidene]benzohydrazide, C14H10ClN3O3
  15. The crystal structure of 3-(1′-deoxy-3′,5′-O-dibenzy-β-d-ribosyl)adenine dichloromethane solvate, C49H52Cl2N10O6
  16. The crystal structure of (Z)-4-amino-N′-(1-(o-tolyl)ethylidene)benzohydrazide, C16H17N3O
  17. The co-crystal structure of etoricoxib–phthalic acid (1/1), C18H15ClN2O2S·C8H6O4
  18. Crystal structure of (glycinto-κ 2 O,N ′)-[5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ 4 N,N ′,N ″,N ‴]nickel(II) perchlorate monohydrate C18H42ClN5NiO7
  19. The crystal structure of catena-poly[bis(1-ethylimidazole-k1 N)-(μ 2-benzene-1-carboxyl-3,5-dicarboxylato-κ 2 O, O′)zinc(II)], C19H20N4O6Zn
  20. Crystal structure of 3-(thiazol-2-ylcarbamoyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic acid, C11H12N2O4S
  21. Rietveld structure analysis of keatite, a rare, metastable SiO2 polymorph
  22. Crystal structure of catena-poly[(μ2-isophthalato-k3 O,O′:O″)(4-(4-pyridyl)-2,5-dipyrazylpyridine-k3 N,N′,N″)cobalt(II)] trihydrate C26H22N6O7Co1
  23. Crystal structure of 3,5–di-O-benzoyl-1,2-O-isopropylidene-α–D-ribose, C22H22O7
  24. The crystal structure of fac-tricarbonyl(6-bromo-2,2-bipyridine-κ2 N,N)-(nitrato-κO)rhenium(I), C13H7BrN3O6Re
  25. The crystal structure of (E)-N′-(4-hydroxy-3-methoxybenzylidene)-2-naphthohydrazide monohydrate, C19H18N2O4
  26. The crystal structure of 5,5′-diselanediyl-bis(2-hydroxybenzaldehyde), C14H10O4Se2
  27. The crystal structure of catena-poly[diaqua-m2-dicyanido-κ2 C:N-dicyanido-κ1 C-bis(4-(pyridin-4-yl)benzaldehyde-κ1N)iron(II)-platinum(II), C28H22N6O4PtFe
  28. Redetermination of the crystal structure of 5,14-dihydro-6,17-dimethyl-8,15-diphenyldibenzo(b,i)(1,4,8,11)tetra-azacyclotetradecine, C32H28N4
  29. Crystal structure of poly[(μ3-2-(3,5-dicarboxyphenyl) benzimidazole-6-carboxylato-κ4O:O:O′:O″)lead(II)] monohydrate, C16H10N2O7Pb
  30. The crystal structure of fac-tricarbonyl(2-pyridin-2-yl-quinoline-κ2 N,N′)-(pyrazole-κN)rhenium(I)nitrate, C20H14N4O3ReNO3
  31. Crystal structure of dibromo-dicarbonyl-bis(tricyclohexylphosphine)-osmium(II) dichloromethane solvate, C38H66Br2O2OsP2
  32. Crystal structure of poly[bis(μ 2-2,6-bis(1-imidazoly)pyridine-κ 2 N:N′)copper(II)] diperchlorate dihydrate, C22H22Cl2CuN10O10
  33. The crystal structure of fac-tricarbonyl(N-benzoyl-N,N-cyclohexylmethylcarbamimidothioato-κ2 S,O)-(pyridine-κN)rhenium(I), C23H24N3O4ReS
  34. Crystal structure of (E)-7-fluoro-2-(4-fluorobenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C17H12F2O
  35. Synthesis and crystal structure of 1-((3R,10S,13S, 17S)-3-((2-methoxyphenyl)amino)-10,13-dimethylhexadecahydro-1H-cyclopenta[α]phenanthren-17-yl)ethan-1-one, C28H41NO2
  36. The crystal structure of fac-tricarbonyl((pyridin-2-yl)methanamino-κ2 N,N′)-((pyridin-2-yl)methanamino-κN)rhenium(I) nitrate, C15H16O3N4Re
  37. The crystal structure of (1-(pyridin-2-yl)-N-(pyridin-2-ylmethyl)-N-((1-(4-vinylbenzyl)-1H-benzo[d]imidazol-2-yl)methyl)methanamine-κ 4 N,N′,N″,N‴)tris(nitrato-kO,O′)-erbium(III), C29H27ErN8O9
  38. Crystal structure of tetracene-5,12-dione, C18H10O2
  39. Crystal structure of (3R,3aS,6R,6aR)-6-hexyl-3-methyltetrahydrofuro[3,4-b]furan-2,4-dione, C13H20O4
  40. The crystal structure of N′1,N′3-bis((E)-thiophen-2-ylmethylene)isophthalohydrazide monohydrate, C18H16N4O3S2
  41. Crystal structure of methyl ((4-aminobenzyl)sulfonyl)-L-prolinate, C13H18N2O4S
  42. Crystal structure of (E)-3-(3-methoxybenzylidene)benzofuran-2(3H)-one, C16H12O3
  43. Synthesis and crystal structure (E)-1-(4-bromo-2-hydroxyphenyl)-3-(dimethylamino)prop-2-en-1-one, C11H12BrNO2
  44. Synthesis and crystal structure of (S,E)-4-hydroxy-3-(2-((4aR,6aS,7R,10aS,10bR)-3,3,6a,10b-tetramethyl-8-methylenedecahydro-1H-naphtho[2,1-d][1,3]dioxin-7-yl)ethylidene)dihydrofuran-2(3H)-one, C23H34O5
  45. The crystal structure of N,N′-(1,2-phenylene)bis (2-((2-oxopropyl)selanyl)benzamide), C26H24N2O4Se2
  46. The crystal structure of 1-ethyl-2-nitro-imidazole oxide, C5H7N3O3
  47. The crystal structure of 2-(2-fluorophenyl)naphtho[2,1-d]thiazole, C17H10FNS
  48. Crystal structure of (E)-2,4-di-tert-butyl-6-(((2-fluorophenyl)imino) methyl)phenol, C21H26FNO
  49. Synthesis and crystal structure of 3-methyl-2-(methylthio)-4H-chromen-4-one, C12H12O2S
  50. Crystal structure of dithieno[2,3-d:2′,3′-d′]benzo[1,2-b:4,5-b′]dithiophene-5,10-dione, C14H4O2S4
  51. The crystal structure of dimethyl 2,2ʹ-((adamantane-1,3-diylbis(4,1-phenylene)) bis(oxy))diacetate, C28H32O6
  52. The crystal structure of N-(6-chloro-2-methyl-2H-indazol-5-yl)acetamide, C10H10ClN3O
  53. Crystal structure of triaqua-(5-bromoisophthalato-κ1 O)-(2,2′-bipyridine-κ2 N:N′)nickel(II) hydrate, C18H19BrN2NiO8
  54. The crystal structure of 2-amino-4-carboxypyridin-1-ium perchlorate, C6H7ClN2O6
  55. The crystal structure of catena-poly[5-aminonicotinic acid-k1 N-m2-bromido-copper(I)], Cu(C6N2H6O2)Br
  56. The crystal structure of 2,2-bis(3-methoxyphenyl)-1-tosyl-1,2-dihydro- 2λ4,3λ4  -[1,3,2]diazaborolo[4,5,1-ij]quinoline - dichloromethane (1/1)
  57. The crystal structure of catena-poly[bis(6-phenylpyridine-2-carboxylato-κ2 N,O)-(μ2-4,4′-bipyridne-κ2 N:N)cadmium(II)], C34H24N4O4Cd
  58. The crystal structure of 5,7-dinitropyrazolo[5,1-b]quinazolin-9(4H)-one, C10H5N5O5
  59. Crystal structure of rac-1,8-bis(2-carbamoylethyl)-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane, C22H46N6O2
  60. The crystal structure of (E)-N ′-(2-bromobenzylidene)-2-naphthohydrazide, C36H26Br2N4O2
  61. The crystal structure of 5-nitronaphthoquinone, C10H5NO4
  62. The crystal structure of (S, R p )-4–benzhydrylideneamino-12-(4-tert-butyl oxazolin-2-yl)[2.2]paracyclophane, C36H36N2O
  63. Synthesis and crystal structure of 2-(2-oxo-2-(o-tolyl)ethyl)-4H-chromen-4-one, C18H14O3
  64. Crystal structure of 2-(thiazol-2-yl)hexahydro-1H-4,7-epoxyisoindole-1,3(2H)-dione, C11H10N2O3S
  65. Crystal structure of N-(diaminomethylene)-1-(dimethylamino)-1-iminiomethanaminium dichloride, C4H13Cl2N5
  66. Crystal structure of poly[(μ3-3, 5-dichloro-2-hydroxy-benzoato-κ4 Cl,O:O′:O″) silver(I)], C7H3AgCl2O3
  67. The crystal structure of tetrakis(1-isopropylimidazole-κ1 N)-[μ2- imidazole-4,5-dicarboxylato-κ4 O,N,O′,N′)]- trioxido-divanadium, C29H41N10O7V2
  68. Crystal structure of catena-[(μ3-bromido)-(1H-1,2,4-triazol-1-yl)benzoato-κ1 N)copper(I)], C9H7BrCuN3O2
  69. The crystal structure of (E)-4-fluoro-N′-(1-(2-hydroxyphenyl)propylidene)benzohydrazide, C16H15FN2O2
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