Startseite The crystal structure of 3-(1′-deoxy-3′,5′-O-dibenzy-β-d-ribosyl)adenine dichloromethane solvate, C49H52Cl2N10O6
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The crystal structure of 3-(1′-deoxy-3′,5′-O-dibenzy-β-d-ribosyl)adenine dichloromethane solvate, C49H52Cl2N10O6

  • Pingqiao Wang , Yunlong Zhu , Haixin Ding ORCID logo und Haiyang Huang ORCID logo EMAIL logo
Veröffentlicht/Copyright: 16. Mai 2023

Abstract

C49H52Cl2N10O6, monoclinic, P21 (no. 4), a = 12.2875(14) Å, b = 8.3031(10) Å, c = 13.1242(15) Å, β =  100.0640 ( 10 ) , V = 1318.4(3) Å3, Z = 1, R g t (F) = 0.0736, w R r e f (F 2) = 0.1545, T = 296 K.

CCDC no.: 2248075

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: Colourless block
Size: 0.28 × 0.26 × 0.20 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.18 mm−1
Diffractometer, scan mode: φ and ω
θ max, completeness: 27.7°, 99%
N(hkl)measured, N(hkl)unique, R int: 10,614, 5454, 0.016
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 4318
N(param)refined: 344
Programs: Bruker [1], SHELX [23], Diamond [4]
Table 2:

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

Atom x y z U iso*/U eq
O1 0.6809 (4) 1.0687 (5) 0.9217 (3) 0.0711 (13)
O2 0.7512 (4) 0.7216 (5) 1.0509 (3) 0.0749 (13)
O3 0.8512 (4) 0.9645 (7) 0.8134 (3) 0.0857 (15)
N1 0.5765 (4) 0.7728 (5) 0.8016 (3) 0.0453 (10)
N2 0.5600 (4) 0.8424 (5) 0.6239 (3) 0.0495 (11)
N3 0.4907 (4) 0.4149 (5) 0.6637 (3) 0.0549 (12)
N4 0.5318 (4) 0.4931 (6) 0.8342 (3) 0.0560 (12)
N5 0.5039 (5) 0.6628 (5) 0.4913 (3) 0.0592 (13)
H5A 0.5087 0.7397 0.4485 0.071*
H5B 0.4835 0.5684 0.4687 0.071*
C1 0.5831 (6) 0.9853 (7) 0.9355 (4) 0.0638 (16)
H1A 0.5194 1.0259 0.8883 0.077*
H1B 0.5700 0.9972 1.0059 0.077*
C2 0.6048 (5) 0.8112 (6) 0.9122 (4) 0.0486 (13)
H2 0.5635 0.7408 0.9516 0.058*
C3 0.7303 (5) 0.7942 (7) 0.9535 (4) 0.0591 (15)
H3 0.7670 0.7358 0.9041 0.071*
C4 0.7709 (6) 0.9690 (8) 0.9659 (4) 0.0691 (18)
H4 0.7889 0.9930 1.0400 0.083*
C5 0.5830 (5) 0.8755 (7) 0.7241 (4) 0.0515 (13)
H5 0.6058 0.9799 0.7423 0.062*
C6 0.5279 (4) 0.6897 (6) 0.5924 (3) 0.0432 (11)
C7 0.5210 (5) 0.5737 (6) 0.6687 (4) 0.0437 (12)
C8 0.5453 (4) 0.6159 (6) 0.7724 (4) 0.0430 (12)
C9 0.4993 (6) 0.3761 (7) 0.7631 (4) 0.0624 (17)
H9 0.4835 0.2725 0.7832 0.075*
C10 0.7479 (7) 0.5497(8) 1.0464 (5) 0.078 (2)
H10A 0.8154 0.5099 1.0267 0.094*
H10B 0.6864 0.5159 0.9940 0.094*
C11 0.7353 (5) 0.4788 (8) 1.1488 (4) 0.0621 (15)
C12 0.7300 (7) 0.3123 (8) 1.1589 (6) 0.080 (2)
H12 0.7342 0.2473 1.1020 0.096*
C13 0.7186 (7) 0.2424 (11) 1.2509 (7) 0.094 (2)
H13 0.7165 0.1308 1.2566 0.112*
C14 0.7102 (6) 0.3392 (11) 1.3363 (6) 0.089 (2)
H14 0.7023 0.2931 1.3992 0.107*
C15 0.7137 (7) 0.5019 (12) 1.3259 (6) 0.089 (2)
H15 0.7061 0.5674 1.3817 0.107*
C16 0.7282 (6) 0.5710 (9) 1.2344 (5) 0.0729 (19)
H16 0.7334 0.6824 1.2302 0.088*
C17 0.8686 (7) 1.0129 (11) 0.9179 (5) 0.094 (3)
H17A 0.8802 1.1285 0.9223 0.113*
H17B 0.9343 0.9607 0.9552 0.113*
C18 0.9365 (7) 1.0161 (12) 0.7630 (6) 0.103 (3)
H18A 1.0063 0.9716 0.7974 0.124*
H18B 0.9419 1.1326 0.7660 0.124*
C19 0.9136 (6) 0.9617 (10) 0.6510 (6) 0.082 (2)
C20 0.8159 (7) 0.9856 (11) 0.5894 (7) 0.091 (2)
H20 0.7604 1.0406 0.6147 0.109*
C21 0.7963 (7) 0.9279 (13) 0.4859 (7) 0.103 (3)
H21 0.7274 0.9398 0.4440 0.123*
C22 0.8845 (11) 0.8519 (15) 0.4485 (8) 0.131 (4)
H22 0.8742 0.8156 0.3804 0.158*
C23 0.9865 (10) 0.8309 (14) 0.5123 (10) 0.126 (4)
H23 1.0455 0.7829 0.4882 0.152*
C24 0.9962 (7) 0.8847 (14) 0.6133 (8) 0.117 (3)
H24 1.0628 0.8673 0.6580 0.141*
C25a 0.8801 (13) 0.5516 (19) 0.7106 (13) 0.118 (11)
H25Aa 0.8501 0.6581 0.7185 0.141*
H25Ba 0.9055 0.5495 0.6446 0.141*
Cl1a 0.9913 (10) 0.5234 (13) 0.8067 (7) 0.137 (4)
Cl2a 0.7787 (6) 0.4180 (14) 0.7065 (16) 0.178 (8)
C25b 0.807 (2) 0.437 (5) 0.7672 (14) 0.035 (9)
H25Cb 0.8028 0.3329 0.8004 0.042*
H25Db 0.7521 0.5071 0.7887 0.042*
Cl1′b 0.9374 (13) 0.5180 (19) 0.8048 (14) 0.081 (6)
Cl2′b 0.780 (2) 0.414 (3) 0.6367 (11) 0.094 (7)
  1. aOccupancy: 0.362(10), boccupancy: 0.138(10).

1 Source of materials

An improved synthesis was performed which was similar to the previous report [5]. To the solution of 3, 5-O-dibenzyl-2-methylsulfonyl-1-deoxy-d-ribose (5.00 g, 12.7 mmol) in anhydrous dimethylformamide (100 mL) was added adenine (3.44 g, 25.5 mmol), K2CO3 (3.52 g, 25.5 mmol) and 18-crown 6-ether (13.47 g, 51.0 mmol) under an argon atmosphere. After addition, the reaction mixture was heated at 110 °C for 10 h. TLC detection showed the reaction was finished. After filtration, the solvent was removed in vacuo. The obtained residue was dissolved in dichloromethane (100 mL), washed with water (50 mL × 2), brine (50 mL × 2), and dried over anhydrous MgSO4. After filtration, the solvent was evaporated in vacuo. The obtained residue was purified by column chromatography to afford white solid of N 9-isoadenosine (4.67 g, 85%) and the title compound N 3-isoadenosine (0.39 g, 7%), which was further purified by recrystallization from dichloromethane and methanol. Crystals were obtained by slow evaporation from the solution at 268–270 K.

2 Experimental details

Restrained distances: C25–Cl1 = C25–Cl2 = C25′–Cl1′ = C25′–Cl2′; U iso/U aniso restraints and constraints: U anis(C25′)1.2U eq: with sigma of 0.01 and sigma for terminal atoms of 0.02; Secondary CH2 refined with riding coordinates: C1(H1A, H1B), C10(H10A, H10B), C17(H17A, H17B), C18(H18A, H18B), C25(H25A, H25B), C25′ (H25C, H25D); Aromatic/amide H refined with riding coordinates: C5(H5), C9(H9), C12(H12),

3 Comment

Isonucleoside (iso-NA) is a nucleoside isomer, in which the nucleobase is moved from C-1 to other positions of ribose, that showed effective activity against a broad spectrum of viruses and good resistance to enzyme hydrolysis [6], [7], [8]. Moreover, Antisense oligonucleotides (ASONs) and siRNA modified with isonucleoside showed promising therapeutic potential and gene silencing activities [910]. It is significant to construct new isonucleoside derivatives for drug candidate [11], [12], [13]. In this paper, 1′-deoxy-2′-d-isonucleosides were synthesized by combining 3,5-O-dibenzyl-2-methylsulfonyl-1-deoxy-d-ribose with adenine by nucleophilic substitution. After the reaction, three isomers, N 9, N 7 and N 3, were obtained with yield of N 9 (85%), N 7 (3%) and N 3 (7%), respectively. In the literature, detailed analysis of all three isomers was not reported before and their NMR spectrum are very similar. Fortunately, the crystal structures of N 3-isoadenosine (3-(1′-deoxy-3′,5′-O-dibenzy-β-d-ribosyl)adenine) was obtained by continuous adjustment of crystallization conditions. It is very helpful for determination of the exact structures of all three isomers. In the meantime, it is very significant for further understanding their interaction with reverse transcriptase. The title structure (see the Figure) contains one isoadenosine and one irregular dichloromethane solvent molecule. The isoadenosine consists of a benzyl-protected 1-deoxyribose and an adenine fragment by a C2–N1 bonding at 1.467(6) Å, where the glycosidic bond is an axial direction on the C2-position of furanose ring with torsion angle of 31 . 26 o (C1–C2–N1–C5) and is in a same orientation to C4–C17 bond (that is, in beta-configuration). The bond lengths and angles are in the expected ranges.


Corresponding author: Haiyang Huang, Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science & Technology Normal University, Nanchang 330013, People’s Republic of China, E-mail:

Acknowledgements

This work was supported by the Jiangxi Provincial Natural Science Foundation (20224BAB203006), the Education Department of Jiangxi Province (No. GJJ2201315), and the Open Foundation (No. 2022KFJJ003) of Jiangxi Science & Technology Normal University.

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

  2. Research funding: Jiangxi Provincial Natural Science Foundation (20224BAB203006), the Education Department of Jiangxi Province (No. GJJ2201315), and the Open Foundation (No. 2022KFJJ003) of Jiangxi Science & Technology Normal University.

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

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Received: 2023-03-16
Accepted: 2023-05-01
Published Online: 2023-05-16
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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  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
Heruntergeladen am 8.9.2025 von https://www.degruyterbrill.com/document/doi/10.1515/ncrs-2023-0126/html
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