X-ray structure of 1,3,4-tri-O-acetyl-2-deoxy-β-d-erythro-pentopyranose

Article abstract of DOI:10.1016/j.carres.2009.06.028

Peracetylated 2-deoxy-d-erythro-pentose (2-deoxy-d-ribose) was synthesized through the acetylation of 2-deoxy-d-ribose with acetic anhydride in pyridine, and the products (including all four ring forms) exist in form of either a white solid or a syrup. A

Full text of DOI:10.1016/j.carres.2009.06.028

Carbohydrate Research 344 (2009) 2056–2059
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Note
X-ray structure of 1,3,4-tri-O-acetyl-2-deoxy-b-D-erythro-pentopyranose
*
Ji-Jun Chen, Jian-Rong Gao, Liang Han , Jian-Hong Jia, Wei-Jian Sheng, Yu-Jing Li
The State Key Laboratory of Green Chemistry-Synthesis Technology, Zhejiang University of Technology, Hang Zhou 310014, PR China
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 5 May 2009
Received in revised form 30 May 2009
Accepted 21 June 2009
Available online 26 June 2009
Peracetylated 2-deoxy-D-erythro-pentose (2-deoxy-D-ribose) was synthesized through the acetylation of
2
-deoxy-
in form of either a white solid or a syrup. A single crystal of 1,3,4-tri-O-acetyl-2-deoxy-b-
pyranose was obtained from the syrup and its structure was determined by X-ray diffraction. The crystal
D
-ribose with acetic anhydride in pyridine, and the products (including all four ring forms) exist
D-erythro-pento-
1
adopts the
4 1 1 1
C conformation, presenting an orthorhombic system, space group P2 2 2 with Z = 4, unit
cell dimensions a = 7.2274 (3) Å, b = 8.0938 (5) Å, and c = 22.0517 (11) Å.
Keywords:
Peracetylated 2-deoxy-
Ó 2009 Elsevier Ltd. All rights reserved.
D-ribose
Pyranose
Crystal structure
OAc
AcO
AcO
O
Deoxynucleoside analogues are small molecules chemically re-
lated to physiological deoxynucleosides, and are widely used for
the treatment of hematological malignancies (cytarabine, fludara-
bine, cladribine, and more recently gemcitabine), and solid tumors
O
OAc
OAc
A
OAc
1
–3
B
(
gemcitabine).
1,3,5-Tri-O-acetyl-2-deoxy-a,b-D-erythro-pentof-
OAc
uranoses (A and B, Fig. 1) have found extensive use in acid-cata-
O
O
0
lyzed fusion syntheses of 2 -deoxy-
D
-ribofuranosyl nucleosides,
OAc
OAc
OAc
and are also a convenient starting point for high yield Lewis
OAc
OAc
C
acid-catalyzed glycosylation of purines and pyrimidines.4 Per-
–6
D
acetylation of 2-deoxy-
D
-ribose provides 1,3,5-tri-O-acetyl-2-
-erythro-pentofuranose and 1,3,4-tri-O-acetyl-2-
-pentopyranose (C and D, Fig. 1). Different reaction
deoxy-a,b-
,b-
D
Figure 1. Isomers of tri-O-acetyl 2-deoxy-D-erythro-pentose.
deoxy-
a
D
conditions offer different products. Earlier work by Zinner indi-
cated that the existence of cyclic forms of pentose depends on
the reaction temperature.7 Reaction with acetic anhydride at a
low temperature of 0ꢀ20 °C gave the tri-O-acetyl pyranose deriva-
tive, while the tri-O-acetyl furanose was obtained in acetic anhy-
dride at reflux. They reported that the b-configuration of the
pyranose and furanose isomers can crystallize from the product
OH
HO
OAc
AcO
O
OH
O
(CH CO) O
OAc
3
2
pyridine
Scheme 1.
mixture, and the remaining oily products were the
a-configured
products. However, other investigations by Efange indicated that
the pyranose product was obtained as a white crystalline product
while the furanose product was left in the syrup form.8 In our
2-Deoxy-D-ribose was dissolved in dry pyridine and acetic
anhydride was added dropwise at 0 °C. The mixture was stirred
for 25 h at room temperature; usual workup gave a yellow syrup
in 97% yield. This yellow syrup became partially crystalline upon
standing at room temperature and then was triturated with iso-
propyl ether. The white crystalline product was obtained after fil-
research, we prepared the peracetyl 2-deoxy-
temperature (Scheme 1) and obtained the single crystal of 1,3,4-
tri-O-acetyl-2-deoxy-b- -erythro-pentopyranose whose structure
was investigated by the X-ray diffraction analysis.
D-ribose at room
D
1
tration, which was assumed to be the pyranose whose H NMR
8
matched that reported previously. The filtrate was concentrated
to remove the isopropyl ether giving a mixture with the furanose
products as a yellow syrup. After standing for 5–7 days, the syrup
*
Corresponding author.
E-mail address: hanliang814@163.com (L. Han).
0
008-6215/$ - see front matter Ó 2009 Elsevier Ltd. All rights reserved.
doi:10.1016/j.carres.2009.06.028

J.-J. Chen et al. / Carbohydrate Research 344 (2009) 2056–2059
2057
Figure 2. Structure of C with thermal ellipsoids shown at 50% probability levels.
yielded single crystal of 1,3,4-tri-O-acetyl-2-deoxy-b-
pentopyranose with the same 1H NMR as that of the white prod-
uct, indicating that the acetylation of 2-deoxy- -ribose gave the
D
-erythro-
(Shanghai Precision & Scientific instrument Co., Ltd) in a 2-dm tube
1
3
at the D line of sodium for a solution in CHCl . The H NMR spectra
D
were recorded at 297 K in CDCl with a Bruker AVANCE III 500
3
b-configuration product as the crystalline white solid.
MHZ spectrometer; d in parts per million.
In the crystal structure, 1,3,4-tri-O-acetyl-2-deoxy-b-
D
-erythro-
1
pentopyranose adopts the
C
4
conformation, presenting
a
1.2. Synthesis of 1,3,4-tri-O-acetyl-2-deoxy-b-D-erythro-
orthorhombic system, space group P2
2
1 1
1
2 , with bond distances
pentopyranose
C1–O1 1.400 (3) Å, C1–C2 1.499 (3) Å, and C1–O2 1.446 (3) Å for
axial anomeric bond. The angle disposition for the endocyclic bond
2-Deoxy-b-D-erythro-pentose (51.3 g, 382 mmol) was dis-
1
C1–O1–C5 is 114.63 (18)°, which is typical for the C
4
chair confor-
solved in pyridine (150 mL). The solution was cooled to an inter-
nal temperature of 0 °C and then acetic anhydride (126 mL) was
added slowly. After the addition was complete, the solution was
stirred at the room temperature for ꢀ25 h. Thereafter, 10 vol-
mation in pyranosides with the aglycone oriented in the axial
position. The perspective view of the molecule shows axial dispo-
sition for all substituents except position 3, is equatorial. The
absolute configurations of the three carbons in the cycle are:
C1 (S), C3 (S), and C4 (R).
3
umes of a saturated solution of NaHCO were added to the reac-
tion mixture at 0 °C, and then the product was extracted with
,2-dichloroethane. The organic phase was washed with 1 M
HCl (100 ml ꢁ 3 times), saturated solution of NaHCO3
1
1
1
. Experimental
(
100 ml ꢁ 1 time), and water (100 ml ꢁ 1 time) successively.
.1. General methods
After being dried and filtered, 96.64 g of a syrup (yield 97%)
was obtained. After several hours, a white solid was precipitated
from the syrup at the room temperature. The solid was filtered
and washed with isopropyl ether (100 mL), and then 22.71 g of
The melting point was uncorrected. The optical rotation was
determined at room temperature with a WZZ-2B polarimeter
Figure 3. A packing diagram for C.

2
058
J.-J. Chen et al. / Carbohydrate Research 344 (2009) 2056–2059
Table 1
Table 3
Crystal data and structure refinement for C
Selected bond lengths (Å) in C
Empirical formula
Formula weight (g/mol)
Temperature (K)
Wavelength (Å)
Crystal system, space group
Unit cell dimensions
a (Å)
C
11
H
16
O
7
Bond lengths
Å
260.24
296(1)
Mo K
C1–O1
C5–O1
C1–O2
C6–O2
C3–O4
C8–O4
C8–O5
C4–O6
C10–O6
C10–O7
C1–C2
C2–C3
C3–C4
C4–C5
C6–C7
C8–C9
O10–C11
1.400(3)
1.424(2)
1.446(3)
1.353(3)
1.445(2)
1.354(2)
1.191(3)
1.447(3)
1.347(3)
1.195(3)
1.499(3)
1.524(2)
1.507(3)
1.521(3)
1.483(4)
1.487(3)
1.487(4)
a
0.71075
1 1 1
Orthorhombic, P2 2 2
7.2274(3)
8.0938(5)
22.5017(11)
90
90
90
1316.28(12)
4, 1.313
0.110
b (Å)
c (Å)
a
(°)
b (°)
(°)
c
3
V (Å )
Z, Dcalcd (Mg/m3)
Absorption coefficient (mm
F(0 0 0)
ꢃ1
)
552.00
Crystal size (mm)
h range for data collection (°)
Limiting indices
Reflections collected/unique [R(int)]
Completeness to h = 27.43 (%)
Absorption correction
0.49 ꢁ 0.47 ꢁ 0.35
3.1–27.4
ꢃ8 6 9, ꢃ10 6 10, -28 6 29
1746/1163 [0.026]
99.5
Multi-scan
Fsqd for F
a
2
Refinement method
Table 4
Data/restraints/parameters
1746/0/164
1.002
R = 0.0361, xR = 0.0840
1 2
1746/1163
None
0.21 and ꢃ0.18
Selected bond angles (°) in C
2
Goodness-of-fit on F
Final R indices [F2 > 2.02r(F2)]
Bond angles
°
2
Observed reflections [F > 2.0
r
(F )]
C1–O1–C5
C1–O2–C6
C3–O4–C8
C4–O6–C10
O1–C1–O2
O1–C1–C2
O2–C1–C2
C1–C2–C3
O4–C3–C2
O4–C3–C4
C2–C3–C4
O6–C4–C3
O6–C4–C5
C3–C4–C5
O1–C5–C4
O2–C6–O3
O2–C6–C7
O3–C6–C7
O4–C8–O5
O4–C8–C9
O5–C8–C9
O6–C10–O7
O6–C10–C11
O7–C10–C11
114.63(18)
117.0(2)
Absolute structure parameter
Largest difference in peak and hole (e Å
ꢃ3
)
116.50(17)
117.41(18)
109.67(19)
113.13(19)
106.68(19)
110.56(17)
107.21(16)
111.41(18)
110.70(18)
109.61(19)
106.5(2)
110.29(19)
112.37(18)
122.8(2)
111.2(2)
126.0(2)
a
Ref. 12.
Table 2
Torsion angles (°) for C
Torsion angles
°
C1–O1–C5–C4
C5–O1–C1–O2
C5–O1–C1–C2
C1–O2–C6–O3
C1–O2–C6–C7
C6–O2–C1–O1
C6–O2–C1–C2
C3–O4–C8–O5
C3–O4–C8–C9
C8–O4–C3–C2
C8–O4–C3–C4
C4–O6–C10–O7
C4–O6–C10–C11
C10–O6–C4–C3
C10–O6–C4–C5
O1–C1–C2–C3
O2–C1–C2–C3
C1–C2–C3–O4
C1–C2–C3–C4
O4–C3–C4–O6
O4–C3–C4–C5
C2–C3–C4–O6
C2–C3–C4–C5
O6–C4–C5–O1
C3–C4–C5–O1
ꢃ54.6(3)
ꢃ63.9(2)
55.1(2)
ꢃ4.8(3)
176.1(2)
ꢃ81.3(2)
155.8(2)
ꢃ2.9(3)
175.6(2)
154.5(2)
ꢃ84.2(2)
0.3(3)
123.2(2)
111.1(2)
125.7(2)
123.7(2)
111.0(2)
125.3(2)
ꢃ179.1(2)
99.3(2)
ꢃ141.4(2)
ꢃ53.2(2)
67.5(2)
174.12(19)
52.4(2)
1.3. X-ray crystallographic study
ꢃ54.5(2)
ꢃ171.45(19)
64.7(2)
Suitable crystals of the title compound were grown at room
temperature and they were mounted on glass fibers. Diffraction
data were collected at 296 K on a Rigaku RAXIS-RAPID diffrac-
ꢃ52.2(2)
ꢃ66.1(2)
52.8(2)
tometer with Mo K
ment was carried out with the PROCESS
crystal structure was solved by direct methods using the SIR97
a radiation (k = 0.71075 Å). The data treat-
AUTO program.9 The
-
1
0
11
package and refined using CRYSTALS. Block-shaped and col-
orless crystal was analyzed by X-ray diffraction. The crystal
1
1
,3,4-tri-O-acetyl-2-deoxy-b-
D
-erythro-pentopyranose (yield 23%)
adopts the
C
4
conformation, presenting an orthorhombic sys-
with Z = 4, unit cell dimensions
was obtained. The filtrate was concentrated and it gave 73.9 g
of a yellow syrup (yield 74%), which was stored at room temper-
ature and yielded a single crystal after several days, mp 89–90 °C
tem, space group P2
a = 7.2274 (3) Å, b = 8.0938 (5) Å, c = 22.0517 (11) Å. All non-
hydrogen atoms were refined anisotropically. The refinement of
the structure, by F full matrix least squares, converged to
1
2 2
1 1
8
20
D
1
2
(
lit. 95–97 °C); ½
aꢂ
ꢃ 284 (c 0.04, CHCl
3
); H NMR (500 MHz,
CDCl
3
) d 1.92 (dd, 1H, 2-H), 2.04 (s, 3H, acetyl), 2.12 (s, 3H, acet-
1 2
R = 0.0361, wR = 0.0840, and goodness-of-fit = 1.002, for
0
2
2
yl), 2.15 (s, 3H, acetyl), 2.26 (ddd, 1H, 2 -H), 3.88 (dd, 1H, 5-H),
F > 2.0 sigma (F ). Figure 2 shows the molecular structure
of the title compound, and part of its crystal structure is
depicted in Figure 3. Crystal and structure refinement data are
0
4
1
.03 (d, 1H, 5-H ), 5.22 (s, 1H, 4-H), 5.311 (dt, 1H, 3-H), 6.27 (t,
H, 1-H).

J.-J. Chen et al. / Carbohydrate Research 344 (2009) 2056–2059
2059
summarized in Table 1. The torsion angles, selected bond
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