Thiosugars, 17. Preparation and structure of a novel deoxythionucleoside

Article abstract of DOI:10.1515/znb-2018-0037

1-(3′,5′-Anhydro-2′-deoxy-3′-thio-D-lyxo-furanosyl)thymine is prepared from the corresponding methyl pentofuranoside by using the silyl Hilbert-Johnson reaction. The α- and β-anomers are separated by column chromatography and their configuration is elucidated by NMR spectroscopy and, in case of the α-anomer, by an X-ray structure determination.

Full text of DOI:10.1515/znb-2018-0037

Z. Naturforsch. 2018; aop
Jürgen Voss*, Dirk Otzen and Gunadi Adiwidjaja
Thiosugars, 17. Preparation and structure of a
novel deoxythionucleoside
https://doi.org/10.1515/znb-2018-0037
Received February 15, 2018; accepted April 22, 2018
2 Results and discussion
Abstract: 1-(3′,5′-Anhydro-2′-deoxy-3′-thio-D-lyxo-furanosyl) In most cases, glycosyl acetates are used as donor reagents
thymine is prepared from the corresponding methyl pento- for the Vorbrüggen synthesis of nucleosides. But methyl
furanoside by using the silyl Hilbert–Johnson reaction. The glycosides are also suitable as glycosyl donors although
α- and β-anomers are separated by column chromatogra- they are less reactive and give lower yields [3, 11–13]. We
phy and their configuration is elucidated by NMR spectro- chose the easily available methyl thietanopentofurano-
scopy and, in case of the α-anomer, by an X-ray structure side 1 [14] as the starting compound. The reaction of 1 in
determination.
dry acetonitrile with in situ-generated bis(trimethylsilyl)
thymine (2) under Lewis acid catalysis with trimethyl-
silyl triflate led, after hydrolytic work-up, to 63% of a
10:1 mixture of the two anomers 3a and 3b. Chromatogra-
phy yielded 46% of the pure α-anomer 3a and 17% of a
mixed 2:1 fraction of the α-anomer 3a and the β-anomer
3b (Scheme 1).
Keywords: NMR spectroscopy; nucleoside analog; thio-
furanoside; X-ray structure.
1 Introduction
The prevailing attack of the nucleobase from the α-
Since more than 50 years ago [1], numerous nucleosides side of the intermediately formed furanosyl carbenium
containing sulfur instead of oxygen in the five-mem- ion can be explained by the anomeric effect and steric hin-
bered ring of the pentofuranose moiety (“4′-thionucleo- drance of an approach from the β-side by the 3′,5′-thioan-
sides”) have been prepared and studied with respect to hydro substructure. This effect is even more pronounced
physiological and, in particular, antiviral including anti- in related cases. For example, exclusively the α-anomers
HIV activity [2–6]. In previous publications, we have of the 2′,5′-thioanhydrothymidine analogs 4 [10] and 5 [9]
reported on the preparation of 3,5-thioanhydro- and are formed from the corresponding donors.
2,5-thioanhydropentofuranosides (“thietano-” and “thi-
olanopentosides”) [7, 8] and some corresponding nucle-
oside analogs [9, 10]. Here we describe the synthesis
and characterization of another novel deoxythymidine
analog containing a bicyclic 3,5-thioanhydropentofura-
noside as the sugar component. We applied the one-pot/
one-step silyl Hilbert–Johnson reaction in the pres-
ence of trimethylsilyl triflate as the Lewis acid catalyst;
this protocol has been introduced by Vorbrüggen et al.
The correct connection of the anomeric center with
[3, 11, 12].
the 1-position of the nucleobase was demonstrated by the
characteristic [15] UV spectrum of 3a with a maximum
absorption at 266 nm.
As we were able to obtain suitable single crystals of
3a, we performed an X-ray structure determination to une-
quivocally prove its configuration. One of the four inde-
*Corresponding author: Jürgen Voss, Department of Chemistry,
pendent but nearly identical molecules in the asymmetric
Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6,
unit is presented in Fig. 1. Table 1 summarizes the crystal
D-20146 Hamburg, Germany, e-mail: voss@chemie.uni-hamburg.de
structure data.
Dirk Otzen and Gunadi Adiwidjaja: Department of Chemistry,
Organic Chemistry, University of Hamburg, D-20146 Hamburg,
Germany
The bond lengths and angles within the thiosugar
part of the four independent molecules A, B, C, and D
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2ꢀ ꢀJ. Voss et al.: Preparation and structure of a novel deoxythionucleoside
Table 1:ꢀCrystal structure data for 3a.
3a
Formula
C10H12N2O3S
240.28
0.28ꢁꢁ×ꢁꢁ0.24ꢁꢁ×ꢁꢁ0.21
Orthorhombic
P212121
Mr
Crystal size, mm3
Crystal system
Space group
a, Å
b, Å
c, Å
V, Å3
Z
9.811(1)
10.823(1)
41.491(1)
4405.7(6)
16
D
calcd, g cm−3
1.449
μ(MoKα), cm−1
F(000), e
hkl range
θmax, deg
0.71073
2016
+11,ꢁ+12,ꢁ+49
25.02
24ꢁ127
4401/0.046
722
Scheme 1:ꢀ(a) TMSOTf, MeCN; (b) NaHCO3, H2O.
Refl. measured
Refl. unique/Rint
Param. refined
R(F)/wR(F2)a,b (all reflexions)
x(Flack)
0.0823/0.1712
0.39(15)
1.089
GoF (F2)c
Δρfin (max/min), e Å−3
0.429/0.351
2
aR(F)ꢁ=ꢁΣ||ꢁFoꢁ|ꢁ – |Fcꢁ||ꢁ/Σꢁ|ꢁFoꢁ|. bwR(F2)ꢁ=ꢁ[Σw(Fo2 – Fc2)2/Σw(Fo )2]1/2
;
wꢁ=ꢁ[σ2(Fo ) + (AP)2 + BP]−1, where Pꢁ=ꢁ(Max(Fo , 0) + 2Fc2)/3.
2
2
cGoFꢁ=ꢁSꢁ=ꢁ[Σw(Fo2 – Fc2)2/(nobs – nparam)]1/2
.
O5′–C1′–N1–C6 and C2′–C1′–N1–C2 in A–D differ consid-
Fig. 1:ꢀOrtep plot of the molecular structure of 3a in the crystal.
Only one of the four crystallographically independent molecules is
shown. Displacement ellipsoids are drawn at the 30% level, H atoms
as spheres with arbitrary radii.
erably from each other (see Table 2).
3
The proton chemical shifts and the JH,H coupling
13
constants as well as the observed C signals in the NMR
spectra of 3a are also in agreement with this assignment
(see the Experimental section). Furthermore, the nuclear
of 3a deviate less than 0.01 Å/2°, respectively, from the Overhauser effect spectroscopy (NOESY) spectrum of 3a
corresponding mean values (see Table 2). Expectedly, clearly shows a through-space coupling between 6-H and
the differences are even smaller in the rigid thymine 4′-H and between 1′-H and 5′-Ha/5′-Hb, whereas, conse-
part. The differences between the dihedral angles in the quently, the corresponding NOESY signals are missing in
thiosugar part of the four molecules, on the other hand, the NMR spectrum of 3b.
are more pronounced (see Table 2). The Ortep plot of
the selected molecule (A) shown in Fig. 1, nevertheless,
correctly reflects the shape of the bicyclic thionucleo-
3 Experimental section
side molecules 3a in the crystal. The thietane ring in A
is folded with S3′ lying above the C3′–C4′–C5′ triangle
by 0.43 Å. The pentose moieties of A–D exhibit the same 3.1 General
envelope conformation as in the related thionucleosides
4 and 5 with C2′ lying 0.343 Å below the nearly planar Melting points were determined by using an electro-
C3′–C4′–O5′–C1′ part. The perfectly planar pyrimidine- thermal apparatus (values are corrected). IR spectra
dione rings of the nucleobase of A–D are significantly were measured with an ATI Mattson Genesis spectro-
tilted around the C1′–N1 bond with respect to the remain- meter. NMR spectra were measured on a Bruker AMX
der of the molecule. The corresponding dihedral angles 400 spectrometer (1H: 400 MHz, 13C: 100.6 MHz) in CDCl3.
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ꢂ3
J. Voss et al.: Preparation and structure of a novel deoxythionucleosideꢂ
Table 2:ꢀSelected bond distances (Å), angles (deg), and dihedral
angles (deg) in the four crystallographically independent molecules
A, B, C, and D in crystals of 3a.a,b
(70–230 mesh). Solvents were purified and dried accord-
ing to standard laboratory procedures [16].
c
̅
M
Distances
ꢁ
A
ꢁ
B
ꢁ
C
ꢁ
D
ꢁ
3.2 1-(3′,5′-Anhydro-2′-deoxy-3′-thio-
α-d-lyxofuranosyl)thymine (3a) and
1-(3′,5′-anhydro-2′-deoxy-3′-thio-β-d-
lyxofuranosyl)thymine (3b)
C1′–C2′
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
1.513ꢃ 1.517ꢃ 1.523 ꢃ 1.524 ꢃ 1.519
1.494ꢃ 1.505ꢃ 1.510 ꢃ 1.506 ꢃ 1.504
1.522ꢃ 1.534ꢃ 1.519 ꢃ 1.514 ꢃ 1.522
1.501ꢃ 1.523ꢃ 1.518 ꢃ 1.503 ꢃ 1.511
1.382ꢃ 1.397ꢃ 1.427 ꢃ 1.413 ꢃ 1.405
1.422ꢃ 1.423ꢃ 1.426 ꢃ 1.398 ꢃ 1.417
1.838ꢃ 1.842ꢃ 1.825 ꢃ 1.792 ꢃ 1.824
1.828ꢃ 1.851ꢃ 1.799 ꢃ 1.811 ꢃ 1.822
C2′–C3′
C3′–C4′
C4′–C5′
C1′–O5′
C4′–O5′
C3′–S3′
Thymine (180 mg, 1.43 mmol) and a catalytic amount of
(NH4)2SO4 were refluxed in 5 mL of hexamethyldisilazane
(HMDS) in a flame-dried vessel in an Ar atmosphere. The
suspension became clear after 2 h. After 3 h, the excess
of HMDS was distilled off and co-distilled (3×) with dry
xylene. The residue was dissolved in 11 mL MeCN. To this
solution, a solution of methyl 3,5-anhydro-2-deoxy-3-thio-
α,d-ribofuranoside 1 [14] (150 mg, 1.03 mmol) in 4 mL
MeCN was added. The mixture was cooled to −40°C, and
trimethylsilyl triflate (0.24 mL, 1.34 mmol) was added
under vigorous stirring which was continued at −30 to
−40°C for 2 h and finally at room temperature for 12 h.
The reaction mixture was diluted with CH2Cl2 and washed
with an aqueous NaHCO3 solution. The organic phase was
dried over Na2SO4 and evaporated. The residue was puri-
fied by chromatography (SiO2, EtOAc) to yield a pure frac-
tion of 113 mg 3a (0.47 mmol, 46%, Rfꢀ=ꢀ0.41) as a colorless,
slowly crystallizing oil, from which single crystals, m.p.
126°C, could be isolated. A second fraction consisted of
42 mg (0.17 mmol, 17%) of an oily 2:1 mixture of 3a and 3b
(Rfꢀ=ꢀ0.35).
C5′–S3′
C1′–N1
1.490ꢃ 1.487ꢃ 1.472 ꢃ 1.475 ꢃ 1.481
c
̅
M
Angles
A
ꢃ
B
ꢃ
C
ꢃ
D
ꢃ
C1′–O5′–C4′
C3′–O5′–C4′
C2–N1–C1′
C6–N1–C1′
O5′–C1′–N1
O5′–C1′–C2′
N1–C1′–C2′
C1′–C2′–C3′
C2′–C3′–C4′
C2′–C3′–S3′
C4′–C3′–S3′
O5′–C4′–C5′
O5′–C4′–C3′
C5′–C4′–C3′
C4′–C5′–S3′
111.6ꢃ 109.8ꢃ 108.5 ꢃ 110.7 ꢃ 110.2
77.3 ꢃ 77.6 ꢃ 77.5 77.5 77.5
ꢃ
ꢃ
117.7ꢃ 116.1ꢃ 118.2 ꢃ 119.0 ꢃ 117.8
121.5ꢃ 121.6ꢃ 120.4 ꢃ 120.2 ꢃ 120.9
108.3ꢃ 107.6ꢃ 107.2 ꢃ 109.0 ꢃ 108.0
108.6ꢃ 105.9ꢃ 106.5 ꢃ 107.2 ꢃ 107.1
113.8ꢃ 114.6ꢃ 114.5 ꢃ 111.8 ꢃ 113.7
103.3ꢃ 101.9ꢃ 102.5 ꢃ 104.7 ꢃ 103.1
105.5ꢃ 104.6ꢃ 105.8 ꢃ 104.1 ꢃ 105.0
118.1ꢃ 116.2ꢃ 115.7 ꢃ 119.1 ꢃ 117.3
90.3 ꢃ 91.0 ꢃ 92.3
ꢃ
91.5
ꢃ
91.3
111.5ꢃ 114.2ꢃ 112.6 ꢃ 113.8 ꢃ 113.0
105.9ꢃ 106.2ꢃ 107.4 ꢃ 109.3 ꢃ 107.2
98.4 ꢃ 98.4 ꢃ 96.7
91.4 ꢃ 91.0 ꢃ 93.4
ꢃ
ꢃ
ꢃ
96.7
91.1
D
ꢃ
ꢃ
ꢃ
97.6
91.7
Dihedral angles ꢃ
C4′–O5′–C1′–N1 ꢃ 133.2ꢃ 152.2ꢃ 152.4 ꢃ 108.9 ꢃ
C4′–O5′–C1′–C2′ꢃ 9.1 29.2 ꢃ 29.6 –12.3 ꢃ
C2–N1–C1′–C2′ ꢃ –73.1ꢃ –91.4ꢃ –121.8ꢃ –111.2ꢃ
C2–N1–C1′–O5′ ꢃ 165.9ꢃ 151.0ꢃ 120.7 ꢃ 130.5 ꢃ
C6–N1–C1′–C2′ ꢃ 103.6ꢃ 85.2 ꢃ 56.9
C6–N1–C1′–O5′ ꢃ –17.3ꢃ –32.3ꢃ –60.6 ꢃ –53.3 ꢃ
A
ꢃ
B
ꢃ
C
ꢃ
ꢃ
ꢃ
65.0
ꢃ
3a: [α]Dꢀ=ꢀ+52° (cꢀ=ꢀ1.0, CHCl3). – UV: λmax (lgε)ꢀ=ꢀ209 nm
(2.57), 266 nm (2.79); λminꢀ=ꢀ234 nm (0.55). – IR (film): 3049,
2981, 2948, 1680, 1469, 1294, 1275, 1111, 1036, 731, 557, 494,
471 cm−1. – 1H NMR: δꢀ=ꢀ1.92 (d, 3H, CH3), 2.05 (ddd, 1H, 2′b-
H), 2.60 (dd, 1H, 2′a-H), 3.14 (dd, 1H, 5′a-H), 3.55 (dd, 1H,
5′b-H), 4.30 (dd, 1H, 3′-H), 5.31 (ddd, 1H, 4′-H), 6.88 (dd,
aThe atomic labels correspond to the IUPAC numbering (see Fig. 1).
They differ from the crystallographic numbering adopted as they are
given in the CIF. bFor esd’s please consult the CIF. cMean values.
Chemical shifts δ (ppm) are relative to Me4Si (1H) and 1H, 1′-H), 7.08 (q, 1H, 6-H), 9.00 (bs, 1H, NH); J1′,2′aꢀ=ꢀ5.5 Hz,
CDCl3 (13C, δꢀꢀ=ꢀꢀ77.05 ppm). To enhance the resolution of
J
1′,2′bꢀ=ꢀ7.9 Hz, J2′a,2′bꢀ=ꢀ13.9 Hz, J2′b,3′ꢀ=ꢀ6.8 Hz, J3′,4′ꢀ=ꢀ6.4 Hz,
1
the H signals, the spectra were recalculated from the
J
4′,5′aꢀ=ꢀ2.5 Hz, J4′,5′bꢀ=ꢀ6.3 Hz, J5′a,5′bꢀ=ꢀ11.1 Hz, J6,Meꢀ=ꢀ1.24 Hz.
13
free induction decay by using the WinNMR software – C NMR: δꢀ=ꢀ12.97 (CH3), 32.76 (C-5′), 39.96 (C-2′), 43.78
(Bruker). NOESY and distortionless enhancement by (C-3′), 81.99 (C-4′), 86.49 (C-1′), 111.95 (C-5), 135.68 (C-6),
polarization transfer experiments were performed to 150.72 (C-2=O), 164.02 (C-4=O).
1
assign the signals. Optical rotations were measured on a
3b: H NMR: δꢀ=ꢀ2.02 (d, 3H, CH3), 2.32 (ddd, 1H, 2′a-
Perkin-Elmer polarimeter 341. UV spectra were recorded H), 2.80 (dd, 1H, 2′b-H), 3.01 (dd, 1H, 5′a-H), 3.58 (dd, 1H,
on a Varian Cary 1E spectrometer in quartz cuvettes. Thin 5b′-H), 4.19 (dd, 1H, 3′-H), 5.08 (m, 1H, 4′-H), 6.42 (dd, 1H,
layer chromatography was carried out on Merck PF254 1′-H), 8.10 (q, 1H, 6-H), 8.90 (bs, 1H, NH); J1′,2′aꢀ=ꢀ7.7 Hz,
foils (detection: UV light, EtOH-H2SO4/200°C or 4-meth-
J
1′,2′bꢀ=ꢀ4.9 Hz, J2′a,2′bꢀ=ꢀ15.1 Hz, J2′a,3′ꢀ=ꢀ2.5 Hz, J3′,4′ꢀ=ꢀ6.2 Hz,
oxybenzaldehyde in 2.5% H2SO4/0.4% AcOH-EtOH),
J
4′,5′aꢀ=ꢀ1.7 Hz, J4′,5′bꢀ=ꢀ5.5 Hz, J5′a,5′bꢀ=ꢀ11.0 Hz, J6,Meꢀ=ꢀ1.24 Hz.
13
and column chromatography on Merck Kieselgel 60 – C NMR: δꢀ=ꢀ13.14 (CH3), 30.24 (C-5′), 41.35 (C-2′), 41.93
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4ꢀ ꢀJ. Voss et al.: Preparation and structure of a novel deoxythionucleoside
[3] H. Vorbrüggen, C. Ruh-Pohlenz, Handbook of Nucleoside Syn-
thesis, John Wiley & Sons, Chichester, 2001.
[4] M. Yokoyama in The Properties of 4′-Thionucleosides in
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p. 173.
(C-3′), 84.09 (C-4′), 88.11 (C-1′), 136.45 (C-6). The signals
of C-5 and C=O could not be detected because the ratio of
signal to noise was too low.
[5] V. A. Mulamoottil, M. S. Majik, G. Chandra, L. S. Jeong in
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4 Crystal structure determination
Data collection was performed with a Nonius Kappa-CCD
diffractometer with graphite-monochromatized MoKα
radiation (λꢀ=ꢀ0.71073 Å) in ϕ scan mode. The structure was
solved by Direct Methods by using the program Sir-97 [17,
18] and refined by full-matrix least squares on F2 using all
unique data (program Shelxl-97 [19, 20]).
The crystal data of 3a and a summary of experimen-
tal details are given in Table 1, and Table 2 summarizes
selected bond distances and angles. The atom labels in
this paper (molecular structure and NMR signals) corre-
spond to the usual chemical numbering. The numbering
chosen in the crystallographic CIF file (see the next para-
graph) is different as, among other aspects, the atoms of
four crystallographically independent molecules had to
be numbered.
CCDC 1450185 contains the supplementary crystallo-
graphic data for this paper. These data can be obtained
free of charge from The Cambridge Crystallographic Data
Centre via www.ccdc.cam.ac.uk/data_request/cif.
Acknowledgments: We thank the University of Hamburg
for financial support. Prof. U. Behrens, University of Ham-
burg, is gratefully acknowledged for help concerning the
X-ray structure determination.
[17] A. Altomare, M. C. Burla, M. Camalli, G. L. Cascarano, C.
Giacovazzo, A. Guagliardi, A. G. G. Moliterni, G. Polidori, R.
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ꢂ2018 | Volume x | Issue x(b)
Graphical synopsis
Jürgen Voss, Dirk Otzen
and Gunadi Adiwidjaja
Thiosugars, 17. Preparation and structure
of a novel deoxythionucleoside
https://doi.org/10.1515/znb-2018-0037
Z. Naturforsch. 2018; x(x)b: xxx–xxx
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