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Volume 68 
Part 10 
Pages o395-o398  
October 2012  

Received 30 August 2012
Accepted 6 September 2012
Online 12 September 2012

5-Ethynyl-2'-deoxycytidine: a DNA building block with a `clickable' side chain

aLaboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany,bLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany, and cAnorganische Chemie II, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
Correspondence e-mail: frank.seela@uni-osnabrueck.de

The title compound [systematic name: 4-amino-1-(2-deoxy-[beta]-D-erythro-pentofuranosyl)-5-ethynylpyrimidin-2(1H)-one], C11H13N3O4, shows two conformations in the crystalline state. The N-glycosylic bonds of both conformers adopt similar conformations, with [chi] = -149.2 (1)° for conformer (I-1) and -151.4 (1)° for conformer (I-2), both in the anti range. The sugar residue of (I-1) shows a C2'-endo envelope conformation (2E, S-type), with P = 164.7 (1)° and [tau]m = 36.9 (1)°, while (I-2) shows a major C3'-exo sugar pucker (C3'-exo-C2'-endo, 3T2, S-type), with P = 189.2 (1)° and [tau]m = 33.3 (1)°. Both conformers participate in the formation of a layered three-dimensional crystal structure with a chain-like arrangement of the conformers. The ethynyl groups do not participate in hydrogen bonding, but are arranged in proximal positions.

Comment

The title compound, 5-ethynyl-2'-deoxycytidine, (I)[link], was first synthesized by Walker and co-workers in 1978 (Barr, Jones et al., 1978[Barr, P. J., Jones, A. S., Serafinowski, P. & Walker, R. T. (1978). J. Chem. Soc. Perkin Trans. 1, pp. 1263-1267.]). Compound (I)[link] is an inhibitor of herpes simplex virus (HSV) and shows enhanced selectivity compared to closely related 5-ethynyl-2'-deoxyuridine, (IV) (De Clercq et al., 1982[De Clercq, E., Balzarini, J., Descamps, J., Huang, G.-F., Torrence, P. E., Bergstrom, D. E., Jones, A. S., Serafinowski, P., Verhelst, G. & Walker, R. T. (1982). Mol. Pharmacol. 21, 217-223.]). Molecular orbital studies were performed on both compounds (Saran, 1988[Saran, A. (1988). J. Mol. Struct. (THEOCHEM), 179, 215-223.]).

The ethynyl group of nucleoside (I)[link] is linked to the 5-position of the pyrimidine moiety, while the related 3'-ethynylcytidine carries this group at the sugar moiety. The latter develops potent cytotoxicity in vitro and in vivo against various human tumour cell lines (Hattori et al., 1996[Hattori, H., Tanaka, M., Fukushima, M., Sasaki, T. & Matsuda, A. (1996). J. Med. Chem. 39, 5005-5011.]).

The terminal triple bond of compound (I)[link] represents a target for the Huisgen-Meldal-Sharpless cycloaddition (`click' reaction; Kolb et al., 2001[Kolb, H. C., Finn, M. G. & Sharpless, K. B. (2001). Angew. Chem. Int. Ed. 40, 2004-2021.]; Kolb & Sharpless, 2003[Kolb, H. C. & Sharpless, K. B. (2003). Drug Discov. Today, 8, 1128-1137.]; Meldal & Tornøe, 2008[Meldal, M. & Tornøe, C. W. (2008). Chem. Rev. 108, 2952-3015.]) and has been functionalized with benzyl azide affording a hydrogel (Seela & Xiong, 2012[Seela, F. & Xiong, H. (2012). Unpublished results.]). Furthermore, this compound can be used in the Glaser coupling for the construction of novel nanostructures (Minakawa et al., 2003[Minakawa, N., Ono, Y. & Matsuda, A. (2003). J. Am. Chem. Soc. 125, 11545-11552.]). A phenyl click derivative of (I)[link] was introduced chemically into oligonucleotides, and improved duplex formation was observed with a complementary RNA oligomer using consecutive incorporations (Andersen et al., 2011[Andersen, N. K., Døssing, H., Jensen, F., Vester, B. & Nielsen, P. (2011). J. Org. Chem. 76, 6177-6187.]). Nucleoside (I)[link] was also incorporated enzymatically in the form of its triphosphate by DNA polymerases (Guan et al., 2011[Guan, L., van der Heijden, G. W., Bortvin, A. & Greenberg, M. M. (2011). ChemBioChem, 12, 2184-2190.]; Macícková-Cahová et al., 2011[Macícková-Cahová, H., Pohl, R. & Hocek, M. (2011). ChemBioChem, 12, 431-438.]). Labelling experiments demonstrated that compound (I)[link] can be used as a specific reporter of DNA replication or cell proliferation (Guan et al., 2011[Guan, L., van der Heijden, G. W., Bortvin, A. & Greenberg, M. M. (2011). ChemBioChem, 12, 2184-2190.]; Qu et al., 2011[Qu, D., Wang, G., Wang, Z., Zhou, L., Chi, W., Cong, S., Ren, X., Liang, P. & Zhang, B. (2011). Anal. Biochem. 417, 112-121.]).

From this background, we became interested in performing a single-crystal X-ray analysis of (I)[link] and the results are reported herein.

[Scheme 1]

The crystal structure of (I)[link] was compared to the two conformers of 5-propynyl-2'-deoxycytidine, (II) (Seela et al., 2007[Seela, F., Budow, S., Eickmeier, H. & Reuter, H. (2007). Acta Cryst. C63, o54-o57.]), 5-methyl-2'-deoxycytidine, (IIIb) (Sato, 1988[Sato, T. (1988). Acta Cryst. C44, 870-872.]; Seela et al., 2000[Seela, F., He, Y., Reuter, H. & Heithoff, E.-M. (2000). Acta Cryst. C56, 989-991.]), and 5-ethynyl-2'-deoxyuridine, (IV) (Barr, Hamor et al., 1978[Barr, P. J., Hamor, T. A. & Walker, R. T. (1978). Acta Cryst. B34, 2799-2802.]). In the asymmetric unit of (I)[link], two molecules were found, which are denoted (I-1) and (I-2). The three-dimensional structures of the two conformers, viz. (I-1) and (I-2), are shown in Fig. 1[link], and selected geometric parameters are summarized in Table 1[link]. For the related crystal structure of (II) (Seela et al., 2007[Seela, F., Budow, S., Eickmeier, H. & Reuter, H. (2007). Acta Cryst. C63, o54-o57.]), two conformers were also formed in the unit cell. Both (I)[link] and (II) crystallize in the same space group (triclinic, P1; Seela et al., 2007[Seela, F., Budow, S., Eickmeier, H. & Reuter, H. (2007). Acta Cryst. C63, o54-o57.]), while the space group of (IIIb) is orthorhombic (P212121; Sato, 1988[Sato, T. (1988). Acta Cryst. C44, 870-872.]) and that of (IV) is monoclinic (P21; Barr, Hamor et al., 1978[Barr, P. J., Hamor, T. A. & Walker, R. T. (1978). Acta Cryst. B34, 2799-2802.]).

Fig. 2[link] shows an overlay of conformers (I-1) and (I-2), indicating that the pyrimidine moieties are almost superimposable, while the major differences between both conformers occur in the sugar moiety.

In the case of conformer (I-1), triple-bonded atoms C5A and C5B together with heterocyclic atom C5 form an almost linear entity with C15B-C15A-C15 = 179.09 (14)°. For the propynyl groups of conformers (II-1) and (II-2), comparable angles were observed [179.3 (3) and 178.7 (3)°, respectively; Seela et al., 2007[Seela, F., Budow, S., Eickmeier, H. & Reuter, H. (2007). Acta Cryst. C63, o54-o57.]]. However, for molecule (I-2), this entity is slightly bent, with C25B-C25A-C25 = 175.83 (14)°. The length of the C5A-C5B triple bond is within the same range for both conformers [1.1978 (18) Å for (I-1) and 1.1925 (18) Å for (I-2)].

In the crystalline state of (I)[link], both types of molecules, (I-1) and (I-2), adopt anti conformations for the glycosylic bond; a conformation that is mainly found in pyrimidine nucleosides (Saenger, 1984[Saenger, W. (1984). Principles of Nucleic Acid Structure, edited by C. R. Cantor, pp. 1-21. New York: Springer-Verlag.]). Both conformers show similar torsion angles around the glycosylic bond (IUPAC-IUB Joint Commission on Biochemical Nomenclature, 1983[IUPAC-IUB Joint Commission on Biochemical Nomenclature (1983). Eur. J. Biochem. 131, 9-15.]), [chi] (O4'-C1'-N1-C2) = -149.17 (10)° for conformer (I-1) and -151.39 (10)° for conformer (I-2). Both conformers of (II) adopt similar anti conformations with [chi] = -135.0 (2) and -156.4 (2)° for (II-1) and (II-2), respectively (Seela et al., 2007[Seela, F., Budow, S., Eickmeier, H. & Reuter, H. (2007). Acta Cryst. C63, o54-o57.]). The glycosylic torsion angle in (IIIb) was also found to be anti with [chi] = -131.7° (Sato, 1988[Sato, T. (1988). Acta Cryst. C44, 870-872.]; Seela et al., 2000[Seela, F., He, Y., Reuter, H. & Heithoff, E.-M. (2000). Acta Cryst. C56, 989-991.]). The length of the glycosylic N1-C1' bond is 1.4773 (14) Å for (I-1) and 1.4869 (14) Å for (I-2), which is almost identical to the bond length observed for the two conformers of (II) [1.475 (2) Å for (II-1) and 1.490 (2) Å for (II-2); Seela et al., 2007[Seela, F., Budow, S., Eickmeier, H. & Reuter, H. (2007). Acta Cryst. C63, o54-o57.]].

The sugar residue of (I-1) shows a C2'-endo envelope conformation (2E, S-type), with P = 164.7 (1)° and [tau]m = 36.9 (1)°, while (I-2) shows a major C3'-exo conformation (C3'-exo-C2'-endo, 3T2, S-type), with P = 189.2 (1)° and [tau]m = 33.3 (1)°. The sugar moieties of (II-1), (II-2) and (IV) also show an S-type conformation and exhibit twisted C2'-endo sugar puckers (Seela et al., 2007[Seela, F., Budow, S., Eickmeier, H. & Reuter, H. (2007). Acta Cryst. C63, o54-o57.]; Barr, Hamor et al., 1978[Barr, P. J., Hamor, T. A. & Walker, R. T. (1978). Acta Cryst. B34, 2799-2802.]). The sugar ring of (IIIb) is also puckered in a typical C2'-endo envelope form (2E, S-type), with P = 161.5° and [tau]m= 37.9° (Sato, 1988[Sato, T. (1988). Acta Cryst. C44, 870-872.]; Seela et al., 2000[Seela, F., He, Y., Reuter, H. & Heithoff, E.-M. (2000). Acta Cryst. C56, 989-991.]).

The [gamma] torsion angle (O5'-C5'-C4'-C3') characterizes the orientation of the exocyclic 5'-hydroxy group relative to the 2'-deoxyribose ring. Molecules (I-1) and (I-2) display similar conformations about the C4'-C5' bond. Both (I-1) and (I-2) show a synclinar (+sc; gauche, gauche) conformation. The torsion angle [gamma] is 55.52 (14)° for (I-1) and 51.66 (14)° for (I-2). In the case of (II), molecule (II-1) shows a similar torsion angle with [gamma] = 57.8 (3)° (+sc; gauche, gauche), while molecule (II-2) adopts an antiperiplanar conformation [+ap; gauche, trans, [gamma] = 166.1 (2)°; Seela et al., 2007[Seela, F., Budow, S., Eickmeier, H. & Reuter, H. (2007). Acta Cryst. C63, o54-o57.]].

In the crystal structure of nucleoside (I)[link], molecules (I-1) and (I-2) are linked into layers by several intermolecular hydrogen bonds (Table 2[link] and Fig. 3[link]) involving all H atoms linked to heteroatoms. Hydrogen bonds between neighbouring bases and sugar units (N14-H14A...N23i, O13'-H13O...O22, N24-H24A...N13iii, O23'-H23O...O12 and O25'-H25O...O15'iv; for symmetry codes and geometry see Table 2[link]) connect the different conformers. One further hydrogen bond was found linking molecules of identical conformation (O15'-H15O...O12ii). Atom O12 of conformer (I-1) functions as an acceptor for a bifurcated hydrogen bond with O15'-H15O of (I-1) and O23'-H23O of (I-2) acting as hydrogen-bond donors.

The layers are built up by alternating chains of conformers (I-1) and (I-2), and each of these chains contains only one type of conformer. Interestingly, the ethynyl group of one conformer is located in a proximal position to the ethynyl group of the other conformer of the neighbouring chain (Fig. 3[link]). However, the ethynyl groups of both conformers do not participate in hydrogen bonding. The individual layers are connected by an intermolecular hydrogen bond (O25'-H25O...O15'iv).

[Figure 1]
Figure 1
Perspective views of conformer (I-1) (left) and conformer (I-2) (right) connected by two hydrogen bonds and showing the atom-numbering schemes. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2]
Figure 2
An overlay of molecules (I-1) (lighter atoms) and (I-2) (darker atoms) (red and black, respectively, in the electronic version of the paper).
[Figure 3]
Figure 3
A detailed view of the two-dimensional hydrogen-bonded (dashed lines) network of (I)[link]. The projection is parallel to the ab plane. For the sake of clarity, H atoms not involved in the intermolecular hydrogen-bonding motifs have been omitted.

Experimental

Compound (I)[link] was synthesized from (IIIa) according to literature procedures (Andersen et al., 2008[Andersen, N. K., Spácilová, L., Jensen, M. D., Kocalka, P., Jensen, F. & Nielsen, P. (2008). Nucleic Acids Symp. Ser. 52, 149-150.], 2011[Andersen, N. K., Døssing, H., Jensen, F., Vester, B. & Nielsen, P. (2011). J. Org. Chem. 76, 6177-6187.]; Dodd et al., 2010[Dodd, D. W., Swanick, K. N., Price, J. T., Brazeau, A. L., Ferguson, M. J., Jones, N. D. & Hudson, R. H. E. (2010). Org. Biomol. Chem. 8, 663-666.]). Slow crystallization from a dichloromethane-methanol mixture afforded (I)[link] as colourless crystals (decomposition at 464 K). For the diffraction experiment, a single crystal was mounted on a MiTeGen Micro-Mountsfibre in a thin smear of oil.

Crystal data
  • C11H13N3O4

  • Mr = 251.24

  • Triclinic, P 1

  • a = 7.8754 (6) Å

  • b = 8.1504 (6) Å

  • c = 10.0893 (7) Å

  • [alpha] = 108.637 (3)°

  • [beta] = 96.327 (3)°

  • [gamma] = 104.562 (3)°

  • V = 580.98 (7) Å3

  • Z = 2

  • Mo K[alpha] radiation

  • [mu] = 0.11 mm-1

  • T = 130 K

  • 0.3 × 0.2 × 0.2 mm

Data collection
  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.710, Tmax = 0.746

  • 37435 measured reflections

  • 3715 independent reflections

  • 3671 reflections with I > 2[sigma](I)

  • Rint = 0.022

Refinement
  • R[F2 > 2[sigma](F2)] = 0.029

  • wR(F2) = 0.080

  • S = 1.06

  • 3715 reflections

  • 329 parameters

  • 3 restraints

  • H-atom parameters constrained

  • [Delta][rho]max = 0.37 e Å-3

  • [Delta][rho]min = -0.29 e Å-3

  • Absolute structure: established by known chemical absolute configuration

Table 1
Selected geometric parameters (Å, °)

N11-C11' 1.4773 (14)
C15-C15A 1.4286 (16)
C15A-C15B 1.1978 (18)
N21-C21' 1.4869 (14)
C25-C25A 1.4259 (16)
C25A-C25B 1.1925 (18)
C15B-C15A-C15 179.09 (14)
O14'-C11'-N11 108.30 (9)
O15'-C15'-C14' 112.24 (10)
C25B-C25A-C25 175.83 (14)
O24'-C21'-N21 108.52 (9)
O25'-C25'-C24' 109.43 (10)
O12-C12-N13-C14 179.23 (10)
N14-C14-C15-C15A -1.28 (17)
C12-N11-C11'-O14' -149.17 (10)
C13'-C14'-C15'-O15' 55.52 (14)
O22-C22-N23-C24 -178.87 (11)
N24-C24-C25-C25A -1.07 (17)
C22-N21-C21'-O24' -151.39 (10)
C23'-C24'-C25'-O25' 51.66 (14)

Table 2
Hydrogen-bond geometry (Å, °)

D-H...A D-H H...A D...A D-H...A
N14-H14A...N23i 0.88 2.09 2.9696 (14) 178
O13'-H13O...O22 0.84 1.88 2.7127 (14) 170
O15'-H15O...O12ii 0.84 2.01 2.8119 (13) 160
N24-H24A...N13iii 0.88 2.11 2.9708 (14) 166
O23'-H23O...O12 0.84 2.00 2.8090 (13) 162
O25'-H25O...O15'iv 0.84 1.97 2.7733 (13) 160
Symmetry codes: (i) x-1, y-1, z-1; (ii) x+1, y, z; (iii) x+1, y+1, z+1; (iv) x-1, y, z+1.

The known configuration of the parent molecule was used to define the enantiomer employed in the refined model. In the absence of suitable anomalous scattering, Friedel equivalents could not be used to determine the absolute structure. Refinement of the Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]) parameter led to inconclusive values for this parameter [-0.3 (3)]. Further confirmation of the configuration was sought by the Hooft analysis. The absolute structure parameter y (Hooft et al., 2008[Hooft, R. W. W., Straver, L. H. & Spek, A. L. (2008). J. Appl. Cryst. 41, 96-103.]) was calculated using PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]). The resulting Hooft analysis parameters were P2(true) = P3(true) = 1.000, P3(false) = 0.2 × 10-27, P3(rac-twin) = 0.1 × 10-8 and y = -0.20 (10) calculated for 3602 Bijvoet pairs (97% coverage), indicating that the known absolute configuration used for analysis is correct. All H atoms were found in a difference Fourier synthesis. In order to maximize the data/parameter ratio, H atoms were placed in geometrically idealized positions, with C-H = 0.95-1.00 Å and N-H = 0.88 Å (AFIX 93; Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C,N). The hydroxy groups were refined as groups allowed to rotate but not tip (AFIX 147), with O-H = 0.84 Å and Uiso(H) = 1.5Ueq(O).

Data collection: APEX2 (Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: APEX2; data reduction: SAINT (Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: DIAMOND (Brandenburg, 1999[Brandenburg, K. (1999). DIAMOND. Crystal Impact GbR, Bonn, Germany.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: SHELXL97.


Supplementary data for this paper are available from the IUCr electronic archives (Reference: FG3269 ). Services for accessing these data are described at the back of the journal.


References

Andersen, N. K., Døssing, H., Jensen, F., Vester, B. & Nielsen, P. (2011). J. Org. Chem. 76, 6177-6187.  [CrossRef] [ChemPort] [PubMed]
Andersen, N. K., Spácilová, L., Jensen, M. D., Kocalka, P., Jensen, F. & Nielsen, P. (2008). Nucleic Acids Symp. Ser. 52, 149-150.
Barr, P. J., Hamor, T. A. & Walker, R. T. (1978). Acta Cryst. B34, 2799-2802.  [CrossRef] [details]
Barr, P. J., Jones, A. S., Serafinowski, P. & Walker, R. T. (1978). J. Chem. Soc. Perkin Trans. 1, pp. 1263-1267.
Brandenburg, K. (1999). DIAMOND. Crystal Impact GbR, Bonn, Germany.
Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
De Clercq, E., Balzarini, J., Descamps, J., Huang, G.-F., Torrence, P. E., Bergstrom, D. E., Jones, A. S., Serafinowski, P., Verhelst, G. & Walker, R. T. (1982). Mol. Pharmacol. 21, 217-223.
Dodd, D. W., Swanick, K. N., Price, J. T., Brazeau, A. L., Ferguson, M. J., Jones, N. D. & Hudson, R. H. E. (2010). Org. Biomol. Chem. 8, 663-666.  [CSD] [CrossRef] [ChemPort] [PubMed]
Flack, H. D. (1983). Acta Cryst. A39, 876-881.  [CrossRef] [details]
Guan, L., van der Heijden, G. W., Bortvin, A. & Greenberg, M. M. (2011). ChemBioChem, 12, 2184-2190.
Hattori, H., Tanaka, M., Fukushima, M., Sasaki, T. & Matsuda, A. (1996). J. Med. Chem. 39, 5005-5011.  [CrossRef] [ChemPort] [PubMed] [ISI]
Hooft, R. W. W., Straver, L. H. & Spek, A. L. (2008). J. Appl. Cryst. 41, 96-103.  [ISI] [CrossRef] [ChemPort] [details]
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Kolb, H. C., Finn, M. G. & Sharpless, K. B. (2001). Angew. Chem. Int. Ed. 40, 2004-2021.  [ISI] [CrossRef] [ChemPort]
Kolb, H. C. & Sharpless, K. B. (2003). Drug Discov. Today, 8, 1128-1137.  [ISI] [CrossRef] [PubMed] [ChemPort]
Macícková-Cahová, H., Pohl, R. & Hocek, M. (2011). ChemBioChem, 12, 431-438.
Meldal, M. & Tornøe, C. W. (2008). Chem. Rev. 108, 2952-3015.  [ISI] [CrossRef] [PubMed] [ChemPort]
Minakawa, N., Ono, Y. & Matsuda, A. (2003). J. Am. Chem. Soc. 125, 11545-11552.
Qu, D., Wang, G., Wang, Z., Zhou, L., Chi, W., Cong, S., Ren, X., Liang, P. & Zhang, B. (2011). Anal. Biochem. 417, 112-121.
Saenger, W. (1984). Principles of Nucleic Acid Structure, edited by C. R. Cantor, pp. 1-21. New York: Springer-Verlag.
Saran, A. (1988). J. Mol. Struct. (THEOCHEM), 179, 215-223.
Sato, T. (1988). Acta Cryst. C44, 870-872.
Seela, F., Budow, S., Eickmeier, H. & Reuter, H. (2007). Acta Cryst. C63, o54-o57.  [CSD] [CrossRef] [details]
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Seela, F. & Xiong, H. (2012). Unpublished results.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.  [CrossRef] [details]
Spek, A. L. (2009). Acta Cryst. D65, 148-155.  [ISI] [CrossRef] [details]


Acta Cryst (2012). C68, o395-o398   [ doi:10.1107/S0108270112038267 ]