organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 69| Part 11| November 2013| Pages o1646-o1647

(2R,3R,4S,5R)-2-(4-Amino-5-iodo-7H-pyrrolo­[2,3-d]pyrimidin-7-yl)-5-methyl­tetra­hydro­furan-3,4-diol

aDepartment Chemie, Fakultät für Naturwissenschaften, Universität Paderborn, Warburgerstrasse 100, D-33098 Paderborn, Germany, and bInstitut für Neurowissenschaften und Medizin, Nuklearchemie (INM-5), Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
*Correspondence e-mail: ulrich.floerke@upb.de

(Received 10 September 2013; accepted 11 October 2013; online 16 October 2013)

The mol­ecular structure of the title compound, C11H13IN4O3, shows a ribo­furanos­yl–pyrrolo O—C—N—C torsion angle of 59.1 (3)°, with the central C—N bond length being 1.446 (3) Å. The C—I bond length is 2.072 (2) Å. The amino group is coplanar with the attached aromatic ring [C—N—C—N torsion angle = −178.8 (2)°] and forms an intra­molecular N—H⋯I hydrogen bond. In the crystal, O—H⋯N and N—H⋯O hydrogen bonds link the mol­ecules into puckered layers parallel to (001). These layers are bound to each other by secondary I⋯O inter­actions [3.2250 (17) Å], forming a three-dimensional framework.

Related literature

For background to the use of marine natural products as therapeutic agents, see: Kazlauskas et al. (1983[Kazlauskas, R., Muphy, P. T., Wells, R. J., Baird-Lambert, J. A. & Jamieson, D. D. (1983). Aust. J. Chem. 36, 165-170.]); Mitchell et al. (1996[Mitchell, S. S., Pomerantz, S. C., Conception, G. P. & Ireland, C. M. (1996). J. Nat. Prod. 59, 1000-1001.]); Wiesner et al. (1999[Wiesner, J. B., Ugarkar, B. G., Castellino, A. J., Barankiewicz, J., Dumas, D. P., Gruber, H. E., Foster, A. C. & Erion, M. D. (1999). J. Pharmacol. Exp. Ther. 289, 1669-1677.]); Ugarkar et al. (2000[Ugarkar, B. G., DaRe, J. M., Kopcho, J. J., Browne, C. E., Schanzer, J. M., Wiesner, J. B. & Erion, M. D. (2000). J. Med. Chem. 43, 2883-2893.]); Song et al. (2011[Song, Y., Ding, H. X., Dou, Y. H., Yang, R. C., Sun, Q., Xiao, Q. & Ju, Y. (2011). Synthesis, 9, 1442-1446.]). For the structures of related compounds, see: Seela et al. (1996[Seela, F., Zulauf, M., Rosemeyer, H. & Reuter, H. (1996). J. Chem. Soc. Perkin Trans. 2, pp. 2373-2376.], 1999[Seela, F., Zulauf, M., Reuter, H. & Kastner, G. (1999). Acta Cryst. C55, 1560-1562.], 2008[Seela, F., Ming, X., Budow, S., Eickmeier, H. & Reuter, H. (2008). Acta Cryst. C64, o293-o295.]).

[Scheme 1]

Experimental

Crystal data
  • C11H13IN4O3

  • Mr = 376.15

  • Orthorhombic, P 21 21 21

  • a = 4.9164 (2) Å

  • b = 14.6490 (5) Å

  • c = 18.0130 (6) Å

  • V = 1297.30 (8) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 2.48 mm−1

  • T = 130 K

  • 0.49 × 0.08 × 0.08 mm

Data collection
  • Bruker SMART APEX diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2004[Sheldrick, G. M. (2004). SADABS. University of Göttingen, Germany.]) Tmin = 0.376, Tmax = 0.826

  • 12307 measured reflections

  • 3103 independent reflections

  • 3056 reflections with I > 2σ(I)

  • Rint = 0.019

Refinement
  • R[F2 > 2σ(F2)] = 0.020

  • wR(F2) = 0.051

  • S = 1.06

  • 3103 reflections

  • 175 parameters

  • H-atom parameters constrained

  • Δρmax = 1.05 e Å−3

  • Δρmin = −0.30 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1274 Friedel pairs

  • Absolute structure parameter: −0.015 (17)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O2—H2⋯N2i 0.84 1.94 2.759 (3) 165
O3—H3⋯N1ii 0.84 2.16 2.907 (3) 149
N4—H4A⋯O2iii 0.88 2.07 2.915 (3) 160
N4—H4B⋯I1 0.88 2.92 3.636 (2) 139
Symmetry codes: (i) x+1, y, z; (ii) [-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (iii) [-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: SMART (Bruker, 2002[Bruker (2002). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2002[Bruker (2002). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and local programs.

Supporting information


Comment top

Marine natural products provide a rich source of chemical diversity that can be used to develop new, potentially useful therapeutic agents. Nucleosides from marine organisms show great potential as lead compounds in medicinal chemistry research. 5'-Deoxy-5-iodotubercidin (5'd-5IT, 4-amino-5-iodo-7-(5-deoxy-β-D-ribofuranosyl)pyrrolo[2,3-d]pyrimidine) was isolated from the marine red alga Hypnea vanlendiae (Kazlauskas et al., 1983) and from the marine ascidian Didemnum voeltzkowi (Mitchell et al., 1996). In vitro, all 5'-deoxytubercidin marine nucleosides show strong inhibitory activity for human adenosine kinase with 5'd-5IT being the most potent one. Therapeutic success of adenosine kinase inhibitors as active agents in animal models is documented for epilepsy and pain and as antiseizure agents (Wiesner et al., 1999; Ugarkar et al., 2000). The molecular structure is related to the derivatives studied previously (Seela et al., 1996, 1999, 2008) and shows no unexpected geometric parameters.

Related literature top

For background to the use of marine natural products as therapeutic agents, see: Kazlauskas et al. (1983); Mitchell et al. (1996); Wiesner et al. (1999); Ugarkar et al. (2000); Song et al. (2011). For the structures of related compounds, see: Seela et al. (1996, 1999, 2008).

Experimental top

The title compound was synthesized according to a known procedure (Song et al., 2011). Recrystallization from ethanol-water (1:1) yielded crystals suitable for X-ray analysis. Spectroscopic analysis: 1H NMR (250 MHz, DMSO-d6, δ): 1.29 (d, J = 6.16 Hz, 3H, CHCH3), 3.87–3.95 [m, 2H, H-3', H-4'], 4.41 (m, 1H, H-2'), 5.11 (s, 1H, 3'-OH), 5.33 (s, 1H, 2'-OH), 6.02 (d, J = 5.28 Hz, 1H, H-1'), 6.69 (s, 2H, 4-NH2), 7.63 (s, 1H, H-6), 8.14 (s, 1H, H-2); 13C NMR (250 MHz, DMSO-d6, δ): 19.6 (CH3, C-5'), 52.8 (C—I, C-5), 73.8 (CH, C-2'), 75.0 (CH, C-3'), 79.8 (CH, C-4'), 87.4 (CH, C-1'), 103.6 (CC, C-4a), 127.4 (CH, C-6), 150.8 (CC, C-7a), 152.5 (CH, C-2), 157.6 (C—NH2, C-4).

Refinement top

Hydrogen atoms were clearly identified in difference syntheses, refined at idealized positions riding on the carbon, nitrogen or oxygen atoms with C—H 0.95–1.00, N—H 0.88, O—H 0.84 Å and with isotropic displacement parameters Uiso(H) = 1.2Ueq(C/N) or 1.5Ueq(—CH3 and —OH H atoms). All CH3 and OH hydrogen atoms were allowed to rotate but not to tip. The max. electron density residual is close (0.9 Å) to the I1 position.

Computing details top

Data collection: SMART (Bruker, 2002); cell refinement: SAINT (Bruker, 2002); data reduction: SAINT (Bruker, 2002); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and local programs.

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound with anisotropic displacement parameters drawn at the 50% probability level. The intramolecular N4–H4b···I1 hydrogen bond depicted as dashed line.
[Figure 2] Fig. 2. Crystal packing viewed along a axis with intermolecular I···O interaction as well as hydrogen bonds as dashed lines.
(2R,3R,4S,5R)-2-(4-Amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-5-methyltetrahydrofuran-3,4-diol top
Crystal data top
C11H13IN4O3F(000) = 736
Mr = 376.15Dx = 1.926 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 8237 reflections
a = 4.9164 (2) Åθ = 2.7–28.3°
b = 14.6490 (5) ŵ = 2.48 mm1
c = 18.0130 (6) ÅT = 130 K
V = 1297.30 (8) Å3Needle, colourless
Z = 40.49 × 0.08 × 0.08 mm
Data collection top
Bruker SMART APEX
diffractometer
3103 independent reflections
Radiation source: sealed tube3056 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.019
ϕ and ω scansθmax = 27.9°, θmin = 1.8°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2004)
h = 66
Tmin = 0.376, Tmax = 0.826k = 1919
12307 measured reflectionsl = 2322
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.020H-atom parameters constrained
wR(F2) = 0.051 w = 1/[σ2(Fo2) + (0.0319P)2 + 0.5639P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.001
3103 reflectionsΔρmax = 1.05 e Å3
175 parametersΔρmin = 0.30 e Å3
0 restraintsAbsolute structure: Flack (1983), 1274 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.015 (17)
Crystal data top
C11H13IN4O3V = 1297.30 (8) Å3
Mr = 376.15Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 4.9164 (2) ŵ = 2.48 mm1
b = 14.6490 (5) ÅT = 130 K
c = 18.0130 (6) Å0.49 × 0.08 × 0.08 mm
Data collection top
Bruker SMART APEX
diffractometer
3103 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2004)
3056 reflections with I > 2σ(I)
Tmin = 0.376, Tmax = 0.826Rint = 0.019
12307 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.020H-atom parameters constrained
wR(F2) = 0.051Δρmax = 1.05 e Å3
S = 1.06Δρmin = 0.30 e Å3
3103 reflectionsAbsolute structure: Flack (1983), 1274 Friedel pairs
175 parametersAbsolute structure parameter: 0.015 (17)
0 restraints
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
I10.89717 (3)0.148805 (10)0.080859 (9)0.02262 (6)
O10.5927 (4)0.52637 (11)0.01354 (9)0.0194 (3)
O21.0140 (4)0.58588 (12)0.16890 (10)0.0197 (4)
H21.12120.54640.18580.030*
O30.7492 (4)0.71478 (11)0.08382 (10)0.0228 (4)
H30.81600.72360.12610.034*
N10.2124 (5)0.28946 (15)0.26704 (12)0.0224 (4)
N20.3108 (4)0.43351 (14)0.20816 (11)0.0189 (4)
N30.6561 (4)0.42430 (13)0.11225 (11)0.0162 (4)
N40.4171 (5)0.15312 (15)0.23436 (11)0.0243 (4)
H4A0.31940.12550.26860.029*
H4B0.53180.12150.20700.029*
C10.8108 (5)0.35459 (17)0.08162 (13)0.0192 (4)
H1A0.94080.36190.04300.023*
C20.7476 (5)0.27404 (16)0.11546 (14)0.0191 (5)
C30.5438 (5)0.29313 (16)0.17014 (13)0.0160 (5)
C40.3910 (6)0.24402 (16)0.22372 (12)0.0185 (5)
C50.1823 (5)0.37938 (18)0.25567 (14)0.0223 (5)
H5A0.05010.40850.28600.027*
C60.4924 (5)0.38688 (16)0.16605 (13)0.0164 (5)
C70.6628 (5)0.51898 (15)0.08971 (13)0.0154 (4)
H7A0.53020.55470.12020.018*
C80.9424 (5)0.56288 (15)0.09505 (12)0.0150 (5)
H8A1.08300.52170.07300.018*
C90.9025 (5)0.64656 (15)0.04619 (12)0.0178 (4)
H9A1.07960.67100.02740.021*
C100.7272 (5)0.60780 (16)0.01690 (13)0.0182 (5)
H10A0.58610.65380.03120.022*
C110.8868 (6)0.58060 (18)0.08480 (14)0.0274 (5)
H11A1.05020.54710.06970.041*
H11B0.93980.63550.11240.041*
H11C0.77420.54150.11650.041*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.02487 (8)0.01568 (8)0.02731 (8)0.00340 (6)0.00081 (7)0.00292 (6)
O10.0223 (8)0.0186 (8)0.0174 (7)0.0041 (7)0.0021 (8)0.0033 (6)
O20.0225 (9)0.0172 (8)0.0193 (8)0.0048 (7)0.0047 (7)0.0027 (7)
O30.0320 (10)0.0158 (7)0.0207 (8)0.0065 (7)0.0005 (9)0.0020 (7)
N10.0230 (11)0.0239 (10)0.0203 (10)0.0025 (9)0.0016 (9)0.0048 (8)
N20.0217 (10)0.0181 (10)0.0170 (9)0.0027 (8)0.0005 (8)0.0030 (8)
N30.0177 (11)0.0120 (9)0.0191 (9)0.0006 (7)0.0022 (8)0.0007 (7)
N40.0286 (11)0.0227 (10)0.0216 (10)0.0061 (12)0.0010 (9)0.0076 (8)
C10.0192 (10)0.0170 (10)0.0213 (10)0.0002 (9)0.0033 (9)0.0001 (11)
C20.0207 (13)0.0160 (11)0.0206 (11)0.0005 (9)0.0014 (10)0.0000 (9)
C30.0162 (12)0.0145 (10)0.0174 (10)0.0010 (8)0.0018 (9)0.0019 (8)
C40.0209 (12)0.0172 (10)0.0175 (10)0.0019 (10)0.0055 (11)0.0043 (8)
C50.0231 (12)0.0227 (11)0.0210 (12)0.0039 (10)0.0030 (10)0.0017 (9)
C60.0167 (10)0.0174 (11)0.0149 (10)0.0008 (9)0.0026 (9)0.0042 (9)
C70.0150 (10)0.0130 (9)0.0182 (11)0.0019 (8)0.0009 (9)0.0020 (8)
C80.0154 (12)0.0135 (10)0.0161 (11)0.0006 (8)0.0007 (8)0.0024 (8)
C90.0205 (10)0.0116 (9)0.0212 (10)0.0014 (12)0.0032 (9)0.0001 (8)
C100.0233 (12)0.0136 (10)0.0177 (11)0.0011 (9)0.0018 (10)0.0027 (9)
C110.0375 (14)0.0256 (12)0.0190 (11)0.0042 (12)0.0058 (15)0.0001 (10)
Geometric parameters (Å, º) top
I1—C22.072 (2)C1—C21.364 (3)
O1—C71.419 (3)C1—H1A0.9500
O1—C101.470 (3)C2—C31.433 (4)
O2—C81.417 (3)C3—C61.398 (3)
O2—H20.8400C3—C41.419 (3)
O3—C91.423 (3)C5—H5A0.9500
O3—H30.8400C7—C81.521 (3)
N1—C51.341 (3)C7—H7A1.0000
N1—C41.350 (3)C8—C91.522 (3)
N2—C51.327 (3)C8—H8A1.0000
N2—C61.356 (3)C9—C101.535 (3)
N3—C61.374 (3)C9—H9A1.0000
N3—C11.388 (3)C10—C111.507 (3)
N3—C71.446 (3)C10—H10A1.0000
N4—C41.351 (3)C11—H11A0.9800
N4—H4A0.8800C11—H11B0.9800
N4—H4B0.8800C11—H11C0.9800
C7—O1—C10108.28 (17)O1—C7—C8104.37 (18)
C8—O2—H2109.5N3—C7—C8114.11 (19)
C9—O3—H3109.5O1—C7—H7A109.5
C5—N1—C4117.9 (2)N3—C7—H7A109.5
C5—N2—C6111.9 (2)C8—C7—H7A109.5
C6—N3—C1107.93 (19)O2—C8—C7112.61 (19)
C6—N3—C7126.5 (2)O2—C8—C9112.55 (18)
C1—N3—C7125.6 (2)C7—C8—C9100.81 (18)
C4—N4—H4A120.0O2—C8—H8A110.2
C4—N4—H4B120.0C7—C8—H8A110.2
H4A—N4—H4B120.0C9—C8—H8A110.2
C2—C1—N3109.5 (2)O3—C9—C8111.00 (18)
C2—C1—H1A125.2O3—C9—C10108.4 (2)
N3—C1—H1A125.2C8—C9—C10101.68 (18)
C1—C2—C3107.3 (2)O3—C9—H9A111.8
C1—C2—I1123.41 (19)C8—C9—H9A111.8
C3—C2—I1128.88 (18)C10—C9—H9A111.8
C6—C3—C4116.0 (2)O1—C10—C11108.81 (19)
C6—C3—C2106.4 (2)O1—C10—C9106.05 (18)
C4—C3—C2137.6 (2)C11—C10—C9114.0 (2)
N1—C4—N4117.7 (2)O1—C10—H10A109.3
N1—C4—C3119.2 (2)C11—C10—H10A109.3
N4—C4—C3123.1 (2)C9—C10—H10A109.3
N2—C5—N1129.3 (2)C10—C11—H11A109.5
N2—C5—H5A115.4C10—C11—H11B109.5
N1—C5—H5A115.4H11A—C11—H11B109.5
N2—C6—N3125.4 (2)C10—C11—H11C109.5
N2—C6—C3125.7 (2)H11A—C11—H11C109.5
N3—C6—C3108.9 (2)H11B—C11—H11C109.5
O1—C7—N3109.84 (18)
C6—N3—C1—C20.2 (3)C2—C3—C6—N2179.6 (2)
C7—N3—C1—C2178.7 (2)C4—C3—C6—N3179.7 (2)
N3—C1—C2—C30.1 (3)C2—C3—C6—N30.4 (3)
N3—C1—C2—I1173.35 (17)C10—O1—C7—N3151.81 (19)
C1—C2—C3—C60.3 (3)C10—O1—C7—C829.1 (2)
I1—C2—C3—C6172.66 (19)C6—N3—C7—O1119.2 (2)
C1—C2—C3—C4179.9 (3)C1—N3—C7—O159.1 (3)
I1—C2—C3—C47.2 (5)C6—N3—C7—C8124.0 (2)
C5—N1—C4—N4178.8 (2)C1—N3—C7—C857.7 (3)
C5—N1—C4—C31.9 (4)O1—C7—C8—O2162.92 (18)
C6—C3—C4—N10.8 (3)N3—C7—C8—O277.2 (2)
C2—C3—C4—N1179.3 (3)O1—C7—C8—C942.8 (2)
C6—C3—C4—N4179.9 (2)N3—C7—C8—C9162.66 (19)
C2—C3—C4—N40.1 (5)O2—C8—C9—O344.0 (3)
C6—N2—C5—N11.1 (4)C7—C8—C9—O376.2 (2)
C4—N1—C5—N22.2 (4)O2—C8—C9—C10159.10 (19)
C5—N2—C6—N3179.8 (2)C7—C8—C9—C1038.9 (2)
C5—N2—C6—C30.2 (4)C7—O1—C10—C11126.7 (2)
C1—N3—C6—N2179.6 (2)C7—O1—C10—C93.7 (2)
C7—N3—C6—N21.1 (4)O3—C9—C10—O194.2 (2)
C1—N3—C6—C30.3 (3)C8—C9—C10—O122.8 (2)
C7—N3—C6—C3178.9 (2)O3—C9—C10—C11146.1 (2)
C4—C3—C6—N20.3 (4)C8—C9—C10—C1196.9 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2···N2i0.841.942.759 (3)165
O3—H3···N1ii0.842.162.907 (3)149
N4—H4A···O2iii0.882.072.915 (3)160
N4—H4B···I10.882.923.636 (2)139
Symmetry codes: (i) x+1, y, z; (ii) x+1, y+1/2, z+1/2; (iii) x+1, y1/2, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2···N2i0.841.942.759 (3)165
O3—H3···N1ii0.842.162.907 (3)149
N4—H4A···O2iii0.882.072.915 (3)160
N4—H4B···I10.882.923.636 (2)139
Symmetry codes: (i) x+1, y, z; (ii) x+1, y+1/2, z+1/2; (iii) x+1, y1/2, z+1/2.
 

References

First citationBruker (2002). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.
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Volume 69| Part 11| November 2013| Pages o1646-o1647
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