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Acta Crystallogr Sect E Struct Rep Online. 2010 July 1; 66(Pt 7): o1688–o1689.
Published online 2010 June 18. doi:  10.1107/S1600536810020179
PMCID: PMC3006811

7-(5-Methyl­sulfanyl-β-d-erythrofuran­osyl)-7H-pyrrolo­[2,3-d]pyrimidin-4-amine monohydrate (MT-tubercidin·H2O)

Abstract

The title compound, C12H16N4O3S·H2O, which has potential as a possible anti­malarial drug, was studied when small deviations in melting points, for two differently aged preparations, were observed. The unexpected existence of a water mol­ecule of crystallization is considered to be the cause of this variation. The 7H-pyrrolo­[2,3-d]pyrimidine unit is very slightly puckered with a total puckering amplitude of 0.035 (2) Å; its mean plane makes an angle of 88.40 (12)° with the mean plane through the ribofuranosyl unit. In the crystal, the mol­ecules are bound by strong O—H(...)N and N—H(...)O hydrogen bonds, utilizing all available protons and linking mainly through the water of crystallization.

Related literature

For details of the synthesis of and for background to the title compound, see: Riegelhaupt et al. (2010 [triangle]). For related structures, see: Seela et al. (2007 [triangle]); Abola & Sundaralingam (1973 [triangle]). For ring conformations, see: Cremer & Pople (1975 [triangle]). For hydrogen-bond motifs, see: Etter et al. (1990 [triangle]); Bernstein et al. (1995 [triangle]).

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Object name is e-66-o1688-scheme1.jpg

Experimental

Crystal data

  • C12H16N4O3S·H2O
  • M r = 314.36
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1688-efi5.jpg
  • a = 4.790 (1) Å
  • b = 16.610 (3) Å
  • c = 18.020 (4) Å
  • V = 1433.7 (5) Å3
  • Z = 4
  • Cu Kα radiation
  • μ = 2.22 mm−1
  • T = 100 K
  • 0.50 × 0.02 × 0.02 mm

Data collection

  • Rigaku Spider diffractometer
  • Absorption correction: multi-scan (ABSCOR; Higashi, 1995 [triangle]) T min = 0.712, T max = 1.0
  • 8013 measured reflections
  • 2582 independent reflections
  • 2422 reflections with I > 2σ(I)
  • R int = 0.045

Refinement

  • R[F 2 > 2σ(F 2)] = 0.039
  • wR(F 2) = 0.091
  • S = 1.08
  • 2582 reflections
  • 209 parameters
  • 2 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.29 e Å−3
  • Δρmin = −0.33 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 986 Friedel pairs
  • Flack parameter: 0.02 (2)

Data collection: CrystalClear (Rigaku Americas, 2005 [triangle]); cell refinement: FSProcess in PROCESS-AUTO (Rigaku, 1998 [triangle]); data reduction: FSProcess in PROCESS-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP in WinGX (Farrugia, 1999 [triangle]) and Mercury (Macrae et al., 2006 [triangle]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810020179/kp2257sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810020179/kp2257Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

We thank the MacDiarmid Institute for Advanced Materials and Nanotechnology for funding of the diffractometer equipment.

supplementary crystallographic information

Comment

The title compound was prepared as part of a study of purine transport or purine salvage pathway inhibitors with potential as alternative anti-malarial drugs (Riegelhaupt et al., 2010). Its common name is 7-(5'Methylthio-β-D-erythrofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-2-amine monohydrate usually shortened to MT-tubercidin.H2O while the conventional name is 2-(4-Amino-pyrrolo[2,3-d]pyrimidin-7-yl)-5-methylsulfanylmethyl -tetrahydrofuran-3,4-diol monohydrate. The structural solution showed that in both batches there was an unexpected water molecule of crystallization, a likely cause of the variation in melting points with differently aged samples. The results for the better crystals are presented here. The asymmetric unit contents are shown in Figure 1.

The absolute configuration is defined as C1'(R), C2'(R), C3'(S) and C4'(S) with the ribofuranosyl unit adopting an (C2'-)endo-envelope Δ conformation (Q(2) 0.434 (3) Å, [var phi](2) 76.3 (3)°, Cremer & Pople (1975)). The 7H-pyrrolo[2,3-d]pyrimidine unit is very slightly puckered with total puckering amplitude of 0.035 (2) Å: its mean plane makes an angle of 88.40 (12)° with the mean plane through the ribofuranosyl unit. The orientation of the C4'–C5' bond is slightly different (with O4'-C1'-N9—C4 torsion angle of -126.6 (2)°) to that found in the related compounds 2'-Deoxy-2-fluorotubercidin (-110.2 (3)°, Seela et al., 2007) and tubercidin (-112.8 (4)°, Abola & Sundaralingam, 1973). Other dimensions are normal.

The molecules are packed in three dimensions using 6 strong hydrogen bonds of the O–H···O and N–H···O types (Table 1). The graph set motifs (Etter et al., 1990; Bernstein et al., 1995) are extensive at the binary level: C22(7), C22(9), C22(11), C22(12), C22(17), D33(10), D33(13), D33(14), D33(15), D33(17) and D33(18) types are found being based mainly on linked chains through the included water molecule (the latter feature is shown in Figure 2). The C–H···π interaction involving the methyl hydrogen H6'A and the 5-membered pyrrolo ring (at 2.80 Å) is considered fortuitous but noted here for completeness.

Experimental

The title compound was prepared as described in the supplementary data section (compound 10) by Riegelhaupt et al. (2010).

Refinement

The H atoms of the ordered hydroxyl, water and amine atoms were placed in the positions indicated by a difference electron density map and their positions were allowed to refine with Uiso(H) = 1.5Ueq(O,N). The water H atoms were restrained to an O–H distance of 0.82 (2) Å. The methyl H atoms were constrained to an ideal geometry (C—H = 0.98 Å) with Uiso(H) = 1.5Ueq(C), but were allowed to rotate freely about the adjacent C—C bonds. All other H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms with C—H distances of 0.95 (aromatic), 0.99 (methylene) or 1.00 (tertiary) Å with Uiso(H) = 1.2Ueq(C,N). Thirty-four high angle outlier reflections identified by having Fo>>Fc and collected in the same area of reciprocal space (and with ΔFo**2/e.s.d. > 5) were omitted from the final cycles of refinement based on the lack of backstop mask corrections.

Figures

Fig. 1.
An ORTEP (Farrugia, 1999) view showing the asymmetric unit of (I) with 50% probabilility ellipsoids. The dotted lines represents an intermolecular hydrogen bond.
Fig. 2.
Mercury cell packing view (Macrae et al., 2006) emphasizing the links with the water of crystallization: conventional hydrogen bonds not running up the a axis are shown (dotted lines).For the complete hydrogen bonding set see Table 1. Contact atoms are ...

Crystal data

C12H16N4O3S·H2OF(000) = 664
Mr = 314.36Dx = 1.456 Mg m3
Orthorhombic, P212121Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2abCell parameters from 1322 reflections
a = 4.790 (1) Åθ = 10.7–72.1°
b = 16.610 (3) ŵ = 2.22 mm1
c = 18.020 (4) ÅT = 100 K
V = 1433.7 (5) Å3Needle, colourless
Z = 40.50 × 0.02 × 0.02 mm

Data collection

Rigaku Spider diffractometer2582 independent reflections
Radiation source: Rigaku MM007 rotating anode2422 reflections with I > 2σ(I)
Rigaku VariMax-HF Confocal Optical SystemRint = 0.045
Detector resolution: 10 pixels mm-1θmax = 71.9°, θmin = 7.3°
ω–scansh = −5→2
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)k = −20→20
Tmin = 0.712, Tmax = 1.0l = −21→19
8013 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.039H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.091w = 1/[σ2(Fo2) + (0.031P)2 + 0.7234P] where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max < 0.001
2582 reflectionsΔρmax = 0.29 e Å3
209 parametersΔρmin = −0.33 e Å3
2 restraintsAbsolute structure: Flack (1983), 986 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.02 (2)

Special details

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)

xyzUiso*/Ueq
S10.97214 (14)0.38389 (4)0.36963 (3)0.01889 (16)
O1W0.2297 (5)0.66101 (10)0.58560 (11)0.0210 (4)
H1A0.363 (5)0.6337 (16)0.5723 (16)0.032*
H1B0.110 (6)0.6336 (16)0.6041 (16)0.032*
O2'0.8902 (4)0.53482 (10)0.64314 (9)0.0155 (4)
H2'O0.971 (7)0.5148 (17)0.6768 (15)0.023*
O3'0.6026 (4)0.56178 (10)0.51450 (10)0.0171 (4)
H3'O0.553 (7)0.5708 (17)0.4704 (16)0.026*
O4'0.4719 (4)0.38417 (10)0.55162 (8)0.0166 (4)
N10.1518 (5)0.40830 (11)0.87950 (11)0.0148 (5)
C20.0798 (6)0.45356 (14)0.82094 (13)0.0152 (5)
H2−0.06810.49060.82930.018*
N30.1866 (5)0.45398 (11)0.75258 (11)0.0132 (4)
C40.3891 (6)0.39748 (13)0.74463 (13)0.0126 (5)
C50.4795 (6)0.34442 (13)0.79930 (13)0.0130 (5)
C60.3551 (5)0.35230 (14)0.87012 (13)0.0144 (5)
N60.4318 (5)0.30707 (13)0.92757 (12)0.0188 (5)
H6A0.355 (7)0.3126 (17)0.9726 (16)0.028*
H6B0.552 (7)0.2722 (17)0.9214 (17)0.028*
C70.6937 (6)0.29487 (14)0.76725 (14)0.0155 (5)
H70.79490.25320.79130.019*
C80.7228 (6)0.31939 (14)0.69593 (14)0.0141 (5)
H80.85010.29710.66110.017*
N90.5374 (4)0.38247 (11)0.68120 (10)0.0128 (4)
C1'0.5393 (6)0.43227 (14)0.61535 (12)0.0139 (5)
H1'0.39710.47600.62080.017*
C2'0.8210 (6)0.46963 (14)0.59653 (13)0.0133 (5)
H2'0.96980.42760.59980.016*
C3'0.7750 (6)0.49214 (14)0.51606 (14)0.0138 (5)
H3'0.95520.50090.48920.017*
C4'0.6191 (6)0.41680 (15)0.48763 (13)0.0139 (5)
H4'0.48150.43280.44860.017*
C5'0.8164 (6)0.35258 (16)0.45686 (13)0.0188 (6)
H5'A0.71160.30190.44920.023*
H5'B0.96600.34190.49350.023*
C6'0.7305 (6)0.34328 (16)0.30226 (15)0.0219 (6)
H6'A0.73580.28430.30410.033*
H6'B0.78350.36150.25250.033*
H6'C0.54120.36200.31370.033*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0145 (4)0.0267 (3)0.0155 (3)−0.0023 (3)0.0037 (3)−0.0050 (3)
O1W0.0206 (12)0.0217 (9)0.0208 (10)−0.0034 (8)0.0045 (8)0.0000 (8)
O2'0.0170 (10)0.0174 (8)0.0120 (9)−0.0004 (7)−0.0028 (8)−0.0007 (7)
O3'0.0200 (11)0.0205 (9)0.0108 (8)0.0075 (8)−0.0027 (8)0.0023 (7)
O4'0.0138 (10)0.0262 (9)0.0096 (8)−0.0044 (9)0.0006 (8)−0.0020 (7)
N10.0160 (12)0.0172 (10)0.0113 (10)0.0002 (8)−0.0001 (9)0.0006 (8)
C20.0135 (14)0.0164 (11)0.0157 (12)0.0007 (10)−0.0020 (11)−0.0023 (10)
N30.0108 (11)0.0172 (9)0.0117 (11)0.0010 (8)−0.0005 (9)−0.0015 (9)
C40.0102 (13)0.0155 (11)0.0121 (12)−0.0032 (9)−0.0034 (10)−0.0014 (10)
C50.0113 (14)0.0155 (10)0.0123 (11)−0.0002 (10)0.0009 (11)0.0012 (9)
C60.0153 (14)0.0157 (11)0.0121 (11)−0.0018 (10)−0.0028 (11)−0.0004 (10)
N60.0235 (15)0.0226 (10)0.0104 (10)0.0066 (10)0.0018 (10)0.0015 (9)
C70.0130 (14)0.0162 (11)0.0174 (12)0.0012 (10)−0.0002 (12)0.0008 (10)
C80.0105 (14)0.0158 (11)0.0160 (13)0.0017 (10)0.0025 (11)−0.0035 (10)
N90.0104 (11)0.0170 (9)0.0110 (10)−0.0010 (9)0.0025 (9)0.0006 (8)
C1'0.0133 (15)0.0196 (11)0.0089 (11)0.0001 (10)−0.0008 (10)−0.0001 (9)
C2'0.0077 (13)0.0178 (11)0.0142 (12)−0.0002 (10)−0.0020 (11)0.0008 (10)
C3'0.0110 (14)0.0174 (11)0.0131 (12)0.0020 (10)0.0011 (11)0.0001 (10)
C4'0.0098 (14)0.0227 (12)0.0091 (11)0.0009 (10)−0.0027 (10)0.0029 (10)
C5'0.0184 (15)0.0227 (12)0.0153 (12)0.0002 (12)−0.0011 (12)−0.0042 (11)
C6'0.0177 (16)0.0283 (14)0.0197 (14)−0.0005 (12)−0.0007 (12)−0.0054 (12)

Geometric parameters (Å, °)

S1—C6'1.808 (3)N6—H6A0.90 (3)
S1—C5'1.816 (3)N6—H6B0.82 (3)
O1W—H1A0.820 (18)C7—C81.355 (3)
O1W—H1B0.805 (18)C7—H70.9500
O2'—C2'1.410 (3)C8—N91.399 (3)
O2'—H2'O0.79 (3)C8—H80.9500
O3'—C3'1.422 (3)N9—C1'1.446 (3)
O3'—H3'O0.84 (3)C1'—C2'1.523 (4)
O4'—C1'1.436 (3)C1'—H1'1.0000
O4'—C4'1.456 (3)C2'—C3'1.514 (3)
N1—C21.341 (3)C2'—H2'1.0000
N1—C61.357 (3)C3'—C4'1.545 (3)
C2—N31.334 (3)C3'—H3'1.0000
C2—H20.9500C4'—C5'1.529 (3)
N3—C41.357 (3)C4'—H4'1.0000
C4—N91.369 (3)C5'—H5'A0.9900
C4—C51.391 (3)C5'—H5'B0.9900
C5—C61.415 (3)C6'—H6'A0.9800
C5—C71.436 (3)C6'—H6'B0.9800
C6—N61.331 (3)C6'—H6'C0.9800
C6'—S1—C5'102.20 (14)O4'—C1'—H1'109.2
H1A—O1W—H1B111 (3)N9—C1'—H1'109.2
C2'—O2'—H2'O104 (2)C2'—C1'—H1'109.2
C3'—O3'—H3'O109 (2)O2'—C2'—C3'114.53 (19)
C1'—O4'—C4'108.50 (17)O2'—C2'—C1'112.9 (2)
C2—N1—C6118.1 (2)C3'—C2'—C1'100.7 (2)
N3—C2—N1129.2 (2)O2'—C2'—H2'109.5
N3—C2—H2115.4C3'—C2'—H2'109.5
N1—C2—H2115.4C1'—C2'—H2'109.5
C2—N3—C4111.6 (2)O3'—C3'—C2'107.7 (2)
N3—C4—N9125.8 (2)O3'—C3'—C4'111.8 (2)
N3—C4—C5125.9 (2)C2'—C3'—C4'100.83 (19)
N9—C4—C5108.3 (2)O3'—C3'—H3'112.0
C4—C5—C6116.7 (2)C2'—C3'—H3'112.0
C4—C5—C7107.5 (2)C4'—C3'—H3'112.0
C6—C5—C7135.8 (2)O4'—C4'—C5'109.07 (19)
N6—C6—N1119.2 (2)O4'—C4'—C3'105.84 (19)
N6—C6—C5122.2 (2)C5'—C4'—C3'112.7 (2)
N1—C6—C5118.6 (2)O4'—C4'—H4'109.7
C6—N6—H6A122 (2)C5'—C4'—H4'109.7
C6—N6—H6B119 (2)C3'—C4'—H4'109.7
H6A—N6—H6B119 (3)C4'—C5'—S1111.59 (18)
C8—C7—C5106.4 (2)C4'—C5'—H5'A109.3
C8—C7—H7126.8S1—C5'—H5'A109.3
C5—C7—H7126.8C4'—C5'—H5'B109.3
C7—C8—N9109.9 (2)S1—C5'—H5'B109.3
C7—C8—H8125.1H5'A—C5'—H5'B108.0
N9—C8—H8125.1S1—C6'—H6'A109.5
C4—N9—C8107.91 (19)S1—C6'—H6'B109.5
C4—N9—C1'125.7 (2)H6'A—C6'—H6'B109.5
C8—N9—C1'125.5 (2)S1—C6'—H6'C109.5
O4'—C1'—N9109.66 (18)H6'A—C6'—H6'C109.5
O4'—C1'—C2'104.34 (19)H6'B—C6'—H6'C109.5
N9—C1'—C2'114.9 (2)
C6—N1—C2—N3−2.3 (4)C4'—O4'—C1'—N9−148.2 (2)
N1—C2—N3—C42.3 (4)C4'—O4'—C1'—C2'−24.6 (2)
C2—N3—C4—N9179.6 (2)C4—N9—C1'—O4'−126.6 (2)
C2—N3—C4—C50.3 (3)C8—N9—C1'—O4'65.6 (3)
N3—C4—C5—C6−2.4 (4)C4—N9—C1'—C2'116.2 (3)
N9—C4—C5—C6178.2 (2)C8—N9—C1'—C2'−51.6 (3)
N3—C4—C5—C7179.5 (2)O4'—C1'—C2'—O2'164.56 (18)
N9—C4—C5—C70.1 (3)N9—C1'—C2'—O2'−75.3 (3)
C2—N1—C6—N6179.5 (2)O4'—C1'—C2'—C3'42.0 (2)
C2—N1—C6—C5−0.2 (3)N9—C1'—C2'—C3'162.11 (19)
C4—C5—C6—N6−177.4 (2)O2'—C2'—C3'—O3'−45.9 (3)
C7—C5—C6—N60.1 (5)C1'—C2'—C3'—O3'75.5 (2)
C4—C5—C6—N12.2 (3)O2'—C2'—C3'—C4'−163.2 (2)
C7—C5—C6—N1179.7 (3)C1'—C2'—C3'—C4'−41.8 (2)
C4—C5—C7—C8−0.1 (3)C1'—O4'—C4'—C5'119.1 (2)
C6—C5—C7—C8−177.8 (3)C1'—O4'—C4'—C3'−2.5 (2)
C5—C7—C8—N90.2 (3)O3'—C3'—C4'—O4'−85.9 (2)
N3—C4—N9—C8−179.4 (2)C2'—C3'—C4'—O4'28.4 (2)
C5—C4—N9—C80.0 (3)O3'—C3'—C4'—C5'155.0 (2)
N3—C4—N9—C1'11.0 (4)C2'—C3'—C4'—C5'−90.8 (2)
C5—C4—N9—C1'−169.5 (2)O4'—C4'—C5'—S1172.20 (16)
C7—C8—N9—C4−0.1 (3)C3'—C4'—C5'—S1−70.5 (2)
C7—C8—N9—C1'169.5 (2)C6'—S1—C5'—C4'−91.9 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2'—H2'O···N3i0.79 (3)1.99 (3)2.776 (3)173 (3)
O1W—H1A···O3'0.82 (3)1.96 (3)2.748 (3)162 (3)
O1W—H1B···O2'ii0.80 (3)2.07 (3)2.848 (3)162 (3)
O3'—H3'O···N1iii0.84 (3)1.94 (3)2.766 (3)166 (3)
N6—H6A···O1Wiv0.90 (3)2.12 (3)2.998 (3)166 (3)
N6—H6B···O1Wv0.82 (3)2.13 (3)2.928 (3)164 (3)

Symmetry codes: (i) x+1, y, z; (ii) x−1, y, z; (iii) −x+1/2, −y+1, z−1/2; (iv) −x+1/2, −y+1, z+1/2; (v) −x+1, y−1/2, −z+3/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: KP2257).

References

  • Abola, E. & Sundaralingam, M. (1973). Acta Cryst. B29, 697–703.
  • Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl.34, 1555–1573.
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