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The asymmetric unit of the title compound, C6H5N3O, consists of discrete mol­ecules of 9-deaza­hypoxanthine [systematic name: 3H-pyrrolo­[3,2-d]pyrimidin-4(5H)-one]. The structure displays N-H...O hydrogen bonding, connecting the mol­ecules into centrosymmetric dimers. These dimers are then connected by N-H...N hydrogen bonds into a ladder-like chain along the c axis. The secondary structure is stabilized by weak noncovalent contacts of the C-H...O and C-H...C types, as well as by [pi]-[pi] stacking inter­actions, which organize the structure into a zigzag architecture.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270112050767/sk3467sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270112050767/sk3467Isup2.hkl
Contains datablock I

cml

Chemical Markup Language (CML) file https://doi.org/10.1107/S0108270112050767/sk3467Isup3.cml
Supplementary material

CCDC reference: 864810

Comment top

3,5-Dihydropyrrolo[3,2-d]pyrimidines, and in particular the title compound, 9-deazahypoxanthine, (I), have become of great interest because of the potential pharmaceutical use of their derivatives (Montgomery et al., 1993; Bzowska et al., 2000). C9-Substituted 9-deazahypoxanthines (immucillins) are powerful inhibitors of purine nucleoside phosphorylase (PNP), which reversibly catalyses the cleavage of purine nucleosides to the corresponding free bases. The activity of this enzyme is most probably required for normal human T-cell proliferation, and therefore PNP inhibitors represent a novel class of potential selective immunosuppressive agents and may be useful for the treatment of autoimmune disorders, such as psoriasis and rheumatoid arthritis, and other T-cell proliferative disorders, such as organ-transplant rejection and adult T-cell leukaemia (Bantia et al., 2001). Moreover, two members of the immucillin family, viz. immucillin-H [BCX-1777, 1-(9-deazahypoxanthin)-1,4-dideoxy-1,4-imino-D-ribitol)] and DADMe-immucillin-H (BCX-4208, 7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-1,5-dihydropyrrolo[3,2-d]pyrimidin-4-one), are currently in human clinical trials for the treatment of T- and B-cell cancers and autoimmune diseases (Clinch et al., 2009). Research on 9-deazahypoxanthine derivatives has been incessant and more derivatives have been prepared and tested as antiproliferative (Otmar et al., 2004) or antidiabetic (Sutton et al., 2012) agents.

Even though (I) has been long known and is well characterized, a search of the Cambridge Structural Database (Version 5.33, August 2012 update; Allen, 2002) gave 17 structures involving the 9-deazahypoxanthine group and none of these showed the structural arrangement of the unsubstituted title molecule. All the data deposited so far describe the structures of, variously, mono-, bi- and tri-substituted 9-deazahypoxanthine derivatives exhibiting different biological properties. For many of these derivatives, (I) served as a synthetic precursor. For example, 6-chloro-9-deazapurine is easily available from 9-deazahypoxanthine, and it may then serve as a perfect precursor for the preparation of 9-deaza-analogues of C6-substituted purines, such as the potent cyclin-dependent kinase inhibitor olomoucine (Čapek et al., 2003). It is well established that the knowledge of the molecular structure and crystal packing of a compound supplies the necessary information for defining possible structure–property relationships, involving different polymorphs with varying physical and chemical properties important in pharmacology, or for identification of possible coordination sites when the compound acts as a ligand in a metal complex. Therefore, in connection with the medicinal potential of 9-deazahypoxanthine derivatives, the constant search for more potent analogues and their potential use as ligands in the preparation of biologically active transition metal complexes, the effort to provide a thorough structural description arising from X-ray structure determination, accompanied by a combination of analytical methods such as multinuclear NMR spectroscopy or mass spectrometry, is unambiguously justified. In this work, we report not only the detailed structural determination of 9-deazahypoxanthine, (I), in the solid state by single-crystal X-ray analysis, but also a thorough characterization of this compound by a wide spectrum of other methods.

Before the isolated title compound was subjected to crystallization attempts, it was fully characterized after preparation in order to confirm its identity and chemical purity. The techniques used for the study of the composition of (I) involved elemental analysis and spectroscopic (IR, MS and NMR) methods. The NMR spectroscopic measurements unambiguously confirmed the composition of (I). It should be pointed out that full interpretations of the 1H, 13C and 15N NMR spectra of (I) have not been reported in the literature thus far.

The molecular structure of (I) consists of discrete molecules of 9-deazahypoxanthine (Fig. 1). The molecule contains nearly coplanar pyrimidine and pyrrole rings [dihedral angle = 0.70 (7)°]. Both rings deviate significantly from planarity (Nardelli, 1995), the maximum deviations from the mean planes being 0.004 (2) and 0.005 (2) Å for atom C4 in the case of the pyrimidine and pyrrole rings, respectively. Additionally, the whole 9-deazapurine skeleton also deviates significantly from planarity, with the maximum deviation being 0.014 (2) Å for atom C9.

The molecule of (I) can be formally derived from the hypoxanthine skeleton by substituting atom N9 for a C atom. Two polymorphs of hypoxanthine have been published so far, the triclinic form (Schmalle et al., 1988) and the monoclinic form (Yang & Xie, 2007). Comparing the structural parameters and focusing on bond angles, the most significant differences would be expected in the vicinity of the substituted C9/N9 atoms, as well as at the N7 site, more concretely in the case of the C5—N7—C8 and C4—C9—C8 angles in (I), and the C5—N7—C8 and C4—N9—C8 angles in hypoxanthine. The expected changes can be explained not only on the basis of the presence of different atoms in the 9-position, but also in connection with the protonation at atom N7 in (I), in contrast with hypoxanthine, where the N9 site is primarily protonated. While the differences in the angles at N7 are conclusively significant, the substitution of N9 in hypoxanthine by C9 in (I) does not bring about a significant difference in the angle at position 9. On the other hand, the bond angles in (I) are comparable with those reported for a monosubstituted derivative of (I), namely 9-deazainosine monohydrate [9-(2-hydroxyethoxymethyl)-9-deazahypoxanthine monohydrate; Otter et al., 1992]. For a comparison of selected bond angles, see Table 2.

The crystal structure consists of the molecules of (I) organized into one-dimensional ladder-like chains along the c axis (Fig. 2) by hydrogen bonding of moderate strength. Two heteroaromatic amine groups are involved in the formation of two main supramolecular ring synthons (Bernstein et al., 1995): (i) a centrosymmetric amide-like R22(8) ring involving the donor N1—H group and atom O1 as an acceptor; (ii) an asymmetric R22(8) ring involving N7—H and C2—H donors, and atoms O1 and N3 as acceptors, respectively. These hydrogen bonds provided by the heteroaromatic amine groups are of different strengths, as can be seen from the donor–acceptor distances (Table 1). This length difference can be rationalized on the basis of the different types of hydrogen-bond acceptors, where the lower electronegativity of N with respect to O determines the different qualities of the noncovalent contacts. The C2—H···O1iii contact is rather long in comparison with the aforementioned hydrogen bonds (Table 1), but its distance classifies this contact in the group of very short C—H···O hydrogen bonds (Desiraju & Steiner, 2001).

The individual one-dimensional ladder-like chains are interconnected by ππ stacking interactions, thus forming a two-dimensional arrangement. The distance between the planes fitted through the non-H atoms of ten molecules in each plane forming the one-dimensional chain is d = 3.193 Å (Fig. 3). The closest C···C contact is found between the atoms C9 and C2iv [3.267 (3) Å; symmetry code: (iv) x - 1, y, z]. The distance between these best-fit planes is significantly shorter than that between the individual aromatic rings, which are thus not placed directly above one another, as demonstrated by the centroid-to-centroid distance [Cg1···Cg2iv = 4.8315 (12) Å, where Cg1 and Cg2 are the centroids of the non-H atoms of (I)]. In other words, neighbouring layers are shifted by 3.626 Å.

Additional stabilization of the secondary structure of (I) is provided by another weak noncovalent contact, C9—H···C8v [3.557 (3) Å; symmetry code: (v) x - 1/2, -y + 1/2, z - 1/2]. This connects the individual infinite ladder-like chains, which results in the organization of the crystal structure into a three-dimensional zigzag architecture, as viewed along the c axis (Fig. 3). The least-squares planes of the molecules in the one-dimensional ladder-like chains organized into the zigzag structure are nearly perpendicular, as the dihedral angle is about 86°.

Related literature top

For related literature, see: Allen (2002); Bantia et al. (2001); Bernstein et al. (1995); Bzowska et al. (2000); Clinch et al. (2009); Desiraju & Steiner (2001); Kamath et al. (2009); Montgomery et al. (1993); Nardelli (1995); Otmar et al. (2004); Otter et al. (1992); Schmalle et al. (1988); Sutton (2012); Yang & Xie (2007); Čapek et al. (2003).

Experimental top

The title compound, (I), was prepared by a modification of the three-step procedure of Kamath et al. (2009) and was characterized as a chemical individuum. The modifications to the published synthesis lie primarily in a shortening of the reaction time and differences in the purification methods for obtaining the intermediates in the reaction process. The first step, as a result of the applied modifications, was complete after ca 4 h, in contrast with the published procedure with a reaction completion time of 24 h. Diethylaminomalonate hydrochloride [Quantity?], ethyl(ethoxymethylene)cyanoacetate [Quantity?] and sodium methoxide [Quantity?] in methanol [Quantity?] were mixed carefully at a temperature below ambient conditions. The reaction solution was then treated with ultrasound for ca 15 min before being refluxed for 4 h. The light-yellow solid product of dimethyl amino-1H-pyrrole-2,4-dicarboxylate was then recrystallized from toluene and [How much?] further reacted with formamidine acetate [Quantity?] in ethanol [Quantity?]. The use of a smaller amount of ethanol [pyrrole–ethanol molar ratio = 1:24, compared with a molar ratio of 1:31 used by Kamath et al. (2009)] enabled direct isolation of the product, methyl 4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidine-7-carboxylate, from the reaction solution. This intermediate was purified by recrystallization from acetic acid. The final reaction step was used without any modifications to achieve (I) as a beige solid [Colourless in CIF data tables - please clarify]. Crystals suitable for X-ray studies were obtained by slow evaporation from a water solution.

IR (νmax, cm-1): 3265 (N—H)ar,3151, 3103, 3021 (C—H)ar, 1663 (CO), 1595, 1542, 1516, 1483 (CC)ring and (C N)ring. 1H NMR (DMF-d7, TMS, 298 K): δ 12.15 (bs, 1H, HN7), 11.82 (bs, 1H, HN1), 7.93 (s, 1H, HC2), 7.49 (d, J = 2.6 Hz, 1H, HC8), 6.43 (d, J = 2.8 Hz, 1H, HC9). 13C NMR (DMF-d7, TMS, 298 K): δ 154.1 (C6), 145.4 (C4), 141.9 (C2), 127.5 (C8), 118.6 (C5), 103.4 (C9). 15N NMR (DMF-d7, relative to DMF, 298 K): δ 140.42 [d, J = 101.2 Hz, 12.15, HN7; s, 7.49, HC8; s, 6.43, HC9 (N7)], 166.6 [s, 47.93, HC2 (N1)], 236.47 [d, J = 10.7 Hz, 7.93, HC2 (N3)]. ESI+MS: m/z 136.1 [M + H]+ (calculated 136.1), 158.1 [M + Na]+ (calculated 158.1). Analysis calculated for C6H5N3O: C 53.33, H 3.73, N 31.10%; found: C 53.46, H 3.70, N 31.44%.

Refinement top

H atoms were located in difference maps and refined using a riding model, with C—H = 0.95 Å and N—H = 0.88 Å, and with Uiso(H) = 1.2Ueq(CH and NH).

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell refinement: CrysAlis RED (Oxford Diffraction, 2009); data reduction: CrysAlis RED (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008) and DIAMOND (Brandenburg, 2011); software used to prepare material for publication: publCIF (Westrip, 2010) and PARST (Nardelli, 1995).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. (a) A view along the a axis, showing the N—H···O and N—H···N hydrogen bonding (dashed lines). (b) A view of the one-dimensional ladder-like chain along the c axis, showing its planarity. [Symmetry codes: (i) -x + 2, -y, -z + 1; (ii) x, y, z + 1.]
[Figure 3] Fig. 3. Part of the crystal structure of (I), showing the formation of layers of ladder-like chains stacked by ππ interactions, with a distance d between neighbouring layers of 3.193 Å, and the formation of the zigzag supramolecular architecture along the c axis. Dotted lines indicate intermolecular interactions.
3H-pyrrolo[3,2-d]pyrimidin-4(5H)-one top
Crystal data top
C6H5N3OF(000) = 280
Mr = 135.13Dx = 1.513 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 1593 reflections
a = 4.8315 (12) Åθ = 3.1–33.3°
b = 19.976 (5) ŵ = 0.11 mm1
c = 6.3551 (13) ÅT = 100 K
β = 104.69 (2)°Prism, colourless
V = 593.3 (2) Å30.20 × 0.15 × 0.10 mm
Z = 4
Data collection top
Oxford Xcalibur
diffractometer with Sapphire2 detector (large Be window)
1050 independent reflections
Radiation source: Enhance (Mo) X-ray Source693 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.063
Detector resolution: 8.3611 pixels mm-1θmax = 25.1°, θmin = 3.5°
ω scansh = 55
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2009)
k = 2322
Tmin = 0.978, Tmax = 0.989l = 77
3740 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.049Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.102H-atom parameters constrained
S = 0.94 w = 1/[σ2(Fo2) + (0.0548P)2]
where P = (Fo2 + 2Fc2)/3
1050 reflections(Δ/σ)max < 0.001
91 parametersΔρmax = 0.27 e Å3
0 restraintsΔρmin = 0.17 e Å3
Crystal data top
C6H5N3OV = 593.3 (2) Å3
Mr = 135.13Z = 4
Monoclinic, P21/nMo Kα radiation
a = 4.8315 (12) ŵ = 0.11 mm1
b = 19.976 (5) ÅT = 100 K
c = 6.3551 (13) Å0.20 × 0.15 × 0.10 mm
β = 104.69 (2)°
Data collection top
Oxford Xcalibur
diffractometer with Sapphire2 detector (large Be window)
1050 independent reflections
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2009)
693 reflections with I > 2σ(I)
Tmin = 0.978, Tmax = 0.989Rint = 0.063
3740 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0490 restraints
wR(F2) = 0.102H-atom parameters constrained
S = 0.94Δρmax = 0.27 e Å3
1050 reflectionsΔρmin = 0.17 e Å3
91 parameters
Special details top

Experimental. Elemental analysis (CHN) was performed on a Thermo Scientific Flash 2000 CHNO-S Analyzer. FT–IR spectra were recorded on a Thermo Nicolet Nexus 670 spectrometer equipped with a micro-ATR module (single reflection diamond ATR crystal) in the 400–4000 cm-1 range. The 1H, 13C and 15N NMR spectra of the DMSO-d6 or DMF-d7 solutions were collected at 300 K on a Varian 400 spectrometer at 400.00, 100.58 and 40.53 MHz, respectively. 1H and 13C spectra were calibrated using tetramethylsilane as a reference. The 15N NMR spectrum was measured relative to the DMF signals. Mass spectra (MS) were recorded on an LTQ Fleet (ThermoFisher Scientific) using the positive electrospray ionization (ESI+) and full scan mode in ca 10-5 M methanolic solutions.

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
N10.7585 (4)0.05060 (9)0.2910 (3)0.0185 (5)
H10.89290.02010.30280.022*
O10.7935 (3)0.04177 (8)0.6563 (2)0.0220 (4)
C20.6453 (5)0.07721 (12)0.0909 (4)0.0213 (6)
H20.71870.06160.02540.026*
N30.4440 (4)0.12250 (10)0.0454 (3)0.0215 (5)
C40.3504 (5)0.14308 (11)0.2234 (4)0.0181 (6)
C50.4583 (5)0.11720 (12)0.4322 (4)0.0173 (5)
C60.6780 (5)0.06798 (11)0.4763 (4)0.0170 (5)
N70.3190 (4)0.14745 (9)0.5707 (3)0.0193 (5)
H70.34750.13960.71080.023*
C80.1282 (5)0.19201 (12)0.4504 (4)0.0209 (6)
H80.00360.21970.50630.025*
C90.1421 (5)0.19112 (12)0.2378 (4)0.0212 (6)
H90.03270.21770.12240.025*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0138 (10)0.0211 (11)0.0202 (11)0.0040 (9)0.0032 (8)0.0018 (8)
O10.0185 (9)0.0274 (10)0.0198 (9)0.0045 (7)0.0045 (7)0.0037 (7)
C20.0183 (13)0.0257 (14)0.0196 (13)0.0007 (12)0.0040 (10)0.0015 (11)
N30.0168 (11)0.0234 (12)0.0237 (12)0.0006 (9)0.0039 (9)0.0004 (9)
C40.0128 (12)0.0188 (13)0.0228 (14)0.0042 (10)0.0046 (10)0.0013 (10)
C50.0135 (12)0.0179 (13)0.0209 (13)0.0034 (10)0.0054 (10)0.0006 (10)
C60.0145 (12)0.0173 (12)0.0197 (13)0.0050 (10)0.0052 (10)0.0014 (10)
N70.0161 (11)0.0213 (11)0.0202 (11)0.0010 (9)0.0042 (8)0.0012 (8)
C80.0113 (11)0.0176 (13)0.0330 (15)0.0001 (10)0.0045 (10)0.0004 (11)
C90.0122 (12)0.0207 (14)0.0278 (15)0.0013 (10)0.0001 (10)0.0037 (11)
Geometric parameters (Å, º) top
N1—C21.358 (3)C4—C91.410 (3)
N1—C61.375 (3)C5—N71.376 (3)
N1—H10.8800C5—C61.422 (3)
O1—C61.253 (3)N7—C81.367 (3)
C2—N31.306 (3)N7—H70.8800
C2—H20.9500C8—C91.370 (3)
N3—C41.383 (3)C8—H80.9500
C4—C51.396 (3)C9—H90.9500
C2—N1—C6124.7 (2)O1—C6—N1121.3 (2)
C2—N1—H1117.7O1—C6—C5127.3 (2)
C6—N1—H1117.7N1—C6—C5111.4 (2)
N3—C2—N1125.4 (2)C8—N7—C5107.34 (18)
N3—C2—H2117.3C8—N7—H7126.3
N1—C2—H2117.3C5—N7—H7126.3
C2—N3—C4113.9 (2)N7—C8—C9110.4 (2)
N3—C4—C5123.1 (2)N7—C8—H8124.8
N3—C4—C9130.0 (2)C9—C8—H8124.8
C5—C4—C9106.9 (2)C8—C9—C4106.7 (2)
N7—C5—C4108.7 (2)C8—C9—H9126.7
N7—C5—C6129.8 (2)C4—C9—H9126.7
C4—C5—C6121.6 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.881.922.799 (3)175
N7—H7···N3ii0.882.092.965 (3)176
C2—H2···O1iii0.952.183.106 (3)165
Symmetry codes: (i) x+2, y, z+1; (ii) x, y, z+1; (iii) x, y, z1.

Experimental details

Crystal data
Chemical formulaC6H5N3O
Mr135.13
Crystal system, space groupMonoclinic, P21/n
Temperature (K)100
a, b, c (Å)4.8315 (12), 19.976 (5), 6.3551 (13)
β (°) 104.69 (2)
V3)593.3 (2)
Z4
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.20 × 0.15 × 0.10
Data collection
DiffractometerOxford Xcalibur
diffractometer with Sapphire2 detector (large Be window)
Absorption correctionMulti-scan
(CrysAlis RED; Oxford Diffraction, 2009)
Tmin, Tmax0.978, 0.989
No. of measured, independent and
observed [I > 2σ(I)] reflections
3740, 1050, 693
Rint0.063
(sin θ/λ)max1)0.596
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.049, 0.102, 0.94
No. of reflections1050
No. of parameters91
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.27, 0.17

Computer programs: CrysAlis CCD (Oxford Diffraction, 2009), CrysAlis RED (Oxford Diffraction, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), Mercury (Macrae et al., 2008) and DIAMOND (Brandenburg, 2011), publCIF (Westrip, 2010) and PARST (Nardelli, 1995).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.881.922.799 (3)175
N7—H7···N3ii0.882.092.965 (3)176
C2—H2···O1iii0.952.183.106 (3)165
Symmetry codes: (i) x+2, y, z+1; (ii) x, y, z+1; (iii) x, y, z1.
Comparison of selected bond angles (°) in (I), hypoxanthine and 9-deazainosine monohydrate top
Bond(I)Hypoxanthine, monoclinicHypoxanthine, triclinic*9-Deazainosine monohydrate
C5—N7—C8107.34 (18)103.81 (11)103.7 (1), 104.8 (1)108.7 (2)
C8—N9/C9—C4106.7 (2)106.41 (11)107.0 (1), 106.6 (1)105.7 (2)
ReferenceThis work(a)(b)(c)
Note: (*) two crystallographically independent molecules within the unit cell. References: (a) Yang & Xie (2007); (b) Schmalle et al. (1988); (c) Otter et al. (1992).
 

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