Supra­molecular structures constructed by 3-(2-amino-6-chloro­pyrimidin-4-yl)-1,1-dimethyl­prop-2-yn-1-ol mono­hydrate and 3-[2-amino-6-(3-hy­droxy-3,3-dimethyl­prop-1-yn-1-yl)pyrimidin-4-yl]-1,1-dimethyl­prop-2-yn-1-ol

The mol­ecule of 3-(2-amino-6-chloropyrimidin-4-yl)-1,1-di­methyl­prop-2-yn-1-ol monohydrate, C₉H₁₀ClN₃O·H₂O, (I), shows a very polarized mol­ecular-electronic structure, while the polarization is slight for 3-[2-amino-6-(3-hy­droxy-3,3-dimethyl­prop-1-yn-1-yl)­pyrimidin-4-yl]-1,1-dimethylprop-2-yn-1-ol, C₁₄H₁₇N₃O₂, (II). In the supra­molecular structure of (I), a combination of hard N-H...N hydrogen bonds and soft C-H...N hydrogen bonds creates a mol­ecular column. Aromatic [pi]-[pi] stackings between the pyrimidine rings stabilize the column with perpendicular and centroid-centroid distances of 3.283 (3) and 3.588 (1) Å, respectively. Short Cl...Cl contacts further link neighbouring mol­ecular columns, creating a hydro­philic tube in which water mol­ecules are fixed by various hydrogen bonds. In the packing of (II), a one-dimensional mol­ecular chain is formed through several contacts involving hard N-H...O(N) and O-H...O(N) and soft C-H...O hydrogen bonds. Inter­chain O-H...O hydrogen bonds link the chains giving a two-dimensional stepped network. It is anti­cipated that study of the influence of hydrogen bonding on the patterns of base pairing and molecular packing in aminopyrimidine structures will shed significant light on nucleic acid structures as well as their functions.

S1. Comment

Aminopyrimidines have attracted considerable attention owing to their biological activities and molecular structures. In this group of compounds, 2-aminopyrimidines are of particular interest as adduct creators because of their potential ability to form stable hydrogen-bonded chains via their stereochemically associated amino groups and annular N atoms (Lynch et al., 2000; Lynch & Jones, 2004). In the crystal structures of 2-aminopyrimidine derivatives that have been reported, the majority are modified by functional groups such as alkyl (Muthiah et al., 2006), aryl (Fun et al., 2006; Gallagher et al., 2004), alkylamino (Lynch et al., 2004; Quesada, Marchal et al., 2002, 2004) and alkoxy (Glidewell et al., 2002; Quesada, Low et al., 2002). However, the acetylenyl moiety may be a good choice as the linker between 2-aminopyrimidine and some other hydrogen-bonding blocks since the low rotational barrier about the sp–sp² bond permits accessibility to favourable binding geometries. The crystal structures of the acetylenyl group bridged pyridine–aminopyrimidine compounds have been described using the pyridine moiety as additional hydrogen-bond acceptors (Aakeröy et al., 2005, 2007, 2009). Our goal is to design and synthesize acetylenyl linker bridged 2-aminopyrimidine derivatives with the OH group potentially acting as both hydrogen-bond acceptor and donor at the same time. Herein we report the crystal structures of two 2-aminopyrimidine compounds containing the acetylenyl and OH groups, namely, 2-amino-4-chloro-6-(3,3-dimethyl-3-hydroxyprop-1-yn-1-yl)-pyrimidine monohydrate, (I), and 2-amino-4,6-bis(3,3-dimethyl-3-hydroxyprop-1-yn-1-yl)-pyrimidine, (II).

Compound (I) crystallizes in space group P2/n as monoalkynyl-substitued aminopyrimidine monohydrate in the asymmetric unit (Fig. 1). The main molecule adopts a conformation in which the amino group, pyrimidine unit, Cl atom and triple bond are almost coplanar. The OH group is slightly twisted out of this plane with the O1—C7—C4—N2 torsion angle of -24.86 (21)°. The H atoms of the OH groups in the main molecule and water solvent are disordered over two sites with the occupation factor of the major conformer being 0.66 (3). In the major conformer, the OH group points to the O atom of the trans water molecule through the intermolecular O1—H1'A···O2 hydrogen bond (Table 1), while in the minor one, the water molecule reversely contects [connects?] with the pyrimidine OH segment via the O2—H2A···O1 hydrogen bond. Such an arrangement may result from the self-assembly in the supramolecular structrue in order to improve the packing efficiency. Compound (II), a dialkynyl-substituted derivative, crystallizes in space group P1 with only one molecule in the asymmetric unit (Fig. 2). Similarly to (I), both OH groups are twisted to the same side of the approximate plane defined by the amino group and pyrimidine ring, with O1—C7—C2—N1 and O2—C12—C4—N2 torsion angles of -57.66 (16) and 24.00 (14)°, respectively. Remarkably, two triple bonds deviate from the approximate plane with C2—C5—C6 and C4—C10—C11 angles of 169.57 (16) and 171.94 (17)°, [respectively?], which are smaller [compared with] those in (I) as well as in similar structrues (Singelenberg & van Eijck, 1987; Pollagi et al.,1994; Aakeröy et al., 2005, 2007, 2009). This bend meets the stereochemical demand for dimer formation in the supramolecular structure.

Some intramolecular bond distances in (I) and (II) are found to be unusual when compared with the typical values (Allen et al., 1987) for similar bond types. For (I), there is a clear distinction between the longer and the shorter C—N bonds of the pyrimidine ring (Table 3). The C1—N2, N3—C1 and C4—N2 bond distances are all short for their types. The extremely short C1—N2 bond [1.306 (3) Å] and N3—C1 bond [1.324 (3) Å] visualize [are] the consequence of the electronic delocalization influenced by the Cl atom. These observations confirm that the charge-separated form (Ia) is a dominant contributor to the overall molecular–electronic structure, as generally found for substituted 2-amino-5-nitropyrimidines (Quesada, Low et al., 2002; Quesada, Marchal et al., 2002; Quesada et al., 2004). By contrast, when the Cl atom is substituted, the distance distinction among the C—N bonds in (II) also exists but is not obvious. This suggests that the polarized form (IIa) is a minor contributor to the overall electronic structure. The triple bond lengths in (I) and (II) range from 1.193 (2) to 1.196 (4) Å and are in agreement with the values reported for similar structrues (Singelenberg & van Eijck, 1987; Pollagi et al.,1994; Aakeröy et al., 2005, 2007, 2009).

In the supramolecular structure of (I), a hydrogen-bonded infinite chain is firstly formed by a combination of intermolecular C9—H9A···N2 (x – 1, y, z) hydrogen bonds (Table 1), which locally creates a C(7) motif (Bernstein et al., 1995) at each link in the chain (Fig. 3). Two adjacent such chains run along the reverse orientation and then generate a molecular column through a pair of N—H···N hydrogen bonds between the amino groups and the pyrimidine N atoms, producing an eight-membered ring motif R₂²(8). In this motif, amino atoms N3 at (x, y, z) and (–x + 3, –y, –z + 1) act as hydrogen-bond donors, via atoms H3A, respectively, to ring atoms N1 at (–x + 3, –y, –z + 1) and (x, y, z). Additionally, π···π contacts (Tsuzuki et al., 2002) occur between the parallel C1/N1/C2/C3/C4/N2 pyrimidine rings at (x, y, z) (centroid Cg1) and (–x + 2, –y, –z + 1) (centroid Cg2). Their perpendicular and Cg1···Cg2 distances are 3.283 (3) and 3.588 (1) Å, respectively. The aromatic π-stacking force is an important factor in the stabilization of the one–dimensional molecular column. Finally, a triangular tube is formed by the intercolumn Cl···Cl short contacts (Fig. 4). The Cl···Cl distance [3.462 (1) Å] is some 0.04 Å shorter than the van der Waals separation based on a radius of 1.75 Å (Bondi, 1964), within the ranges discussed by Price et al. (1994) and Lommerse et al. (1996), and both C—Cl···Cl angles are 142.64 (9)°. This kind of arrangement results in the tube being more hydrophilic with the hydrophilic NH₂, OH groups, N atoms of pyrimidine rings and Cl atoms inboard. As a result, water molecules are sequentially fixed in this hydrophilic cavity by a combination of O—H···O, N—H···O and O—H···N hydrogen bonds (Table 1) between waters and these hydrophilic moieties, alternately creating R₄⁴(8) and R₄⁴(12) ring motifs which cross at O atoms of the filled water molecules (Fig. 4a).

In the packing of (II), a number of hard N—H···O(N), O—H···O(N) hydrogen bonds and soft C—H···O hydrogen bonds are also observed (Table 2). Firstly, a dimer is formed with the two pyrimidine rings in an adjacent parallel plane by N—H···N and N—H···O hydrogen bonds (Fig. 5). In this dimer, either [both?] amino group acts as a double hydrogen-bond donor, where the acceptors are the annular N atom and the hydroxy O atom. Amino atoms N3 at (x, y, z) and (–x + 1, –y + 1, –z + 1) act as hydrogen-bond donors, via atoms H3B, to ring atoms N2 at (–x + 1, –y + 1, –z + 1) and (x, y, z), so creating an R₂²(8) motif (Bernstein et al., 1995), and via atoms H3A, to hydroxy O2 atoms at (–x + 1, –y + 1, –z + 1) and (x, y, z), then producing an R₂²(18) motif including one R₂²(8) [as described above?] and two R₂²(9) motifs. Next, each dimer is linked to its neighbours to produce a one-dimensional molecular chain by a combination of interdimer N3—H3A···O1 (–x, –y + 2, –z), O1—H1···N1 (–x, –y + 2, –z) and C9—H9C···O2 (x – 1, y + 1, z – 1) hydrogen bonds, locally generating one R₂²(14) and two distinct R₂²(6) motifs. One R₂²(6) motif invovles two molecules, while the other invovles three molecules. Finally, the interchain O2—H2···O1 (–x + 1, –y + 1, –z) hydrogen bonds associate these chains into a two-dimensional stepping plane (Fig. 6).

Related literature

For related literature, see: Aakeröy et al. (2005, 2007, 2009); Allen et al. (1987); Bernstein et al. (1995); Bondi (1964); Fun et al. (2006); Gallagher et al. (2004); Glidewell et al. (2002); Lommerse et al. (1996); Lynch & Jones (2004); Lynch et al. (2000); Muthiah et al. (2006); Pollagi et al. (1994); Price et al. (1994); Quesada et al. (2004); Quesada, Low, Melguizo, Nogueras & Glidewell (2002); Quesada, Marchal, Melguizo, Nogueras, Sánchez, Low, Cannon, Farrell & Glidewell (2002); Singelenberg & van Eijck (1987); Tsuzuki et al. (2002).

S2. Experimental

2-Methylbut-3-yn-2-ol (0.293 ml, 3.00 mmol), Et₃N (1 ml) and CH₃CN (5 ml) were added to a nitrogen-purged flask containing 2-amino-4,6-dichloropyrimidine (0.164 g, 1.00 mmol), CuI (0.019 g, 0.10 mmol), 5% Pd/C (0.106 g, 0.05 mmol), PPh₃ (0.026 g, 0.10 mmol) and the mixture was stirred at 313 K for 6 h. The resulting mixture was cooled to room temperatrue and filtered. After removal of the solvent under reduced pressure, the residue was dissolved in EtOAc and washed with brine. The organic layer was dried over anhydrous MgSO₄. The solvent was evaporated in vacuo and the crude products were chromatographed on a silica gel column (EtOAc/petroleum ether = 3:2) to give (I) (water-free) as a white solid (yield 35%, R_F = 0.6, m.p. 431 K) and (II) as a white solid (yield 42%, R_F = 0.3, m.p. 460 K). ¹H NMR (300 MHz, DMSO-d₆) for (I) (water-free): δ 7.24 (s, 2H), 6.67 (s, 1H), 5.64 (s, 1H), 1.43 (s, 6H); for (II): δ 6.87 (s, 2H), 6.55 (s, 1H), 5.60 (s, 2H), 1.43 (s, 12H). Single crystals of (I) and (II) suitable for X-ray diffraction analysis were obtained by slow vapour diffusion of pentane into a solution of (I) (no water) in EtOAc at 298 K, and slow evaporation of a solution of (II) in EtOAc at 298 K.

S3. Refinement

In the absence of significant anomalous scattering effects, Friedel pairs were averaged. For (I), H atoms attached to C atoms were included in calculated positions and refined as riding [C—H = 0.98 Å and U_iso(H) = 1.5U_eq(C) (methyl); C—H = 0.95 Å and U_iso(H) = 1.2U_eq(C) (aromatic)]. H atoms attached to N atoms were initially refined with restrained distances to their hosts [N—H = 0.88 Å and U_iso(H) = 1.2U_eq(N)]. The H atoms of the hydrate molecule and the OH group were located in a difference map and subsequently refined with restraints of O—H = 0.85 Å and U_iso(H) = 1.2U_eq(O). The water molecule is rotationally disordered, in which one of the H atoms has full occupancy, while the other is disordered over two sites with refined site-occupation factors of 0.5. The H atom of the OH group is also disordered over two positions of equal occupancy. For (II), H atoms attached to C atoms were included in calculated positions and refined as riding [C—H = 0.96 Å and U_iso(H)=1.5U_eq(C) (methyl); C—H = 0.93 Å and U_iso(H) = 1.2U_eq(C) (aromatic)]. H atoms attached to N and O atoms were initially refined with restrained distances to their hosts [N—H = 0.86 Å and U_iso(H) = 1.2U_eq(N); O—H = 0.82 Å and U_iso(H) = 1.5U_eq(O)].

Computing details

For both compounds, data collection: SMART (Bruker, 1999); cell refinement: SMART (Bruker, 1999); data reduction: SAINT (Bruker, 1999); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures

	Fig. 1. The molecular structure of (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level for non-H atoms and H atoms are shown as small spheres of arbitrary radii. The disordered H atoms have been omitted for clarity. The dashed line represents a hydrogen bond between the main molecule and water.
	Fig. 2. The molecular structure of (II), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level for non-H atoms and H atoms are shown as small spheres of arbitrary radii.
	Fig. 3. The molecular column of (I), consisting of two hydrogen-bonded one-dimensional chains in the reverse orientation, showing the perpendicular distances between Cg1 and Cg2. The H atoms not involved in the motifs and water molecules have been omitted for clarity. Atoms marked with an asterisk (*), hash (#) and dollar ($) are at the symmetry positions (x + 1, y, z), (x - 1, y, z) and (-x + 3, -y, -z + 1), respectively.
	Fig. 4. (a) The hydrophilic tube of (I), viewed along the a axis. H atoms not involved in hydrogen bonding have been omitted for clarity. (b) Part of the hydrophilic tube, showing the R4^4(8) and R4^4(12) motifs; methyl groups and H atoms not involved in the hydrogen bonding have been omitted for clarity. Atoms marked with asterisks (*), hashes (#) and dollar ($) signs are at the symmetry positions (-x+3/2, y, -z+3/2), (-x+5/2, y, -z+3/2) and (x+1, y, z), respectively. Dashed lines represent hydrogen bonds and Cl···Cl contacts.
	Fig. 5. The hydrogen-bonded one-dimensional chain of (II), showing the supramolecular motifs; H atoms not involved have been omitted for clarity. Atoms marked with an asterisk (*), hash (#) and dollar ($) are at the symmetry positions (-x + 1, -y + 1, -z + 1), (-x, -y + 2, -z) and (x - 1, y + 1, z - 1), respectively.
	Fig. 6. The two-dimensional stepped network of (II), formed via O—H···O hydrogen bonds, with H atoms not involved omitted for clarity.

(I) 3-(2-amino-6-chloropyrimidin-4-yl)-1,1-dimethylprop-2-yn-1-ol monohydrate

Crystal data

C9H10ClN3O·H2O	F(000) = 480
Mr = 229.67	Dx = 1.363 Mg m^−3
Monoclinic, P2/n	Mo Kα radiation, λ = 0.71073 Å
a = 6.0021 (15) Å	Cell parameters from 2092 reflections
b = 11.003 (3) Å	θ = 2.2–27.4°
c = 16.960 (4) Å	µ = 0.33 mm^−1
β = 92.566 (4)°	T = 173 K
V = 1119.0 (5) Å^3	Block, colourless
Z = 4	0.40 × 0.16 × 0.12 mm

Data collection

Bruker SMART CCD area-detector diffractometer	1988 independent reflections
Radiation source: fine-focus sealed tube	1767 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.030
ϕ and ω scans	θmax = 25.1°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Bruker, 1999)	h = −7→6
Tmin = 0.881, Tmax = 0.962	k = −11→13
5489 measured reflections	l = −19→20

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.052	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.115	H-atom parameters constrained
S = 1.21	w = 1/[s^2(Fo^2) + (0.040P)^2 + 0.7037P] where P = (Fo^2 + 2Fc^2)/3
1988 reflections	(Δ/σ)max < 0.001
139 parameters	Δρmax = 0.27 e Å^−3
0 restraints	Δρmin = −0.28 e Å^−3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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 (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
C1	1.2361 (4)	0.1139 (2)	0.55133 (14)	0.0219 (5)
C2	1.0747 (4)	0.1294 (2)	0.42912 (14)	0.0241 (6)
C3	0.9068 (4)	0.2030 (2)	0.45481 (14)	0.0256 (6)
H3	0.7906	0.2331	0.4203	0.031*
C4	0.9200 (4)	0.2299 (2)	0.53445 (14)	0.0221 (5)
C5	0.7662 (4)	0.3131 (2)	0.56846 (14)	0.0233 (5)
C6	0.6515 (4)	0.3880 (2)	0.59771 (14)	0.0216 (5)
C7	0.5210 (4)	0.4801 (2)	0.63971 (13)	0.0202 (5)
C8	0.6238 (5)	0.6055 (2)	0.62907 (17)	0.0317 (6)
H8A	0.5459	0.6649	0.6608	0.048*
H8B	0.6098	0.6288	0.5733	0.048*
H8C	0.7819	0.6032	0.6462	0.048*
C9	0.2774 (4)	0.4778 (2)	0.61274 (15)	0.0282 (6)
H9A	0.2158	0.3968	0.6219	0.042*
H9B	0.2630	0.4970	0.5563	0.042*
H9C	0.1955	0.5382	0.6425	0.042*
Cl1	1.07907 (13)	0.09441 (6)	0.32955 (4)	0.0362 (2)
N1	1.2382 (3)	0.08482 (18)	0.47357 (11)	0.0241 (5)
N2	1.0805 (3)	0.18474 (18)	0.58374 (11)	0.0219 (5)
N3	1.3968 (4)	0.0691 (2)	0.59888 (12)	0.0297 (5)
H3A	1.5041	0.0264	0.5793	0.036*
H3B	1.4138	0.0959	0.6475	0.036*
O1	0.5352 (3)	0.45132 (16)	0.72198 (9)	0.0271 (4)
O2	0.5163 (3)	0.20125 (16)	0.74861 (9)	0.0293 (4)
H2'B	0.4736	0.1941	0.7956	0.035*
H1'A	0.5136	0.3760	0.7289	0.035*	0.50
H2'A	0.6550	0.1901	0.7443	0.035*	0.50
H2A	0.4733	0.2733	0.7395	0.035*	0.50
H1A	0.6667	0.4656	0.7403	0.035*	0.50

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0209 (13)	0.0171 (12)	0.0279 (13)	−0.0006 (10)	0.0048 (10)	−0.0014 (10)
C2	0.0286 (14)	0.0214 (13)	0.0227 (12)	−0.0029 (11)	0.0058 (10)	−0.0013 (10)
C3	0.0258 (14)	0.0254 (14)	0.0256 (12)	0.0049 (11)	0.0012 (10)	0.0001 (11)
C4	0.0204 (13)	0.0185 (12)	0.0279 (13)	−0.0004 (10)	0.0054 (10)	0.0009 (10)
C5	0.0217 (13)	0.0251 (13)	0.0232 (12)	0.0019 (11)	0.0005 (10)	0.0022 (11)
C6	0.0188 (13)	0.0230 (13)	0.0230 (12)	0.0012 (11)	−0.0002 (10)	0.0023 (10)
C7	0.0197 (13)	0.0202 (12)	0.0209 (12)	0.0029 (10)	0.0025 (10)	0.0009 (10)
C8	0.0278 (15)	0.0250 (14)	0.0424 (16)	0.0007 (11)	0.0034 (12)	0.0000 (12)
C9	0.0198 (13)	0.0306 (14)	0.0342 (14)	0.0028 (11)	0.0011 (11)	0.0023 (11)
Cl1	0.0470 (5)	0.0399 (4)	0.0222 (3)	0.0034 (3)	0.0059 (3)	−0.0054 (3)
N1	0.0247 (12)	0.0230 (11)	0.0252 (11)	−0.0003 (9)	0.0061 (9)	−0.0024 (9)
N2	0.0214 (11)	0.0211 (11)	0.0234 (10)	0.0029 (9)	0.0041 (8)	−0.0015 (8)
N3	0.0267 (13)	0.0327 (13)	0.0295 (11)	0.0100 (10)	−0.0009 (9)	−0.0079 (10)
O1	0.0297 (10)	0.0298 (10)	0.0218 (9)	0.0025 (8)	0.0019 (7)	−0.0001 (7)
O2	0.0271 (10)	0.0365 (11)	0.0246 (9)	−0.0014 (8)	0.0033 (7)	0.0006 (8)

Geometric parameters (Å, º)

C1—N3	1.325 (3)	C7—C8	1.525 (3)
C1—N2	1.352 (3)	C8—H8A	0.9800
C1—N1	1.358 (3)	C8—H8B	0.9800
C2—N1	1.306 (3)	C8—H8C	0.9800
C2—C3	1.378 (4)	C9—H9A	0.9800
C2—Cl1	1.734 (2)	C9—H9B	0.9800
C3—C4	1.381 (3)	C9—H9C	0.9800
C3—H3	0.9500	N3—H3A	0.8752
C4—N2	1.342 (3)	N3—H3B	0.8764
C4—C5	1.439 (3)	O1—H1'A	0.8479
C5—C6	1.196 (3)	O1—H1A	0.8500
C6—C7	1.482 (3)	O2—H2'B	0.8519
C7—O1	1.430 (3)	O2—H2'A	0.8479
C7—C9	1.513 (3)	O2—H2A	0.8462
N3—C1—N2	117.7 (2)	H8A—C8—H8B	109.5
N3—C1—N1	117.7 (2)	C7—C8—H8C	109.5
N2—C1—N1	124.6 (2)	H8A—C8—H8C	109.5
N1—C2—C3	125.4 (2)	H8B—C8—H8C	109.5
N1—C2—Cl1	115.79 (19)	C7—C9—H9A	109.5
C3—C2—Cl1	118.8 (2)	C7—C9—H9B	109.5
C2—C3—C4	115.1 (2)	H9A—C9—H9B	109.5
C2—C3—H3	122.5	C7—C9—H9C	109.5
C4—C3—H3	122.5	H9A—C9—H9C	109.5
N2—C4—C3	122.6 (2)	H9B—C9—H9C	109.5
N2—C4—C5	116.2 (2)	C2—N1—C1	115.6 (2)
C3—C4—C5	121.2 (2)	C4—N2—C1	116.7 (2)
C6—C5—C4	175.1 (3)	C1—N3—H3A	119.8
C5—C6—C7	175.4 (3)	C1—N3—H3B	119.9
O1—C7—C6	107.95 (19)	H3A—N3—H3B	118.7
O1—C7—C9	107.81 (19)	C7—O1—H1'A	110.4
C6—C7—C9	111.6 (2)	C7—O1—H1A	109.2
O1—C7—C8	108.0 (2)	H1'A—O1—H1A	106.0
C6—C7—C8	109.6 (2)	H2'B—O2—H2'A	113.9
C9—C7—C8	111.7 (2)	H2'B—O2—H2A	99.0
C7—C8—H8A	109.5	H2'A—O2—H2A	114.4
C7—C8—H8B	109.5
N1—C2—C3—C4	0.3 (4)	C5—C6—C7—C8	87 (3)
Cl1—C2—C3—C4	−177.84 (18)	C3—C2—N1—C1	0.8 (4)
C2—C3—C4—N2	−1.9 (4)	Cl1—C2—N1—C1	179.03 (17)
C2—C3—C4—C5	175.2 (2)	N3—C1—N1—C2	179.0 (2)
N2—C4—C5—C6	65 (3)	N2—C1—N1—C2	−0.5 (3)
C3—C4—C5—C6	−112 (3)	C3—C4—N2—C1	2.2 (3)
C4—C5—C6—C7	−59 (5)	C5—C4—N2—C1	−175.0 (2)
C5—C6—C7—O1	−30 (3)	N3—C1—N2—C4	179.6 (2)
C5—C6—C7—C9	−148 (3)	N1—C1—N2—C4	−0.9 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···O1^i	0.85	1.88	2.708 (4)	164
O1—H1′A···O2	0.85	1.95	2.791 (3)	171
O2—H2A···O1	0.85	2.02	2.791 (3)	152
O2—H2′A···O2^i	0.85	1.97	2.803 (4)	165
O2—H2′B···N2^i	0.85	2.09	2.933 (3)	171
C9—H9A···N2^ii	0.98	2.55	3.462 (3)	156
N3—H3A···N1^iii	0.88	2.19	3.069 (3)	177
N3—H3B···O2^iv	0.88	2.14	2.986 (3)	163

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

(II) 3-[2-amino-6-(3-hydroxy-3,3-dimethylprop-1-yn-1-yl)pyrimidin-4-yl]-1,1- dimethylprop-2-yn-1-ol

Crystal data

C14H17N3O2	Z = 2
Mr = 259.31	F(000) = 276
Triclinic, P1	Dx = 1.198 Mg m^−3
a = 7.9966 (17) Å	Mo Kα radiation, λ = 0.71073 Å
b = 9.737 (2) Å	Cell parameters from 1820 reflections
c = 9.833 (2) Å	θ = 2.2–27.9°
α = 78.976 (3)°	µ = 0.08 mm^−1
β = 86.217 (3)°	T = 173 K
γ = 73.104 (3)°	Block, colourless
V = 719.0 (3) Å^3	0.38 × 0.32 × 0.19 mm

Data collection

Bruker SMART CCD area-detector diffractometer	2644 independent reflections
Radiation source: fine-focus sealed tube	2316 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.016
ϕ and ω scans	θmax = 25.6°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 1999)	h = −7→9
Tmin = 0.969, Tmax = 0.985	k = −11→11
3832 measured reflections	l = −11→10

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.045	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.112	H-atom parameters constrained
S = 1.02	w = 1/[s^2(Fo^2) + (0.057P)^2 + 0.1916P] where P = (Fo^2 + 2Fc^2)/3
2644 reflections	(Δ/σ)max < 0.001
178 parameters	Δρmax = 0.16 e Å^−3
0 restraints	Δρmin = −0.23 e Å^−3

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 (Ų)

	x	y	z	Uiso*/Ueq
C1	0.34240 (19)	0.66320 (16)	0.32687 (15)	0.0248 (3)
C2	0.34401 (19)	0.75848 (16)	0.09525 (15)	0.0246 (3)
C3	0.50003 (19)	0.65441 (16)	0.07843 (15)	0.0264 (3)
H3	0.5511	0.6468	−0.0086	0.032*
C4	0.57674 (19)	0.56205 (15)	0.19699 (15)	0.0243 (3)
C5	0.2707 (2)	0.86548 (16)	−0.02401 (15)	0.0270 (3)
C6	0.23337 (19)	0.94368 (16)	−0.13373 (15)	0.0270 (3)
C7	0.1960 (2)	1.03140 (16)	−0.27470 (15)	0.0272 (3)
C8	0.2097 (3)	1.18504 (19)	−0.28019 (19)	0.0443 (5)
H8A	0.1894	1.2388	−0.3731	0.066*
H8B	0.3244	1.1799	−0.2522	0.066*
H8C	0.1240	1.2333	−0.2188	0.066*
C9	0.3231 (2)	0.9527 (2)	−0.37571 (17)	0.0405 (4)
H9A	0.3109	0.8565	−0.3699	0.061*
H9B	0.4405	0.9457	−0.3527	0.061*
H9C	0.2981	1.0062	−0.4682	0.061*
C10	0.7498 (2)	0.46297 (16)	0.19517 (15)	0.0276 (4)
C11	0.8969 (2)	0.38734 (16)	0.20745 (15)	0.0270 (4)
C12	1.0798 (2)	0.29629 (16)	0.23353 (16)	0.0270 (3)
C13	1.1890 (2)	0.39394 (19)	0.2572 (2)	0.0394 (4)
H13A	1.1429	0.4395	0.3354	0.059*
H13B	1.1854	0.4677	0.1763	0.059*
H13C	1.3078	0.3363	0.2748	0.059*
C14	1.1506 (2)	0.21818 (18)	0.11305 (18)	0.0343 (4)
H14A	1.2697	0.1614	0.1306	0.051*
H14B	1.1455	0.2888	0.0295	0.051*
H14C	1.0815	0.1551	0.1029	0.051*
N1	0.26248 (16)	0.76481 (13)	0.21849 (12)	0.0261 (3)
N2	0.49961 (16)	0.56418 (13)	0.32144 (12)	0.0256 (3)
N3	0.26122 (18)	0.65977 (14)	0.44984 (13)	0.0330 (3)
H3A	0.1631	0.7245	0.4595	0.040*
H3B	0.3173	0.5997	0.5208	0.040*
O1	0.02489 (13)	1.03693 (11)	−0.31459 (11)	0.0275 (3)
H1	−0.0486	1.0899	−0.2708	0.041*
O2	1.08389 (16)	0.19577 (12)	0.36028 (11)	0.0341 (3)
H2	1.0464	0.1294	0.3475	0.051*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0262 (8)	0.0242 (7)	0.0229 (8)	−0.0058 (6)	−0.0007 (6)	−0.0036 (6)
C2	0.0262 (8)	0.0259 (8)	0.0223 (7)	−0.0092 (6)	−0.0020 (6)	−0.0022 (6)
C3	0.0268 (8)	0.0294 (8)	0.0222 (8)	−0.0075 (6)	0.0033 (6)	−0.0050 (6)
C4	0.0251 (8)	0.0226 (7)	0.0252 (8)	−0.0071 (6)	−0.0002 (6)	−0.0042 (6)
C5	0.0253 (8)	0.0284 (8)	0.0254 (8)	−0.0052 (6)	0.0002 (6)	−0.0043 (6)
C6	0.0256 (8)	0.0268 (8)	0.0269 (8)	−0.0055 (6)	0.0007 (6)	−0.0043 (6)
C7	0.0258 (8)	0.0296 (8)	0.0240 (8)	−0.0073 (6)	−0.0022 (6)	0.0000 (6)
C8	0.0565 (12)	0.0369 (10)	0.0415 (10)	−0.0224 (9)	−0.0144 (9)	0.0071 (8)
C9	0.0295 (9)	0.0554 (11)	0.0279 (9)	−0.0033 (8)	0.0011 (7)	−0.0004 (8)
C10	0.0304 (9)	0.0275 (8)	0.0229 (8)	−0.0069 (7)	0.0019 (6)	−0.0023 (6)
C11	0.0311 (9)	0.0259 (8)	0.0221 (8)	−0.0075 (7)	0.0024 (6)	−0.0019 (6)
C12	0.0257 (8)	0.0242 (8)	0.0278 (8)	−0.0040 (6)	−0.0005 (6)	−0.0013 (6)
C13	0.0361 (10)	0.0360 (9)	0.0481 (11)	−0.0128 (8)	−0.0026 (8)	−0.0081 (8)
C14	0.0288 (9)	0.0342 (9)	0.0389 (9)	−0.0072 (7)	0.0063 (7)	−0.0093 (7)
N1	0.0265 (7)	0.0255 (6)	0.0230 (7)	−0.0037 (5)	−0.0008 (5)	−0.0022 (5)
N2	0.0264 (7)	0.0248 (6)	0.0231 (7)	−0.0044 (5)	0.0009 (5)	−0.0029 (5)
N3	0.0321 (8)	0.0352 (7)	0.0219 (7)	0.0033 (6)	0.0013 (6)	−0.0018 (5)
O1	0.0255 (6)	0.0277 (6)	0.0268 (6)	−0.0027 (4)	−0.0017 (4)	−0.0054 (4)
O2	0.0418 (7)	0.0290 (6)	0.0298 (6)	−0.0093 (5)	−0.0087 (5)	0.0004 (5)

Geometric parameters (Å, º)

C1—N3	1.333 (2)	C9—H9A	0.9600
C1—N2	1.3487 (19)	C9—H9B	0.9600
C1—N1	1.3573 (19)	C9—H9C	0.9600
C2—N1	1.3410 (19)	C10—C11	1.193 (2)
C2—C3	1.383 (2)	C11—C12	1.483 (2)
C2—C5	1.440 (2)	C12—O2	1.4257 (18)
C3—C4	1.385 (2)	C12—C14	1.519 (2)
C3—H3	0.9300	C12—C13	1.522 (2)
C4—N2	1.3346 (19)	C13—H13A	0.9600
C4—C10	1.440 (2)	C13—H13B	0.9600
C5—C6	1.196 (2)	C13—H13C	0.9600
C6—C7	1.481 (2)	C14—H14A	0.9600
C7—O1	1.4312 (18)	C14—H14B	0.9600
C7—C9	1.520 (2)	C14—H14C	0.9600
C7—C8	1.522 (2)	N3—H3A	0.8648
C8—H8A	0.9600	N3—H3B	0.8733
C8—H8B	0.9600	O1—H1	0.8200
C8—H8C	0.9600	O2—H2	0.8200
N3—C1—N2	116.37 (13)	H9A—C9—H9C	109.5
N3—C1—N1	118.26 (13)	H9B—C9—H9C	109.5
N2—C1—N1	125.37 (13)	C11—C10—C4	171.94 (17)
N1—C2—C3	122.33 (13)	C10—C11—C12	175.54 (16)
N1—C2—C5	119.54 (13)	O2—C12—C11	108.54 (12)
C3—C2—C5	118.11 (13)	O2—C12—C14	111.61 (12)
C2—C3—C4	116.98 (13)	C11—C12—C14	110.48 (13)
C2—C3—H3	121.5	O2—C12—C13	105.95 (13)
C4—C3—H3	121.5	C11—C12—C13	108.54 (13)
N2—C4—C3	122.43 (14)	C14—C12—C13	111.55 (13)
N2—C4—C10	115.51 (13)	C12—C13—H13A	109.5
C3—C4—C10	121.97 (13)	C12—C13—H13B	109.5
C6—C5—C2	169.57 (16)	H13A—C13—H13B	109.5
C5—C6—C7	175.59 (16)	C12—C13—H13C	109.5
O1—C7—C6	109.55 (12)	H13A—C13—H13C	109.5
O1—C7—C9	106.30 (13)	H13B—C13—H13C	109.5
C6—C7—C9	108.24 (13)	C12—C14—H14A	109.5
O1—C7—C8	110.21 (13)	C12—C14—H14B	109.5
C6—C7—C8	110.85 (13)	H14A—C14—H14B	109.5
C9—C7—C8	111.56 (14)	C12—C14—H14C	109.5
C7—C8—H8A	109.5	H14A—C14—H14C	109.5
C7—C8—H8B	109.5	H14B—C14—H14C	109.5
H8A—C8—H8B	109.5	C2—N1—C1	116.12 (13)
C7—C8—H8C	109.5	C4—N2—C1	116.47 (12)
H8A—C8—H8C	109.5	C1—N3—H3A	119.7
H8B—C8—H8C	109.5	C1—N3—H3B	117.8
C7—C9—H9A	109.5	H3A—N3—H3B	121.9
C7—C9—H9B	109.5	C7—O1—H1	109.5
H9A—C9—H9B	109.5	C12—O2—H2	109.5
C7—C9—H9C	109.5
N1—C2—C3—C4	−4.6 (2)	C4—C10—C11—C12	14 (3)
C5—C2—C3—C4	173.66 (14)	C10—C11—C12—O2	55 (2)
C2—C3—C4—N2	4.9 (2)	C10—C11—C12—C14	178 (2)
C2—C3—C4—C10	−171.43 (14)	C10—C11—C12—C13	−60 (2)
N1—C2—C5—C6	175.6 (8)	C3—C2—N1—C1	0.3 (2)
C3—C2—C5—C6	−2.7 (10)	C5—C2—N1—C1	−177.91 (13)
C2—C5—C6—C7	24 (3)	N3—C1—N1—C2	−176.14 (13)
C5—C6—C7—O1	105 (2)	N2—C1—N1—C2	4.2 (2)
C5—C6—C7—C9	−11 (2)	C3—C4—N2—C1	−0.9 (2)
C5—C6—C7—C8	−133 (2)	C10—C4—N2—C1	175.66 (13)
N2—C4—C10—C11	−44.9 (12)	N3—C1—N2—C4	176.42 (13)
C3—C4—C10—C11	131.7 (11)	N1—C1—N2—C4	−3.9 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3B···N2^i	0.87	2.26	3.1207 (18)	170
N3—H3A···O2^i	0.86	2.61	3.3390 (19)	143
N3—H3A···O1^ii	0.86	2.58	3.2705 (17)	137
O1—H1···N1^ii	0.82	1.99	2.7808 (16)	163
C9—H9C···O2^iii	0.96	2.56	3.4167 (18)	149
O2—H2···O1^iv	0.82	1.95	2.7710 (16)	176

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