The molecule of 3-(2-amino-6-chloropyrimidin-4-yl)-1,1-dimethylprop-2-yn-1-ol monohydrate, C
9H
10ClN
3O·H
2O, (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, C
14H
17N
3O
2, (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
-
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.
Supporting information
CCDC references: 838159; 838160
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%, RF = 0.6,
m.p. 431 K) and (II) as a white solid (yield 42%, RF = 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.
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 Uiso(H) =
1.5Ueq(C) (methyl); C—H = 0.95 Å and Uiso(H) =
1.2Ueq(C) (aromatic)]. H atoms attached to N atoms were initially
refined with restrained distances to their hosts [N—H = 0.88 Å and
Uiso(H) = 1.2Ueq(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 Uiso(H) = 1.2Ueq(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 Uiso(H)=1.5Ueq(C) (methyl); C—H = 0.93 Å and
Uiso(H) = 1.2Ueq(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 Uiso(H) = 1.2Ueq(N); O—H = 0.82 Å and
Uiso(H) = 1.5Ueq(O)].
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).
(I) 3-(2-amino-6-chloropyrimidin-4-yl)-1,1-dimethylprop-2-yn-1-ol monohydrate
top
Crystal data top
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) Å3 | Block, colourless |
Z = 4 | 0.40 × 0.16 × 0.12 mm |
Data collection top
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 top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.052 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.115 | H-atom parameters constrained |
S = 1.21 | w = 1/[s2(Fo2) + (0.040P)2 + 0.7037P] where P = (Fo2 + 2Fc2)/3 |
1988 reflections | (Δ/σ)max < 0.001 |
139 parameters | Δρmax = 0.27 e Å−3 |
0 restraints | Δρmin = −0.28 e Å−3 |
Crystal data top
C9H10ClN3O·H2O | V = 1119.0 (5) Å3 |
Mr = 229.67 | Z = 4 |
Monoclinic, P2/n | Mo Kα radiation |
a = 6.0021 (15) Å | µ = 0.33 mm−1 |
b = 11.003 (3) Å | T = 173 K |
c = 16.960 (4) Å | 0.40 × 0.16 × 0.12 mm |
β = 92.566 (4)° | |
Data collection top
Bruker SMART CCD area-detector diffractometer | 1988 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 1999) | 1767 reflections with I > 2σ(I) |
Tmin = 0.881, Tmax = 0.962 | Rint = 0.030 |
5489 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.052 | 0 restraints |
wR(F2) = 0.115 | H-atom parameters constrained |
S = 1.21 | Δρmax = 0.27 e Å−3 |
1988 reflections | Δρmin = −0.28 e Å−3 |
139 parameters | |
Special details top
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 (Å2) top | 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 (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
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) top
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) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1A···O1i | 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···O2i | 0.85 | 1.97 | 2.803 (4) | 165 |
O2—H2′B···N2i | 0.85 | 2.09 | 2.933 (3) | 171 |
C9—H9A···N2ii | 0.98 | 2.55 | 3.462 (3) | 156 |
N3—H3A···N1iii | 0.88 | 2.19 | 3.069 (3) | 177 |
N3—H3B···O2iv | 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
top
Crystal data top
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) Å3 | 0.38 × 0.32 × 0.19 mm |
Data collection top
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 top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.045 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.112 | H-atom parameters constrained |
S = 1.02 | w = 1/[s2(Fo2) + (0.057P)2 + 0.1916P] where P = (Fo2 + 2Fc2)/3 |
2644 reflections | (Δ/σ)max < 0.001 |
178 parameters | Δρmax = 0.16 e Å−3 |
0 restraints | Δρmin = −0.23 e Å−3 |
Crystal data top
C14H17N3O2 | γ = 73.104 (3)° |
Mr = 259.31 | V = 719.0 (3) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.9966 (17) Å | Mo Kα radiation |
b = 9.737 (2) Å | µ = 0.08 mm−1 |
c = 9.833 (2) Å | T = 173 K |
α = 78.976 (3)° | 0.38 × 0.32 × 0.19 mm |
β = 86.217 (3)° | |
Data collection top
Bruker SMART CCD area-detector diffractometer | 2644 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 1999) | 2316 reflections with I > 2σ(I) |
Tmin = 0.969, Tmax = 0.985 | Rint = 0.016 |
3832 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.045 | 0 restraints |
wR(F2) = 0.112 | H-atom parameters constrained |
S = 1.02 | Δρmax = 0.16 e Å−3 |
2644 reflections | Δρmin = −0.23 e Å−3 |
178 parameters | |
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 | 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 (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
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) top
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) top
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3B···N2i | 0.87 | 2.26 | 3.1207 (18) | 170 |
N3—H3A···O2i | 0.86 | 2.61 | 3.3390 (19) | 143 |
N3—H3A···O1ii | 0.86 | 2.58 | 3.2705 (17) | 137 |
O1—H1···N1ii | 0.82 | 1.99 | 2.7808 (16) | 163 |
C9—H9C···O2iii | 0.96 | 2.56 | 3.4167 (18) | 149 |
O2—H2···O1iv | 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. |
Experimental details
| (I) | (II) |
Crystal data |
Chemical formula | C9H10ClN3O·H2O | C14H17N3O2 |
Mr | 229.67 | 259.31 |
Crystal system, space group | Monoclinic, P2/n | Triclinic, P1 |
Temperature (K) | 173 | 173 |
a, b, c (Å) | 6.0021 (15), 11.003 (3), 16.960 (4) | 7.9966 (17), 9.737 (2), 9.833 (2) |
α, β, γ (°) | 90, 92.566 (4), 90 | 78.976 (3), 86.217 (3), 73.104 (3) |
V (Å3) | 1119.0 (5) | 719.0 (3) |
Z | 4 | 2 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.33 | 0.08 |
Crystal size (mm) | 0.40 × 0.16 × 0.12 | 0.38 × 0.32 × 0.19 |
|
Data collection |
Diffractometer | Bruker SMART CCD area-detector diffractometer | Bruker SMART CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 1999) | Multi-scan (SADABS; Bruker, 1999) |
Tmin, Tmax | 0.881, 0.962 | 0.969, 0.985 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5489, 1988, 1767 | 3832, 2644, 2316 |
Rint | 0.030 | 0.016 |
(sin θ/λ)max (Å−1) | 0.597 | 0.608 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.052, 0.115, 1.21 | 0.045, 0.112, 1.02 |
No. of reflections | 1988 | 2644 |
No. of parameters | 139 | 178 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.27, −0.28 | 0.16, −0.23 |
Hydrogen-bond geometry (Å, º) for (I) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1A···O1i | 0.85 | 1.88 | 2.708 (4) | 164.4 |
O1—H1'A···O2 | 0.85 | 1.95 | 2.791 (3) | 170.6 |
O2—H2A···O1 | 0.85 | 2.02 | 2.791 (3) | 151.6 |
O2—H2'A···O2i | 0.85 | 1.97 | 2.803 (4) | 165.4 |
O2—H2'B···N2i | 0.85 | 2.09 | 2.933 (3) | 171.0 |
C9—H9A···N2ii | 0.98 | 2.55 | 3.462 (3) | 155.7 |
N3—H3A···N1iii | 0.88 | 2.19 | 3.069 (3) | 177.3 |
N3—H3B···O2iv | 0.88 | 2.14 | 2.986 (3) | 162.5 |
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. |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3B···N2i | 0.87 | 2.26 | 3.1207 (18) | 170.3 |
N3—H3A···O2i | 0.86 | 2.61 | 3.3390 (19) | 142.5 |
N3—H3A···O1ii | 0.86 | 2.58 | 3.2705 (17) | 137.2 |
O1—H1···N1ii | 0.82 | 1.99 | 2.7808 (16) | 162.9 |
C9—H9C···O2iii | 0.96 | 2.56 | 3.4167 (18) | 149.2 |
O2—H2···O1iv | 0.82 | 1.95 | 2.7710 (16) | 175.7 |
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. |
Selected bond lengths (Å) for (I) and (II). top | (I) | (II) |
N1–C2 | 1.306 (3) | 1.3410 (19) |
N2–C1 | 1.352 (3) | 1.3487 (19) |
N3–C1 | 1.325 (3) | 1.333 (2) |
C1–N1 | 1.358 (3) | 1.3573 (19) |
C2–C3 | 1.378 (4) | 1.383 (2) |
C3–C4 | 1.381 (3) | 1.385 (2) |
C4–N2 | 1.342 (3) | 1.3346 (19) |
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).