Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270102005632/sk1546sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270102005632/sk1546Isup2.hkl | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270102005632/sk1546IIsup3.hkl | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270102005632/sk1546IIIsup4.hkl |
CCDC references: 187936; 187937; 187938
A sample of (I) was purchased from Aldrich. For the synthesis of (II), (I) (19.3 mmol) was added to a stirred solution of sodium benzylate (96 mmol) in toluene (100 ml). The resulting mixture was heated under reflux, with stirring, for 60 h. Diethyl ether (30 ml) and toluene (15 ml) were then added and the mixture was filtered through silica gel. The silica gel was washed with toluene (3 × 40 ml) and diethyl ether (3 × 40 ml), and the filtrate and the washings were pooled together. After removal of the solvent, the oily residue was dissolved in a hexane-ethyl ether mixture (60:40 v/v) and cooled. The product, (II), precipitated at 253 K and was collected by filtration, washed with hexane and dried in vacuo (yield 70%, m.p. 355 K). Analysis, found: C 75.2, H 5.8, N 10.6%; C25H23N3O2 requires: C 75.5, H 5.8, N 10.6%. Spectroscopic analysis: 1H NMR (DMSO-d6, δ, p.p.m.): 4.46 (d, 2H, N—CH2, J = 6.02 Hz), 5.27 (s, 4H, O—CH2), 5.45 (s, 1H, C5—H), 7.29 (m, 15H, Ph), 7.75 (t, H, NH, J = 6.59 Hz, exchanges with D2O); 13C NMR (δ, p.p.m): 44.1, 66.7, 78.1, 126.4, 128,2, 136.8, 140.4, 161.2, 170.8. For the synthesis of (III), pyrrolidine (21.3 mmol) and triethylamine (18.3 mmol) were added to a stirred solution of 2-amino-4,6-dichloropyrimidine (Aldrich; 6.1 mmol) in n-butyl alcohol (40 ml). The resulting mixture was heated under reflux, with stirring, for 56 h. After filtration and removal of the solvent, hot ethyl acetate (100 ml) was added, and the product, (III), was filtered off (yield 68%, m.p. 497 K). Analysis, found: C 61.7, H 7.9, N 29.9%; C12H19N5 requires: C 61.8, H 8.2, N 30.0%. Spectroscopic analysis: 1H NMR (DMSO-d6, δ, p.p.m.): 1.85 (m, 8H, CH2), 3.27 (m, 8H, N—CH2, partially obscured by solvent DMSO-d6), 5.31 (s, 2H, NH2, exchanges with D2O); 13C NMR (δ, p.p.m.): 24.6, 45.7, 73.2, 161.3, 161.6. Crystals of (I), (II) and (III) suitable for single-crystal X-ray diffraction were grown by slow evaporation of solutions in acetone, methanol and dichloromethane-ethyl acetate (1:1 v/v), respectively.
Compounds (I) and (III) are monoclinic and the systematic absences permitted space groups C2/c and Cc. For each, C2/c was chosen and confirmed by the analysis. Compound (II) is triclinic; space group P1 was selected, and confirmed by the analysis. H atoms were treated as riding, with C—H = 0.95–0.98 Å and N—H 0.88 Å.
Data collection: KappaCCD Server Software (Nonius, 1997) for (I), (III); SMART (Bruker, 1997) for (II). Cell refinement: DENZO-SMN (Otwinowski & Minor, 1997) for (I), (III); SMART for (II). Data reduction: DENZO-SMN (Otwinowski & Minor, 1997) for (I); SHELXTL (Bruker, 1997) for (II); DENZO-SMN for (III). For all compounds, program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2002); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).
C6H9N3O2 | F(000) = 656 |
Mr = 155.16 | Dx = 1.429 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 1642 reflections |
a = 12.3971 (5) Å | θ = 2.9–27.4° |
b = 8.3608 (5) Å | µ = 0.11 mm−1 |
c = 14.5237 (7) Å | T = 120 K |
β = 106.585 (3)° | Block, colourless |
V = 1442.75 (13) Å3 | 0.20 × 0.15 × 0.05 mm |
Z = 8 |
Nonius KappaCCD area-detector diffractometer | 1642 independent reflections |
Radiation source: fine-focus sealed X-ray tube | 1090 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.066 |
ϕ scans, and ω scans with κ offsets | θmax = 27.4°, θmin = 2.9° |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | h = −16→14 |
Tmin = 0.978, Tmax = 0.994 | k = −9→10 |
5248 measured reflections | l = −17→18 |
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)] = 0.049 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.132 | H-atom parameters constrained |
S = 1.01 | w = 1/[σ2(Fo2) + (0.0727P)2] where P = (Fo2 + 2Fc2)/3 |
1642 reflections | (Δ/σ)max < 0.001 |
102 parameters | Δρmax = 0.22 e Å−3 |
0 restraints | Δρmin = −0.37 e Å−3 |
C6H9N3O2 | V = 1442.75 (13) Å3 |
Mr = 155.16 | Z = 8 |
Monoclinic, C2/c | Mo Kα radiation |
a = 12.3971 (5) Å | µ = 0.11 mm−1 |
b = 8.3608 (5) Å | T = 120 K |
c = 14.5237 (7) Å | 0.20 × 0.15 × 0.05 mm |
β = 106.585 (3)° |
Nonius KappaCCD area-detector diffractometer | 1642 independent reflections |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | 1090 reflections with I > 2σ(I) |
Tmin = 0.978, Tmax = 0.994 | Rint = 0.066 |
5248 measured reflections |
R[F2 > 2σ(F2)] = 0.049 | 0 restraints |
wR(F2) = 0.132 | H-atom parameters constrained |
S = 1.01 | Δρmax = 0.22 e Å−3 |
1642 reflections | Δρmin = −0.37 e Å−3 |
102 parameters |
Experimental. The program DENZO-SMN (Otwinowski & Minor, 1997) uses a scaling algorithm [Fox, G. C. & Holmes, K. C. (1966). Acta Cryst. 20, 886–891] which effectively corrects for absorption effects. High-redundancy data were used in the scaling program, hence the `multi-scan' code word was used. No transmission coefficients are available from the program (only scale factors for each frame). |
x | y | z | Uiso*/Ueq | ||
N1 | 0.14019 (11) | 0.48401 (17) | 0.48098 (9) | 0.0206 (4) | |
N2 | −0.01762 (11) | 0.37392 (19) | 0.37859 (10) | 0.0285 (4) | |
N3 | 0.14982 (11) | 0.31903 (17) | 0.34783 (9) | 0.0205 (4) | |
C2 | 0.09446 (13) | 0.3937 (2) | 0.40367 (11) | 0.0196 (4) | |
O4 | 0.32450 (9) | 0.26690 (14) | 0.32742 (8) | 0.0244 (3) | |
C4 | 0.26097 (13) | 0.3388 (2) | 0.37614 (11) | 0.0200 (4) | |
C41 | 0.27005 (15) | 0.1574 (2) | 0.25231 (12) | 0.0266 (4) | |
C5 | 0.31797 (13) | 0.4311 (2) | 0.45409 (11) | 0.0209 (4) | |
O6 | 0.29165 (9) | 0.59379 (15) | 0.58250 (8) | 0.0253 (3) | |
C6 | 0.25158 (13) | 0.5009 (2) | 0.50419 (10) | 0.0205 (4) | |
C61 | 0.41058 (14) | 0.6223 (2) | 0.61287 (13) | 0.0307 (5) | |
H2A | −0.0576 | 0.4195 | 0.4126 | 0.034* | |
H2B | −0.0511 | 0.3154 | 0.3282 | 0.034* | |
H41A | 0.2195 | 0.0873 | 0.2749 | 0.040* | |
H41B | 0.3270 | 0.0925 | 0.2347 | 0.040* | |
H41C | 0.2265 | 0.2176 | 0.1961 | 0.040* | |
H5 | 0.3973 | 0.4451 | 0.4717 | 0.025* | |
H61A | 0.4505 | 0.5200 | 0.6270 | 0.046* | |
H61B | 0.4296 | 0.6889 | 0.6708 | 0.046* | |
H61C | 0.4329 | 0.6774 | 0.5616 | 0.046* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0176 (8) | 0.0247 (8) | 0.0192 (7) | 0.0026 (6) | 0.0048 (6) | −0.0002 (6) |
N2 | 0.0161 (8) | 0.0425 (10) | 0.0265 (8) | 0.0012 (7) | 0.0051 (6) | −0.0114 (7) |
N3 | 0.0207 (8) | 0.0233 (8) | 0.0185 (7) | 0.0011 (6) | 0.0071 (6) | 0.0008 (6) |
C2 | 0.0196 (9) | 0.0207 (10) | 0.0186 (8) | 0.0022 (7) | 0.0055 (7) | 0.0038 (7) |
O4 | 0.0221 (7) | 0.0297 (7) | 0.0224 (6) | 0.0025 (5) | 0.0081 (5) | −0.0049 (5) |
C4 | 0.0208 (9) | 0.0219 (10) | 0.0186 (8) | 0.0050 (7) | 0.0077 (7) | 0.0055 (7) |
C41 | 0.0307 (10) | 0.0255 (10) | 0.0258 (9) | 0.0012 (8) | 0.0114 (8) | −0.0046 (8) |
C5 | 0.0153 (8) | 0.0248 (10) | 0.0222 (8) | 0.0006 (7) | 0.0047 (7) | 0.0003 (7) |
O6 | 0.0191 (7) | 0.0349 (8) | 0.0213 (6) | −0.0007 (5) | 0.0046 (5) | −0.0076 (5) |
C6 | 0.0210 (9) | 0.0223 (10) | 0.0173 (8) | 0.0016 (7) | 0.0042 (7) | 0.0006 (7) |
C61 | 0.0174 (9) | 0.0414 (12) | 0.0303 (10) | −0.0002 (8) | 0.0018 (8) | −0.0118 (8) |
N1—C2 | 1.338 (2) | O6—C61 | 1.433 (2) |
C2—N3 | 1.355 (2) | N2—H2A | 0.8800 |
N3—C4 | 1.331 (2) | N2—H2B | 0.8800 |
C4—C5 | 1.386 (2) | C41—H41A | 0.9800 |
C5—C6 | 1.375 (2) | C41—H41B | 0.9800 |
C6—N1 | 1.332 (2) | C41—H41C | 0.9800 |
C2—N2 | 1.342 (2) | C5—H5 | 0.9500 |
C4—O4 | 1.342 (2) | C61—H61A | 0.9800 |
O4—C41 | 1.437 (2) | C61—H61B | 0.9800 |
C6—O6 | 1.3492 (19) | C61—H61C | 0.9800 |
C6—N1—C2 | 115.64 (13) | H41A—C41—H41C | 109.5 |
C2—N2—H2A | 120.0 | H41B—C41—H41C | 109.5 |
C2—N2—H2B | 120.0 | C6—C5—C4 | 115.24 (15) |
H2A—N2—H2B | 120.0 | C6—C5—H5 | 122.4 |
C4—N3—C2 | 114.49 (14) | C4—C5—H5 | 122.4 |
N1—C2—N2 | 117.07 (14) | C6—O6—C61 | 117.00 (13) |
N1—C2—N3 | 126.64 (14) | N1—C6—O6 | 112.34 (13) |
N2—C2—N3 | 116.28 (15) | N1—C6—C5 | 123.70 (15) |
C4—O4—C41 | 117.81 (12) | O6—C6—C5 | 123.96 (15) |
N3—C4—O4 | 119.56 (15) | O6—C61—H61A | 109.5 |
N3—C4—C5 | 124.27 (15) | O6—C61—H61B | 109.5 |
O4—C4—C5 | 116.17 (14) | H61A—C61—H61B | 109.5 |
O4—C41—H41A | 109.5 | O6—C61—H61C | 109.5 |
O4—C41—H41B | 109.5 | H61A—C61—H61C | 109.5 |
H41A—C41—H41B | 109.5 | H61B—C61—H61C | 109.5 |
O4—C41—H41C | 109.5 | ||
C6—N1—C2—N2 | 179.80 (15) | N3—C4—C5—C6 | 1.6 (2) |
C6—N1—C2—N3 | 0.1 (2) | O4—C4—C5—C6 | −178.70 (14) |
C4—N3—C2—N1 | 1.1 (2) | C2—N1—C6—O6 | 179.78 (13) |
C4—N3—C2—N2 | −178.68 (14) | C2—N1—C6—C5 | −0.4 (2) |
C2—N3—C4—O4 | 178.40 (14) | C61—O6—C6—N1 | −178.95 (15) |
C2—N3—C4—C5 | −1.9 (2) | C61—O6—C6—C5 | 1.3 (2) |
C41—O4—C4—N3 | −6.5 (2) | C4—C5—C6—N1 | −0.3 (3) |
C41—O4—C4—C5 | 173.81 (15) | C4—C5—C6—O6 | 179.44 (15) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···N1i | 0.88 | 2.23 | 3.106 (2) | 171 |
N2—H2B···N3ii | 0.88 | 2.50 | 3.261 (2) | 145 |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x, y, −z+1/2. |
C25H23N3O2 | Z = 2 |
Mr = 397.46 | F(000) = 420 |
Triclinic, P1 | Dx = 1.272 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 5.8083 (6) Å | Cell parameters from 4785 reflections |
b = 12.3104 (13) Å | θ = 1.8–29.0° |
c = 15.7260 (16) Å | µ = 0.08 mm−1 |
α = 68.549 (2)° | T = 120 K |
β = 85.978 (2)° | Needle, colourless |
γ = 82.737 (2)° | 0.14 × 0.05 × 0.04 mm |
V = 1037.81 (19) Å3 |
Bruker SMART 1000 diffractometer | 4785 independent reflections |
Radiation source: fine-focus sealed X-ray tube | 3697 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.010 |
ϕ scans, and ω scans with κ offsets | θmax = 29.0°, θmin = 1.8° |
Absorption correction: multi-scan (SADABS; Bruker, 1997) | h = −7→7 |
Tmin = 0.989, Tmax = 0.997 | k = −13→16 |
6639 measured reflections | l = −20→19 |
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)] = 0.041 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.111 | H-atom parameters constrained |
S = 1.07 | w = 1/[σ2(Fo2) + (0.0612P)2 + 0.0805P] where P = (Fo2 + 2Fc2)/3 |
4785 reflections | (Δ/σ)max < 0.001 |
271 parameters | Δρmax = 0.25 e Å−3 |
0 restraints | Δρmin = −0.22 e Å−3 |
C25H23N3O2 | γ = 82.737 (2)° |
Mr = 397.46 | V = 1037.81 (19) Å3 |
Triclinic, P1 | Z = 2 |
a = 5.8083 (6) Å | Mo Kα radiation |
b = 12.3104 (13) Å | µ = 0.08 mm−1 |
c = 15.7260 (16) Å | T = 120 K |
α = 68.549 (2)° | 0.14 × 0.05 × 0.04 mm |
β = 85.978 (2)° |
Bruker SMART 1000 diffractometer | 4785 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 1997) | 3697 reflections with I > 2σ(I) |
Tmin = 0.989, Tmax = 0.997 | Rint = 0.010 |
6639 measured reflections |
R[F2 > 2σ(F2)] = 0.041 | 0 restraints |
wR(F2) = 0.111 | H-atom parameters constrained |
S = 1.07 | Δρmax = 0.25 e Å−3 |
4785 reflections | Δρmin = −0.22 e Å−3 |
271 parameters |
x | y | z | Uiso*/Ueq | ||
N1 | 1.06020 (18) | 0.15079 (9) | 0.43312 (7) | 0.0245 (2) | |
C2 | 0.9040 (2) | 0.14975 (10) | 0.37413 (8) | 0.0234 (2) | |
N2 | 0.81278 (19) | 0.04843 (9) | 0.39253 (7) | 0.0279 (2) | |
C27 | 0.6332 (2) | 0.03365 (11) | 0.33940 (8) | 0.0261 (3) | |
C21 | 0.7221 (2) | −0.00571 (10) | 0.26110 (8) | 0.0231 (3) | |
C22 | 0.5881 (2) | −0.07097 (11) | 0.23235 (8) | 0.0275 (3) | |
C23 | 0.6605 (2) | −0.10549 (11) | 0.15896 (9) | 0.0328 (3) | |
C24 | 0.8691 (2) | −0.07512 (12) | 0.11369 (9) | 0.0334 (3) | |
C25 | 1.0057 (2) | −0.01108 (12) | 0.14225 (9) | 0.0317 (3) | |
C26 | 0.9327 (2) | 0.02341 (11) | 0.21554 (8) | 0.0272 (3) | |
N3 | 0.82976 (18) | 0.24202 (8) | 0.29875 (6) | 0.0249 (2) | |
C4 | 0.9258 (2) | 0.33947 (10) | 0.28374 (8) | 0.0238 (3) | |
O4 | 0.85807 (15) | 0.43613 (7) | 0.21106 (6) | 0.0280 (2) | |
C47 | 0.6792 (2) | 0.42567 (11) | 0.15532 (9) | 0.0321 (3) | |
C41 | 0.6113 (2) | 0.54692 (11) | 0.08775 (8) | 0.0278 (3) | |
C42 | 0.7715 (3) | 0.60873 (13) | 0.02532 (11) | 0.0409 (3) | |
C43 | 0.7082 (3) | 0.72002 (13) | −0.03715 (11) | 0.0454 (4) | |
C44 | 0.4837 (3) | 0.77170 (12) | −0.03714 (10) | 0.0392 (3) | |
C45 | 0.3238 (3) | 0.71142 (13) | 0.02456 (10) | 0.0396 (3) | |
C46 | 0.3856 (2) | 0.59913 (12) | 0.08676 (9) | 0.0334 (3) | |
C5 | 1.0904 (2) | 0.35194 (10) | 0.33882 (8) | 0.0257 (3) | |
C6 | 1.1484 (2) | 0.25220 (10) | 0.41456 (8) | 0.0237 (3) | |
O6 | 1.29228 (15) | 0.24744 (7) | 0.48017 (6) | 0.0284 (2) | |
C67 | 1.3823 (3) | 0.35596 (11) | 0.47016 (9) | 0.0338 (3) | |
C61 | 1.5029 (2) | 0.34046 (10) | 0.55579 (8) | 0.0264 (3) | |
C62 | 1.3964 (2) | 0.38608 (11) | 0.61912 (9) | 0.0280 (3) | |
C63 | 1.5120 (3) | 0.37561 (11) | 0.69647 (9) | 0.0332 (3) | |
C64 | 1.7358 (2) | 0.32039 (11) | 0.71061 (9) | 0.0347 (3) | |
C65 | 1.8430 (2) | 0.27374 (12) | 0.64840 (10) | 0.0355 (3) | |
C66 | 1.7265 (2) | 0.28324 (11) | 0.57154 (9) | 0.0320 (3) | |
H2 | 0.8652 | −0.0127 | 0.4397 | 0.033* | |
H27A | 0.5340 | 0.1092 | 0.3143 | 0.031* | |
H27B | 0.5343 | −0.0248 | 0.3807 | 0.031* | |
H22 | 0.4449 | −0.0923 | 0.2633 | 0.033* | |
H23 | 0.5667 | −0.1499 | 0.1399 | 0.039* | |
H24 | 0.9185 | −0.0981 | 0.0633 | 0.040* | |
H25 | 1.1497 | 0.0093 | 0.1116 | 0.038* | |
H26 | 1.0274 | 0.0673 | 0.2347 | 0.033* | |
H47A | 0.5433 | 0.3942 | 0.1940 | 0.039* | |
H47B | 0.7393 | 0.3720 | 0.1230 | 0.039* | |
H42 | 0.9273 | 0.5743 | 0.0253 | 0.049* | |
H43 | 0.8199 | 0.7608 | −0.0801 | 0.054* | |
H44 | 0.4401 | 0.8484 | −0.0795 | 0.047* | |
H45 | 0.1687 | 0.7468 | 0.0249 | 0.048* | |
H46 | 0.2725 | 0.5581 | 0.1288 | 0.040* | |
H5 | 1.1575 | 0.4230 | 0.3256 | 0.031* | |
H67A | 1.2535 | 0.4200 | 0.4589 | 0.041* | |
H67B | 1.4928 | 0.3774 | 0.4173 | 0.041* | |
H62 | 1.2431 | 0.4248 | 0.6094 | 0.034* | |
H63 | 1.4371 | 0.4065 | 0.7398 | 0.040* | |
H64 | 1.8158 | 0.3145 | 0.7630 | 0.042* | |
H65 | 1.9964 | 0.2352 | 0.6583 | 0.043* | |
H66 | 1.8002 | 0.2503 | 0.5293 | 0.038* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0330 (5) | 0.0203 (5) | 0.0203 (5) | −0.0065 (4) | −0.0032 (4) | −0.0059 (4) |
C2 | 0.0304 (6) | 0.0205 (6) | 0.0201 (5) | −0.0048 (5) | −0.0013 (5) | −0.0075 (5) |
N2 | 0.0402 (6) | 0.0199 (5) | 0.0222 (5) | −0.0094 (4) | −0.0091 (4) | −0.0023 (4) |
C27 | 0.0303 (6) | 0.0233 (6) | 0.0243 (6) | −0.0088 (5) | −0.0026 (5) | −0.0057 (5) |
C21 | 0.0271 (6) | 0.0169 (5) | 0.0217 (6) | −0.0023 (5) | −0.0078 (5) | −0.0015 (4) |
C22 | 0.0299 (6) | 0.0247 (6) | 0.0260 (6) | −0.0081 (5) | −0.0049 (5) | −0.0046 (5) |
C23 | 0.0461 (8) | 0.0262 (7) | 0.0279 (6) | −0.0101 (6) | −0.0085 (6) | −0.0085 (5) |
C24 | 0.0446 (8) | 0.0274 (7) | 0.0271 (6) | 0.0002 (6) | −0.0030 (6) | −0.0093 (5) |
C25 | 0.0284 (6) | 0.0323 (7) | 0.0296 (7) | −0.0019 (5) | −0.0005 (5) | −0.0061 (5) |
C26 | 0.0274 (6) | 0.0247 (6) | 0.0275 (6) | −0.0041 (5) | −0.0068 (5) | −0.0056 (5) |
N3 | 0.0324 (5) | 0.0193 (5) | 0.0218 (5) | −0.0053 (4) | −0.0045 (4) | −0.0046 (4) |
C4 | 0.0309 (6) | 0.0191 (6) | 0.0203 (6) | −0.0023 (5) | −0.0010 (5) | −0.0059 (5) |
O4 | 0.0378 (5) | 0.0181 (4) | 0.0256 (4) | −0.0051 (4) | −0.0107 (4) | −0.0022 (3) |
C47 | 0.0411 (7) | 0.0227 (6) | 0.0307 (7) | −0.0063 (5) | −0.0142 (6) | −0.0042 (5) |
C41 | 0.0355 (7) | 0.0226 (6) | 0.0256 (6) | −0.0041 (5) | −0.0099 (5) | −0.0072 (5) |
C42 | 0.0337 (7) | 0.0290 (7) | 0.0494 (9) | −0.0022 (6) | −0.0051 (6) | −0.0015 (6) |
C43 | 0.0456 (9) | 0.0336 (8) | 0.0448 (9) | −0.0112 (7) | −0.0049 (7) | 0.0031 (7) |
C44 | 0.0516 (9) | 0.0231 (7) | 0.0382 (8) | −0.0018 (6) | −0.0217 (7) | −0.0028 (6) |
C45 | 0.0378 (7) | 0.0342 (8) | 0.0469 (8) | 0.0060 (6) | −0.0136 (7) | −0.0156 (7) |
C46 | 0.0377 (7) | 0.0339 (7) | 0.0286 (7) | −0.0040 (6) | −0.0035 (5) | −0.0109 (6) |
C5 | 0.0347 (7) | 0.0187 (6) | 0.0234 (6) | −0.0082 (5) | −0.0031 (5) | −0.0051 (5) |
C6 | 0.0297 (6) | 0.0229 (6) | 0.0200 (6) | −0.0063 (5) | −0.0017 (5) | −0.0082 (5) |
O6 | 0.0403 (5) | 0.0219 (4) | 0.0230 (4) | −0.0114 (4) | −0.0085 (4) | −0.0041 (3) |
C67 | 0.0506 (8) | 0.0252 (6) | 0.0265 (6) | −0.0170 (6) | −0.0090 (6) | −0.0046 (5) |
C61 | 0.0326 (6) | 0.0216 (6) | 0.0247 (6) | −0.0114 (5) | −0.0025 (5) | −0.0048 (5) |
C62 | 0.0293 (6) | 0.0215 (6) | 0.0316 (7) | −0.0060 (5) | −0.0022 (5) | −0.0064 (5) |
C63 | 0.0482 (8) | 0.0250 (6) | 0.0285 (7) | −0.0104 (6) | 0.0007 (6) | −0.0104 (5) |
C64 | 0.0466 (8) | 0.0259 (7) | 0.0298 (7) | −0.0120 (6) | −0.0142 (6) | −0.0030 (5) |
C65 | 0.0272 (7) | 0.0272 (7) | 0.0466 (8) | −0.0065 (5) | −0.0068 (6) | −0.0048 (6) |
C66 | 0.0340 (7) | 0.0276 (7) | 0.0341 (7) | −0.0084 (5) | 0.0068 (6) | −0.0106 (5) |
N1—C2 | 1.3466 (15) | C47—H47A | 0.9900 |
C2—N3 | 1.3582 (15) | C47—H47B | 0.9900 |
N3—C4 | 1.3227 (15) | C41—C42 | 1.3831 (19) |
C4—C5 | 1.3925 (17) | C41—C46 | 1.3833 (19) |
C5—C6 | 1.3863 (16) | C42—C43 | 1.384 (2) |
C6—N1 | 1.3342 (15) | C42—H42 | 0.9500 |
C2—N2 | 1.3424 (15) | C43—C44 | 1.377 (2) |
N2—C27 | 1.4495 (15) | C43—H43 | 0.9500 |
C4—O4 | 1.3516 (14) | C44—C45 | 1.370 (2) |
O4—C47 | 1.4522 (14) | C44—H44 | 0.9500 |
C6—O6 | 1.3530 (14) | C45—C46 | 1.390 (2) |
O6—C67 | 1.4470 (15) | C45—H45 | 0.9500 |
N2—H2 | 0.8800 | C46—H46 | 0.9500 |
C27—C21 | 1.5172 (17) | C5—H5 | 0.9500 |
C27—H27A | 0.9900 | C67—C61 | 1.5005 (17) |
C27—H27B | 0.9900 | C67—H67A | 0.9900 |
C21—C22 | 1.3886 (16) | C67—H67B | 0.9900 |
C21—C26 | 1.3923 (17) | C61—C62 | 1.3872 (18) |
C22—C23 | 1.3910 (18) | C61—C66 | 1.3894 (18) |
C22—H22 | 0.9500 | C62—C63 | 1.3872 (18) |
C23—C24 | 1.383 (2) | C62—H62 | 0.9500 |
C23—H23 | 0.9500 | C63—C64 | 1.381 (2) |
C24—C25 | 1.3854 (19) | C63—H63 | 0.9500 |
C24—H24 | 0.9500 | C64—C65 | 1.382 (2) |
C25—C26 | 1.3900 (18) | C64—H64 | 0.9500 |
C25—H25 | 0.9500 | C65—C66 | 1.3871 (19) |
C26—H26 | 0.9500 | C65—H65 | 0.9500 |
C47—C41 | 1.5042 (17) | C66—H66 | 0.9500 |
C6—N1—C2 | 116.12 (10) | C41—C42—H42 | 119.5 |
N2—C2—N1 | 116.63 (10) | C43—C42—H42 | 119.5 |
N2—C2—N3 | 117.54 (10) | C44—C43—C42 | 120.14 (14) |
N1—C2—N3 | 125.83 (11) | C44—C43—H43 | 119.9 |
C2—N2—C27 | 123.94 (10) | C42—C43—H43 | 119.9 |
C2—N2—H2 | 118.0 | C45—C44—C43 | 119.33 (13) |
C27—N2—H2 | 118.0 | C45—C44—H44 | 120.3 |
N2—C27—C21 | 114.73 (10) | C43—C44—H44 | 120.3 |
N2—C27—H27A | 108.6 | C44—C45—C46 | 120.80 (13) |
C21—C27—H27A | 108.6 | C44—C45—H45 | 119.6 |
N2—C27—H27B | 108.6 | C46—C45—H45 | 119.6 |
C21—C27—H27B | 108.6 | C41—C46—C45 | 120.26 (13) |
H27A—C27—H27B | 107.6 | C41—C46—H46 | 119.9 |
C22—C21—C26 | 118.55 (11) | C45—C46—H46 | 119.9 |
C22—C21—C27 | 119.33 (11) | C6—C5—C4 | 114.53 (11) |
C26—C21—C27 | 122.11 (10) | C6—C5—H5 | 122.7 |
C21—C22—C23 | 120.98 (12) | C4—C5—H5 | 122.7 |
C21—C22—H22 | 119.5 | N1—C6—O6 | 112.10 (10) |
C23—C22—H22 | 119.5 | N1—C6—C5 | 123.60 (11) |
C24—C23—C22 | 119.95 (12) | O6—C6—C5 | 124.24 (10) |
C24—C23—H23 | 120.0 | C6—O6—C67 | 116.37 (9) |
C22—C23—H23 | 120.0 | O6—C67—C61 | 109.25 (10) |
C23—C24—C25 | 119.68 (12) | O6—C67—H67A | 109.8 |
C23—C24—H24 | 120.2 | C61—C67—H67A | 109.8 |
C25—C24—H24 | 120.2 | O6—C67—H67B | 109.8 |
C24—C25—C26 | 120.23 (12) | C61—C67—H67B | 109.8 |
C24—C25—H25 | 119.9 | H67A—C67—H67B | 108.3 |
C26—C25—H25 | 119.9 | C62—C61—C66 | 118.87 (11) |
C25—C26—C21 | 120.61 (12) | C62—C61—C67 | 120.71 (12) |
C25—C26—H26 | 119.7 | C66—C61—C67 | 120.39 (12) |
C21—C26—H26 | 119.7 | C61—C62—C63 | 120.57 (12) |
C4—N3—C2 | 115.00 (10) | C61—C62—H62 | 119.7 |
N3—C4—O4 | 118.75 (10) | C63—C62—H62 | 119.7 |
N3—C4—C5 | 124.90 (11) | C64—C63—C62 | 120.07 (12) |
O4—C4—C5 | 116.34 (10) | C64—C63—H63 | 120.0 |
C4—O4—C47 | 116.87 (9) | C62—C63—H63 | 120.0 |
O4—C47—C41 | 106.83 (10) | C63—C64—C65 | 119.89 (12) |
O4—C47—H47A | 110.4 | C63—C64—H64 | 120.1 |
C41—C47—H47A | 110.4 | C65—C64—H64 | 120.1 |
O4—C47—H47B | 110.4 | C64—C65—C66 | 119.99 (12) |
C41—C47—H47B | 110.4 | C64—C65—H65 | 120.0 |
H47A—C47—H47B | 108.6 | C66—C65—H65 | 120.0 |
C42—C41—C46 | 118.45 (12) | C65—C66—C61 | 120.59 (12) |
C42—C41—C47 | 121.14 (12) | C65—C66—H66 | 119.7 |
C46—C41—C47 | 120.41 (12) | C61—C66—H66 | 119.7 |
C41—C42—C43 | 121.02 (13) | ||
C27—N2—C2—N3 | −3.0 (2) | C67—O6—C6—C5 | 2.1 (2) |
C47—O4—C4—N3 | 1.1 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···N1i | 0.88 | 2.13 | 2.997 (2) | 170 |
C66—H66···N1ii | 0.95 | 2.58 | 3.516 (2) | 170 |
Symmetry codes: (i) −x+2, −y, −z+1; (ii) x+1, y, z. |
C12H19N5 | F(000) = 1008 |
Mr = 233.32 | Dx = 1.308 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 2485 reflections |
a = 12.5654 (8) Å | θ = 2.2–27.6° |
b = 13.2735 (8) Å | µ = 0.08 mm−1 |
c = 14.2279 (9) Å | T = 120 K |
β = 93.090 (2)° | Prism, colourless |
V = 2369.6 (3) Å3 | 0.3 × 0.2 × 0.2 mm |
Z = 8 |
Nonius KappaCCD area-detector diffractometer | 2485 independent reflections |
Radiation source: fine-focus sealed X-ray tube | 2109 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.022 |
ϕ scans, and ω scans with κ offsets | θmax = 27.0°, θmin = 2.2° |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | h = −16→15 |
Tmin = 0.975, Tmax = 0.990 | k = −16→17 |
7257 measured reflections | l = −15→17 |
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)] = 0.041 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.117 | H-atom parameters constrained |
S = 1.08 | w = 1/[σ2(Fo2) + (0.0753P)2 + 0.6604P] where P = (Fo2 + 2Fc2)/3 |
2485 reflections | (Δ/σ)max < 0.001 |
154 parameters | Δρmax = 0.24 e Å−3 |
0 restraints | Δρmin = −0.31 e Å−3 |
C12H19N5 | V = 2369.6 (3) Å3 |
Mr = 233.32 | Z = 8 |
Monoclinic, C2/c | Mo Kα radiation |
a = 12.5654 (8) Å | µ = 0.08 mm−1 |
b = 13.2735 (8) Å | T = 120 K |
c = 14.2279 (9) Å | 0.3 × 0.2 × 0.2 mm |
β = 93.090 (2)° |
Nonius KappaCCD area-detector diffractometer | 2485 independent reflections |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | 2109 reflections with I > 2σ(I) |
Tmin = 0.975, Tmax = 0.990 | Rint = 0.022 |
7257 measured reflections |
R[F2 > 2σ(F2)] = 0.041 | 0 restraints |
wR(F2) = 0.117 | H-atom parameters constrained |
S = 1.08 | Δρmax = 0.24 e Å−3 |
2485 reflections | Δρmin = −0.31 e Å−3 |
154 parameters |
Experimental. The program DENZO-SMN (Otwinowski & Minor, 1997) uses a scaling algorithm [Fox, G. C. & Holmes, K. C. (1966). Acta Cryst. 20, 886–891] which effectively corrects for absorption effects. High-redundancy data were used in the scaling program, hence the `multi-scan' code word was used. No transmission coefficients are available from the program (only scale factors for each frame). |
x | y | z | Uiso*/Ueq | ||
N1 | 0.14234 (7) | 0.42768 (7) | 0.04220 (6) | 0.0167 (2) | |
C2 | 0.08934 (9) | 0.41017 (8) | 0.12032 (8) | 0.0169 (3) | |
N2 | −0.01134 (8) | 0.44606 (8) | 0.12240 (7) | 0.0226 (3) | |
N3 | 0.12512 (7) | 0.36133 (7) | 0.19908 (6) | 0.0177 (2) | |
C4 | 0.22452 (9) | 0.32333 (8) | 0.19736 (8) | 0.0168 (3) | |
N4 | 0.25920 (7) | 0.27045 (8) | 0.27487 (7) | 0.0210 (3) | |
C41 | 0.19010 (9) | 0.24157 (9) | 0.34986 (8) | 0.0200 (3) | |
C42 | 0.25113 (10) | 0.15405 (9) | 0.39630 (9) | 0.0247 (3) | |
C43 | 0.36722 (10) | 0.18595 (10) | 0.38874 (9) | 0.0248 (3) | |
C44 | 0.36740 (9) | 0.23140 (9) | 0.28994 (8) | 0.0203 (3) | |
C5 | 0.28893 (9) | 0.33753 (8) | 0.12149 (8) | 0.0181 (3) | |
C6 | 0.24377 (9) | 0.39189 (8) | 0.04469 (8) | 0.0163 (3) | |
N6 | 0.30145 (7) | 0.41109 (7) | −0.03098 (7) | 0.0190 (2) | |
C61 | 0.41069 (9) | 0.37530 (9) | −0.03849 (8) | 0.0193 (3) | |
C62 | 0.44028 (10) | 0.41074 (9) | −0.13600 (8) | 0.0228 (3) | |
C63 | 0.36687 (9) | 0.50100 (9) | −0.15631 (8) | 0.0216 (3) | |
C64 | 0.26383 (9) | 0.47094 (9) | −0.11223 (8) | 0.0188 (3) | |
H2A | −0.0398 | 0.4794 | 0.0738 | 0.027* | |
H2B | −0.0484 | 0.4360 | 0.1723 | 0.027* | |
H41A | 0.1190 | 0.2200 | 0.3240 | 0.024* | |
H41B | 0.1814 | 0.2976 | 0.3947 | 0.024* | |
H42A | 0.2360 | 0.0901 | 0.3623 | 0.030* | |
H42B | 0.2334 | 0.1461 | 0.4628 | 0.030* | |
H43A | 0.4158 | 0.1273 | 0.3950 | 0.030* | |
H43B | 0.3885 | 0.2365 | 0.4374 | 0.030* | |
H44A | 0.4207 | 0.2861 | 0.2871 | 0.024* | |
H44B | 0.3827 | 0.1794 | 0.2426 | 0.024* | |
H5 | 0.3595 | 0.3118 | 0.1218 | 0.022* | |
H61A | 0.4142 | 0.3010 | −0.0336 | 0.023* | |
H61B | 0.4589 | 0.4051 | 0.0114 | 0.023* | |
H62A | 0.4272 | 0.3570 | −0.1835 | 0.027* | |
H62B | 0.5161 | 0.4311 | −0.1355 | 0.027* | |
H63A | 0.3970 | 0.5631 | −0.1270 | 0.026* | |
H63B | 0.3550 | 0.5120 | −0.2249 | 0.026* | |
H64A | 0.2238 | 0.5309 | −0.0926 | 0.023* | |
H64B | 0.2178 | 0.4305 | −0.1565 | 0.023* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0156 (5) | 0.0198 (5) | 0.0148 (5) | 0.0000 (4) | 0.0009 (4) | 0.0007 (4) |
C2 | 0.0159 (5) | 0.0186 (5) | 0.0161 (6) | −0.0027 (4) | 0.0003 (4) | −0.0009 (4) |
N2 | 0.0161 (5) | 0.0349 (6) | 0.0172 (5) | 0.0040 (4) | 0.0034 (4) | 0.0079 (4) |
N3 | 0.0152 (5) | 0.0231 (5) | 0.0147 (5) | −0.0005 (4) | 0.0009 (4) | 0.0016 (4) |
C4 | 0.0182 (6) | 0.0173 (5) | 0.0148 (5) | −0.0023 (4) | −0.0007 (4) | −0.0001 (4) |
N4 | 0.0162 (5) | 0.0288 (5) | 0.0183 (5) | 0.0021 (4) | 0.0023 (4) | 0.0070 (4) |
C41 | 0.0205 (6) | 0.0244 (6) | 0.0149 (6) | −0.0020 (5) | 0.0005 (4) | 0.0031 (4) |
C42 | 0.0292 (7) | 0.0246 (6) | 0.0203 (6) | −0.0008 (5) | −0.0002 (5) | 0.0053 (5) |
C43 | 0.0252 (7) | 0.0264 (6) | 0.0225 (6) | 0.0037 (5) | −0.0027 (5) | 0.0047 (5) |
C44 | 0.0176 (6) | 0.0234 (6) | 0.0197 (6) | 0.0029 (5) | −0.0001 (4) | 0.0005 (5) |
C5 | 0.0154 (5) | 0.0210 (6) | 0.0179 (6) | 0.0024 (4) | 0.0017 (4) | 0.0011 (4) |
C6 | 0.0175 (6) | 0.0162 (5) | 0.0151 (6) | −0.0011 (4) | 0.0016 (4) | −0.0020 (4) |
N6 | 0.0173 (5) | 0.0249 (5) | 0.0152 (5) | 0.0049 (4) | 0.0038 (4) | 0.0037 (4) |
C61 | 0.0163 (6) | 0.0237 (6) | 0.0181 (6) | 0.0033 (4) | 0.0040 (4) | 0.0004 (4) |
C62 | 0.0215 (6) | 0.0283 (6) | 0.0191 (6) | 0.0021 (5) | 0.0068 (5) | 0.0009 (5) |
C63 | 0.0203 (6) | 0.0282 (6) | 0.0166 (6) | 0.0001 (5) | 0.0028 (4) | 0.0028 (5) |
C64 | 0.0190 (6) | 0.0229 (6) | 0.0144 (6) | 0.0002 (4) | −0.0004 (4) | 0.0016 (4) |
N1—C2 | 1.3464 (15) | C43—H43A | 0.9900 |
C2—N3 | 1.3506 (14) | C43—H43B | 0.9900 |
N3—C4 | 1.3484 (15) | C44—H44A | 0.9900 |
C4—C5 | 1.3965 (16) | C44—H44B | 0.9900 |
C5—C6 | 1.4035 (15) | C5—H5 | 0.9500 |
C6—N1 | 1.3588 (14) | C6—N6 | 1.3540 (15) |
C2—N2 | 1.3537 (15) | N6—C64 | 1.4602 (14) |
N2—H2A | 0.8800 | N6—C61 | 1.4619 (14) |
N2—H2B | 0.8800 | C61—C62 | 1.5296 (16) |
C4—N4 | 1.3590 (14) | C61—H61A | 0.9900 |
N4—C44 | 1.4601 (14) | C61—H61B | 0.9900 |
N4—C41 | 1.4625 (15) | C62—C63 | 1.5300 (16) |
C41—C42 | 1.5230 (16) | C62—H62A | 0.9900 |
C41—H41A | 0.9900 | C62—H62B | 0.9900 |
C41—H41B | 0.9900 | C63—C64 | 1.5219 (16) |
C42—C43 | 1.5283 (18) | C63—H63A | 0.9900 |
C42—H42A | 0.9900 | C63—H63B | 0.9900 |
C42—H42B | 0.9900 | C64—H64A | 0.9900 |
C43—C44 | 1.5298 (16) | C64—H64B | 0.9900 |
C2—N1—C6 | 115.03 (10) | C43—C44—H44B | 111.1 |
N1—C2—N3 | 127.63 (10) | H44A—C44—H44B | 109.1 |
N1—C2—N2 | 117.50 (10) | C4—C5—C6 | 116.39 (10) |
N3—C2—N2 | 114.87 (10) | C4—C5—H5 | 121.8 |
C2—N2—H2A | 120.0 | C6—C5—H5 | 121.8 |
C2—N2—H2B | 120.0 | N6—C6—N1 | 117.06 (10) |
H2A—N2—H2B | 120.0 | N6—C6—C5 | 120.30 (10) |
C4—N3—C2 | 115.58 (10) | N1—C6—C5 | 122.64 (10) |
N3—C4—N4 | 115.80 (10) | C6—N6—C61 | 122.82 (9) |
N3—C4—C5 | 122.65 (10) | C6—N6—C64 | 124.58 (9) |
N4—C4—C5 | 121.55 (10) | C61—N6—C64 | 112.58 (9) |
C4—N4—C41 | 123.39 (9) | N6—C61—C62 | 103.98 (9) |
C4—N4—C44 | 123.91 (10) | N6—C61—H61A | 111.0 |
C41—N4—C44 | 112.62 (9) | C62—C61—H61A | 111.0 |
N4—C41—C42 | 102.22 (9) | N6—C61—H61B | 111.0 |
N4—C41—H41A | 111.3 | C62—C61—H61B | 111.0 |
C42—C41—H41A | 111.3 | H61A—C61—H61B | 109.0 |
N4—C41—H41B | 111.3 | C61—C62—C63 | 103.80 (9) |
C42—C41—H41B | 111.3 | C61—C62—H62A | 111.0 |
H41A—C41—H41B | 109.2 | C63—C62—H62A | 111.0 |
C41—C42—C43 | 102.61 (9) | C61—C62—H62B | 111.0 |
C41—C42—H42A | 111.2 | C63—C62—H62B | 111.0 |
C43—C42—H42A | 111.2 | H62A—C62—H62B | 109.0 |
C41—C42—H42B | 111.2 | C64—C63—C62 | 103.56 (9) |
C43—C42—H42B | 111.2 | C64—C63—H63A | 111.0 |
H42A—C42—H42B | 109.2 | C62—C63—H63A | 111.0 |
C42—C43—C44 | 102.87 (9) | C64—C63—H63B | 111.0 |
C42—C43—H43A | 111.2 | C62—C63—H63B | 111.0 |
C44—C43—H43A | 111.2 | H63A—C63—H63B | 109.0 |
C42—C43—H43B | 111.2 | N6—C64—C63 | 102.86 (9) |
C44—C43—H43B | 111.2 | N6—C64—H64A | 111.2 |
H43A—C43—H43B | 109.1 | C63—C64—H64A | 111.2 |
N4—C44—C43 | 103.14 (9) | N6—C64—H64B | 111.2 |
N4—C44—H44A | 111.1 | C63—C64—H64B | 111.2 |
C43—C44—H44A | 111.1 | H64A—C64—H64B | 109.1 |
N4—C44—H44B | 111.1 | ||
C6—N1—C2—N3 | −0.43 (17) | N3—C4—C5—C6 | −1.63 (16) |
C6—N1—C2—N2 | 178.66 (9) | N4—C4—C5—C6 | 178.90 (10) |
N1—C2—N3—C4 | −2.19 (17) | C2—N1—C6—N6 | −177.58 (9) |
N2—C2—N3—C4 | 178.70 (9) | C2—N1—C6—C5 | 2.18 (16) |
C2—N3—C4—N4 | −177.32 (9) | C4—C5—C6—N6 | 178.52 (10) |
C2—N3—C4—C5 | 3.17 (16) | C4—C5—C6—N1 | −1.23 (17) |
N3—C4—N4—C44 | −174.24 (10) | C5—C6—N6—C64 | −176.89 (10) |
N3—C4—N4—C41 | 9.39 (16) | N1—C6—N6—C61 | −178.70 (9) |
C5—C4—N4—C44 | 5.27 (17) | C5—C6—N6—C61 | 1.53 (17) |
C5—C4—N4—C41 | −171.10 (11) | N1—C6—N6—C64 | 2.88 (16) |
C4—N4—C41—C42 | 158.93 (11) | C6—N6—C61—C62 | 177.59 (10) |
N4—C41—C42—C43 | 35.48 (12) | N6—C64—C63—C62 | 33.10 (11) |
C41—C42—C43—C44 | −40.59 (12) | C64—C63—C62—C61 | −35.97 (12) |
C42—C43—C44—N4 | 29.44 (12) | C63—C62—C61—N6 | 24.55 (12) |
C43—C44—N4—C41 | −7.37 (13) | C62—C61—N6—C64 | −3.82 (13) |
C44—N4—C41—C42 | −17.80 (13) | C61—N6—C64—C63 | −18.54 (12) |
C4—N4—C44—C43 | 175.92 (11) | C6—N6—C64—C63 | 160.02 (11) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···N1i | 0.88 | 2.38 | 3.2538 (14) | 170 |
N2—H2B···N3ii | 0.88 | 2.33 | 3.1862 (13) | 163 |
Symmetry codes: (i) −x, −y+1, −z; (ii) −x, y, −z+1/2. |
Experimental details
(I) | (II) | (III) | |
Crystal data | |||
Chemical formula | C6H9N3O2 | C25H23N3O2 | C12H19N5 |
Mr | 155.16 | 397.46 | 233.32 |
Crystal system, space group | Monoclinic, C2/c | Triclinic, P1 | Monoclinic, C2/c |
Temperature (K) | 120 | 120 | 120 |
a, b, c (Å) | 12.3971 (5), 8.3608 (5), 14.5237 (7) | 5.8083 (6), 12.3104 (13), 15.7260 (16) | 12.5654 (8), 13.2735 (8), 14.2279 (9) |
α, β, γ (°) | 90, 106.585 (3), 90 | 68.549 (2), 85.978 (2), 82.737 (2) | 90, 93.090 (2), 90 |
V (Å3) | 1442.75 (13) | 1037.81 (19) | 2369.6 (3) |
Z | 8 | 2 | 8 |
Radiation type | Mo Kα | Mo Kα | Mo Kα |
µ (mm−1) | 0.11 | 0.08 | 0.08 |
Crystal size (mm) | 0.20 × 0.15 × 0.05 | 0.14 × 0.05 × 0.04 | 0.3 × 0.2 × 0.2 |
Data collection | |||
Diffractometer | Nonius KappaCCD area-detector diffractometer | Bruker SMART 1000 diffractometer | Nonius KappaCCD area-detector diffractometer |
Absorption correction | Multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | Multi-scan (SADABS; Bruker, 1997) | Multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.978, 0.994 | 0.989, 0.997 | 0.975, 0.990 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5248, 1642, 1090 | 6639, 4785, 3697 | 7257, 2485, 2109 |
Rint | 0.066 | 0.010 | 0.022 |
(sin θ/λ)max (Å−1) | 0.648 | 0.683 | 0.639 |
Refinement | |||
R[F2 > 2σ(F2)], wR(F2), S | 0.049, 0.132, 1.01 | 0.041, 0.111, 1.07 | 0.041, 0.117, 1.08 |
No. of reflections | 1642 | 4785 | 2485 |
No. of parameters | 102 | 271 | 154 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.22, −0.37 | 0.25, −0.22 | 0.24, −0.31 |
Computer programs: KappaCCD Server Software (Nonius, 1997), SMART (Bruker, 1997), DENZO-SMN (Otwinowski & Minor, 1997), SMART, SHELXTL (Bruker, 1997), DENZO-SMN, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2002), SHELXL97 and PRPKAPPA (Ferguson, 1999).
N1—C2 | 1.338 (2) | C2—N2 | 1.342 (2) |
C2—N3 | 1.355 (2) | C4—O4 | 1.342 (2) |
N3—C4 | 1.331 (2) | O4—C41 | 1.437 (2) |
C4—C5 | 1.386 (2) | C6—O6 | 1.3492 (19) |
C5—C6 | 1.375 (2) | O6—C61 | 1.433 (2) |
C6—N1 | 1.332 (2) | ||
C41—O4—C4—N3 | −6.5 (2) | C61—O6—C6—C5 | 1.3 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···N1i | 0.88 | 2.23 | 3.106 (2) | 171 |
N2—H2B···N3ii | 0.88 | 2.50 | 3.261 (2) | 145 |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x, y, −z+1/2. |
N1—C2 | 1.3466 (15) | C2—N2 | 1.3424 (15) |
C2—N3 | 1.3582 (15) | N2—C27 | 1.4495 (15) |
N3—C4 | 1.3227 (15) | C4—O4 | 1.3516 (14) |
C4—C5 | 1.3925 (17) | O4—C47 | 1.4522 (14) |
C5—C6 | 1.3863 (16) | C6—O6 | 1.3530 (14) |
C6—N1 | 1.3342 (15) | O6—C67 | 1.4470 (15) |
C27—N2—C2—N3 | −3.0 (2) | C67—O6—C6—C5 | 2.1 (2) |
C47—O4—C4—N3 | 1.1 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···N1i | 0.88 | 2.13 | 2.997 (2) | 170 |
Symmetry code: (i) −x+2, −y, −z+1. |
N1—C2 | 1.3464 (15) | C6—N1 | 1.3588 (14) |
C2—N3 | 1.3506 (14) | C2—N2 | 1.3537 (15) |
N3—C4 | 1.3484 (15) | C4—N4 | 1.3590 (14) |
C4—C5 | 1.3965 (16) | C6—N6 | 1.3540 (15) |
C5—C6 | 1.4035 (15) | ||
C4—N4—C41 | 123.39 (9) | C6—N6—C61 | 122.82 (9) |
C4—N4—C44 | 123.91 (10) | C6—N6—C64 | 124.58 (9) |
C41—N4—C44 | 112.62 (9) | C61—N6—C64 | 112.58 (9) |
N3—C4—N4—C41 | 9.39 (16) | C5—C6—N6—C61 | 1.53 (17) |
C5—C4—N4—C44 | 5.27 (17) | N1—C6—N6—C64 | 2.88 (16) |
N4—C41—C42—C43 | 35.48 (12) | N6—C64—C63—C62 | 33.10 (11) |
C41—C42—C43—C44 | −40.59 (12) | C64—C63—C62—C61 | −35.97 (12) |
C42—C43—C44—N4 | 29.44 (12) | C63—C62—C61—N6 | 24.55 (12) |
C43—C44—N4—C41 | −7.37 (13) | C62—C61—N6—C64 | −3.82 (13) |
C44—N4—C41—C42 | −17.80 (13) | C61—N6—C64—C63 | −18.54 (12) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···N1i | 0.88 | 2.38 | 3.2538 (14) | 170 |
N2—H2B···N3ii | 0.88 | 2.33 | 3.1862 (13) | 163 |
Symmetry codes: (i) −x, −y+1, −z; (ii) −x, y, −z+1/2. |
4,6-Dialkoxypyrimidines are key intermediates for the synthesis of a wide range of alkoxy and amino substituted O6-benzyloxy-5-nitrosopyrimidines (Marchal et al., 1998, 2000; Quesada et al., 2000), which are important as potential, or proven, in vitro inhibitors of the human DNA-repair protein O6-alkylguanine-DNA-transferase (Chae et al., 1995; Quesada et al., 2002). Here, we report the molecular and supramolecular structures of two examples of this class of pyrimidine, 2-amino-4,6-dimethoxypyrimidine (I) and 2-benzylamino-4,6-bis(benzyloxy)pyrimidine (II). \sch
Compound (I) could, in principle, adopt a conformation having C2v (mm2) molecular symmetry. In the event, the conformations of the two independent methoxy substituents are such that there is no exact molecular symmetry, although there is approximate Cs (m) symmetry (Fig. 1, Table 1). The C—N distances in (I) span the rather small range 1.331 (2)–1.355 (2) Å, with no significant bond fixation within the pyrimidine ring (Table 1). In this respect, the molecular-electronic structure of (I) is markedly different from those in a large number of analogous pyrimidines carrying a 5-nitroso substituent, where highly polarized structures are the norm (Low et al., 2000; Low, Cannon et al., 2001; Low, Moreno et al., 2001; Quesada et al., 2002).
The amino group in (I) acts as a double donor in N—H···N hydrogen bonds, while the two ring N atoms act as the acceptors. The O atoms play no part in the intermolecular aggregation (Table 2). Amino atom N2 at (x, y, z) acts as a hydrogen-bond donor, via atom H2A, to atom N1 at (-x, 1 - y, 1 - z), so generating a centrosymmetric R22(8) ring centred at (0, 1/2, 1/2). This amino atom N2 at (x, y, z) also acts as a donor, this time via atom H2B, to atom N3 at (-x, y, 1/2 - z), so producing a second R22(8) motif, generated by the twofold rotation axis along (0, y, 1/4). Propagation of these two hydrogen-bonding motifs by inversion and rotation generates a chain of fused rings running parallel to the [001] direction (Fig. 2). The supramolecular structure can alternatively be viewed as a molecular ladder, in which paired C22(6) chains form the uprights and the C2—N2 covalent bonds form the rungs, so that the full graph-set designation is C22(6)[R22(8)][R22(8)].
Two chains of this type, related by the C-centring operation, run through each unit cell, along the lines (0, 1/2, z) and (1/2, 1, z), and the parallel chains are linked by aromatic π···π stacking interactions to form a three-dimensional continuum. The pyrimidine rings of the molecules at (x, y, z) and (1/2 - x, 1/2 - y, 1 - z) have parallel planes separated by 3.319 (2) Å; the centroid separation is 3.412 (2) Å and the centroid offset is only ca 0.79 Å (Fig. 3). In this manner, the chain along (0, 1/2, z) is linked to each of the chains along (1/2, 0, z), (1/2, 1, z), (-1/2, 0, z) and (-1/2, 1, z), so forming a continuous bundle of chains.
In compound (II) (Fig. 4), the atoms C27, C47 and C67 are also nearly coplanar with the pyrimidine ring, and the conformation of the alkoxy groups is similar to that in (I) (Fig. 4, Table 3), although the phenyl groups each add two further rotational degrees of freedom. As in (I), there is no evidence of bond fixation or charge separation in the pyrimidine ring (Table 3). With only one N—H per molecule available for N—H···N hydrogen-bond formation, the supramolecular structure of (II) is much simpler than that of (I). The molecules are linked by the hydrogen bonds into centrosymmetric dimers (Fig. 5, Table 4), and there are no aromatic π···π stacking interactions, so that the supramolecular aggregation consists simply of one finite zero-dimensional dimer per unit cell, with no direction-specific interactions between these units.
We also report here the structure of the closely-related compound 2-amino-4,6-bis(N-pyrrolidino)pyrimidine, (III). We have recently investigated the structure of the 5-nitroso analogue, (IV) (Quesada et al., 2002). However, not only were the crystals of (II) should this be (IV)?, obtainable only as a partial hydrate, of consistently poor quality [indeed, analogues of (IV) containing other secondary amino substituents cannot be crystallized at all], but the structure of (IV) was characterized by pseudosymmetry between the two independent molecules, by multiple disorder, both in the orientations of the two nitroso groups and in the conformations of the four independent pyrrolidine rings, and by partial occupancy of each of the two independent water sites. Because of the poor diffraction data and the multiple disorder, no meaningful conclusions could be drawn about the intramolecular structural parameters for (IV), although the supramolecular structure, which takes the form of centrosymmetric six-molecule aggregates, was readily established.
In compound (III) (Fig. 6), by contrast, the intramolecular distances and angles are all well defined (Table 5). The four C—N distances within the pyrimidine ring, as well as the three exocyclic C—N distances involving three-connected C, all lie within the rather narrow range 1.346 (2)–1.359 (2) Å. This range of values is somewhat higher than the mean value of 1.333 Å for pyrimidines in general (Allen et al., 1987) but, overall, the C—N and C—C distances within the pyrimidine ring of (I) should this be (III)? are consistent with aromatic delocalization, with no significant bond fixation. At each of N4 and N6, the sum of the bond angles indicates planar N, consistent with the C4—N4 and C6—N6 distances (Allen et al., 1987), and typical of amino N bonded to an aromatic or heteroaromatic ring. While the pyrrolidine rings exhibit the puckered conformation characteristic of saturated five-membered rings, there is no evidence, either from difference maps or from the displacement parameters, for any positional disorder of the C atoms in these rings. The CNC2 planes centred on N4 and N6 are only very slightly twisted out of the plane of the pyrimidine ring (Table 5). The overall conformation of the molecule of (III) is very close to having local twofold rotational symmetry. This is illustrated not only by the torsion angles within the pyrrolidine rings (Table 5) but, perhaps more strikingly, by the location of the H atoms in these rings (Fig. 6). However, a search for possible additional symmetry revealed none.
The supramolecular structure of (III) takes the form of a chain of fused rings, similar to that found in (I). The amino group acts as a double donor in the intermolecular N—H···N hydrogen bonds, where the acceptors are the two ring N atoms (Table 6); the planar pyrrolidine N atoms play no part in the supramolecular aggregation. Amino atom N2 at (x, y, z) acts as a hydrogen-bond donor, via atom H2A, to ring atom N1 at (x, 1 - y, -z), so forming an R22(8) motif centred at (0, 1/2, 0). This amino atom N2 at (x, y, z) also acts as a donor, via atom H2B, to ring atom N3 at (-x, y, 1/2 - z), so forming a second R22(8) motif, this time generated by the twofold rotation axis along (0, y, 1/4). The combination of these two distinct R22(8) motifs, the one containing atoms N1 and N2 and the other containing atoms N2 and N3, generates a chain of fused rings running parallel to the [001] direction (Fig. 6), generated by inversion centres at (0, 1/2, n/2) (for n = zero or integer) and twofold axes along (0, y, 1/4 + n/2) (n = zero or integer). Two of these chains run through each unit cell, but there are no direction-specific interactions between adjacent chains. In particular, the π···π stacking interactions found in (I) are absent from the structure of (III). We note that this type of supramolecular aggregation would be possible even if the molecules of (III) had been located on twofold rotation axes.
It is of interest to compare the conformations and supramolecular aggregation in compounds (I) and (II) with those in the related compound, (V) (Quesada et al., 2002), which is analogous to (I) in containing an unsubstituted amino group, and to (II) in containing two benzyloxy substituents. In (V), where the conformation of the alkoxy substitutents is identical to those in (I) and (II), hydrogen-bonded R22(8) dimers precisely analogous to those in (II) are linked into a molecular ladder by N—H···O hydrogen bonds, with atom O4 as the acceptor. By contrast, the O atoms in (I) and (II) play no role in the hydrogen bonding, as noted above. Likewise, the supramolecular structures of (I), (III) and (V) can be contrasted with that of 2-aminopyrimidine, (VI), itself (Scheinbeim & Schempp, 1976; Furberg et al., 1979). The molecules of (VI) act as double donors and double acceptors of N—H···N hydrogen bonds and two motifs are generated, by a centre of inversion and by a glide plane, leading to the formation of sheets.