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In both 1-(2-cyanoethyl)thymine [systematic name: 3-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)propanenitrile], C
8H
9N
3O
2, (I), and 1-(3-cyanopropyl)thymine [systematic name: 4-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)butanenitrile], C
9H
11N
3O
2, (II), the core of the supramolecular structure is formed by centrosymmetric dimers generated by N—H
O hydrogen bonds. Further weak hydrogen bonds of C—H
O and C—H
N types generate molecular tapes and sheets that resemble those in uracil and its methyl derivatives. The steric hindrance that arises from the cyanoalkyl substituents perturbs the conformations of the tapes and sheets.
Supporting information
CCDC references: 641821; 641822
The synthesis of 1-(3-cyanopropyl)thymine, (II), was described by Spychała
(2000). Crystals of (II) suitable for X-ray data collection were grown from a
solution in methanol by slow cooling. 1-(2-Cyanoethyl)thymine, (I), was
prepared by the same N-alkylation procedure from thymine and
3-bromopropionitrile and recrystallized from methanol (m.p. 472–474 K).
Spectroscopic analysis: 1H NMR (DMSO-d6, TMS, δ, p.p.m.): 1.75
(s, 3H, CH3), 2.88 (t, 2H, J = 6.4 Hz, CH2), 3.89
(t, 2H, J = 6.6 Hz, CH2), 7.55 (s, 1H, C6H), 11.33
(br s, 1H, N3H); 13C NMR (DMSO-d6, TMS, δ, p.p.m.): 11.9,
16.8, 43.0, 99.8, 108.8, 118.8, 150.7, 164.2; FT–IR (KBr, νmax, cm-1):
3032, 2831, 2245, 1720, 1666, 1480, 1459, 1430, 1389; HRMS (EI): M+,
found 179.0693; C8H9N3O2 requires 179.0695. The instrumentation and
analysis methods have been described by Spychała (2000).
For both compounds, data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell refinement: CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Stereochemical Workstation Operation Manual (Siemens, 1989) and Mercury (Macrae et al., 2006); software used to prepare material for publication: Please provide missing details.
(I) 3-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)propanenitrile
top
Crystal data top
C8H9N3O2 | F(000) = 376 |
Mr = 179.18 | Dx = 1.374 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
a = 11.2597 (4) Å | Cell parameters from 3997 reflections |
b = 4.4118 (2) Å | θ = 2.3–29.6° |
c = 17.6256 (6) Å | µ = 0.10 mm−1 |
β = 98.253 (3)° | T = 293 K |
V = 866.49 (6) Å3 | Block, colourless |
Z = 4 | 0.45 × 0.2 × 0.2 mm |
Data collection top
Kuma KM4 CCD area-detector diffractometer | 2187 independent reflections |
Radiation source: fine-focus sealed tube | 1423 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.018 |
ω scans | θmax = 29.6°, θmin = 2.3° |
Absorption correction: multi-scan CrysAlis RED (Oxford Diffraction 2006) | h = −15→15 |
Tmin = 0.837, Tmax = 0.980 | k = −5→5 |
8802 measured reflections | l = −23→22 |
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)] = 0.037 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.117 | All H-atom parameters refined |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0659P)2 + 0.0478P] where P = (Fo2 + 2Fc2)/3 |
2187 reflections | (Δ/σ)max < 0.001 |
154 parameters | Δρmax = 0.19 e Å−3 |
0 restraints | Δρmin = −0.20 e Å−3 |
Crystal data top
C8H9N3O2 | V = 866.49 (6) Å3 |
Mr = 179.18 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 11.2597 (4) Å | µ = 0.10 mm−1 |
b = 4.4118 (2) Å | T = 293 K |
c = 17.6256 (6) Å | 0.45 × 0.2 × 0.2 mm |
β = 98.253 (3)° | |
Data collection top
Kuma KM4 CCD area-detector diffractometer | 2187 independent reflections |
Absorption correction: multi-scan CrysAlis RED (Oxford Diffraction 2006) | 1423 reflections with I > 2σ(I) |
Tmin = 0.837, Tmax = 0.980 | Rint = 0.018 |
8802 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.037 | 0 restraints |
wR(F2) = 0.117 | All H-atom parameters refined |
S = 1.04 | Δρmax = 0.19 e Å−3 |
2187 reflections | Δρmin = −0.20 e Å−3 |
154 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 | |
N1 | 0.69015 (9) | 0.4338 (2) | 0.16614 (5) | 0.0330 (3) | |
C2 | 0.57613 (10) | 0.5355 (3) | 0.13772 (7) | 0.0328 (3) | |
O2 | 0.48757 (8) | 0.4579 (2) | 0.16478 (5) | 0.0470 (3) | |
N3 | 0.57166 (9) | 0.7327 (3) | 0.07725 (6) | 0.0355 (3) | |
H3 | 0.4986 (15) | 0.804 (3) | 0.0571 (8) | 0.048 (4)* | |
C4 | 0.66662 (11) | 0.8317 (3) | 0.04233 (7) | 0.0349 (3) | |
O4 | 0.65004 (8) | 1.0135 (2) | −0.01110 (5) | 0.0503 (3) | |
C5 | 0.78282 (10) | 0.7107 (3) | 0.07342 (7) | 0.0345 (3) | |
C6 | 0.78883 (11) | 0.5213 (3) | 0.13305 (7) | 0.0341 (3) | |
C11 | 0.70402 (13) | 0.2323 (3) | 0.23290 (7) | 0.0375 (3) | |
H11A | 0.7741 (13) | 0.116 (3) | 0.2274 (8) | 0.042 (4)* | |
H11B | 0.6311 (13) | 0.113 (4) | 0.2313 (8) | 0.044 (4)* | |
C12 | 0.72076 (13) | 0.4038 (4) | 0.30899 (8) | 0.0416 (3) | |
H12A | 0.7238 (13) | 0.257 (3) | 0.3547 (8) | 0.053 (4)* | |
H12B | 0.6548 (15) | 0.530 (4) | 0.3159 (9) | 0.055 (4)* | |
C13 | 0.83109 (14) | 0.5819 (4) | 0.31961 (8) | 0.0483 (4) | |
N13 | 0.91629 (13) | 0.7239 (4) | 0.32592 (8) | 0.0734 (5) | |
C51 | 0.88965 (13) | 0.8001 (5) | 0.03697 (9) | 0.0513 (4) | |
H51A | 0.8989 (17) | 1.027 (5) | 0.0298 (12) | 0.086 (6)* | |
H51B | 0.8827 (15) | 0.719 (4) | −0.0157 (11) | 0.071 (5)* | |
H51C | 0.9619 (16) | 0.713 (4) | 0.0613 (10) | 0.070 (5)* | |
H6 | 0.8604 (13) | 0.430 (3) | 0.1547 (8) | 0.039 (4)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0316 (5) | 0.0355 (6) | 0.0317 (5) | 0.0039 (4) | 0.0033 (4) | 0.0017 (4) |
C2 | 0.0300 (6) | 0.0359 (7) | 0.0325 (6) | 0.0004 (5) | 0.0046 (5) | −0.0016 (5) |
O2 | 0.0339 (5) | 0.0557 (6) | 0.0534 (6) | 0.0004 (4) | 0.0129 (4) | 0.0100 (5) |
N3 | 0.0261 (5) | 0.0456 (7) | 0.0341 (6) | 0.0046 (4) | 0.0018 (4) | 0.0051 (5) |
C4 | 0.0316 (6) | 0.0435 (8) | 0.0291 (6) | 0.0011 (5) | 0.0027 (5) | 0.0019 (5) |
O4 | 0.0372 (5) | 0.0688 (7) | 0.0443 (6) | 0.0050 (4) | 0.0033 (4) | 0.0213 (5) |
C5 | 0.0279 (6) | 0.0453 (8) | 0.0305 (6) | 0.0024 (5) | 0.0045 (5) | −0.0017 (5) |
C6 | 0.0279 (6) | 0.0408 (7) | 0.0330 (6) | 0.0059 (5) | 0.0024 (5) | −0.0020 (5) |
C11 | 0.0412 (7) | 0.0340 (7) | 0.0367 (7) | 0.0031 (6) | 0.0041 (6) | 0.0051 (5) |
C12 | 0.0444 (8) | 0.0461 (8) | 0.0342 (7) | 0.0010 (6) | 0.0052 (6) | 0.0030 (6) |
C13 | 0.0531 (9) | 0.0515 (9) | 0.0362 (7) | −0.0002 (7) | −0.0071 (6) | 0.0060 (6) |
N13 | 0.0664 (9) | 0.0809 (11) | 0.0661 (10) | −0.0210 (8) | −0.0135 (7) | 0.0097 (8) |
C51 | 0.0337 (7) | 0.0759 (13) | 0.0463 (9) | 0.0046 (7) | 0.0127 (6) | 0.0107 (8) |
Geometric parameters (Å, º) top
N1—C6 | 1.3820 (16) | C2—N3 | 1.3709 (16) |
N1—C2 | 1.3841 (15) | N3—C4 | 1.3791 (16) |
N1—C11 | 1.4652 (15) | N3—H3 | 0.903 (16) |
C11—C12 | 1.5279 (18) | C4—O4 | 1.2306 (15) |
C11—H11A | 0.958 (15) | C4—C5 | 1.4462 (17) |
C11—H11B | 0.972 (15) | C5—C6 | 1.3365 (18) |
C12—C13 | 1.459 (2) | C5—C51 | 1.4958 (18) |
C12—H12A | 1.030 (15) | C51—H51A | 1.02 (2) |
C12—H12B | 0.951 (17) | C51—H51B | 0.988 (18) |
C13—N13 | 1.1378 (19) | C51—H51C | 0.945 (17) |
C2—O2 | 1.2148 (14) | C6—H6 | 0.933 (14) |
| | | |
C6—N1—C2 | 121.12 (10) | C2—N3—C4 | 127.13 (10) |
C6—N1—C11 | 120.60 (10) | C2—N3—H3 | 117.0 (9) |
C2—N1—C11 | 118.28 (10) | C4—N3—H3 | 115.8 (9) |
N1—C11—C12 | 112.95 (11) | O4—C4—N3 | 120.39 (11) |
N1—C11—H11A | 103.8 (9) | O4—C4—C5 | 124.07 (11) |
C12—C11—H11A | 110.8 (8) | N3—C4—C5 | 115.54 (11) |
N1—C11—H11B | 108.2 (8) | C6—C5—C4 | 118.01 (11) |
C12—C11—H11B | 106.9 (8) | C6—C5—C51 | 123.33 (12) |
H11A—C11—H11B | 114.2 (13) | C4—C5—C51 | 118.65 (12) |
C13—C12—C11 | 112.01 (12) | C5—C51—H51A | 114.6 (11) |
C13—C12—H12A | 107.8 (8) | C5—C51—H51B | 110.3 (10) |
C11—C12—H12A | 111.2 (8) | H51A—C51—H51B | 103.6 (16) |
C13—C12—H12B | 109.5 (10) | C5—C51—H51C | 112.9 (10) |
C11—C12—H12B | 113.8 (9) | H51A—C51—H51C | 111.2 (16) |
H12A—C12—H12B | 102.0 (12) | H51B—C51—H51C | 103.1 (14) |
N13—C13—C12 | 178.12 (15) | C5—C6—N1 | 123.60 (11) |
O2—C2—N3 | 122.92 (11) | C5—C6—H6 | 122.4 (8) |
O2—C2—N1 | 122.51 (12) | N1—C6—H6 | 113.9 (8) |
N3—C2—N1 | 114.56 (10) | | |
| | | |
C6—N1—C11—C12 | 92.05 (14) | C2—N3—C4—C5 | 0.37 (19) |
C2—N1—C11—C12 | −87.42 (14) | O4—C4—C5—C6 | 178.10 (12) |
N1—C11—C12—C13 | −63.62 (15) | N3—C4—C5—C6 | −1.20 (18) |
C6—N1—C2—O2 | 178.61 (11) | O4—C4—C5—C51 | −2.6 (2) |
C11—N1—C2—O2 | −1.93 (18) | N3—C4—C5—C51 | 178.13 (13) |
C6—N1—C2—N3 | −2.00 (17) | C4—C5—C6—N1 | 0.44 (19) |
C11—N1—C2—N3 | 177.47 (10) | C51—C5—C6—N1 | −178.86 (13) |
O2—C2—N3—C4 | −179.40 (12) | C2—N1—C6—C5 | 1.27 (19) |
N1—C2—N3—C4 | 1.21 (18) | C11—N1—C6—C5 | −178.19 (12) |
C2—N3—C4—O4 | −178.96 (11) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3···O4i | 0.903 (16) | 1.929 (17) | 2.8301 (14) | 174.8 (14) |
C11—H11B···O2ii | 0.972 (15) | 2.513 (14) | 3.2386 (17) | 131.4 (10) |
C12—H12B···O2iii | 0.951 (17) | 2.530 (18) | 3.4645 (18) | 167.6 (13) |
C6—H6···N13iv | 0.933 (14) | 2.649 (15) | 3.5468 (19) | 161.7 (11) |
Symmetry codes: (i) −x+1, −y+2, −z; (ii) −x+1, y−1/2, −z+1/2; (iii) −x+1, y+1/2, −z+1/2; (iv) −x+2, y−1/2, −z+1/2. |
(II) 4-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)butanenitrile
top
Crystal data top
C9H11N3O2 | Z = 2 |
Mr = 193.21 | F(000) = 204 |
Triclinic, P1 | Dx = 1.345 Mg m−3 |
a = 4.8591 (8) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 9.8205 (12) Å | Cell parameters from 2362 reflections |
c = 10.5979 (11) Å | θ = 2.6–29.7° |
α = 75.815 (10)° | µ = 0.10 mm−1 |
β = 78.364 (12)° | T = 293 K |
γ = 80.780 (11)° | Plate, colourless |
V = 476.94 (11) Å3 | 0.6 × 0.3 × 0.1 mm |
Data collection top
Kuma KM4 CCD area-detector diffractometer | 2368 independent reflections |
Radiation source: fine-focus sealed tube | 1842 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.011 |
ω scans | θmax = 29.7°, θmin = 2.6° |
Absorption correction: multi-scan CrysAlis RED (Oxford Diffraction 2006) | h = −6→4 |
Tmin = 0.969, Tmax = 1.000 | k = −13→13 |
4787 measured reflections | l = −14→14 |
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)] = 0.039 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.121 | All H-atom parameters refined |
S = 1.07 | w = 1/[σ2(Fo2) + (0.0762P)2 + 0.0211P] where P = (Fo2 + 2Fc2)/3 |
2368 reflections | (Δ/σ)max < 0.001 |
171 parameters | Δρmax = 0.22 e Å−3 |
0 restraints | Δρmin = −0.24 e Å−3 |
Crystal data top
C9H11N3O2 | γ = 80.780 (11)° |
Mr = 193.21 | V = 476.94 (11) Å3 |
Triclinic, P1 | Z = 2 |
a = 4.8591 (8) Å | Mo Kα radiation |
b = 9.8205 (12) Å | µ = 0.10 mm−1 |
c = 10.5979 (11) Å | T = 293 K |
α = 75.815 (10)° | 0.6 × 0.3 × 0.1 mm |
β = 78.364 (12)° | |
Data collection top
Kuma KM4 CCD area-detector diffractometer | 2368 independent reflections |
Absorption correction: multi-scan CrysAlis RED (Oxford Diffraction 2006) | 1842 reflections with I > 2σ(I) |
Tmin = 0.969, Tmax = 1.000 | Rint = 0.011 |
4787 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.039 | 0 restraints |
wR(F2) = 0.121 | All H-atom parameters refined |
S = 1.07 | Δρmax = 0.22 e Å−3 |
2368 reflections | Δρmin = −0.24 e Å−3 |
171 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 | |
N1 | 0.50209 (17) | 0.33709 (9) | 0.79194 (8) | 0.0372 (2) | |
C2 | 0.2855 (2) | 0.43986 (11) | 0.75638 (10) | 0.0361 (2) | |
O2 | 0.16684 (18) | 0.52289 (9) | 0.82454 (8) | 0.0500 (2) | |
N3 | 0.20966 (17) | 0.44027 (9) | 0.63776 (8) | 0.0364 (2) | |
H3 | 0.068 (3) | 0.5047 (16) | 0.6142 (14) | 0.051 (3)* | |
C4 | 0.3384 (2) | 0.35642 (11) | 0.55030 (10) | 0.0342 (2) | |
O4 | 0.25319 (16) | 0.37071 (9) | 0.44499 (8) | 0.0464 (2) | |
C5 | 0.5724 (2) | 0.25585 (10) | 0.59085 (10) | 0.0370 (2) | |
C6 | 0.6387 (2) | 0.25031 (11) | 0.70908 (10) | 0.0378 (2) | |
H6 | 0.786 (3) | 0.1834 (15) | 0.7423 (15) | 0.056 (4)* | |
C11 | 0.5778 (2) | 0.31798 (13) | 0.92343 (11) | 0.0413 (3) | |
H11B | 0.754 (3) | 0.2562 (15) | 0.9210 (14) | 0.053 (4)* | |
H11A | 0.620 (3) | 0.4062 (16) | 0.9349 (14) | 0.054 (4)* | |
C12 | 0.3514 (2) | 0.25179 (14) | 1.03188 (11) | 0.0458 (3) | |
H12B | 0.174 (3) | 0.3214 (17) | 1.0369 (16) | 0.070 (4)* | |
H12A | 0.311 (3) | 0.1647 (15) | 1.0101 (14) | 0.050 (3)* | |
C13 | 0.4400 (3) | 0.21409 (16) | 1.16776 (12) | 0.0543 (3) | |
H13B | 0.274 (4) | 0.1850 (18) | 1.237 (2) | 0.086 (5)* | |
H13A | 0.497 (4) | 0.296 (2) | 1.1906 (17) | 0.080 (5)* | |
C14 | 0.6690 (3) | 0.09841 (14) | 1.17855 (12) | 0.0532 (3) | |
N14 | 0.8451 (3) | 0.00833 (16) | 1.18472 (16) | 0.0857 (5) | |
C51 | 0.7281 (3) | 0.16313 (16) | 0.50001 (15) | 0.0551 (3) | |
H51C | 0.809 (4) | 0.225 (2) | 0.412 (2) | 0.095 (6)* | |
H51B | 0.614 (4) | 0.100 (2) | 0.485 (2) | 0.095 (6)* | |
H51A | 0.876 (4) | 0.106 (2) | 0.536 (2) | 0.099 (6)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0355 (4) | 0.0418 (5) | 0.0327 (4) | 0.0032 (3) | −0.0084 (3) | −0.0077 (3) |
C2 | 0.0341 (5) | 0.0386 (5) | 0.0334 (5) | 0.0011 (4) | −0.0051 (4) | −0.0077 (4) |
O2 | 0.0535 (5) | 0.0530 (5) | 0.0428 (4) | 0.0127 (4) | −0.0094 (4) | −0.0202 (4) |
N3 | 0.0323 (4) | 0.0397 (5) | 0.0354 (4) | 0.0056 (3) | −0.0086 (3) | −0.0091 (4) |
C4 | 0.0316 (5) | 0.0366 (5) | 0.0339 (5) | −0.0027 (4) | −0.0048 (4) | −0.0084 (4) |
O4 | 0.0434 (4) | 0.0575 (5) | 0.0407 (4) | 0.0060 (3) | −0.0143 (3) | −0.0173 (3) |
C5 | 0.0362 (5) | 0.0334 (5) | 0.0409 (5) | 0.0011 (4) | −0.0059 (4) | −0.0109 (4) |
C6 | 0.0346 (5) | 0.0354 (5) | 0.0404 (5) | 0.0043 (4) | −0.0081 (4) | −0.0068 (4) |
C11 | 0.0396 (5) | 0.0491 (6) | 0.0366 (5) | 0.0002 (5) | −0.0137 (4) | −0.0096 (4) |
C12 | 0.0417 (6) | 0.0579 (7) | 0.0354 (5) | 0.0019 (5) | −0.0102 (4) | −0.0080 (5) |
C13 | 0.0618 (8) | 0.0637 (8) | 0.0346 (6) | 0.0053 (6) | −0.0124 (5) | −0.0104 (5) |
C14 | 0.0564 (7) | 0.0564 (7) | 0.0427 (6) | −0.0067 (6) | −0.0151 (5) | 0.0025 (5) |
N14 | 0.0721 (8) | 0.0768 (9) | 0.0889 (10) | 0.0134 (7) | −0.0226 (7) | 0.0109 (8) |
C51 | 0.0574 (7) | 0.0521 (7) | 0.0595 (8) | 0.0139 (6) | −0.0144 (6) | −0.0286 (6) |
Geometric parameters (Å, º) top
N1—C6 | 1.3743 (14) | C2—O2 | 1.2203 (13) |
N1—C2 | 1.3788 (13) | C2—N3 | 1.3786 (12) |
N1—C11 | 1.4728 (13) | N3—C4 | 1.3797 (13) |
C11—C12 | 1.5191 (17) | N3—H3 | 0.888 (15) |
C11—H11B | 0.966 (15) | C4—O4 | 1.2362 (12) |
C11—H11A | 0.962 (16) | C4—C5 | 1.4427 (13) |
C12—C13 | 1.5277 (15) | C5—C6 | 1.3420 (14) |
C12—H12B | 1.010 (16) | C5—C51 | 1.4977 (16) |
C12—H12A | 0.996 (14) | C51—H51C | 1.02 (2) |
C13—C14 | 1.4578 (19) | C51—H51B | 0.96 (2) |
C13—H13B | 1.00 (2) | C51—H51A | 0.92 (2) |
C13—H13A | 0.988 (18) | C6—H6 | 0.953 (14) |
C14—N14 | 1.1272 (18) | | |
| | | |
C6—N1—C2 | 121.12 (8) | O2—C2—N3 | 122.29 (9) |
C6—N1—C11 | 120.22 (8) | O2—C2—N1 | 123.18 (9) |
C2—N1—C11 | 118.61 (9) | N3—C2—N1 | 114.53 (9) |
N1—C11—C12 | 111.35 (9) | C2—N3—C4 | 126.95 (8) |
N1—C11—H11B | 104.9 (8) | C2—N3—H3 | 115.6 (9) |
C12—C11—H11B | 110.8 (9) | C4—N3—H3 | 117.3 (9) |
N1—C11—H11A | 110.0 (9) | O4—C4—N3 | 120.22 (9) |
C12—C11—H11A | 113.2 (9) | O4—C4—C5 | 124.29 (9) |
H11B—C11—H11A | 106.1 (11) | N3—C4—C5 | 115.49 (8) |
C11—C12—C13 | 112.52 (10) | C6—C5—C4 | 117.84 (9) |
C11—C12—H12B | 109.2 (9) | C6—C5—C51 | 123.33 (10) |
C13—C12—H12B | 107.2 (9) | C4—C5—C51 | 118.83 (10) |
C11—C12—H12A | 108.5 (8) | C5—C51—H51C | 109.4 (11) |
C13—C12—H12A | 109.4 (8) | C5—C51—H51B | 113.8 (13) |
H12B—C12—H12A | 110.0 (12) | H51C—C51—H51B | 109.3 (17) |
C14—C13—C12 | 112.22 (11) | C5—C51—H51A | 110.1 (13) |
C14—C13—H13B | 108.2 (10) | H51C—C51—H51A | 108.7 (17) |
C12—C13—H13B | 109.6 (10) | H51B—C51—H51A | 105.5 (17) |
C14—C13—H13A | 108.9 (11) | C5—C6—N1 | 123.91 (9) |
C12—C13—H13A | 112.3 (10) | C5—C6—H6 | 121.4 (9) |
H13B—C13—H13A | 105.3 (15) | N1—C6—H6 | 114.7 (9) |
N14—C14—C13 | 178.63 (15) | | |
| | | |
C6—N1—C11—C12 | −106.37 (12) | C2—N3—C4—O4 | −177.87 (9) |
C2—N1—C11—C12 | 71.29 (13) | C2—N3—C4—C5 | 1.72 (15) |
N1—C11—C12—C13 | 173.01 (10) | O4—C4—C5—C6 | −178.88 (10) |
C11—C12—C13—C14 | −68.41 (16) | N3—C4—C5—C6 | 1.55 (14) |
C6—N1—C2—O2 | −176.83 (10) | O4—C4—C5—C51 | 0.99 (17) |
C11—N1—C2—O2 | 5.53 (16) | N3—C4—C5—C51 | −178.57 (11) |
C6—N1—C2—N3 | 4.14 (15) | C4—C5—C6—N1 | −1.78 (17) |
C11—N1—C2—N3 | −173.50 (9) | C51—C5—C6—N1 | 178.35 (11) |
O2—C2—N3—C4 | 176.44 (10) | C2—N1—C6—C5 | −1.24 (17) |
N1—C2—N3—C4 | −4.51 (15) | C11—N1—C6—C5 | 176.36 (10) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3···O4i | 0.888 (15) | 1.932 (16) | 2.8165 (12) | 173.6 (13) |
C6—H6···N14ii | 0.953 (14) | 2.472 (15) | 3.4211 (16) | 173.6 (11) |
C13—H13A···O2iii | 0.988 (18) | 2.557 (18) | 3.4751 (19) | 154.5 (14) |
C12—H12B···O2iv | 1.010 (16) | 2.560 (17) | 3.4454 (15) | 146.3 (12) |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x+2, −y, −z+2; (iii) −x+1, −y+1, −z+2; (iv) −x, −y+1, −z+2. |
Experimental details
| (I) | (II) |
Crystal data |
Chemical formula | C8H9N3O2 | C9H11N3O2 |
Mr | 179.18 | 193.21 |
Crystal system, space group | Monoclinic, P21/c | Triclinic, P1 |
Temperature (K) | 293 | 293 |
a, b, c (Å) | 11.2597 (4), 4.4118 (2), 17.6256 (6) | 4.8591 (8), 9.8205 (12), 10.5979 (11) |
α, β, γ (°) | 90, 98.253 (3), 90 | 75.815 (10), 78.364 (12), 80.780 (11) |
V (Å3) | 866.49 (6) | 476.94 (11) |
Z | 4 | 2 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.10 | 0.10 |
Crystal size (mm) | 0.45 × 0.2 × 0.2 | 0.6 × 0.3 × 0.1 |
|
Data collection |
Diffractometer | Kuma KM4 CCD area-detector diffractometer | Kuma KM4 CCD area-detector diffractometer |
Absorption correction | Multi-scan CrysAlis RED (Oxford Diffraction 2006) | Multi-scan CrysAlis RED (Oxford Diffraction 2006) |
Tmin, Tmax | 0.837, 0.980 | 0.969, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8802, 2187, 1423 | 4787, 2368, 1842 |
Rint | 0.018 | 0.011 |
(sin θ/λ)max (Å−1) | 0.695 | 0.697 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.117, 1.04 | 0.039, 0.121, 1.07 |
No. of reflections | 2187 | 2368 |
No. of parameters | 154 | 171 |
H-atom treatment | All H-atom parameters refined | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.19, −0.20 | 0.22, −0.24 |
Hydrogen-bond geometry (Å, º) for (I) top
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3···O4i | 0.903 (16) | 1.929 (17) | 2.8301 (14) | 174.8 (14) |
C11—H11B···O2ii | 0.972 (15) | 2.513 (14) | 3.2386 (17) | 131.4 (10) |
C12—H12B···O2iii | 0.951 (17) | 2.530 (18) | 3.4645 (18) | 167.6 (13) |
C6—H6···N13iv | 0.933 (14) | 2.649 (15) | 3.5468 (19) | 161.7 (11) |
Symmetry codes: (i) −x+1, −y+2, −z; (ii) −x+1, y−1/2, −z+1/2; (iii) −x+1, y+1/2, −z+1/2; (iv) −x+2, y−1/2, −z+1/2. |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3···O4i | 0.888 (15) | 1.932 (16) | 2.8165 (12) | 173.6 (13) |
C6—H6···N14ii | 0.953 (14) | 2.472 (15) | 3.4211 (16) | 173.6 (11) |
C13—H13A···O2iii | 0.988 (18) | 2.557 (18) | 3.4751 (19) | 154.5 (14) |
C12—H12B···O2iv | 1.010 (16) | 2.560 (17) | 3.4454 (15) | 146.3 (12) |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x+2, −y, −z+2; (iii) −x+1, −y+1, −z+2; (iv) −x, −y+1, −z+2. |
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In the course of our studies of the hierarchy of intermolecular interactions in crystals (Borowiak et al., 2006; Kubicki et al., 2001, 2002; Kubicki, 2004), the supramolecular structures of two thymine derivatives, 1-(2-cyanoethyl)thymine, (I), and 1-(3-cyanopropyl)thymine, (II), have been determined. Both molecules contain a planar thymine ring and, of the several possible tautomeric forms for the ring, the diketo tautomer is observed in the solid state (Figs. 1 and 2). Appreciable differences are observed in the values of the C═O bond lengths [C2═O2 = 1.216 (1) and 1.221 (1) Å for (I) and (II), respectively; C4═O4 = 1.233 (1) and 1.237 (2) Å for (I) and (II), respectively]. The existence of two different C═O groups can be easily rationalized by observing the respective crystal structures.
In (I) and (II), centrosymmetric dimers are formed via N3—H3···O4═ C4 hydrogen bonds. For this reason, C4═O4 is longer than the standard carbonyl double bond (Standard reference?). The second carbonyl group, C2═O2, is involved only in weak C—H···O hydrogen bonds (Table 1 and 2), and this bond is shorter [Than what?]. The geometric perturbation is mainly due to self-association and confirms the fundamental role of conjugative stabilization of the intermolecular hydrogen bonding.
The C═O bond-length pattern in (I) and (II) is in agreement with those in other uracil derivatives. In the structure of (1-thyminyl)acetamide (Borowiak et al., 2006), the centrosymmetric dimers are formed via N3—H3···O2═C2 hydrogen bonds and, in consequence, the C2═O2 bond is longer. Similar appreciable discrepancies in the C═O bond lengths have also been found in the structures of uracil (Portalone et al., 1999), thymine (Portalone et al., 1999) or 1-methyluracil (McMullan & Craven, 1989). The hydrogen bonding in the crystal structures of uracil and 1-methyluracil involves atom O4 as acceptor of a strong hydrogen bond but not atom O2. In the structure of 1,3-dimethyluracil, the equivalence of the carbonyl groups is explained by the fact that no C═O···H—N hydrogen bond is possible (Banerjee et al., 1977).
Although the molecules of (I) and (II) differ only by one CH2 group in the substituent at N1 and intermolecular interactions are of the same type, the supramolecular motifs in their crystal structures differ due to the steric factor determined by the length of the chain. The centrosymmetric dimers form the cores of the supramolecular structures, which are further based on continuous tapes.
In (I), the planar N3—H3···O4 dimers are connected by C12—H12B···O2 and C11—H11B···O2 hydrogen bonds, thus forming the second kind of dimer, a non-centrosymmetric one (Fig. 3a). These two consecutive dimers extend to form a molecular tape. On the other hand, two centrosymmetric dimers separated by a non-centrosymmetric one in each tape are set almost perpendicular to one another, giving rise to a sinusoidal shape of tapes (the angle between the planes of two flat dimers is about 78° (Fig. 3b).
The tapes are connected in turn by weak C6—H6···N13 hydrogen bonds. Moreover, the thymine moieties of (I) are mutually oriented in a parallel mode along the shortest unit cell axis [b = 4.412 (1) Å] (Fig. 3b). As a consequence of the tape conformation, two different orientations of columns are observed, with the distance between mutually parallel rings being 3.42 (1) Å. The stacking of molecules in (I) occurs with no overlap of pyrimidine rings.
In (II), the core of the supramolecular structure is also defined by centrosymmetric dimers formed via the same type of hydrogen bonds, N3—H3···O4 (Table 2). These dimers are further connected by weak C12—H12B···O2 hydrogen bonds that form another centrosymmetric dimer (Fig. 4a). These consecutive dimers are linked into continuous tapes which are, however, not planar, as small steps are found in their conformation (Fig. 4b).
The tapes are further connected into sheets by the third type of centrosymmetric dimer created via weak C6—H6···N14 hydrogen bonds (Fig. 4a). The same steps occur in the conformation of the sheets. As in (I), the uracil moieties in (II) also form a parallel mode of packing along the shortest unit cell axis [a = 4.859 (1) Å]. Also in (II), no overlap of the pyrimidine rings is observed.
The features of the supramolecular structures of uracil and its methyl derivatives are retained in compounds (I) and (II), although steric hindrance causes disturbances in the conformations of the tapes and sheets. No carbonyl–carbonyl interactions are found, although this kind of interaction is able to compete successfully with hydrogen bonds (Allen et al., 1998).