The crystal structure of isocytosine, 2-aminopyrimidin-4-(3H)-one, C4H5N3O, has been redetermined with higher precision. The asymmetric unit comprises a triply hydrogen-bonded adduct of two tautomers in an exact 1:1 ratio. Watson-Crick base pairing occurs between tautomers.
Supporting information
CCDC reference: 643081
Key indicators
- Single-crystal X-ray study
- T = 298 K
- Mean (C-C) = 0.003 Å
- R factor = 0.054
- wR factor = 0.187
- Data-to-parameter ratio = 16.4
checkCIF/PLATON results
No syntax errors found
Alert level C
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.22
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.41
0 ALERT level A = In general: serious problem
0 ALERT level B = Potentially serious problem
2 ALERT level C = Check and explain
0 ALERT level G = General alerts; check
0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
2 ALERT type 2 Indicator that the structure model may be wrong or deficient
0 ALERT type 3 Indicator that the structure quality may be low
0 ALERT type 4 Improvement, methodology, query or suggestion
0 ALERT type 5 Informative message, check
Data collection: XCS (Colapietro et al., 1992); cell refinement: XCS; data reduction: XCS; program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997).
Crystal data top
C4H5N3O | F(000) = 464 |
Mr = 111.11 | Dx = 1.415 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71069 Å |
Hall symbol: -P 2yn | Cell parameters from 54 reflections |
a = 8.7211 (6) Å | θ = 10–15° |
b = 11.4222 (8) Å | µ = 0.11 mm−1 |
c = 10.5027 (9) Å | T = 298 K |
β = 94.605 (14)° | Plate, colourless |
V = 1042.84 (14) Å3 | 0.20 × 0.20 × 0.10 mm |
Z = 8 | |
Data collection top
Huber CS four-circle diffractometer | Rint = 0.026 |
Radiation source: X-Ray tube | θmax = 30.0°, θmin = 2.6° |
Graphite monochromator | h = 0→13 |
ω scan | k = 0→16 |
3354 measured reflections | l = −15→15 |
2968 independent reflections | 3 standard reflections every 97 reflections |
2250 reflections with I > 2σ(I) | intensity decay: 1% |
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)] = 0.054 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.187 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.16 | w = 1/[σ2(Fo2) + (0.0743P)2 + 0.515P] where P = (Fo2 + 2Fc2)/3 |
2968 reflections | (Δ/σ)max < 0.001 |
181 parameters | Δρmax = 0.46 e Å−3 |
0 restraints | Δρmin = −0.24 e Å−3 |
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 | |
O1 | 0.51952 (17) | 0.46691 (14) | 0.22033 (16) | 0.0570 (4) | |
N1 | 0.11747 (17) | 0.42809 (17) | 0.38667 (17) | 0.0496 (4) | |
N3 | 0.35323 (16) | 0.52327 (14) | 0.36292 (15) | 0.0405 (3) | |
N4 | 0.1873 (2) | 0.5916 (2) | 0.5053 (2) | 0.0610 (5) | |
C2 | 0.21776 (19) | 0.51276 (17) | 0.41855 (18) | 0.0428 (4) | |
C4 | 0.3947 (2) | 0.44871 (17) | 0.26879 (19) | 0.0436 (4) | |
C5 | 0.2887 (2) | 0.35842 (19) | 0.2348 (2) | 0.0500 (4) | |
H5 | 0.3111 | 0.2952 | 0.1608 | 0.070* | |
C6 | 0.1581 (2) | 0.35235 (19) | 0.2967 (2) | 0.0493 (4) | |
O11 | 0.41213 (16) | 0.76237 (14) | 0.59008 (14) | 0.0536 (4) | |
N11 | 0.77190 (19) | 0.83352 (16) | 0.39455 (18) | 0.0519 (4) | |
N13 | 0.56682 (16) | 0.71040 (14) | 0.43765 (14) | 0.0396 (3) | |
N14 | 0.7220 (2) | 0.6647 (2) | 0.2788 (2) | 0.0617 (5) | |
C12 | 0.68681 (19) | 0.73568 (17) | 0.37174 (18) | 0.0435 (4) | |
C14 | 0.52788 (19) | 0.78428 (17) | 0.53182 (17) | 0.0409 (4) | |
C15 | 0.6200 (2) | 0.8877 (2) | 0.5593 (2) | 0.0525 (5) | |
C16 | 0.7385 (2) | 0.9085 (2) | 0.4887 (2) | 0.0552 (5) | |
H3 | 0.424 (3) | 0.586 (3) | 0.392 (3) | 0.070 (8)* | |
H4 | 0.089 (4) | 0.583 (3) | 0.541 (3) | 0.078 (8)* | |
H41 | 0.258 (3) | 0.643 (2) | 0.534 (3) | 0.063 (7)* | |
H6 | 0.076 (3) | 0.290 (2) | 0.273 (2) | 0.063 (7)* | |
H11 | 0.850 (4) | 0.858 (3) | 0.344 (3) | 0.086 (9)* | |
H14 | 0.792 (3) | 0.685 (2) | 0.226 (3) | 0.066 (8)* | |
H141 | 0.659 (3) | 0.598 (3) | 0.259 (3) | 0.073 (8)* | |
H15 | 0.594 (4) | 0.937 (3) | 0.628 (3) | 0.090 (10)* | |
H16 | 0.807 (3) | 0.971 (3) | 0.507 (3) | 0.074 (8)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0496 (7) | 0.0559 (9) | 0.0703 (9) | 0.0020 (6) | 0.0338 (7) | −0.0076 (7) |
N1 | 0.0358 (7) | 0.0598 (10) | 0.0547 (9) | −0.0103 (7) | 0.0136 (6) | −0.0105 (8) |
N3 | 0.0337 (6) | 0.0445 (8) | 0.0455 (8) | −0.0029 (6) | 0.0159 (5) | −0.0040 (6) |
N4 | 0.0444 (8) | 0.0738 (12) | 0.0690 (12) | −0.0198 (9) | 0.0305 (8) | −0.0285 (10) |
C2 | 0.0345 (7) | 0.0499 (10) | 0.0459 (9) | −0.0066 (7) | 0.0158 (6) | −0.0047 (8) |
C4 | 0.0397 (8) | 0.0445 (9) | 0.0486 (9) | 0.0049 (7) | 0.0168 (7) | −0.0002 (7) |
C5 | 0.0482 (10) | 0.0510 (10) | 0.0516 (10) | 0.0009 (8) | 0.0094 (8) | −0.0118 (9) |
C6 | 0.0420 (9) | 0.0520 (11) | 0.0542 (11) | −0.0057 (8) | 0.0055 (8) | −0.0084 (9) |
O11 | 0.0446 (7) | 0.0629 (9) | 0.0571 (8) | −0.0130 (6) | 0.0278 (6) | −0.0125 (7) |
N11 | 0.0415 (8) | 0.0568 (10) | 0.0599 (10) | −0.0140 (7) | 0.0201 (7) | 0.0073 (8) |
N13 | 0.0335 (6) | 0.0456 (8) | 0.0421 (7) | −0.0054 (6) | 0.0167 (5) | 0.0019 (6) |
N14 | 0.0593 (10) | 0.0672 (12) | 0.0643 (11) | −0.0117 (9) | 0.0404 (9) | −0.0058 (9) |
C12 | 0.0355 (7) | 0.0503 (10) | 0.0469 (9) | −0.0026 (7) | 0.0169 (7) | 0.0081 (8) |
C14 | 0.0329 (7) | 0.0478 (9) | 0.0435 (8) | −0.0021 (7) | 0.0125 (6) | 0.0006 (7) |
C15 | 0.0507 (10) | 0.0515 (11) | 0.0569 (11) | −0.0107 (9) | 0.0147 (9) | −0.0068 (9) |
C16 | 0.0476 (10) | 0.0538 (11) | 0.0653 (13) | −0.0175 (9) | 0.0108 (9) | 0.0016 (10) |
Geometric parameters (Å, º) top
O1—C4 | 1.255 (2) | O11—C14 | 1.2471 (19) |
N1—C2 | 1.329 (2) | N11—C12 | 1.352 (3) |
N1—C6 | 1.350 (3) | N11—C16 | 1.357 (3) |
N3—C2 | 1.365 (2) | N11—H11 | 0.94 (3) |
N3—C4 | 1.375 (2) | N13—C12 | 1.3318 (19) |
N3—H3 | 0.98 (3) | N13—C14 | 1.364 (2) |
N4—C2 | 1.323 (3) | N14—C12 | 1.324 (3) |
N4—H4 | 0.97 (3) | N14—H14 | 0.89 (3) |
N4—H41 | 0.89 (3) | N14—H141 | 0.95 (3) |
C4—C5 | 1.412 (3) | C14—C15 | 1.445 (3) |
C5—C6 | 1.357 (3) | C15—C16 | 1.340 (3) |
C5—H5 | 1.0900 | C15—H15 | 0.96 (3) |
C6—H6 | 1.03 (3) | C16—H16 | 0.95 (3) |
| | | |
C2—N1—C6 | 116.01 (15) | C12—N11—C16 | 120.23 (16) |
C2—N3—C4 | 122.68 (16) | C12—N11—H11 | 124 (2) |
C2—N3—H3 | 118.3 (16) | C16—N11—H11 | 116 (2) |
C4—N3—H3 | 119.0 (16) | C12—N13—C14 | 119.65 (16) |
C2—N4—H4 | 115.5 (18) | C12—N14—H14 | 120.7 (18) |
C2—N4—H41 | 121.2 (18) | C12—N14—H141 | 119.2 (18) |
H4—N4—H41 | 123 (3) | H14—N14—H141 | 119 (3) |
N4—C2—N1 | 120.29 (15) | N14—C12—N13 | 119.24 (18) |
N4—C2—N3 | 117.61 (16) | N14—C12—N11 | 118.74 (16) |
N1—C2—N3 | 122.09 (17) | N13—C12—N11 | 122.00 (18) |
O1—C4—N3 | 118.40 (18) | O11—C14—N13 | 119.35 (17) |
O1—C4—C5 | 126.18 (18) | O11—C14—C15 | 121.69 (17) |
N3—C4—C5 | 115.42 (15) | N13—C14—C15 | 118.94 (15) |
C6—C5—C4 | 118.31 (18) | C16—C15—C14 | 118.4 (2) |
C6—C5—H5 | 120.8 | C16—C15—H15 | 124 (2) |
C4—C5—H5 | 120.8 | C14—C15—H15 | 118 (2) |
N1—C6—C5 | 125.45 (19) | C15—C16—N11 | 120.77 (19) |
N1—C6—H6 | 113.5 (15) | C15—C16—H16 | 122.0 (18) |
C5—C6—H6 | 120.9 (15) | N11—C16—H16 | 117.0 (18) |
| | | |
C6—N1—C2—N4 | 179.5 (2) | C14—N13—C12—N14 | −178.69 (19) |
C6—N1—C2—N3 | 0.6 (3) | C14—N13—C12—N11 | −0.4 (3) |
C4—N3—C2—N4 | −177.9 (2) | C16—N11—C12—N14 | 179.7 (2) |
C4—N3—C2—N1 | 1.1 (3) | C16—N11—C12—N13 | 1.4 (3) |
C2—N3—C4—O1 | 177.96 (18) | C12—N13—C14—O11 | 177.42 (18) |
C2—N3—C4—C5 | −1.2 (3) | C12—N13—C14—C15 | −1.1 (3) |
O1—C4—C5—C6 | −179.4 (2) | O11—C14—C15—C16 | −176.9 (2) |
N3—C4—C5—C6 | −0.3 (3) | N13—C14—C15—C16 | 1.6 (3) |
C2—N1—C6—C5 | −2.2 (3) | C14—C15—C16—N11 | −0.7 (4) |
C4—C5—C6—N1 | 2.1 (4) | C12—N11—C16—C15 | −0.8 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3···N13 | 0.98 (3) | 1.92 (3) | 2.902 (2) | 176 (2) |
N4—H4···N1i | 0.97 (3) | 2.01 (3) | 2.981 (2) | 177 (3) |
N4—H41···O11 | 0.89 (3) | 1.97 (3) | 2.857 (2) | 177 (3) |
N11—H11···O1ii | 0.94 (3) | 1.85 (3) | 2.727 (2) | 154 (3) |
N14—H14···O11iii | 0.89 (3) | 1.93 (3) | 2.811 (2) | 169 (3) |
N14—H141···O1 | 0.95 (3) | 1.95 (3) | 2.902 (3) | 176 (3) |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x+3/2, y+1/2, −z+1/2; (iii) x+1/2, −y+3/2, z−1/2. |
Selected geometric parameters (Å,°) for IsoCyt
tautomers Ia (n=nil) and Ib (n=1) top | | n = nil | n = 1 |
On1-Cn4 | | 1.255 (2) | 1.247 (2) |
Nn1-Cn2 | | 1.329 (2) | 1.352 (3) |
Nn1-Cn6 | | 1.350 (3) | 1.357 (3) |
Nn3-Cn2 | | 1.365 (2) | 1.332 (2) |
Nn3-Cn4 | | 1.375 (2) | 1.364 (2) |
Nn4-Cn2 | | 1.323 (2) | 1.324 (3) |
Cn4-Cn5 | | 1.412 (3) | 1.445 (3) |
Cn5-Cn6 | | 1.357 (3) | 1.340 (3) |