Redetermination of isocytosine

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.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](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

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Computing details

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).

(I)

Crystal data

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) Å^3	0.20 × 0.20 × 0.10 mm
Z = 8

Data collection

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

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.054	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.187	H atoms treated by a mixture of independent and constrained refinement
S = 1.16	w = 1/[σ^2(Fo^2) + (0.0743P)^2 + 0.515P] where P = (Fo^2 + 2Fc^2)/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

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

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
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 (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

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)

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···N1^i	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···O1^ii	0.94 (3)	1.85 (3)	2.727 (2)	154 (3)
N14—H14···O11^iii	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.