The surprising pairing of 2-amino­imidazo[1,2-a][1,3,5]triazin-4-one, a component of an expanded DNA alphabet

Synthetic biologists demonstrate their command over natural biology by reproducing the behaviors of natural living systems on synthetic biomolecular platforms. For nucleic acids, this is being done stepwise, first by adding replicable nucleotides to DNA, and then removing its standard nucleotides. This challenge has been met in vitro with `six-letter' DNA and RNA, where the Watson–Crick pairing `concept' is recruited to increase the number of independently replicable nucleotides from four to six. The two nucleobases most successfully added so far are Z and P, which present a donor–donor–acceptor and an acceptor–acceptor–donor pattern, respectively. This pair of nucleobases are part of an `artificially expanded genetic information system' (AEGIS). The Z nucleobase has been already crystallized, characterized, and published in this journal [Matsuura et al. (2016). Acta Cryst. C72, 952–959]. More recently, variants of Taq polymerase have been crystallized with the pair P:Z trapped in the active site. Here we report the crystal structure of the nucleobase 2-amino­imidazo[1,2-a][1,3,5]triazin-4-one (trivially named P) as the monohydrate, C₅H₅N₅O·H₂O. The nucleobase P was crystallized from water and characterized by X-ray diffraction. Inter­estingly, the crystal structure shows two tautomers of P packed in a Watson–Crick fashion that cocrystallized in a 1:1 ratio.

Computing details

Data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2017 (Sheldrick, 2015b) and ShelXle (Hübschle et al., 2011); molecular graphics: XP in SHELXTL-Plus (Sheldrick, 2008); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015b).

2-Aminoimidazo[1,2-a][1,3,5]triazin-4(3H)-one monohydrate

Crystal data

C5H5N5O·H2O	F(000) = 704
Mr = 169.16	Dx = 1.663 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 16.357 (13) Å	Cell parameters from 9591 reflections
b = 3.712 (3) Å	θ = 2.6–26.3°
c = 22.723 (19) Å	µ = 0.13 mm^−1
β = 101.72 (3)°	T = 100 K
V = 1350.9 (19) Å^3	Very thin needle, colourless
Z = 8	0.40 × 0.10 × 0.10 mm

Data collection

Bruker D8 VENTURE diffractometer	1086 reflections with I > 2σ(I)
Multilayer mirror monochromator	Rint = 0.089
φ and ω scans	θmax = 26.4°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2013)	h = −20→20
	k = −4→4
33557 measured reflections	l = −28→28
1397 independent reflections

Refinement

Refinement on F^2	0 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F^2 > 2σ(F^2)] = 0.060	H-atom parameters constrained
wR(F^2) = 0.166	w = 1/[σ^2(Fo^2) + (0.0742P)^2 + 4.2384P] where P = (Fo^2 + 2Fc^2)/3
S = 1.16	(Δ/σ)max < 0.001
1397 reflections	Δρmax = 0.27 e Å^−3
112 parameters	Δρmin = −0.56 e Å^−3

Special details

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. The structure was solved and refined using the Bruker SHELXTL software package (Bruker, 2014; Hübschle et al., 2011; Sheldrick, 2015b), in the space group C2/c, with Z = 8 for the formula unit, C₅H₇N₅O₂. The final anisotropic full-matrix least-squares refinement on F² with 116 variables converged at R₁ = 7.14%, for the observed data and wR₂ = 19.41% for all data. The goodness-of-fit was 1.089. The largest peak in the final difference electron density was 0.269 e Å^-3 and the largest hole was -0.562 e Å^-3 with an r.m.s. deviation of 0.086 e Å^-3. On the basis of the final model, the calculated density was 1.663 Mg m^-3 and F(000) = 704 e.

All H atoms bound to C atoms were positioned geometrically ( C—H = 0.93/1.00 Å) and allowed to ride with U_iso(H)= 1.2/1.5U_eq(C).

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

	x	y	z	Uiso*/Ueq	Occ. (<1)
O2	0.6958 (3)	0.6401 (14)	0.23204 (16)	0.0541 (13)	0.75
H2Y	0.730670	0.854966	0.242044	0.081*	0.75
H2X	0.667110	0.607746	0.265584	0.081*	0.75
O2'	0.7846 (9)	0.953 (4)	0.2572 (6)	0.0541 (13)	0.25
H2W	0.774086	1.213329	0.255700	0.081*	0.25
H2Z	0.752094	0.765008	0.232740	0.081*	0.25
O1	0.61373 (11)	0.3616 (5)	0.51107 (8)	0.0169 (5)
N1	0.64639 (13)	0.5857 (6)	0.34214 (9)	0.0136 (5)
N2	0.77095 (14)	0.8537 (6)	0.38555 (10)	0.0156 (6)
H2A	0.780006	0.902557	0.349521	0.019*
H2B	0.807740	0.918339	0.417693	0.019*
C9	0.57886 (16)	0.4099 (7)	0.35240 (11)	0.0123 (6)
N8	0.51426 (13)	0.2871 (6)	0.31270 (10)	0.0152 (5)
H8	0.506724	0.304919	0.273345	0.018*	0.5
C7	0.46028 (17)	0.1238 (8)	0.34504 (12)	0.0164 (6)
H7	0.408713	0.013066	0.327525	0.020*
C6	0.49153 (16)	0.1454 (8)	0.40446 (12)	0.0156 (6)
H6	0.467115	0.056609	0.436123	0.019*
N3	0.69230 (13)	0.6152 (6)	0.44912 (9)	0.0140 (5)
H3	0.730825	0.692018	0.479352	0.017*	0.5
C4	0.62514 (16)	0.4336 (7)	0.46086 (12)	0.0132 (6)
N5	0.56777 (13)	0.3267 (6)	0.40962 (9)	0.0127 (5)
C2	0.70163 (16)	0.6820 (7)	0.39144 (11)	0.0124 (6)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O2	0.050 (2)	0.087 (4)	0.0280 (18)	0.019 (2)	0.0143 (17)	0.0103 (19)
O2'	0.050 (2)	0.087 (4)	0.0280 (18)	0.019 (2)	0.0143 (17)	0.0103 (19)
O1	0.0200 (10)	0.0225 (11)	0.0088 (9)	−0.0018 (8)	0.0047 (7)	0.0009 (8)
N1	0.0149 (11)	0.0170 (12)	0.0082 (11)	0.0019 (9)	0.0007 (9)	0.0000 (9)
N2	0.0163 (12)	0.0230 (13)	0.0076 (11)	−0.0035 (10)	0.0025 (9)	0.0007 (9)
C9	0.0143 (13)	0.0118 (13)	0.0107 (13)	0.0045 (10)	0.0021 (10)	−0.0002 (10)
N8	0.0129 (11)	0.0185 (12)	0.0135 (11)	0.0021 (9)	0.0006 (9)	−0.0022 (9)
C7	0.0143 (13)	0.0166 (14)	0.0178 (14)	0.0019 (11)	0.0020 (11)	−0.0023 (11)
C6	0.0148 (13)	0.0163 (14)	0.0170 (14)	0.0008 (11)	0.0063 (11)	−0.0001 (11)
N3	0.0136 (11)	0.0183 (12)	0.0096 (11)	0.0010 (9)	0.0014 (9)	0.0005 (9)
C4	0.0146 (13)	0.0137 (13)	0.0108 (13)	0.0046 (11)	0.0015 (10)	−0.0019 (10)
N5	0.0129 (11)	0.0153 (12)	0.0096 (11)	0.0024 (9)	0.0016 (9)	0.0009 (9)
C2	0.0144 (13)	0.0126 (13)	0.0104 (13)	0.0046 (11)	0.0029 (10)	0.0012 (10)

Geometric parameters (Å, º)

O2—H2Y	0.9800	C9—N5	1.384 (3)
O2—H2X	0.9802	N8—C7	1.397 (4)
O2'—H2W	0.9800	N8—H8	0.8800
O2'—H2Z	0.9800	C7—C6	1.345 (4)
O1—C4	1.223 (3)	C7—H7	0.9500
N1—C2	1.337 (3)	C6—N5	1.401 (4)
N1—C9	1.343 (4)	C6—H6	0.9500
N2—C2	1.331 (4)	N3—C4	1.361 (4)
N2—H2A	0.8800	N3—C2	1.373 (3)
N2—H2B	0.8800	N3—H3	0.8800
C9—N8	1.323 (4)	C4—N5	1.396 (3)
H2Y—O2—H2X	105.5	C7—C6—N5	105.2 (2)
H2W—O2'—H2Z	127.7	C7—C6—H6	127.4
C2—N1—C9	115.1 (2)	N5—C6—H6	127.4
C2—N2—H2A	120.0	C4—N3—C2	121.8 (2)
C2—N2—H2B	120.0	C4—N3—H3	119.1
H2A—N2—H2B	120.0	C2—N3—H3	119.1
N8—C9—N1	128.3 (2)	O1—C4—N3	125.0 (2)
N8—C9—N5	108.9 (2)	O1—C4—N5	120.8 (2)
N1—C9—N5	122.7 (2)	N3—C4—N5	114.2 (2)
C9—N8—C7	107.1 (2)	C9—N5—C4	121.7 (2)
C9—N8—H8	126.5	C9—N5—C6	108.2 (2)
C7—N8—H8	126.5	C4—N5—C6	130.0 (2)
C6—C7—N8	110.5 (2)	N2—C2—N1	119.2 (2)
C6—C7—H7	124.7	N2—C2—N3	116.4 (2)
N8—C7—H7	124.7	N1—C2—N3	124.4 (2)
C2—N1—C9—N8	179.2 (3)	N1—C9—N5—C6	179.9 (2)
C2—N1—C9—N5	−1.4 (4)	O1—C4—N5—C9	179.0 (2)
N1—C9—N8—C7	179.9 (3)	N3—C4—N5—C9	−1.5 (4)
N5—C9—N8—C7	0.4 (3)	O1—C4—N5—C6	2.3 (4)
C9—N8—C7—C6	−0.1 (3)	N3—C4—N5—C6	−178.2 (2)
N8—C7—C6—N5	−0.2 (3)	C7—C6—N5—C9	0.5 (3)
C2—N3—C4—O1	179.0 (2)	C7—C6—N5—C4	177.5 (3)
C2—N3—C4—N5	−0.4 (4)	C9—N1—C2—N2	179.2 (2)
N8—C9—N5—C4	−177.9 (2)	C9—N1—C2—N3	−0.6 (4)
N1—C9—N5—C4	2.5 (4)	C4—N3—C2—N2	−178.3 (2)
N8—C9—N5—C6	−0.6 (3)	C4—N3—C2—N1	1.6 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2Y···O2^i	0.98	1.62	2.582 (6)	166
O2—H2X···N1	0.98	1.84	2.788 (5)	162
O2′—H2W···O2′^i	0.98	1.30	2.164 (15)	143
O2′—H2Z···O2′^ii	0.98	1.34	2.164 (15)	137
N3—H3···N3^iii	0.88	1.98	2.853 (5)	174
N2—H2A···O2^i	0.88	2.16	3.026 (5)	168
N2—H2A···O2′	0.88	2.12	2.993 (12)	170
N2—H2B···O1^iii	0.88	2.02	2.897 (3)	172
N8—H8···N8^iv	0.88	1.92	2.792 (5)	173
C7—H7···O2^v	0.95	2.39	3.315 (5)	163
C6—H6···O1^vi	0.95	2.50	3.396 (4)	158

Symmetry codes: (i) −x+3/2, y+1/2, −z+1/2; (ii) −x+3/2, y−1/2, −z+1/2; (iii) −x+3/2, −y+3/2, −z+1; (iv) −x+1, y, −z+1/2; (v) −x+1, y−1, −z+1/2; (vi) −x+1, −y, −z+1.