Cytosinium 3,5-di­nitro­salicyl­ate

The crystal structure of cytosinium 3,5-di­nitro­salicyl­icate (systematic name: 6-amino-2-oxo-2,3-di­hydro­pyrimidinium 3,5-di­nitro­salicyl­ate), C₄H₆N₃O⁺·C₇H₃N₂O₇^-, shows the presence of a primary heteroionic cyclic R₂²(8) interaction between the H-atom donors of the protonated cytosinium cation and the carboxyl­ate O-atom acceptors of the 3,5-di­nitro­salicyl­ate anion. Additional peripheral hydrogen-bonding interactions involving all available cytosinium H-atom donors and both phenol and nitro O-atom acceptors of the anion species give a three-dimensional polymeric structure.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.044
• wR factor = 0.160
• Data-to-parameter ratio = 13.1

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT430_ALERT_2_B Short Inter D...A Contact  O32    ..  O32     ..       2.78 Ang.

Alert level C
PLAT430_ALERT_2_C Short Inter D...A Contact  O32    ..  N3      ..       2.88 Ang.
PLAT432_ALERT_2_C Short Inter X...Y Contact  O21    ..  C21     ..       2.97 Ang.

   0 ALERT level A = In general: serious problem
   1 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
   3 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

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Computing details

Data collection: MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1999); cell refinement: MSC/AFC Diffractometer Control Software; data reduction: TEXSAN for Windows (Molecular Structure Corporation, 1999); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: PLATON.

6-amino-2-oxo-2,3-dihydropyrimidinium 3,5-dinitrosalicylate

Crystal data

C7H3N2O7^+·C4H6N3O^−	F(000) = 696
Mr = 339.23	Dx = 1.697 Mg m^−3
Monoclinic, P21/n	Melting point = 527.3–529.6 K
Hall symbol: -P 2yn	Mo Kα radiation, λ = 0.71069 Å
a = 9.339 (3) Å	Cell parameters from 25 reflections
b = 5.766 (3) Å	θ = 12.7–17.3°
c = 24.662 (9) Å	µ = 0.15 mm^−1
β = 90.07 (3)°	T = 298 K
V = 1328.0 (9) Å^3	Prismatic, yellow
Z = 4	0.55 × 0.30 × 0.15 mm

Data collection

Rigaku AFC-7R diffractometer	Rint = 0.025
Radiation source: Rigaku rotating anode	θmax = 27.5°, θmin = 3.3°
Graphite monochromator	h = −5→12
ω–2θ scans	k = −7→3
3572 measured reflections	l = −32→32
3059 independent reflections	3 standard reflections every 150 min
1728 reflections with F^2 > 2σ(F^2)	intensity decay: 1.0%

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)] = 0.044	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.160	H atoms treated by a mixture of independent and constrained refinement
S = 0.93	w = 1/[σ^2(Fo^2) + (0.1P)^2 + 0.9288P] where P = (Fo^2 + 2Fc^2)/3
3059 reflections	(Δ/σ)max = 0.002
233 parameters	Δρmax = 0.24 e Å^−3
0 restraints	Δρmin = −0.29 e Å^−3

Special details

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All e.s.d.'s are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

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
O2	0.1595 (2)	−0.1388 (3)	0.49099 (7)	0.0409 (6)
O31	0.3281 (2)	0.1442 (4)	0.55255 (8)	0.0518 (7)
O32	0.5042 (2)	0.2595 (3)	0.50223 (9)	0.0490 (7)
O51	0.3458 (2)	0.6928 (4)	0.34537 (9)	0.0586 (8)
O52	0.1785 (3)	0.5501 (5)	0.29555 (10)	0.0761 (10)
O71	−0.0799 (2)	−0.1564 (4)	0.35375 (8)	0.0518 (7)
O72	−0.0214 (2)	−0.3111 (3)	0.43315 (8)	0.0436 (6)
N3	0.3791 (2)	0.2005 (4)	0.50868 (9)	0.0366 (7)
N5	0.2518 (2)	0.5503 (4)	0.33644 (9)	0.0425 (7)
C1	0.0987 (2)	0.0323 (4)	0.40605 (10)	0.0318 (7)
C2	0.1803 (2)	0.0250 (4)	0.45504 (10)	0.0315 (7)
C3	0.2862 (2)	0.1980 (4)	0.46090 (10)	0.0316 (7)
C4	0.3111 (2)	0.3664 (4)	0.42249 (10)	0.0324 (7)
C5	0.2267 (3)	0.3690 (5)	0.37655 (10)	0.0336 (7)
C6	0.1210 (3)	0.2035 (5)	0.36799 (10)	0.0344 (7)
C7	−0.0096 (3)	−0.1554 (5)	0.39615 (10)	0.0360 (7)
O21	0.6400 (2)	0.7167 (3)	0.24766 (8)	0.0463 (6)
N11	0.5412 (2)	0.3624 (4)	0.26503 (9)	0.0374 (7)
N31	0.6948 (2)	0.5337 (4)	0.32702 (8)	0.0325 (6)
N41	0.7608 (3)	0.3521 (4)	0.40595 (9)	0.0400 (7)
C21	0.6268 (3)	0.5494 (5)	0.27722 (10)	0.0346 (7)
C41	0.6847 (2)	0.3507 (4)	0.36125 (9)	0.0299 (7)
C51	0.5911 (3)	0.1668 (5)	0.34676 (10)	0.0353 (8)
C61	0.5244 (3)	0.1779 (5)	0.29864 (11)	0.0372 (8)
H4	0.384600	0.478300	0.427400	0.0390*
H6	0.064300	0.208300	0.336100	0.0410*
H72	0.0513	−0.2664	0.4652	0.0490*
H11	0.506 (3)	0.363 (5)	0.2334 (12)	0.043 (8)*
H31	0.762 (4)	0.639 (6)	0.3336 (14)	0.069 (11)*
H41A	0.754 (3)	0.229 (5)	0.4304 (12)	0.048 (9)*
H41B	0.828 (3)	0.466 (6)	0.4142 (12)	0.055 (9)*
H51	0.576300	0.038800	0.370400	0.0420*
H61	0.463600	0.054000	0.287900	0.0450*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O2	0.0439 (10)	0.0407 (11)	0.0382 (10)	−0.0088 (9)	−0.0115 (8)	0.0068 (9)
O31	0.0629 (13)	0.0589 (14)	0.0337 (10)	0.0002 (11)	−0.0133 (9)	0.0010 (10)
O32	0.0404 (10)	0.0380 (11)	0.0687 (13)	−0.0090 (9)	−0.0248 (9)	0.0048 (10)
O51	0.0658 (14)	0.0483 (13)	0.0616 (14)	−0.0189 (11)	−0.0088 (11)	0.0114 (11)
O52	0.0797 (17)	0.0863 (19)	0.0625 (15)	−0.0210 (14)	−0.0347 (13)	0.0349 (14)
O71	0.0543 (12)	0.0609 (13)	0.0403 (10)	−0.0240 (11)	−0.0151 (9)	−0.0013 (10)
O72	0.0421 (10)	0.0407 (11)	0.0479 (11)	−0.0112 (9)	−0.0097 (9)	0.0011 (9)
N3	0.0396 (12)	0.0267 (11)	0.0434 (12)	0.0006 (9)	−0.0168 (10)	−0.0033 (9)
N5	0.0425 (13)	0.0436 (13)	0.0415 (12)	0.0006 (11)	−0.0030 (10)	0.0066 (11)
C1	0.0271 (11)	0.0361 (14)	0.0322 (12)	−0.0025 (10)	−0.0034 (9)	−0.0052 (10)
C2	0.0298 (11)	0.0322 (13)	0.0326 (12)	0.0009 (10)	−0.0053 (9)	−0.0025 (10)
C3	0.0297 (12)	0.0342 (13)	0.0308 (12)	0.0034 (10)	−0.0083 (9)	−0.0046 (10)
C4	0.0293 (12)	0.0291 (12)	0.0389 (13)	−0.0005 (10)	−0.0035 (9)	−0.0038 (11)
C5	0.0327 (12)	0.0343 (13)	0.0337 (12)	0.0027 (11)	−0.0033 (10)	0.0017 (11)
C6	0.0307 (12)	0.0398 (14)	0.0326 (12)	0.0008 (11)	−0.0061 (10)	−0.0029 (11)
C7	0.0328 (12)	0.0398 (14)	0.0353 (12)	−0.0038 (11)	−0.0028 (10)	−0.0043 (11)
O21	0.0576 (12)	0.0413 (11)	0.0401 (10)	−0.0037 (9)	−0.0069 (9)	0.0087 (9)
N11	0.0432 (12)	0.0379 (12)	0.0312 (11)	−0.0016 (10)	−0.0136 (9)	−0.0017 (10)
N31	0.0335 (11)	0.0299 (11)	0.0342 (11)	−0.0047 (9)	−0.0047 (9)	−0.0036 (9)
N41	0.0461 (13)	0.0393 (13)	0.0345 (11)	−0.0108 (11)	−0.0120 (10)	0.0018 (10)
C21	0.0356 (12)	0.0353 (14)	0.0329 (12)	0.0005 (11)	−0.0041 (10)	−0.0014 (11)
C41	0.0305 (12)	0.0318 (13)	0.0274 (11)	0.0001 (10)	−0.0019 (9)	−0.0013 (10)
C51	0.0369 (13)	0.0310 (13)	0.0381 (13)	−0.0057 (11)	−0.0056 (10)	0.0008 (11)
C61	0.0368 (13)	0.0333 (14)	0.0414 (13)	−0.0051 (11)	−0.0093 (11)	−0.0073 (11)

Geometric parameters (Å, º)

O2—C2	1.310 (3)	N31—H31	0.89 (4)
O31—N3	1.225 (3)	N41—H41B	0.93 (3)
O32—N3	1.227 (3)	N41—H41A	0.93 (3)
O51—N5	1.223 (3)	C1—C6	1.378 (4)
O52—N5	1.220 (3)	C1—C2	1.430 (3)
O71—C7	1.235 (3)	C1—C7	1.501 (4)
O72—C7	1.285 (3)	C2—C3	1.412 (3)
O72—H72	1.070	C3—C4	1.376 (3)
O21—C21	1.215 (3)	C4—C5	1.381 (4)
N3—C3	1.464 (3)	C5—C6	1.389 (4)
N5—C5	1.458 (4)	C4—H4	0.9499
N11—C21	1.376 (4)	C6—H6	0.9491
N11—C61	1.358 (4)	C41—C51	1.420 (4)
N31—C21	1.386 (3)	C51—C61	1.342 (4)
N31—C41	1.355 (3)	C51—H51	0.9505
N41—C41	1.312 (3)	C61—H61	0.9504
N11—H11	0.85 (3)
C7—O72—H72	107.6	C3—C4—C5	118.4 (2)
O31—N3—O32	123.8 (2)	C4—C5—C6	121.6 (2)
O32—N3—C3	117.6 (2)	N5—C5—C6	120.2 (2)
O31—N3—C3	118.55 (19)	N5—C5—C4	118.2 (2)
O51—N5—C5	118.3 (2)	C1—C6—C5	119.7 (2)
O51—N5—O52	123.6 (3)	O71—C7—O72	123.6 (3)
O52—N5—C5	118.1 (2)	O72—C7—C1	116.4 (2)
C21—N11—C61	123.2 (2)	O71—C7—C1	120.0 (2)
C21—N31—C41	124.8 (2)	C3—C4—H4	120.87
C61—N11—H11	121 (2)	C5—C4—H4	120.69
C21—N11—H11	115 (2)	C1—C6—H6	120.09
C41—N31—H31	118 (2)	C5—C6—H6	120.21
C21—N31—H31	116 (2)	O21—C21—N11	123.3 (2)
C41—N41—H41B	123.6 (19)	O21—C21—N31	122.5 (3)
C41—N41—H41A	120.1 (18)	N11—C21—N31	114.2 (2)
H41A—N41—H41B	116 (3)	N31—C41—N41	118.8 (2)
C2—C1—C7	118.4 (2)	N31—C41—C51	117.9 (2)
C6—C1—C7	120.5 (2)	N41—C41—C51	123.4 (2)
C2—C1—C6	121.1 (2)	C41—C51—C61	118.2 (2)
C1—C2—C3	116.1 (2)	N11—C61—C51	121.6 (3)
O2—C2—C3	122.9 (2)	C41—C51—H51	120.96
O2—C2—C1	121.0 (2)	C61—C51—H51	120.79
N3—C3—C2	120.3 (2)	N11—C61—H61	119.18
C2—C3—C4	123.1 (2)	C51—C61—H61	119.24
N3—C3—C4	116.57 (19)
O32—N3—C3—C4	−34.6 (3)	C6—C1—C2—C3	−1.8 (3)
O32—N3—C3—C2	143.6 (2)	C7—C1—C2—O2	−1.3 (3)
O31—N3—C3—C2	−36.5 (3)	C6—C1—C2—O2	−179.6 (2)
O31—N3—C3—C4	145.3 (2)	C2—C1—C7—O72	0.2 (4)
O51—N5—C5—C6	−180.0 (2)	C7—C1—C6—C5	−176.7 (2)
O51—N5—C5—C4	−0.4 (4)	C2—C1—C7—O71	−178.6 (2)
O52—N5—C5—C4	178.9 (2)	C1—C2—C3—N3	−177.7 (2)
O52—N5—C5—C6	−0.6 (4)	O2—C2—C3—N3	0.0 (3)
C61—N11—C21—N31	−0.1 (4)	C1—C2—C3—C4	0.3 (3)
C61—N11—C21—O21	−178.6 (3)	O2—C2—C3—C4	178.1 (2)
C21—N11—C61—C51	0.2 (4)	N3—C3—C4—C5	179.4 (2)
C41—N31—C21—N11	2.0 (4)	C2—C3—C4—C5	1.3 (3)
C21—N31—C41—N41	176.3 (2)	C3—C4—C5—C6	−1.6 (4)
C21—N31—C41—C51	−3.9 (3)	C3—C4—C5—N5	178.9 (2)
C41—N31—C21—O21	−179.4 (2)	N5—C5—C6—C1	179.7 (2)
C6—C1—C7—O72	178.5 (2)	C4—C5—C6—C1	0.2 (4)
C7—C1—C2—C3	176.5 (2)	N31—C41—C51—C61	3.8 (4)
C2—C1—C6—C5	1.5 (4)	N41—C41—C51—C61	−176.4 (3)
C6—C1—C7—O71	−0.3 (4)	C41—C51—C61—N11	−2.1 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O72—H72···O2	1.07	1.40	2.425 (3)	156
N11—H11···O52^i	0.85 (3)	2.60 (3)	3.113 (4)	121 (2)
N11—H11···O71^ii	0.85 (3)	2.26 (3)	2.953 (3)	139 (2)
N31—H31···O71^iii	0.89 (4)	1.95 (4)	2.839 (3)	173 (3)
N41—H41A···O2^iv	0.93 (3)	2.16 (3)	2.921 (3)	137 (2)
N41—H41A···O31^iv	0.93 (3)	2.32 (3)	3.150 (4)	148 (2)
N41—H41B···O72^iii	0.93 (3)	1.96 (3)	2.892 (3)	176 (3)
C4—H4···O32^v	0.95	2.53	3.329 (3)	142
C51—H51···O31^iv	0.95	2.35	3.155 (4)	142
C61—H61···O52^i	0.95	2.45	3.089 (4)	124

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