A redetermination from the original data of the crystal structure of 2-amino-4,6-di­meth­oxy­pyrimidin-1-ium 4-amino­benzoate

The title structure, 2-amino-4,6-di­meth­oxy­pyrimidine-(μ₂-hydrogen)-4-amino­benzoate, has been redetermined from the data published by Thanigaimani, Mu­thiah & Lynch [Acta Cryst. (2006), E62, o2976–o2978]. The improvement of the present redetermination consists in a released geometry of the primary amine groups, which were originally been assumed as planar, as well as in a redetermination of the position of the hy­droxy H atom. This H atom, whose parameters were originally constrained, turns out to be situated about the centre of the O...N hydrogen bond in two disordered positions, each with 0.5 occupancy.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.037
• wR factor = 0.084
• Data-to-parameter ratio = 15.0

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT934_ALERT_3_B Number of (Iobs-Icalc)/SigmaW > 10 Outliers ....          4 Check

Alert level C
PLAT420_ALERT_2_C D-H Without Acceptor       N4     --  H4B    ...     Please Check
PLAT910_ALERT_3_C Missing # of FCF Reflection(s) Below Theta(Min)           6 Note
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600          4 Report

Alert level G
PLAT005_ALERT_5_G No Embedded Refinement Details found  in the CIF     Please Do !
PLAT042_ALERT_1_G Calc. and Reported MoietyFormula Strings  Differ     Please Check
PLAT199_ALERT_1_G Reported _cell_measurement_temperature ..... (K)        293 Check
PLAT200_ALERT_1_G Reported   _diffrn_ambient_temperature ..... (K)        293 Check
PLAT300_ALERT_4_G Atom Site Occupancy of *H4N1   is Constrained at        0.5 Check
PLAT300_ALERT_4_G Atom Site Occupancy of *H4O4   is Constrained at        0.5 Check
PLAT304_ALERT_4_G Non-Integer Number of Atoms (  20.50) in Resd. #          1 Check
PLAT304_ALERT_4_G Non-Integer Number of Atoms (  16.50) in Resd. #          2 Check
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........          2 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         25 Note
PLAT913_ALERT_3_G Missing # of Very Strong Reflections in FCF ....          1 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density           2 Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
   1 ALERT level B = A potentially serious problem, consider carefully
   3 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  12 ALERT level G = General information/check it is not something unexpected

   3 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
   4 ALERT type 3 Indicator that the structure quality may be low
   6 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

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Computing details

Data collection: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); cell refinement: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); data reduction: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: JANA2006 (Petříček et al., 2014); molecular graphics: PLATON (Spek, 2009), DIAMOND (Brandenburg & Putz, 2005) and JANA2006 (Petříček et al., 2014); software used to prepare material for publication: JANA2006 (Petříček et al., 2014).

2-Amino-4,6-dimethoxypyrimidin-1-ium 4-aminobenzoate

Crystal data

C6H9.5N3O20.5+·C7H6.5NO20.5−−	F(000) = 616
Mr = 292.30	Dx = 1.416 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 50 reflections
a = 6.6358 (4) Å	θ = 3.5–27.5°
b = 7.5560 (5) Å	µ = 0.11 mm^−1
c = 27.4226 (16) Å	T = 293 K
β = 94.418 (2)°	Block, colourless
V = 1370.89 (15) Å^3	0.44 × 0.32 × 0.08 mm
Z = 4

Data collection

Bruker–Nonius KappaCCD area-detector diffractometer	2302 reflections with I > 3σ(I)
Radiation source: Bruker–Nonius FR591 rotating anode	Rint = 0.032
Graphite monochromator	θmax = 27.5°, θmin = 3.5°
φ and ω scans	h = −8→8
14577 measured reflections	k = −9→9
3130 independent reflections	l = −35→35

Refinement

Refinement on F^2	50 constraints
R[F > 3σ(F)] = 0.037	H atoms treated by a mixture of independent and constrained refinement
wR(F) = 0.084	Weighting scheme based on measured s.u.'s w = 1/(σ^2(I) + 0.0004I^2)
S = 1.91	(Δ/σ)max = 0.021
3130 reflections	Δρmax = 0.21 e Å^−3
208 parameters	Δρmin = −0.23 e Å^−3
0 restraints

Special details

Refinement. This part differs from the original article by Thanigaimani et al. (2006). It also differs from the refinement by Thanigaimani et al. (2006) by a different threshold for the consideration of the observed diffractions: F² > 3σ(F²) has been used as criterion for observed diffractions by JANA2006 which was used for the calculation of the corrected structural model.

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

	x	y	z	Uiso*/Ueq	Occ. (<1)
O1	−0.31928 (12)	0.65273 (11)	−0.06555 (3)	0.0245 (3)
O2	−0.10295 (12)	0.62305 (10)	0.10293 (3)	0.0220 (3)
N1	0.08195 (15)	0.75282 (13)	0.04894 (4)	0.0190 (3)
N2	0.29136 (17)	0.87608 (15)	−0.00426 (4)	0.0257 (4)
N3	−0.01303 (15)	0.76827 (13)	−0.03671 (3)	0.0195 (3)
C2	0.11662 (18)	0.79867 (15)	0.00265 (4)	0.0187 (4)
C4	−0.18261 (18)	0.68662 (15)	−0.02786 (4)	0.0194 (4)
C5	−0.23220 (18)	0.62937 (15)	0.01815 (4)	0.0201 (4)
C6	−0.09140 (18)	0.66647 (15)	0.05581 (4)	0.0186 (4)
C7	−0.26609 (18)	0.70054 (18)	−0.11374 (4)	0.0261 (4)
C8	−0.26910 (18)	0.51184 (16)	0.11446 (4)	0.0244 (4)
O3	0.54244 (13)	0.93439 (11)	0.08178 (3)	0.0263 (3)
O4	0.31630 (13)	0.82158 (12)	0.12916 (3)	0.0258 (3)
N4	0.9485 (2)	1.16699 (16)	0.28973 (4)	0.0366 (4)
C9	0.60450 (18)	0.96745 (15)	0.16726 (4)	0.0198 (4)
C10	0.5334 (2)	0.95948 (16)	0.21374 (5)	0.0252 (4)
C11	0.6456 (2)	1.02612 (16)	0.25407 (5)	0.0286 (4)
C12	0.8340 (2)	1.10412 (16)	0.24933 (4)	0.0251 (4)
C13	0.90630 (19)	1.11079 (16)	0.20281 (5)	0.0254 (4)
C14	0.79433 (19)	1.04458 (15)	0.16262 (5)	0.0227 (4)
C15	0.48369 (18)	0.90491 (15)	0.12288 (4)	0.0202 (4)
H2a	0.3827 (19)	0.8954 (17)	0.0219 (5)	0.0308*
H2b	0.3152 (19)	0.9139 (17)	−0.0336 (5)	0.0308*
H5	−0.352188	0.570355	0.022827	0.0241*
H7a	−0.38336	0.691873	−0.13641	0.0391*
H7b	−0.163259	0.621794	−0.123627	0.0391*
H7c	−0.216204	0.819832	−0.113329	0.0391*
H8a	−0.266284	0.403993	0.096019	0.0365*
H8b	−0.257451	0.484961	0.148775	0.0365*
H8c	−0.394276	0.572471	0.106262	0.0365*
H4a	0.878 (2)	1.1906 (19)	0.3166 (6)	0.0439*
H4b	1.050 (2)	1.237 (2)	0.2829 (5)	0.0439*
H10	0.408167	0.908373	0.217631	0.0302*
H11	0.595299	1.019027	0.284732	0.0344*
H13	1.032145	1.160827	0.198977	0.0305*
H14	0.845086	1.051013	0.131987	0.0273*
H4N1	0.157 (5)	0.771 (4)	0.0756 (12)	0.0285*	0.5
H4O4	0.251 (5)	0.797 (4)	0.1004 (12)	0.0387*	0.5

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0216 (5)	0.0332 (5)	0.0179 (5)	−0.0044 (4)	−0.0040 (4)	0.0017 (4)
O2	0.0211 (5)	0.0274 (5)	0.0173 (5)	−0.0059 (4)	0.0009 (4)	0.0032 (4)
N1	0.0188 (6)	0.0218 (6)	0.0161 (5)	−0.0025 (5)	0.0004 (4)	−0.0001 (4)
N2	0.0232 (6)	0.0371 (7)	0.0165 (6)	−0.0107 (5)	−0.0004 (5)	0.0015 (5)
N3	0.0190 (6)	0.0212 (5)	0.0179 (5)	−0.0008 (4)	−0.0012 (4)	−0.0006 (4)
C2	0.0203 (7)	0.0184 (6)	0.0173 (6)	−0.0003 (5)	0.0008 (5)	−0.0010 (5)
C4	0.0188 (7)	0.0188 (6)	0.0201 (6)	0.0027 (5)	−0.0026 (5)	−0.0015 (5)
C5	0.0178 (7)	0.0212 (6)	0.0211 (7)	−0.0029 (5)	0.0000 (5)	0.0002 (5)
C6	0.0212 (7)	0.0171 (6)	0.0175 (6)	0.0015 (5)	0.0024 (5)	0.0007 (5)
C7	0.0260 (7)	0.0347 (8)	0.0169 (7)	0.0014 (6)	−0.0024 (6)	0.0022 (5)
C8	0.0228 (7)	0.0268 (7)	0.0239 (7)	−0.0055 (6)	0.0043 (6)	0.0043 (5)
O3	0.0258 (5)	0.0358 (5)	0.0172 (5)	−0.0057 (4)	0.0016 (4)	−0.0019 (4)
O4	0.0243 (5)	0.0324 (5)	0.0204 (5)	−0.0089 (4)	−0.0002 (4)	0.0003 (4)
N4	0.0480 (8)	0.0393 (7)	0.0209 (6)	−0.0112 (6)	−0.0072 (6)	−0.0028 (5)
C9	0.0236 (7)	0.0177 (6)	0.0176 (6)	0.0004 (5)	−0.0009 (5)	0.0006 (5)
C10	0.0294 (8)	0.0246 (7)	0.0214 (7)	−0.0043 (6)	0.0017 (6)	0.0008 (5)
C11	0.0400 (9)	0.0287 (7)	0.0171 (7)	−0.0048 (6)	0.0017 (6)	0.0005 (5)
C12	0.0341 (8)	0.0189 (6)	0.0207 (7)	0.0012 (6)	−0.0076 (6)	−0.0002 (5)
C13	0.0239 (7)	0.0261 (7)	0.0255 (7)	−0.0033 (6)	−0.0031 (6)	0.0001 (5)
C14	0.0252 (7)	0.0240 (7)	0.0189 (7)	0.0016 (6)	0.0004 (6)	0.0002 (5)
C15	0.0211 (7)	0.0196 (6)	0.0199 (7)	0.0019 (5)	0.0017 (5)	0.0010 (5)

Geometric parameters (Å, º)

O1—C4	1.3462 (14)	O4—H4O4	0.89 (3)
O1—C7	1.4400 (14)	N4—C12	1.3786 (17)
O2—C6	1.3411 (14)	N4—H4a	0.918 (15)
O2—C8	1.4405 (15)	N4—H4b	0.886 (15)
N1—C2	1.3525 (16)	C9—C10	1.3940 (17)
N1—C6	1.3483 (16)	C9—C14	1.4026 (17)
N1—H4N1	0.86 (3)	C9—C15	1.4821 (16)
N2—C2	1.3253 (16)	C10—C11	1.3799 (17)
N2—H2a	0.914 (13)	C10—H10	0.93
N2—H2b	0.880 (14)	C11—C12	1.3973 (19)
N3—C2	1.3472 (15)	C11—H11	0.93
N3—C4	1.3221 (15)	C12—C13	1.3980 (18)
C4—C5	1.3969 (17)	C13—C14	1.3751 (17)
C5—C6	1.3672 (16)	C13—H13	0.93
C5—H5	0.93	C14—H14	0.93
C7—H7a	0.96	H2a—H2b	1.559 (19)
C7—H7b	0.96	H7a—H7b	1.5677
C7—H7c	0.96	H7a—H7c	1.5677
C8—H8a	0.96	H7b—H7c	1.5677
C8—H8b	0.96	H8a—H8b	1.5677
C8—H8c	0.96	H8a—H8c	1.5677
O3—C15	1.2409 (15)	H8b—H8c	1.5677
O4—C15	1.2998 (15)	H4a—H4b	1.56 (2)
C4—O1—C7	117.31 (9)	H8a—C8—H8b	109.47
C6—O2—C8	117.11 (8)	H8a—C8—H8c	109.47
C2—N1—C6	117.63 (10)	H8b—C8—H8c	109.47
C2—N1—H4N1	129 (2)	C15—O4—H4O4	110 (2)
C6—N1—H4N1	114 (2)	C12—N4—H4a	115.4 (9)
C2—N2—H2a	119.5 (8)	C12—N4—H4b	114.5 (9)
C2—N2—H2b	119.7 (8)	H4a—N4—H4b	119.5 (13)
H2a—N2—H2b	120.7 (12)	C10—C9—C14	118.07 (11)
C2—N3—C4	115.62 (10)	C10—C9—C15	122.49 (11)
N1—C2—N2	117.46 (11)	C14—C9—C15	119.39 (11)
N1—C2—N3	124.33 (11)	C9—C10—C11	121.15 (12)
N2—C2—N3	118.20 (11)	C9—C10—H10	119.43
O1—C4—N3	118.71 (10)	C11—C10—H10	119.43
O1—C4—C5	116.29 (10)	C10—C11—C12	120.73 (12)
N3—C4—C5	125.00 (10)	C10—C11—H11	119.64
C4—C5—C6	115.08 (11)	C12—C11—H11	119.64
C4—C5—H5	122.46	N4—C12—C11	120.82 (12)
C6—C5—H5	122.46	N4—C12—C13	120.96 (12)
O2—C6—N1	111.45 (10)	C11—C12—C13	118.18 (11)
O2—C6—C5	126.24 (11)	C12—C13—C14	121.08 (12)
N1—C6—C5	122.31 (11)	C12—C13—H13	119.46
O1—C7—H7a	109.47	C14—C13—H13	119.46
O1—C7—H7b	109.47	C9—C14—C13	120.80 (12)
O1—C7—H7c	109.47	C9—C14—H14	119.6
H7a—C7—H7b	109.47	C13—C14—H14	119.6
H7a—C7—H7c	109.47	O3—C15—O4	122.60 (11)
H7b—C7—H7c	109.47	O3—C15—C9	120.04 (11)
O2—C8—H8a	109.47	O4—C15—C9	117.35 (11)
O2—C8—H8b	109.47	N1—H4N1—H4O4	171 (5)
O2—C8—H8c	109.47	O4—H4O4—H4N1	165 (5)

Hydrogen-bond geometry (Å, º)

Cg1 is the centroid of the C9–C14 ring.

D—H···A	D—H	H···A	D···A	D—H···A
N1—H4N1···O4	0.86 (3)	1.78 (3)	2.6459 (14)	176 (2)
O4—H4O4···N1	0.89 (3)	1.77 (3)	2.6459 (14)	170 (3)
N2—H2A···O3	0.92 (1)	1.91 (1)	2.8163 (14)	172 (1)
N2—H2B···O3^i	0.88 (1)	2.04 (1)	2.8544 (14)	154 (1)
N4—H4A···O4^ii	0.92 (2)	2.27 (2)	3.1625 (15)	164 (1)
C7—H7B···O2^iii	0.96	2.59	3.4571 (15)	150
N4—H4b···Cg1^iv	0.89 (2)	2.724 (15)	3.5472 (14)	154.7 (12)

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