The asymmetric unit of the title compound, C
6H
10N
3O
2+·C
7H
5O
3−, contains one 2-amino-4,6-dimethoxypyrimidinium cation and a salicylate anion. The 2-amino-4,6-dimethoxypyrimidinium cation interacts with the carboxylate group of the salicylate anion through a pair of nearly parallel N—H
O hydrogen bonds, forming an
R22(8) ring motif. These motifs are centrosymmetrically paired
via N—H
O hydrogen bonds, forming a complementary
DDAA array. The typical intramolecular O—H
O hydrogen bond is observed in the anion. The salicylate ions form a hydrogen-bonded supramolecular chain along the
c axis
via C—H
O hydrogen bonds involving a benzene hydrogen and one of the O atoms of the carboxylate group.
Supporting information
CCDC reference: 672829
Key indicators
- Single-crystal X-ray study
- T = 120 K
- Mean (C-C) = 0.003 Å
- R factor = 0.054
- wR factor = 0.137
- Data-to-parameter ratio = 16.2
checkCIF/PLATON results
No syntax errors found
Alert level C
DIFMN02_ALERT_2_C The minimum difference density is < -0.1*ZMAX*0.75
_refine_diff_density_min given = -0.719
Test value = -0.600
DIFMN03_ALERT_1_C The minimum difference density is < -0.1*ZMAX*0.75
The relevant atom site should be identified.
DIFMX01_ALERT_2_C The maximum difference density is > 0.1*ZMAX*0.75
_refine_diff_density_max given = 0.662
Test value = 0.600
DIFMX02_ALERT_1_C The maximum difference density is > 0.1*ZMAX*0.75
The relevant atom site should be identified.
PLAT097_ALERT_2_C Maximum (Positive) Residual Density ............ 0.66 e/A
PLAT098_ALERT_2_C Minimum (Negative) Residual Density ............ -0.72 e/A
0 ALERT level A = In general: serious problem
0 ALERT level B = Potentially serious problem
6 ALERT level C = Check and explain
0 ALERT level G = General alerts; check
2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
4 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
A hot methanolic solution (20 ml) of 2-amino-4,6-dimethoxy pyrimidine (38 mg,
Aldrich) and salicylic acid (34 mg, Loba chemie) was warmed for half an hour
over a water bath. The mixture was cooled slowly and kept at room temperature.
After a few days colourless plate-like crystals were obtained.
All H atoms were positioned geometrically and were refined using a riding model.
The C—H, O—H and N—H bond lengths are 0.93–0.96, 0.82 and 0.86 Å,
respectively [Uiso (H)=1.2 Ueq(parent atom)]. The highest
peak in the final difference map (0.66 e Å-3) is at 1.55 Å from N1, the
deepest hole (-0.72 e Å-3) is at 0.75 Å from N2.
Data collection: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); cell refinement: DENZO and COLLECT; data reduction: DENZO and COLLECT; 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.
2-amino-4,6-dimethoxypyrimidinium salicylate
top
Crystal data top
C6H10N3O2+·C7H5O3− | F(000) = 616 |
Mr = 293.28 | Dx = 1.414 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 25 reflections |
a = 9.1071 (3) Å | θ = 3.8–27.5° |
b = 14.7657 (6) Å | µ = 0.11 mm−1 |
c = 12.2829 (6) Å | T = 120 K |
β = 123.465 (3)° | Plate-like, colourless |
V = 1377.90 (11) Å3 | 0.30 × 0.30 × 0.08 mm |
Z = 4 | |
Data collection top
Bruker–Nonius Kappa CCD area-detector diffractometer | 2465 reflections with I > 2σ(I) |
Radiation source: Bruker–Nonius FR591 rotating anode | Rint = 0.034 |
Graphite monochromator | θmax = 27.5°, θmin = 3.9° |
ϕ and ω scans | h = −11→11 |
14310 measured reflections | k = −17→19 |
3136 independent reflections | l = −15→15 |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.054 | H-atom parameters constrained |
wR(F2) = 0.137 | w = 1/[σ2(Fo2) + (0.0773P)2 + 0.2362P] where P = (Fo2 + 2Fc2)/3 |
S = 1.11 | (Δ/σ)max < 0.001 |
3136 reflections | Δρmax = 0.66 e Å−3 |
194 parameters | Δρmin = −0.72 e Å−3 |
0 restraints | Extinction correction: SHELXL, FC*=KFC[1+0.001XFC2Λ3/SIN(2Θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.068 (6) |
Crystal data top
C6H10N3O2+·C7H5O3− | V = 1377.90 (11) Å3 |
Mr = 293.28 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 9.1071 (3) Å | µ = 0.11 mm−1 |
b = 14.7657 (6) Å | T = 120 K |
c = 12.2829 (6) Å | 0.30 × 0.30 × 0.08 mm |
β = 123.465 (3)° | |
Data collection top
Bruker–Nonius Kappa CCD area-detector diffractometer | 2465 reflections with I > 2σ(I) |
14310 measured reflections | Rint = 0.034 |
3136 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.054 | 0 restraints |
wR(F2) = 0.137 | H-atom parameters constrained |
S = 1.11 | Δρmax = 0.66 e Å−3 |
3136 reflections | Δρmin = −0.72 e Å−3 |
194 parameters | |
Special details top
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 on F2 for ALL reflections except those flagged by the user
for potential systematic errors. Weighted R-factors wR and all
goodnesses of fit S are based on F2, conventional
R-factors R are based on F, with F set to zero for
negative F2. The observed criterion of F2 > σ(F2)
is used only for calculating -R-factor-obs 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 | 0.20130 (12) | −0.06793 (7) | 0.72454 (10) | 0.0246 (3) | |
O2 | 0.37869 (12) | 0.09584 (7) | 0.48494 (10) | 0.0217 (3) | |
N1 | 0.56670 (15) | 0.04949 (8) | 0.68864 (12) | 0.0189 (3) | |
N2 | 0.77862 (15) | 0.00635 (9) | 0.89739 (12) | 0.0250 (4) | |
N3 | 0.49174 (15) | −0.03420 (8) | 0.81536 (12) | 0.0199 (4) | |
C2 | 0.61084 (17) | 0.00665 (9) | 0.80033 (14) | 0.0192 (4) | |
C4 | 0.32600 (18) | −0.03031 (10) | 0.71396 (14) | 0.0194 (4) | |
C5 | 0.26878 (18) | 0.01071 (10) | 0.59397 (14) | 0.0206 (4) | |
C6 | 0.39631 (17) | 0.05140 (9) | 0.58543 (14) | 0.0184 (4) | |
C7 | 0.2563 (2) | −0.11184 (12) | 0.84644 (17) | 0.0301 (5) | |
C8 | 0.20153 (17) | 0.10678 (10) | 0.37204 (14) | 0.0216 (4) | |
O3 | 0.81007 (12) | 0.13044 (7) | 0.66450 (10) | 0.0246 (3) | |
O4 | 1.03098 (13) | 0.07809 (7) | 0.85566 (10) | 0.0238 (3) | |
O5 | 0.86976 (14) | 0.22213 (8) | 0.51703 (11) | 0.0291 (3) | |
C9 | 1.10073 (18) | 0.16797 (9) | 0.72967 (14) | 0.0189 (4) | |
C10 | 1.04166 (19) | 0.21540 (10) | 0.61315 (15) | 0.0223 (4) | |
C11 | 1.1641 (2) | 0.25754 (10) | 0.59510 (17) | 0.0275 (5) | |
C12 | 1.3417 (2) | 0.25220 (11) | 0.69058 (17) | 0.0292 (5) | |
C13 | 1.4024 (2) | 0.20592 (11) | 0.80650 (17) | 0.0281 (5) | |
C14 | 1.28197 (18) | 0.16428 (10) | 0.82527 (15) | 0.0229 (4) | |
C15 | 0.97425 (18) | 0.12227 (9) | 0.75325 (14) | 0.0187 (4) | |
H1 | 0.64680 | 0.07550 | 0.68300 | 0.0230* | |
H2A | 0.81090 | −0.02000 | 0.96980 | 0.0300* | |
H2B | 0.85550 | 0.03250 | 0.88820 | 0.0300* | |
H5 | 0.15130 | 0.01020 | 0.52460 | 0.0250* | |
H7A | 0.32260 | −0.16530 | 0.85630 | 0.0450* | |
H7B | 0.15440 | −0.12830 | 0.84660 | 0.0450* | |
H7C | 0.32830 | −0.07110 | 0.91750 | 0.0450* | |
H8A | 0.14990 | 0.04830 | 0.33880 | 0.0320* | |
H8B | 0.20420 | 0.13990 | 0.30590 | 0.0320* | |
H8C | 0.13260 | 0.13940 | 0.39630 | 0.0320* | |
H5A | 0.81080 | 0.19490 | 0.53830 | 0.0440* | |
H11 | 1.12590 | 0.28930 | 0.51850 | 0.0330* | |
H12 | 1.42210 | 0.28000 | 0.67710 | 0.0350* | |
H13 | 1.52220 | 0.20300 | 0.87050 | 0.0340* | |
H14 | 1.32190 | 0.13330 | 0.90270 | 0.0280* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0199 (5) | 0.0316 (6) | 0.0247 (6) | −0.0019 (4) | 0.0139 (4) | 0.0051 (5) |
O2 | 0.0179 (5) | 0.0281 (6) | 0.0174 (5) | −0.0004 (4) | 0.0086 (4) | 0.0049 (4) |
N1 | 0.0159 (6) | 0.0222 (6) | 0.0192 (6) | −0.0008 (4) | 0.0101 (5) | 0.0018 (5) |
N2 | 0.0186 (6) | 0.0342 (8) | 0.0209 (7) | 0.0001 (5) | 0.0100 (5) | 0.0089 (5) |
N3 | 0.0193 (6) | 0.0209 (6) | 0.0210 (7) | 0.0020 (5) | 0.0120 (5) | 0.0025 (5) |
C2 | 0.0197 (7) | 0.0185 (7) | 0.0209 (7) | 0.0027 (5) | 0.0121 (6) | 0.0018 (5) |
C4 | 0.0221 (7) | 0.0175 (7) | 0.0227 (8) | 0.0006 (5) | 0.0150 (6) | −0.0003 (6) |
C5 | 0.0181 (6) | 0.0223 (8) | 0.0210 (7) | −0.0008 (5) | 0.0105 (6) | −0.0002 (6) |
C6 | 0.0194 (7) | 0.0185 (7) | 0.0167 (7) | 0.0019 (5) | 0.0096 (6) | −0.0005 (5) |
C7 | 0.0276 (8) | 0.0366 (9) | 0.0314 (9) | 0.0020 (7) | 0.0197 (7) | 0.0108 (7) |
C8 | 0.0184 (7) | 0.0246 (8) | 0.0170 (7) | 0.0006 (5) | 0.0067 (6) | 0.0029 (6) |
O3 | 0.0181 (5) | 0.0307 (6) | 0.0212 (6) | −0.0016 (4) | 0.0085 (4) | 0.0052 (4) |
O4 | 0.0224 (5) | 0.0291 (6) | 0.0186 (6) | −0.0017 (4) | 0.0105 (4) | 0.0045 (4) |
O5 | 0.0305 (6) | 0.0311 (6) | 0.0234 (6) | −0.0006 (5) | 0.0135 (5) | 0.0056 (5) |
C9 | 0.0226 (7) | 0.0155 (7) | 0.0211 (8) | −0.0019 (5) | 0.0137 (6) | −0.0029 (5) |
C10 | 0.0283 (8) | 0.0184 (7) | 0.0231 (8) | −0.0005 (6) | 0.0160 (6) | −0.0020 (6) |
C11 | 0.0428 (9) | 0.0189 (8) | 0.0317 (9) | −0.0017 (6) | 0.0274 (8) | 0.0008 (6) |
C12 | 0.0364 (8) | 0.0213 (8) | 0.0456 (10) | −0.0066 (6) | 0.0325 (8) | −0.0055 (7) |
C13 | 0.0239 (7) | 0.0245 (8) | 0.0388 (10) | −0.0025 (6) | 0.0191 (7) | −0.0058 (7) |
C14 | 0.0236 (7) | 0.0195 (7) | 0.0279 (8) | −0.0019 (5) | 0.0156 (6) | −0.0029 (6) |
C15 | 0.0212 (7) | 0.0164 (7) | 0.0186 (7) | −0.0014 (5) | 0.0111 (6) | −0.0023 (5) |
Geometric parameters (Å, º) top
O1—C4 | 1.333 (2) | C5—H5 | 0.9303 |
O1—C7 | 1.444 (2) | C7—H7A | 0.9601 |
O2—C6 | 1.3272 (18) | C7—H7C | 0.9604 |
O2—C8 | 1.4439 (19) | C7—H7B | 0.9604 |
O3—C15 | 1.281 (2) | C8—H8B | 0.9600 |
O4—C15 | 1.2482 (18) | C8—H8C | 0.9598 |
O5—C10 | 1.348 (2) | C8—H8A | 0.9600 |
O5—H5A | 0.8203 | C9—C14 | 1.403 (2) |
N1—C2 | 1.3548 (19) | C9—C15 | 1.495 (3) |
N1—C6 | 1.359 (2) | C9—C10 | 1.407 (2) |
N2—C2 | 1.322 (2) | C10—C11 | 1.397 (3) |
N3—C4 | 1.326 (2) | C11—C12 | 1.380 (3) |
N3—C2 | 1.340 (2) | C12—C13 | 1.390 (2) |
N1—H1 | 0.8603 | C13—C14 | 1.383 (3) |
N2—H2B | 0.8598 | C11—H11 | 0.9302 |
N2—H2A | 0.8605 | C12—H12 | 0.9305 |
C4—C5 | 1.401 (2) | C13—H13 | 0.9297 |
C5—C6 | 1.362 (3) | C14—H14 | 0.9298 |
| | | |
O1···C8i | 3.224 (2) | C11···H8Bx | 2.8439 |
O2···C6ii | 3.410 (2) | C12···H8Bx | 2.8406 |
O2···N1ii | 3.2507 (17) | C13···H8Bx | 2.9028 |
O3···O5 | 2.5486 (17) | C14···H8Bx | 2.9551 |
O3···N1 | 2.675 (2) | C15···H8Aii | 2.7368 |
O4···N2 | 2.822 (2) | C15···H5A | 2.4500 |
O4···N2iii | 2.8216 (16) | C15···H2B | 2.7661 |
O5···O3 | 2.5486 (17) | C15···H1 | 2.6975 |
O1···H8Ci | 2.7542 | C15···H11iv | 3.0438 |
O1···H8Ai | 2.8592 | H1···O3 | 1.8147 |
O3···H5A | 1.8221 | H1···C15 | 2.6975 |
O3···H8Aii | 2.6676 | H1···H2B | 2.2550 |
O3···H1 | 1.8147 | H2A···O4iii | 2.0002 |
O4···H2Aiii | 2.0002 | H2A···H2Biii | 2.5421 |
O4···H14 | 2.5159 | H2B···H1 | 2.2550 |
O4···H8Aii | 2.7499 | H2B···N2iii | 2.9478 |
O4···H11iv | 2.5836 | H2B···C15 | 2.7661 |
O4···H2B | 1.9676 | H2B···O4 | 1.9676 |
O5···H7Bv | 2.8527 | H2B···H2Aiii | 2.5421 |
O5···H13vi | 2.8631 | H5···H8A | 2.3437 |
N1···O2ii | 3.2507 (17) | H5···C8 | 2.5884 |
N1···O3 | 2.675 (2) | H5···H5i | 2.4927 |
N2···O4 | 2.822 (2) | H5···H8C | 2.4199 |
N2···O4iii | 2.8216 (16) | H5A···C15 | 2.4500 |
N2···H2Biii | 2.9478 | H5A···O3 | 1.8221 |
N3···H7C | 2.4791 | H7A···N3 | 2.6883 |
N3···H12vii | 2.8409 | H7B···C8i | 2.8670 |
N3···H7A | 2.6883 | H7B···O5xi | 2.8527 |
C2···C13viii | 3.525 (2) | H7C···N3 | 2.4791 |
C4···C14viii | 3.300 (2) | H8A···C5 | 2.7498 |
C5···C14viii | 3.585 (2) | H8A···C15ii | 2.7368 |
C6···C13viii | 3.524 (2) | H8A···H5 | 2.3437 |
C6···O2ii | 3.410 (2) | H8A···O1i | 2.8592 |
C6···C12viii | 3.379 (2) | H8A···O3ii | 2.6676 |
C7···C8i | 3.500 (3) | H8A···O4ii | 2.7499 |
C8···O1i | 3.224 (2) | H8B···C10vi | 2.9149 |
C8···C7i | 3.500 (3) | H8B···C11vi | 2.8439 |
C8···C14vi | 3.572 (2) | H8B···C9vi | 2.9732 |
C12···C6ix | 3.379 (2) | H8B···C12vi | 2.8406 |
C13···C6ix | 3.524 (2) | H8B···C13vi | 2.9028 |
C13···C2ix | 3.525 (2) | H8B···C14vi | 2.9551 |
C14···C8x | 3.572 (2) | H8C···C11viii | 2.8836 |
C14···C5ix | 3.585 (2) | H8C···H5 | 2.4199 |
C14···C4ix | 3.300 (2) | H8C···O1i | 2.7542 |
C5···H8C | 2.7790 | H8C···C5 | 2.7790 |
C5···H8A | 2.7498 | H11···O4xii | 2.5836 |
C8···H7Bi | 2.8670 | H11···C15xii | 3.0438 |
C8···H5 | 2.5884 | H12···N3xiii | 2.8409 |
C9···H8Bx | 2.9732 | H13···O5x | 2.8631 |
C10···H8Bx | 2.9149 | H14···O4 | 2.5159 |
C11···H8Cix | 2.8836 | | |
| | | |
C4—O1—C7 | 117.45 (13) | O2—C8—H8A | 109.49 |
C6—O2—C8 | 116.52 (13) | O2—C8—H8C | 109.50 |
C10—O5—H5A | 109.45 | H8A—C8—H8B | 109.47 |
C2—N1—C6 | 120.19 (15) | O2—C8—H8B | 109.48 |
C2—N3—C4 | 116.08 (13) | H8B—C8—H8C | 109.46 |
C2—N1—H1 | 119.91 | H8A—C8—H8C | 109.43 |
C6—N1—H1 | 119.90 | C10—C9—C15 | 121.24 (15) |
H2A—N2—H2B | 120.00 | C14—C9—C15 | 119.80 (13) |
C2—N2—H2A | 119.99 | C10—C9—C14 | 118.96 (16) |
C2—N2—H2B | 120.01 | O5—C10—C11 | 118.12 (14) |
N2—C2—N3 | 119.69 (13) | C9—C10—C11 | 119.48 (16) |
N1—C2—N3 | 122.61 (15) | O5—C10—C9 | 122.40 (17) |
N1—C2—N2 | 117.70 (15) | C10—C11—C12 | 120.23 (16) |
O1—C4—C5 | 116.09 (15) | C11—C12—C13 | 121.08 (19) |
N3—C4—C5 | 125.24 (17) | C12—C13—C14 | 119.03 (18) |
O1—C4—N3 | 118.67 (13) | C9—C14—C13 | 121.22 (15) |
C4—C5—C6 | 115.68 (15) | O3—C15—C9 | 117.08 (13) |
N1—C6—C5 | 120.17 (14) | O4—C15—C9 | 119.75 (15) |
O2—C6—C5 | 128.23 (15) | O3—C15—O4 | 123.17 (16) |
O2—C6—N1 | 111.60 (15) | C10—C11—H11 | 119.93 |
C4—C5—H5 | 122.19 | C12—C11—H11 | 119.84 |
C6—C5—H5 | 122.13 | C11—C12—H12 | 119.47 |
O1—C7—H7B | 109.43 | C13—C12—H12 | 119.45 |
O1—C7—H7C | 109.49 | C12—C13—H13 | 120.49 |
O1—C7—H7A | 109.53 | C14—C13—H13 | 120.48 |
H7A—C7—H7C | 109.49 | C9—C14—H14 | 119.42 |
H7B—C7—H7C | 109.44 | C13—C14—H14 | 119.37 |
H7A—C7—H7B | 109.44 | | |
| | | |
C7—O1—C4—N3 | −0.8 (2) | C15—C9—C10—O5 | −0.2 (2) |
C7—O1—C4—C5 | 179.19 (14) | C15—C9—C10—C11 | 179.72 (14) |
C8—O2—C6—N1 | −176.54 (12) | C10—C9—C14—C13 | −0.3 (2) |
C8—O2—C6—C5 | 3.4 (2) | C15—C9—C14—C13 | −179.94 (16) |
C2—N1—C6—O2 | −179.69 (13) | C10—C9—C15—O3 | −1.9 (2) |
C2—N1—C6—C5 | 0.4 (2) | C10—C9—C15—O4 | 177.55 (14) |
C6—N1—C2—N2 | 179.57 (13) | C14—C9—C15—O3 | 177.71 (13) |
C6—N1—C2—N3 | −0.8 (2) | C14—C9—C15—O4 | −2.8 (2) |
C4—N3—C2—N2 | 179.46 (14) | C14—C9—C10—C11 | 0.1 (2) |
C4—N3—C2—N1 | −0.2 (2) | C14—C9—C10—O5 | −179.83 (14) |
C2—N3—C4—C5 | 1.6 (2) | C9—C10—C11—C12 | 0.4 (2) |
C2—N3—C4—O1 | −178.40 (13) | O5—C10—C11—C12 | −179.73 (15) |
O1—C4—C5—C6 | 178.04 (13) | C10—C11—C12—C13 | −0.6 (3) |
N3—C4—C5—C6 | −2.0 (2) | C11—C12—C13—C14 | 0.4 (3) |
C4—C5—C6—N1 | 0.9 (2) | C12—C13—C14—C9 | 0.1 (3) |
C4—C5—C6—O2 | −179.03 (14) | | |
Symmetry codes: (i) −x, −y, −z+1; (ii) −x+1, −y, −z+1; (iii) −x+2, −y, −z+2; (iv) x, −y+1/2, z+1/2; (v) −x+1, y+1/2, −z+3/2; (vi) x−1, −y+1/2, z−1/2; (vii) −x+2, y−1/2, −z+3/2; (viii) x−1, y, z; (ix) x+1, y, z; (x) x+1, −y+1/2, z+1/2; (xi) −x+1, y−1/2, −z+3/2; (xii) x, −y+1/2, z−1/2; (xiii) −x+2, y+1/2, −z+3/2. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O3 | 0.86 | 1.81 | 2.675 (2) | 178 |
N2—H2A···O4iii | 0.86 | 2.00 | 2.8216 (16) | 159 |
N2—H2B···O4 | 0.86 | 1.97 | 2.822 (2) | 173 |
O5—H5A···O3 | 0.82 | 1.82 | 2.5486 (17) | 147 |
C11—H11···O4xii | 0.93 | 2.58 | 3.4753 (19) | 161 |
Symmetry codes: (iii) −x+2, −y, −z+2; (xii) x, −y+1/2, z−1/2. |
Experimental details
Crystal data |
Chemical formula | C6H10N3O2+·C7H5O3− |
Mr | 293.28 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 120 |
a, b, c (Å) | 9.1071 (3), 14.7657 (6), 12.2829 (6) |
β (°) | 123.465 (3) |
V (Å3) | 1377.90 (11) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.30 × 0.30 × 0.08 |
|
Data collection |
Diffractometer | Bruker–Nonius Kappa CCD area-detector diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 14310, 3136, 2465 |
Rint | 0.034 |
(sin θ/λ)max (Å−1) | 0.650 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.054, 0.137, 1.11 |
No. of reflections | 3136 |
No. of parameters | 194 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.66, −0.72 |
Selected geometric parameters (Å, º) topO1—C4 | 1.333 (2) | O5—C10 | 1.348 (2) |
O1—C7 | 1.444 (2) | N1—C2 | 1.3548 (19) |
O2—C6 | 1.3272 (18) | N1—C6 | 1.359 (2) |
O2—C8 | 1.4439 (19) | N2—C2 | 1.322 (2) |
O3—C15 | 1.281 (2) | N3—C4 | 1.326 (2) |
O4—C15 | 1.2482 (18) | N3—C2 | 1.340 (2) |
| | | |
C4—O1—C7 | 117.45 (13) | O1—C4—N3 | 118.67 (13) |
C6—O2—C8 | 116.52 (13) | N1—C6—C5 | 120.17 (14) |
C2—N1—C6 | 120.19 (15) | O2—C6—C5 | 128.23 (15) |
C2—N3—C4 | 116.08 (13) | O2—C6—N1 | 111.60 (15) |
N2—C2—N3 | 119.69 (13) | O5—C10—C11 | 118.12 (14) |
N1—C2—N3 | 122.61 (15) | O5—C10—C9 | 122.40 (17) |
N1—C2—N2 | 117.70 (15) | O3—C15—C9 | 117.08 (13) |
O1—C4—C5 | 116.09 (15) | O4—C15—C9 | 119.75 (15) |
N3—C4—C5 | 125.24 (17) | O3—C15—O4 | 123.17 (16) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O3 | 0.8600 | 1.8100 | 2.675 (2) | 178.00 |
N2—H2A···O4i | 0.8600 | 2.0000 | 2.8216 (16) | 159.00 |
N2—H2B···O4 | 0.8600 | 1.9700 | 2.822 (2) | 173.00 |
O5—H5A···O3 | 0.8200 | 1.8200 | 2.5486 (17) | 147.00 |
C11—H11···O4ii | 0.9300 | 2.5800 | 3.4753 (19) | 161.00 |
Symmetry codes: (i) −x+2, −y, −z+2; (ii) x, −y+1/2, z−1/2. |
Aminopyrimidine-carboxylate interactions are of fundamental importance since they are involved in protein-nucleic acids recognition and protein-drug binding (Hunt et al., 1980; Baker & Santi, 1965). Hydrogen bonding plays a key role in molecular recognition and crystal engineering research (Desiraju, 1989). 2-Aminopyrimidine forms 1:1 adduct with different mono and dicarboxylic acids (Etter & Adsmond, 1990) rather than individual self-assembly compounds (Scheinbeim & Schempp, 1976). The adducts of carboxylic acid with 2-amino heterocylic ring system have a graph-set motif [R22(8)] (Lynch & Jones, 2004). This motif is very robust in aminopyrimidine- carboxylic acid/ carboxylate systems. The crystal structures of aminopyrimidine derivatives (Schwalbe & Williams, 1982), aminopyrimidine carboxylates (Muthiah, Francis et al., 2006) and co-crystals (Chinnakali et al., 1999) have been reported. Salicylic acid (Cochran et al., 1953) and its derivatives are widely used as analgesic. They are also used for various gastric tympany and also used externally as antiseptic and antifungal agents for various skin conditions. The crystal structure of salicylic acid and its complexes, for example, antipyrine-salicylic acid (salipyrine) (Singh & Vijayan, 1974) and piperazinedione-salicylic acid (1:2) (Varughese & Kartha, 1982) have been reported in literature. The crystal structure of 2-amino-4,6-dimethoxy pyrimidine has also been reported (Low et al., 2002). The crystal structures of 2-amino-4,6-dimethylpyrimidinium salicylate (Muthiah, Balasubramani et al. 2006), 2-amino-4,6-dimethoxy pyrimidine-4-aminobenzoic acid (1/1) (Thanigaimani et al., 2006) and 2-amino-4,6-dimethoxy pyrimidine phthalic acid (1/1) (Thanigaimani et al., 2007a) and 2-amino-4,6- dimethoxypyrimidinium 4-hydroxybenzoate monohydrate, 2-amino-4,6- dimethoxypyrimidinium 6-carboxypyridine-2-carboxylate monohydrate and 2-amino-4,6-dimethoxypyrimidinium hydrogen (2R, 3R)-tartrate 2-amino-4,6-dimethoxypyrimidine (Thanigaimani et al., 2007b)have been recently reported from our laboratory. The present study investigates the hydrogen bonding patterns in 2-amino-4,6-dimethoxy pyrimidinium salicylate (I).
The asymmetric unit (Fig 1) contains one 2-amino-4,6-dimethoxypyrimidinium cation and a salicylate anion, The 2-amino-4,6-dimethoxy pyrimidinium cation is protonated at N1. Protonation of the pyrimidine base on the N1 site is reflected by an increase in bond angle. The C2—N3—C4 angle of the unprotonated atom N3 is 116.08 (13)° while for protonated atom N1, the C2—N1—C6 angle is 120.19 (15)°. The carboxylate group of the salicylate anion interacts with the protonated atom N1 and the 2-amino group of the pyrimidine moiety through a pair of N—H···O hydrogen bonds, forming an eight membered R22(8) ring motif (Etter, 1990; Bernstein et al., 1995). These motifs are centrosymmetrically paired via N—H···O hydrogen bonds to produce the DDAA (D=donor in hydrogen bonds, A=acceptor in hydrogen bonds) array of quadruple hydrogen bonds. This can be represented by the graph-set notation R22(8), R42(8) and R22(8) (Fig. 2). This type of array has also been identified in trimethoprim hydrogen glutarate (Robert et al., 2001), trimethoprim formate (Umadevi et al., 2002), trimethoprim- m-chlorobenzoate (Raj et al., 2003) and pyrimethaminium 3,5-dinitrobenzoate (Subashini et al., 2007). But this array is absent in the crystal structure of a related compound, 2-amino-4,6-dimethylpyrimidinium salicylate (Muthiah, Balasubramani et al. 2006) where the bases are paired. In the title compound, these arrays are further connected via C—H···O hydrogen bonds. The salicylate ions form a hydrogen-bonded supramolecular chain along the c axis, via C—H···O hydrogen bonds involving benzene hydrogen (C11) and one of the oxygen atoms of the carboxylate group, as shown in Fig 3. There is a typical intramolecular hydrogen bond between the phenolic –OH group and the carboxylate group of the salicylate anion [S(6)]. π-π stacking interactions between the aromatic rings are also observed. The pyrimidine ring of 2-amino-4,6-dimethoxy pyrimidinium cation has stacking interactions with the benzene rings of salicylate anion, with a perpendicular separation of 3.280 Å, a centroid-to-centroid distance of 3.6363 (8) and slip angle (the angle between the centroid vector and the normal to the plan) of 21.03°. These are typical aromatic stacking values (Hunter, 1994).