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In the title compound, 2,4-di­amino-5-(3,4,5-tri­methoxy­benzyl)­pyrimidinium hydrogen malonate, C14H19N4O3+·C3H3O4, the trimethoprim mol­ecule is protonated at one of the pyrimidine N atoms. The carboxyl­ate group of the hydrogen malonate ion accepts a pair of N—H...O hydrogen bonds from an adjacent trimethoprim mol­ecule, which is similar to the carboxyl­ate–trimethoprim cation interaction present in the complex of di­hydro­folate reductase with trimethoprim. An O atom of the carboxyl group forms an intramolecular O—H...O hydrogen bond with the carboxyl­ate group, leading to a folded conformation for the hydrogen malonate ion. Each hydrogen malonate ion bridges two di­amino­pyrimidine cations, via N—H...O and C—H...N hydrogen bonds, leading to a supramolecular ribbon made up of alternating cations and anions. Two such inversion-related ribbons are cross-linked by (amino)N—H...O(methoxy) hydrogen bonds, (pyrimidine)C—H...O(methoxy) hydrogen bonds and π–π stacking involving the benzene planes.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536804028867/hb6113sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536804028867/hb6113Isup2.hkl
Contains datablock I

CCDC reference: 259588

Key indicators

  • Single-crystal X-ray study
  • T = 293 K
  • Mean [sigma](C-C) = 0.002 Å
  • R factor = 0.054
  • wR factor = 0.155
  • Data-to-parameter ratio = 12.7

checkCIF/PLATON results

No syntax errors found



Alert level A PLAT029_ALERT_3_A _diffrn_measured_fraction_theta_full Low ....... 0.92
Alert level C REFLT03_ALERT_3_C Reflection count < 95% complete From the CIF: _diffrn_reflns_theta_max 68.90 From the CIF: _diffrn_reflns_theta_full 0.00 From the CIF: _reflns_number_total 3268 TEST2: Reflns within _diffrn_reflns_theta_max Count of symmetry unique reflns 3567 Completeness (_total/calc) 91.62% PLAT022_ALERT_3_C Ratio Unique / Expected Reflections too Low .... 0.92 PLAT063_ALERT_3_C Crystal Probably too Large for Beam Size ....... 0.68 mm PLAT244_ALERT_4_C Low Solvent U(eq) as Compared to Neighbors for C19 PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.25
1 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 5 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 1 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 1 ALERT type 4 Improvement, methodology, query or suggestion

Computing details top

Data collection: XSCANS (Bruker, 2001); cell refinement: XSCANS; data reduction: SHELXTL (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 1990); software used to prepare material for publication: PLATON.

2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidinium hydrogen malonate top
Crystal data top
C14H19N4O3+·C3H3O4Z = 2
Mr = 394.39F(000) = 416
Triclinic, P1Dx = 1.366 Mg m3
Hall symbol: -P 1Cu Kα radiation, λ = 1.54178 Å
a = 8.4851 (2) ÅCell parameters from 50 reflections
b = 8.6566 (2) Åθ = 2.1–28.1°
c = 13.6425 (3) ŵ = 0.91 mm1
α = 106.360 (3)°T = 293 K
β = 91.712 (2)°Plate, colorless
γ = 92.950 (3)°0.68 × 0.65 × 0.35 mm
V = 959.08 (4) Å3
Data collection top
Bruker P4
diffractometer
3029 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.020
Graphite monochromatorθmax = 68.9°, θmin = 3.4°
ω scansh = 010
Absorption correction: part of the refinement model (ΔF)
SHELXA (Bruker, 2001)
k = 109
Tmin = 0.549, Tmax = 0.726l = 1616
3484 measured reflections3 standard reflections every 97 reflections
3268 independent reflections intensity decay: none
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.054H-atom parameters constrained
wR(F2) = 0.156 w = 1/[σ2(Fo2) + (0.0825P)2 + 0.208P]
where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max < 0.001
3268 reflectionsΔρmax = 0.15 e Å3
258 parametersΔρmin = 0.20 e Å3
0 restraintsExtinction correction: SHELXL97, FC*=KFC[1+0.001XFC2Λ3/SIN(2Θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.016 (2)
Special details top

Experimental. The low data completeness (92%) arose due to problems in accessing all parts of reciprocal space at high angles (2θ = 138°) for a triclinic crystal collected using copper radiation.

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
xyzUiso*/Ueq
O10.60422 (16)0.19447 (18)0.66944 (10)0.0635 (5)
O20.29781 (16)0.11037 (17)0.64647 (10)0.0620 (4)
O30.12262 (16)0.1503 (2)0.48835 (10)0.0722 (5)
N10.3900 (2)0.41033 (18)0.11787 (11)0.0578 (5)
N20.2603 (2)0.2447 (2)0.02719 (13)0.0746 (7)
N30.3824 (2)0.12923 (18)0.08431 (12)0.0595 (5)
N40.4950 (2)0.0105 (2)0.19461 (13)0.0676 (6)
C20.3453 (2)0.2601 (2)0.05907 (14)0.0564 (6)
C40.4633 (2)0.1467 (2)0.17320 (14)0.0546 (6)
C50.5132 (2)0.3023 (2)0.24014 (13)0.0539 (6)
C60.4728 (2)0.4284 (2)0.20754 (14)0.0558 (6)
C70.6048 (2)0.3261 (3)0.34030 (14)0.0603 (6)
C80.5172 (2)0.2756 (2)0.42258 (13)0.0513 (5)
C90.6041 (2)0.2604 (2)0.50718 (13)0.0524 (6)
C100.5297 (2)0.2106 (2)0.58268 (13)0.0508 (5)
C110.3677 (2)0.1733 (2)0.57452 (13)0.0512 (6)
C120.2803 (2)0.1915 (2)0.49096 (13)0.0544 (6)
C130.3555 (2)0.2447 (2)0.41588 (14)0.0567 (6)
C140.0276 (2)0.1698 (3)0.40559 (18)0.0797 (9)
C150.2035 (3)0.2178 (3)0.71531 (16)0.0734 (8)
C160.7715 (3)0.2277 (4)0.68101 (17)0.0807 (9)
O40.3144 (2)0.67550 (18)0.06300 (12)0.0779 (6)
O50.1735 (2)0.52666 (18)0.07463 (13)0.0841 (6)
O60.0763 (3)0.9271 (2)0.15728 (14)0.0982 (8)
O70.0414 (3)0.6641 (2)0.19174 (13)0.0942 (7)
C170.2203 (3)0.6593 (2)0.01213 (15)0.0624 (7)
C180.1600 (3)0.8112 (2)0.02884 (16)0.0700 (8)
C190.0895 (3)0.8053 (3)0.13153 (16)0.0686 (7)
H10.366300.493300.098900.0690*
H2A0.230100.150300.065900.0900*
H2B0.235700.329100.044200.0900*
H4A0.464000.081000.152600.0810*
H4B0.546500.014000.250500.0810*
H60.502800.532100.248000.0670*
H7A0.638800.439400.366800.0720*
H7B0.699000.266000.326900.0720*
H90.712700.283900.512900.0630*
H130.296400.259500.361100.0680*
H14A0.078500.128100.409300.1200*
H14B0.069800.112200.342100.1200*
H14C0.027200.282300.409500.1200*
H15A0.140000.158700.751300.1100*
H15B0.136000.268900.677700.1100*
H15C0.270600.298500.763500.1100*
H16A0.810000.207500.742800.1210*
H16B0.796100.338600.684300.1210*
H16C0.820700.159300.623600.1210*
H70.055300.595000.162400.1410*
H18A0.081100.848700.021000.0840*
H18B0.247200.892600.013300.0840*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0627 (8)0.0821 (9)0.0515 (7)0.0097 (7)0.0057 (6)0.0283 (7)
O20.0719 (8)0.0663 (8)0.0520 (7)0.0025 (6)0.0085 (6)0.0236 (6)
O30.0555 (7)0.1081 (12)0.0538 (8)0.0108 (7)0.0041 (6)0.0277 (8)
N10.0766 (10)0.0482 (9)0.0496 (8)0.0046 (7)0.0040 (7)0.0163 (7)
N20.1130 (15)0.0535 (10)0.0560 (9)0.0054 (9)0.0241 (9)0.0164 (8)
N30.0798 (10)0.0494 (9)0.0499 (8)0.0066 (8)0.0045 (7)0.0156 (7)
N40.0924 (12)0.0582 (10)0.0557 (9)0.0137 (9)0.0052 (8)0.0210 (8)
C20.0721 (11)0.0511 (10)0.0470 (9)0.0047 (8)0.0016 (8)0.0160 (8)
C40.0645 (10)0.0546 (10)0.0483 (9)0.0083 (8)0.0046 (8)0.0197 (8)
C50.0587 (10)0.0598 (11)0.0450 (9)0.0006 (8)0.0036 (7)0.0183 (8)
C60.0657 (11)0.0540 (10)0.0458 (9)0.0018 (8)0.0001 (8)0.0124 (8)
C70.0586 (10)0.0742 (13)0.0511 (10)0.0040 (9)0.0026 (8)0.0246 (9)
C80.0571 (9)0.0523 (10)0.0441 (9)0.0032 (8)0.0002 (7)0.0135 (7)
C90.0522 (9)0.0576 (11)0.0475 (9)0.0032 (8)0.0014 (7)0.0155 (8)
C100.0593 (10)0.0505 (9)0.0421 (8)0.0078 (8)0.0022 (7)0.0120 (7)
C110.0597 (10)0.0512 (10)0.0426 (9)0.0010 (8)0.0010 (7)0.0137 (7)
C120.0527 (9)0.0631 (11)0.0452 (9)0.0019 (8)0.0011 (7)0.0131 (8)
C130.0571 (10)0.0674 (12)0.0462 (9)0.0001 (8)0.0045 (7)0.0186 (8)
C140.0554 (11)0.1133 (19)0.0723 (14)0.0038 (11)0.0119 (10)0.0325 (13)
C150.0799 (14)0.0850 (15)0.0553 (11)0.0033 (11)0.0167 (10)0.0189 (10)
C160.0608 (12)0.122 (2)0.0631 (12)0.0161 (12)0.0080 (10)0.0319 (13)
O40.1069 (12)0.0603 (9)0.0689 (9)0.0083 (8)0.0197 (8)0.0241 (7)
O50.1248 (14)0.0512 (8)0.0736 (10)0.0058 (8)0.0188 (9)0.0154 (7)
O60.1482 (17)0.0711 (11)0.0812 (11)0.0053 (10)0.0288 (11)0.0349 (9)
O70.1392 (16)0.0670 (10)0.0708 (10)0.0016 (10)0.0343 (10)0.0151 (8)
C170.0801 (13)0.0551 (11)0.0542 (10)0.0060 (9)0.0008 (9)0.0192 (9)
C180.0935 (15)0.0553 (12)0.0602 (12)0.0097 (10)0.0121 (11)0.0153 (9)
C190.0872 (14)0.0592 (12)0.0602 (12)0.0069 (10)0.0071 (10)0.0189 (9)
Geometric parameters (Å, º) top
O1—C101.370 (2)C7—C81.515 (3)
O1—C161.429 (3)C8—C91.392 (2)
O2—C111.384 (2)C8—C131.380 (2)
O2—C151.420 (3)C9—C101.381 (2)
O3—C121.364 (2)C10—C111.390 (2)
O3—C141.421 (3)C11—C121.392 (2)
O4—C171.252 (3)C12—C131.394 (3)
O5—C171.259 (3)C6—H60.9296
O6—C191.211 (3)C7—H7B0.9700
O7—C191.303 (3)C7—H7A0.9699
O7—H70.8193C9—H90.9295
N1—C61.358 (2)C13—H130.9298
N1—C21.350 (2)C14—H14B0.9595
N2—C21.332 (2)C14—H14C0.9603
N3—C21.323 (2)C14—H14A0.9607
N3—C41.342 (2)C15—H15A0.9602
N4—C41.330 (3)C15—H15C0.9604
N1—H10.8600C15—H15B0.9609
N2—H2B0.8599C16—H16B0.9600
N2—H2A0.8599C16—H16A0.9593
N4—H4A0.8595C16—H16C0.9602
N4—H4B0.8596C17—C181.508 (3)
C4—C51.433 (3)C18—C191.493 (3)
C5—C61.345 (3)C18—H18A0.9701
C5—C71.508 (2)C18—H18B0.9704
C10—O1—C16117.44 (16)C5—C6—H6118.69
C11—O2—C15114.76 (16)C5—C7—H7B108.29
C12—O3—C14117.60 (15)C8—C7—H7A108.26
C19—O7—H7109.49C5—C7—H7A108.30
C2—N1—C6118.94 (16)H7A—C7—H7B107.44
C2—N3—C4118.74 (16)C8—C7—H7B108.35
C6—N1—H1120.52C10—C9—H9119.83
C2—N1—H1120.53C8—C9—H9119.88
C2—N2—H2A119.96C8—C13—H13119.89
C2—N2—H2B120.02C12—C13—H13119.84
H2A—N2—H2B120.01O3—C14—H14B109.49
C4—N4—H4A120.04O3—C14—H14C109.50
H4A—N4—H4B119.98O3—C14—H14A109.43
C4—N4—H4B119.98H14A—C14—H14C109.48
N2—C2—N3119.40 (17)H14B—C14—H14C109.43
N1—C2—N2118.16 (17)H14A—C14—H14B109.48
N1—C2—N3122.44 (17)O2—C15—H15A109.48
N3—C4—C5121.97 (16)O2—C15—H15C109.52
N4—C4—C5122.32 (17)H15A—C15—H15B109.46
N3—C4—N4115.72 (17)O2—C15—H15B109.46
C6—C5—C7121.47 (18)H15B—C15—H15C109.48
C4—C5—C6115.24 (16)H15A—C15—H15C109.42
C4—C5—C7123.29 (17)O1—C16—H16B109.46
N1—C6—C5122.65 (17)O1—C16—H16C109.44
C5—C7—C8115.91 (15)O1—C16—H16A109.46
C7—C8—C9118.33 (15)H16A—C16—H16C109.50
C9—C8—C13119.59 (16)H16B—C16—H16C109.46
C7—C8—C13122.08 (16)H16A—C16—H16B109.50
C8—C9—C10120.29 (16)O4—C17—C18117.03 (18)
O1—C10—C11114.89 (15)O5—C17—C18117.93 (19)
C9—C10—C11120.43 (16)O4—C17—O5125.03 (19)
O1—C10—C9124.69 (16)C17—C18—C19118.88 (18)
O2—C11—C12121.21 (15)O6—C19—C18121.2 (2)
O2—C11—C10119.40 (15)O7—C19—C18117.3 (2)
C10—C11—C12119.29 (16)O6—C19—O7121.5 (2)
O3—C12—C11115.42 (15)C17—C18—H18A107.63
C11—C12—C13120.06 (16)C17—C18—H18B107.62
O3—C12—C13124.50 (16)C19—C18—H18A107.62
C8—C13—C12120.27 (16)C19—C18—H18B107.52
N1—C6—H6118.66H18A—C18—H18B107.03
C16—O1—C10—C91.7 (3)C5—C7—C8—C9165.84 (17)
C16—O1—C10—C11178.6 (2)C13—C8—C9—C101.7 (3)
C15—O2—C11—C10108.4 (2)C7—C8—C13—C12177.10 (18)
C15—O2—C11—C1275.3 (2)C9—C8—C13—C122.9 (3)
C14—O3—C12—C11178.76 (18)C7—C8—C9—C10178.30 (18)
C14—O3—C12—C132.9 (3)C8—C9—C10—C110.8 (3)
C6—N1—C2—N31.7 (3)C8—C9—C10—O1178.89 (17)
C6—N1—C2—N2178.11 (17)C9—C10—C11—O2174.43 (16)
C2—N1—C6—C50.4 (3)C9—C10—C11—C122.0 (3)
C4—N3—C2—N2177.67 (17)O1—C10—C11—C12177.68 (16)
C4—N3—C2—N12.1 (3)O1—C10—C11—O25.9 (2)
C2—N3—C4—C51.3 (3)O2—C11—C12—C13175.57 (16)
C2—N3—C4—N4179.15 (17)C10—C11—C12—C130.8 (3)
N4—C4—C5—C6179.66 (17)O2—C11—C12—O32.9 (3)
N3—C4—C5—C60.2 (3)C10—C11—C12—O3179.22 (16)
N4—C4—C5—C70.3 (3)C11—C12—C13—C81.7 (3)
N3—C4—C5—C7179.74 (16)O3—C12—C13—C8176.60 (17)
C6—C5—C7—C8113.4 (2)O4—C17—C18—C19161.5 (2)
C4—C5—C7—C866.7 (2)O5—C17—C18—C1918.0 (3)
C4—C5—C6—N10.3 (3)C17—C18—C19—O719.6 (3)
C7—C5—C6—N1179.80 (16)C17—C18—C19—O6161.1 (2)
C5—C7—C8—C1314.2 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O40.861.852.708 (2)178
N2—H2A···O6i0.862.303.129 (3)163
N2—H2B···O50.861.962.822 (2)176
N4—H4A···O4i0.862.393.229 (2)164
N4—H4B···O2ii0.862.403.182 (2)151
O7—H7···O50.821.782.515 (3)148
C6—H6···O1iii0.932.543.331 (2)143
C15—H15B···O30.962.493.035 (3)116
C18—H18B···N3iv0.972.333.228 (3)154
Symmetry codes: (i) x, y1, z; (ii) x+1, y, z+1; (iii) x+1, y+1, z+1; (iv) x, y+1, z.
 

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