Literature DB >> 23476187

4-Meth-oxy-benzamidinium hydrogen oxalate monohydrate.

Simona Irrera1, Gustavo Portalone.   

Abstract

The title hydrated salt, C8H11N2O(+)·C2HO4(-)·H2O, was synthesized by a reaction of 4-meth-oxy-benzamidine (4-amidino-anisole) and oxalic acid in water solution. In the cation, the amidinium group forms a dihedral angle of 15.60 (6)° with the mean plane of the benzene ring. In the crystal, each amidinium unit is bound to three acetate anions and one water mol-ecule by six distinct N-H⋯O hydrogen bonds. The ion pairs of the asymmetric unit are joined by two N-H⋯O hydrogen bonds into ionic dimers in which the carbonyl O atom of the semi-oxalate anion acts as a bifurcated acceptor, thus generating an R(1)2(6) motif. These subunits are then joined through the remaining N-H⋯O hydrogen bonds to adjacent semi-oxalate anions into linear tetra-meric chains running approximately along the b axis. The structure is stabilized by N-H⋯O and O-H⋯O inter-molecular hydrogen bonds. The water mol-ecule plays an important role in the cohesion and the stability of the crystal structure being involved in three hydrogen bonds connecting two semi-oxalate anions as donor and a benzamidinium cation as acceptor.

Entities:  

Year:  2012        PMID: 23476187      PMCID: PMC3588951          DOI: 10.1107/S1600536812046351

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For the biological and pharmacological relevance of benzamidine, see: Powers & Harper (1999 ▶). For structural analysis of proton-transfer adducts containing mol­ecules of biological inter­est, see: Portalone, (2011a ▶); Portalone & Irrera (2011 ▶). For supra­molecular association in proton-transfer adducts containing benzamidinium cations, see; Portalone (2010 ▶, 2011b ▶, 2012 ▶); Irrera et al. (2012 ▶); Irrera & Portalone (2012a ▶,b ▶,c ▶). For hydrogen-bond motifs, see Bernstein et al. (1995 ▶).

Experimental

Crystal data

C8H11N2O+·C2HO4 −·H2O M = 258.23 Monoclinic, a = 7.1444 (8) Å b = 9.0428 (7) Å c = 18.115 (2) Å β = 93.156 (10)° V = 1168.5 (2) Å3 Z = 4 Mo Kα radiation μ = 0.12 mm−1 T = 298 K 0.18 × 0.12 × 0.09 mm

Data collection

Oxford Diffraction Xcalibur S CCD diffractometer Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011 ▶) T min = 0.978, T max = 0.989 15203 measured reflections 2135 independent reflections 1693 reflections with I > 2σ(I) R int = 0.046

Refinement

R[F 2 > 2σ(F 2)] = 0.047 wR(F 2) = 0.110 S = 1.09 2135 reflections 201 parameters 2 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.16 e Å−3 Δρmin = −0.15 e Å−3 Data collection: CrysAlis CCD (Oxford Diffraction, 2006 ▶); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2006 ▶); program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 (Farrugia, 2012 ▶); software used to prepare material for publication: WinGX (Farrugia, 2012 ▶). Click here for additional data file. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812046351/kp2440sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812046351/kp2440Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C8H11N2O+·C2HO4·H2OF(000) = 544
Mr = 258.23Dx = 1.468 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71069 Å
Hall symbol: -P 2ybcCell parameters from 4235 reflections
a = 7.1444 (8) Åθ = 3.0–29.1°
b = 9.0428 (7) ŵ = 0.12 mm1
c = 18.115 (2) ÅT = 298 K
β = 93.156 (10)°Tablets, colourless
V = 1168.5 (2) Å30.18 × 0.12 × 0.09 mm
Z = 4
Oxford Diffraction Xcalibur S CCD diffractometer2135 independent reflections
Radiation source: Enhance (Mo) X-ray Source1693 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.046
Detector resolution: 16.0696 pixels mm-1θmax = 25.4°, θmin = 3.2°
ω and φ scansh = −8→8
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011)k = −10→10
Tmin = 0.978, Tmax = 0.989l = −21→21
15203 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.110H atoms treated by a mixture of independent and constrained refinement
S = 1.09w = 1/[σ2(Fo2) + (0.0502P)2 + 0.2028P] where P = (Fo2 + 2Fc2)/3
2135 reflections(Δ/σ)max < 0.001
201 parametersΔρmax = 0.16 e Å3
2 restraintsΔρmin = −0.15 e Å3
Experimental. Absorption correction: CrysAlisPro, Agilent Technologies, Version 1.171.35.19 (release 27-10-2011 CrysAlis171 .NET) (compiled Oct 27 2011,15:02:11) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'s involving l.s. planes.
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 > 2σ(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.
xyzUiso*/UeqOcc. (<1)
O10.8980 (2)0.07501 (16)0.24710 (8)0.0511 (4)
N10.7104 (3)−0.2554 (2)−0.06019 (12)0.0484 (5)
H1A0.671 (4)−0.287 (3)−0.1070 (16)0.084 (9)*
H1B0.728 (3)−0.326 (3)−0.0238 (13)0.060 (7)*
N20.6975 (3)−0.0163 (2)−0.09613 (11)0.0439 (5)
H2A0.668 (3)−0.043 (2)−0.1409 (14)0.055 (7)*
H2B0.702 (3)0.080 (3)−0.0883 (12)0.053 (7)*
C10.7801 (2)−0.0672 (2)0.03205 (10)0.0327 (4)
C20.8530 (3)−0.1659 (2)0.08440 (11)0.0420 (5)
H20.8730−0.26350.07070.050*
C30.8970 (3)−0.1231 (2)0.15668 (11)0.0414 (5)
H30.9472−0.19080.19100.050*
C40.8654 (3)0.0217 (2)0.17730 (11)0.0371 (5)
C50.7954 (3)0.1222 (2)0.12537 (11)0.0440 (5)
H50.77610.21990.13900.053*
C60.7543 (3)0.0788 (2)0.05387 (11)0.0395 (5)
H60.70850.14780.01940.047*
C70.7288 (2)−0.1139 (2)−0.04408 (10)0.0346 (5)
C80.9800 (3)−0.0223 (3)0.30183 (12)0.0542 (6)
H8A0.9075 (15)−0.1129 (14)0.3028 (6)0.081*
H8B0.981 (2)0.0250 (9)0.3499 (7)0.081*
H8C1.1076 (19)−0.0452 (14)0.2900 (5)0.081*
O30.6035 (2)−0.17989 (15)−0.22870 (8)0.0506 (4)
O40.4130 (2)−0.35402 (14)−0.27537 (8)0.0448 (4)
H40.454 (4)−0.412 (3)−0.2291 (15)0.086 (8)*
O50.4872 (2)0.00180 (14)−0.34351 (8)0.0478 (4)
O60.3608 (2)−0.19541 (15)−0.39997 (8)0.0517 (4)
C90.4936 (3)−0.22516 (19)−0.27658 (11)0.0354 (5)
C100.4403 (3)−0.1325 (2)−0.34652 (11)0.0383 (5)
O2W0.7296 (9)−0.5215 (3)0.02842 (17)0.0531 (13)0.85 (2)
H21W0.646 (3)−0.530 (3)0.0600 (14)0.080*
H22W0.699 (4)−0.578 (3)−0.0102 (12)0.080*
O21W0.845 (10)−0.520 (2)0.008 (2)0.101 (17)0.15 (2)
U11U22U33U12U13U23
O10.0703 (10)0.0445 (8)0.0369 (8)0.0073 (7)−0.0118 (7)−0.0061 (7)
N10.0728 (13)0.0325 (10)0.0385 (11)−0.0018 (9)−0.0083 (10)−0.0023 (9)
N20.0607 (12)0.0371 (11)0.0328 (11)−0.0035 (8)−0.0074 (9)0.0024 (8)
C10.0334 (10)0.0303 (10)0.0341 (11)−0.0011 (8)0.0007 (8)−0.0002 (8)
C20.0576 (13)0.0273 (10)0.0406 (12)0.0026 (9)−0.0034 (10)−0.0015 (9)
C30.0513 (13)0.0332 (10)0.0386 (12)0.0015 (9)−0.0080 (10)0.0052 (9)
C40.0373 (11)0.0383 (11)0.0353 (11)−0.0010 (8)−0.0021 (8)−0.0038 (9)
C50.0572 (13)0.0292 (10)0.0449 (13)0.0061 (9)−0.0045 (10)−0.0041 (9)
C60.0494 (12)0.0315 (10)0.0370 (11)0.0048 (9)−0.0043 (9)0.0042 (9)
C70.0354 (11)0.0333 (10)0.0348 (11)−0.0016 (8)−0.0007 (8)0.0009 (9)
C80.0646 (15)0.0563 (14)0.0402 (13)0.0030 (11)−0.0105 (11)0.0007 (11)
O30.0705 (10)0.0363 (8)0.0427 (9)−0.0050 (7)−0.0184 (8)−0.0008 (6)
O40.0650 (10)0.0293 (7)0.0386 (9)−0.0066 (6)−0.0096 (7)0.0046 (6)
O50.0765 (11)0.0278 (7)0.0379 (8)−0.0054 (7)−0.0081 (7)0.0019 (6)
O60.0857 (11)0.0329 (8)0.0343 (9)−0.0044 (7)−0.0164 (8)−0.0001 (6)
C90.0458 (12)0.0257 (9)0.0345 (11)0.0045 (8)−0.0006 (9)−0.0040 (8)
C100.0511 (12)0.0289 (10)0.0346 (11)0.0007 (9)−0.0014 (9)−0.0016 (8)
O2W0.074 (3)0.0401 (12)0.0453 (15)−0.0055 (13)0.0009 (14)−0.0065 (9)
O21W0.15 (4)0.067 (10)0.078 (16)0.022 (14)−0.04 (2)−0.021 (9)
O1—C41.361 (2)C5—C61.370 (3)
O1—C81.427 (2)C5—H50.9300
N1—C71.317 (3)C6—H60.9300
N1—H1A0.92 (3)C8—H8A0.9696
N1—H1B0.92 (2)C8—H8B0.9697
N2—C71.302 (2)C8—H8C0.9696
N2—H2A0.86 (2)O3—C91.209 (2)
N2—H2B0.88 (2)O4—C91.300 (2)
C1—C21.383 (3)O4—H41.02 (3)
C1—C61.393 (3)O5—C101.260 (2)
C1—C71.470 (3)O6—C101.234 (2)
C2—C31.385 (3)C9—C101.549 (3)
C2—H20.9300O2W—O21W0.92 (8)
C3—C41.383 (3)O2W—H21W0.854 (17)
C3—H30.9300O2W—H22W0.883 (17)
C4—C51.382 (3)O21W—H22W1.20 (6)
C4—O1—C8118.00 (16)C5—C6—H6119.5
C7—N1—H1A121.5 (18)C1—C6—H6119.5
C7—N1—H1B120.6 (14)N2—C7—N1119.1 (2)
H1A—N1—H1B118 (2)N2—C7—C1120.56 (18)
C7—N2—H2A121.0 (15)N1—C7—C1120.28 (18)
C7—N2—H2B123.3 (14)O1—C8—H8A109.5
H2A—N2—H2B116 (2)O1—C8—H8B109.5
C2—C1—C6117.90 (17)H8A—C8—H8B109.5
C2—C1—C7121.50 (17)O1—C8—H8C109.5
C6—C1—C7120.59 (17)H8A—C8—H8C109.5
C1—C2—C3121.65 (18)H8B—C8—H8C109.5
C1—C2—H2119.2C9—O4—H4111.6 (15)
C3—C2—H2119.2O3—C9—O4124.20 (18)
C4—C3—C2119.22 (18)O3—C9—C10121.61 (17)
C4—C3—H3120.4O4—C9—C10114.18 (17)
C2—C3—H3120.4O6—C10—O5126.03 (18)
O1—C4—C5115.88 (17)O6—C10—C9118.28 (16)
O1—C4—C3124.32 (18)O5—C10—C9115.68 (17)
C5—C4—C3119.80 (18)O21W—O2W—H21W161 (2)
C6—C5—C4120.39 (18)O21W—O2W—H22W83 (2)
C6—C5—H5119.8H21W—O2W—H22W109 (3)
C4—C5—H5119.8O2W—O21W—H22W47 (3)
C5—C6—C1121.01 (18)
C6—C1—C2—C30.9 (3)C2—C1—C6—C5−1.6 (3)
C7—C1—C2—C3−178.30 (18)C7—C1—C6—C5177.63 (18)
C1—C2—C3—C40.7 (3)C2—C1—C7—N2−165.77 (19)
C8—O1—C4—C5−176.59 (18)C6—C1—C7—N215.0 (3)
C8—O1—C4—C33.7 (3)C2—C1—C7—N115.5 (3)
C2—C3—C4—O1177.98 (18)C6—C1—C7—N1−163.68 (19)
C2—C3—C4—C5−1.7 (3)O3—C9—C10—O6164.7 (2)
O1—C4—C5—C6−178.67 (17)O4—C9—C10—O6−14.1 (3)
C3—C4—C5—C61.1 (3)O3—C9—C10—O5−13.9 (3)
C4—C5—C6—C10.6 (3)O4—C9—C10—O5167.33 (17)
D—H···AD—HH···AD···AD—H···A
N1—H1A···O30.92 (3)2.43 (3)3.180 (3)138 (2)
N1—H1B···O2W0.92 (2)2.00 (2)2.891 (3)161 (2)
N1—H1A···O5i0.92 (3)2.37 (3)3.096 (2)135 (2)
N2—H2A···O30.86 (2)2.05 (2)2.869 (2)159 (2)
N2—H2A···O4ii0.86 (2)2.34 (2)2.827 (2)116.4 (18)
N2—H2B···O6ii0.88 (2)2.09 (3)2.932 (2)159.5 (19)
O4—H4···O5i1.02 (3)1.56 (3)2.5840 (19)178 (2)
O2W—H21W···O5iii0.85 (2)2.15 (2)2.976 (6)163 (3)
O2W—H22W···O6i0.88 (2)1.97 (2)2.853 (3)177 (3)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
N1—H1A⋯O30.92 (3)2.43 (3)3.180 (3)138 (2)
N1—H1B⋯O2W 0.92 (2)2.00 (2)2.891 (3)161 (2)
N1—H1A⋯O5i 0.92 (3)2.37 (3)3.096 (2)135 (2)
N2—H2A⋯O30.86 (2)2.05 (2)2.869 (2)159 (2)
N2—H2A⋯O4ii 0.86 (2)2.34 (2)2.827 (2)116.4 (18)
N2—H2B⋯O6ii 0.88 (2)2.09 (3)2.932 (2)159.5 (19)
O4—H4⋯O5i 1.02 (3)1.56 (3)2.5840 (19)178 (2)
O2W—H21W⋯O5iii 0.85 (2)2.15 (2)2.976 (6)163 (3)
O2W—H22W⋯O6i 0.88 (2)1.97 (2)2.853 (3)177 (3)

Symmetry codes: (i) ; (ii) ; (iii) .

  9 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  Supramolecular association in proton-transfer adducts containing benzamidinium cations. I. Four molecular salts with uracil derivatives.

Authors:  Gustavo Portalone
Journal:  Acta Crystallogr C       Date:  2010-05-13       Impact factor: 1.172

3.  Supramolecular association in proton-transfer adducts containing benzamidinium cations. II. Concomitant polymorphs of the molecular salt of 2,6-dimethoxybenzoic acid with benzamidine.

Authors:  Simona Irrera; Giancarlo Ortaggi; Gustavo Portalone
Journal:  Acta Crystallogr C       Date:  2012-10-18       Impact factor: 1.172

4.  Solid-phase molecular recognition of cytosine based on proton-transfer reaction. Part II. supramolecular architecture in the cocrystals of cytosine and its 5-Fluoroderivative with 5-Nitrouracil.

Authors:  Gustavo Portalone
Journal:  Chem Cent J       Date:  2011-09-02       Impact factor: 4.215

5.  4-Meth-oxy-benzamidinium 2,6-dimeth-oxy-benzoate.

Authors:  Gustavo Portalone
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-01-07

6.  A new polymorph of 2,6-dimeth-oxy-benzoic acid.

Authors:  Gustavo Portalone
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-11-23

7.  4-Meth-oxy-benzamidinium acetate.

Authors:  Simona Irrera; Gustavo Portalone
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-11-03

8.  4-Meth-oxy-benzamidinium hydrogen sulfate.

Authors:  Simona Irrera; Gustavo Portalone
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-10-31

9.  4-Meth-oxy-benzamidinium chloride monohydrate.

Authors:  Simona Irrera; Gustavo Portalone
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-10-06
  9 in total
  1 in total

1.  4-Meth-oxy-benzamidinium bromide.

Authors:  Simona Irrera; Gustavo Portalone
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-12-08
  1 in total

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