Literature DB >> 22346912

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

Gustavo Portalone1.   

Abstract

The title compound, C(8)H(11)N(2)O(+)·C(9)H(9)O(4) (-), was synthesized by the reaction of 4-meth-oxy-benzamidine (4-amidino-anisole) and 2,6-dimeth-oxy-benzoic acid. The structure consists of non-planar pairs of hydrogen-bonded 4-meth-oxy-benzamidinium cations and 2,6-dimeth-oxy-benzoate anions. In the cation, the amidinium group is tilted by 27.94 (10)° with respect to the benzene ring. In the anion, the sterically bulky ortho-meth-oxy substituents force the carb-oxy-ate group to be twisted away from the plane of the benzene ring by 73.24 (6)°. The ions are further associated in the crystal into chains along the b-axis direction by inter-molecular N-H⋯O hydrogen bonds.

Entities:  

Year:  2012        PMID: 22346912      PMCID: PMC3274967          DOI: 10.1107/S160053681105519X

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: Marquart et al. (1983 ▶); Sprang et al. (1987 ▶); Bode et al. (1990 ▶); Powers & Harper (1999 ▶); Grzesiak et al. (2000 ▶). For the structure of benzamidine, see: Barker et al. (1996 ▶). For supra­molecular association in proton-transfer adducts containing benzamidinium cations, see; Papoutsakis et al. (1999 ▶); Portalone (2008 ▶, 2010 ▶). For the structure of benzdiamidine, see: Jokić et al. (2001) ▶. For the ortho­rhom­bic and tetra­gonal polymorphs of 2,6-dimeth­oxy­benzoic acid, see: Swaminathan et al. (1976 ▶); Bryan & White (1982 ▶); Portalone (2009 ▶, 2011 ▶). For the analysis of benzene ring deformations induced by substitution, see: Schultz et al. (1993 ▶); Portalone et al. (1998 ▶); For computation of ring patterns formed by hydrogen bonds in crystal structures, see: Etter et al. (1990 ▶); Bernstein et al. (1995 ▶); Motherwell et al. (1999 ▶).

Experimental

Crystal data

C8H11N2O+·C9H9O4 M = 332.35 Monoclinic, a = 12.6594 (3) Å b = 9.6754 (2) Å c = 13.7923 (4) Å β = 99.241 (2)° V = 1667.42 (7) Å3 Z = 4 Mo Kα radiation μ = 0.10 mm−1 T = 298 K 0.30 × 0.30 × 0.25 mm

Data collection

Oxford Diffraction Xcalibur S CCD diffractometer Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006 ▶) T min = 0.971, T max = 0.976 76316 measured reflections 4217 independent reflections 3914 reflections with I > 2σ(I) R int = 0.026

Refinement

R[F 2 > 2σ(F 2)] = 0.060 wR(F 2) = 0.131 S = 1.17 4217 reflections 239 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.32 e Å−3 Δρmin = −0.18 e Å−3 Data collection: CrysAlis CCD (Oxford Diffraction, 2006 ▶); cell refinement: CrysAlis RED (Oxford Diffraction, 2006 ▶); data reduction: CrysAlis RED; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: WinGX (Farrugia, 1997 ▶); software used to prepare material for publication: WinGX (Farrugia, 1999 ▶). Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S160053681105519X/rz2691sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681105519X/rz2691Isup2.hkl Supplementary material file. DOI: 10.1107/S160053681105519X/rz2691Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C8H11N2O+·C9H9O4F(000) = 704
Mr = 332.35Dx = 1.324 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71069 Å
Hall symbol: -P 2ybcCell parameters from 41031 reflections
a = 12.6594 (3) Åθ = 2.9–34.8°
b = 9.6754 (2) ŵ = 0.10 mm1
c = 13.7923 (4) ÅT = 298 K
β = 99.241 (2)°Tablets, colourless
V = 1667.42 (7) Å30.30 × 0.30 × 0.25 mm
Z = 4
Oxford Diffraction Xcalibur S CCD diffractometer4217 independent reflections
Radiation source: Enhance (Mo) X-ray source3914 reflections with I > 2σ(I)
graphiteRint = 0.026
Detector resolution: 16.0696 pixels mm-1θmax = 28.5°, θmin = 2.9°
ω and φ scansh = −16→16
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006)k = −12→12
Tmin = 0.971, Tmax = 0.976l = −18→18
76316 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)] = 0.060Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.131H atoms treated by a mixture of independent and constrained refinement
S = 1.17w = 1/[σ2(Fo2) + (0.0405P)2 + 0.878P] where P = (Fo2 + 2Fc2)/3
4217 reflections(Δ/σ)max < 0.001
239 parametersΔρmax = 0.32 e Å3
0 restraintsΔρmin = −0.18 e Å3
Experimental. CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.32.29 (release 10-06-2008 CrysAlis171 .NET) (compiled Jun 10 2008,16:49:55) 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*/Ueq
O50.10799 (10)−0.11594 (17)−0.24016 (10)0.0540 (4)
N10.44446 (13)−0.09706 (15)0.15597 (11)0.0413 (4)
H1A0.4973 (17)−0.110 (2)0.2099 (16)0.049 (6)*
H1B0.4294 (17)−0.011 (2)0.1385 (15)0.045 (5)*
N20.39964 (14)−0.32294 (16)0.15666 (14)0.0467 (4)
H2A0.442 (2)−0.329 (3)0.2161 (19)0.063 (7)*
H2B0.3761 (19)−0.396 (3)0.1250 (18)0.059 (7)*
C10.31657 (12)−0.17948 (16)0.02049 (11)0.0303 (3)
C20.33754 (13)−0.07531 (19)−0.04288 (12)0.0376 (4)
H20.4006−0.0181−0.02500.045*
C30.27065 (13)−0.0509 (2)−0.13109 (13)0.0408 (4)
H30.28710.0216−0.17490.049*
C40.17991 (13)−0.13163 (19)−0.15559 (12)0.0375 (4)
C50.15748 (13)−0.2361 (2)−0.09328 (14)0.0426 (4)
H50.0939−0.2924−0.11090.051*
C60.22544 (13)−0.26050 (18)−0.00599 (13)0.0388 (4)
H60.2096−0.33440.03700.047*
C70.38977 (12)−0.20070 (15)0.11435 (12)0.0316 (3)
C170.12111 (18)0.0003 (3)−0.30073 (15)0.0591 (6)
H17A0.1146 (14)0.0864 (14)−0.2636 (7)0.089*
H17B0.0653 (12)−0.0014 (10)−0.3597 (11)0.089*
H17C0.1925 (12)−0.0034 (10)−0.3209 (11)0.089*
O10.61718 (10)−0.11290 (12)0.30539 (9)0.0400 (3)
O20.55414 (10)−0.31629 (12)0.34359 (10)0.0421 (3)
O30.63894 (11)−0.06691 (15)0.52149 (10)0.0517 (4)
O40.78817 (10)−0.40567 (14)0.34411 (9)0.0447 (3)
C80.71797 (11)−0.23514 (15)0.43547 (11)0.0276 (3)
C90.72422 (14)−0.15283 (17)0.51889 (12)0.0366 (4)
C100.81319 (17)−0.1596 (2)0.59275 (14)0.0523 (5)
H100.8165−0.10420.65180.063*
C110.89636 (15)−0.2462 (2)0.58046 (15)0.0524 (5)
H110.9593−0.24910.63080.063*
C120.89261 (13)−0.3286 (2)0.49875 (13)0.0425 (4)
H120.9522−0.38850.49140.051*
C130.80189 (12)−0.32480 (16)0.42671 (11)0.0315 (3)
C140.62180 (11)−0.22199 (15)0.35457 (10)0.0270 (3)
C150.62678 (17)−0.0059 (2)0.61327 (15)0.0523 (5)
H15A0.6294 (13)−0.0783 (10)0.6634 (8)0.078*
H15B0.5577 (11)0.0421 (16)0.6066 (3)0.078*
H15C0.6849 (11)0.0606 (15)0.6329 (7)0.078*
C160.86484 (16)−0.5108 (2)0.33788 (14)0.0477 (5)
H16A0.9338 (10)−0.4683 (6)0.3302 (11)0.071*
H16B0.8399 (7)−0.5704 (12)0.2808 (10)0.071*
H16C0.8742 (9)−0.5669 (13)0.3984 (9)0.071*
U11U22U33U12U13U23
O50.0399 (7)0.0729 (10)0.0426 (7)−0.0057 (7)−0.0136 (6)−0.0001 (7)
N10.0484 (8)0.0244 (7)0.0428 (8)0.0029 (6)−0.0181 (7)0.0010 (6)
N20.0499 (9)0.0259 (7)0.0573 (10)0.0001 (6)−0.0121 (8)0.0043 (7)
C10.0278 (7)0.0275 (7)0.0339 (7)0.0028 (6)−0.0002 (6)−0.0054 (6)
C20.0279 (7)0.0432 (9)0.0391 (9)−0.0068 (7)−0.0025 (6)0.0002 (7)
C30.0344 (8)0.0496 (10)0.0363 (8)−0.0056 (7)−0.0002 (6)0.0046 (7)
C40.0280 (7)0.0481 (10)0.0340 (8)0.0026 (7)−0.0022 (6)−0.0077 (7)
C50.0310 (8)0.0456 (10)0.0478 (10)−0.0105 (7)−0.0042 (7)−0.0070 (8)
C60.0371 (8)0.0335 (8)0.0440 (9)−0.0063 (7)0.0005 (7)−0.0015 (7)
C70.0307 (7)0.0247 (7)0.0372 (8)0.0049 (6)−0.0013 (6)−0.0019 (6)
C170.0533 (12)0.0791 (16)0.0397 (10)0.0039 (11)−0.0081 (8)0.0063 (10)
O10.0410 (6)0.0318 (6)0.0416 (6)−0.0013 (5)−0.0104 (5)0.0114 (5)
O20.0363 (6)0.0267 (6)0.0568 (8)−0.0032 (5)−0.0126 (5)0.0046 (5)
O30.0525 (8)0.0551 (8)0.0425 (7)0.0201 (6)−0.0072 (6)−0.0171 (6)
O40.0446 (7)0.0508 (7)0.0354 (6)0.0217 (6)−0.0034 (5)−0.0049 (5)
C80.0273 (7)0.0251 (7)0.0279 (7)−0.0004 (5)−0.0027 (5)0.0048 (5)
C90.0378 (8)0.0331 (8)0.0356 (8)0.0037 (6)−0.0043 (6)−0.0027 (6)
C100.0547 (11)0.0540 (12)0.0405 (10)0.0065 (9)−0.0154 (8)−0.0128 (9)
C110.0418 (10)0.0579 (12)0.0486 (11)0.0046 (9)−0.0204 (8)−0.0008 (9)
C120.0302 (8)0.0475 (10)0.0459 (10)0.0094 (7)−0.0052 (7)0.0060 (8)
C130.0310 (7)0.0326 (8)0.0295 (7)0.0035 (6)−0.0001 (6)0.0054 (6)
C140.0272 (7)0.0237 (7)0.0281 (7)0.0064 (5)−0.0018 (5)−0.0015 (5)
C150.0532 (11)0.0604 (12)0.0452 (10)0.0034 (9)0.0133 (9)−0.0112 (9)
C160.0494 (10)0.0501 (11)0.0445 (10)0.0213 (9)0.0103 (8)0.0032 (8)
O5—C41.3680 (19)O1—C141.2509 (18)
O5—C171.427 (3)O2—C141.2440 (18)
N1—C71.299 (2)O3—C91.368 (2)
N1—H1A0.93 (2)O3—C151.427 (2)
N1—H1B0.88 (2)O4—C131.370 (2)
N2—C71.316 (2)O4—C161.418 (2)
N2—H2A0.91 (3)C8—C91.391 (2)
N2—H2B0.86 (3)C8—C131.392 (2)
C1—C21.387 (2)C8—C141.5189 (18)
C1—C61.394 (2)C9—C101.394 (2)
C1—C71.480 (2)C10—C111.377 (3)
C2—C31.386 (2)C10—H100.9700
C2—H20.9700C11—C121.375 (3)
C3—C41.386 (2)C11—H110.9700
C3—H30.9700C12—C131.393 (2)
C4—C51.385 (3)C12—H120.9700
C5—C61.383 (2)C15—H15A0.9817
C5—H50.9700C15—H15B0.9817
C6—H60.9700C15—H15C0.9817
C17—H17A0.9877C16—H16A0.9865
C17—H17B0.9877C16—H16B0.9865
C17—H17C0.9877C16—H16C0.9865
C4—O5—C17117.56 (15)C13—O4—C16117.61 (13)
C7—N1—H1A120.8 (13)C9—C8—C13119.07 (13)
C7—N1—H1B122.1 (14)C9—C8—C14119.47 (13)
H1A—N1—H1B116.8 (19)C13—C8—C14121.43 (13)
C7—N2—H2A117.3 (16)O3—C9—C8115.43 (13)
C7—N2—H2B120.8 (16)O3—C9—C10123.91 (16)
H2A—N2—H2B121 (2)C8—C9—C10120.65 (16)
C2—C1—C6118.52 (14)C11—C10—C9118.85 (17)
C2—C1—C7119.69 (14)C11—C10—H10120.6
C6—C1—C7121.78 (15)C9—C10—H10120.6
C3—C2—C1121.67 (15)C12—C11—C10121.83 (16)
C3—C2—H2119.2C12—C11—H11119.1
C1—C2—H2119.2C10—C11—H11119.1
C4—C3—C2118.91 (16)C11—C12—C13119.02 (16)
C4—C3—H3120.5C11—C12—H12120.5
C2—C3—H3120.5C13—C12—H12120.5
O5—C4—C5115.80 (15)O4—C13—C8115.57 (13)
O5—C4—C3123.89 (17)O4—C13—C12123.92 (15)
C5—C4—C3120.31 (15)C8—C13—C12120.52 (15)
C6—C5—C4120.24 (15)O2—C14—O1125.56 (13)
C6—C5—H5119.9O2—C14—C8118.88 (13)
C4—C5—H5119.9O1—C14—C8115.54 (13)
C5—C6—C1120.34 (16)O3—C15—H15A109.5
C5—C6—H6119.8O3—C15—H15B109.5
C1—C6—H6119.8H15A—C15—H15B109.5
N1—C7—N2119.47 (15)O3—C15—H15C109.5
N1—C7—C1119.60 (14)H15A—C15—H15C109.5
N2—C7—C1120.93 (15)H15B—C15—H15C109.5
O5—C17—H17A109.5O4—C16—H16A109.5
O5—C17—H17B109.5O4—C16—H16B109.5
H17A—C17—H17B109.5H16A—C16—H16B109.5
O5—C17—H17C109.5O4—C16—H16C109.5
H17A—C17—H17C109.5H16A—C16—H16C109.5
H17B—C17—H17C109.5H16B—C16—H16C109.5
C9—O3—C15118.21 (14)
C6—C1—C2—C3−0.2 (3)C14—C8—C9—O31.5 (2)
C7—C1—C2—C3−179.38 (16)C13—C8—C9—C100.1 (3)
C1—C2—C3—C40.9 (3)C14—C8—C9—C10−177.89 (17)
C17—O5—C4—C5172.81 (18)O3—C9—C10—C11−177.5 (2)
C17—O5—C4—C3−7.5 (3)C8—C9—C10—C111.9 (3)
C2—C3—C4—O5179.46 (17)C9—C10—C11—C12−1.8 (3)
C2—C3—C4—C5−0.8 (3)C10—C11—C12—C13−0.3 (3)
O5—C4—C5—C6179.86 (17)C16—O4—C13—C8−172.11 (15)
C3—C4—C5—C60.1 (3)C16—O4—C13—C128.1 (3)
C4—C5—C6—C10.6 (3)C9—C8—C13—O4177.88 (15)
C2—C1—C6—C5−0.5 (3)C14—C8—C13—O4−4.2 (2)
C7—C1—C6—C5178.64 (16)C9—C8—C13—C12−2.3 (2)
C2—C1—C7—N127.6 (2)C14—C8—C13—C12175.68 (15)
C6—C1—C7—N1−151.54 (17)C11—C12—C13—O4−177.78 (17)
C2—C1—C7—N2−152.93 (18)C11—C12—C13—C82.4 (3)
C6—C1—C7—N227.9 (2)C9—C8—C14—O2−107.53 (17)
C15—O3—C9—C8164.66 (17)C13—C8—C14—O274.5 (2)
C15—O3—C9—C10−15.9 (3)C9—C8—C14—O171.0 (2)
C13—C8—C9—O3179.53 (15)C13—C8—C14—O1−106.91 (17)
D—H···AD—HH···AD···AD—H···A
N1—H1A···O10.93 (2)1.84 (2)2.7576 (18)169 (2)
N1—H1B···O2i0.88 (2)1.91 (2)2.7166 (18)152 (2)
N2—H2B···O1ii0.86 (3)2.31 (2)2.868 (2)123 (2)
N2—H2A···O20.91 (3)2.08 (3)2.976 (2)170 (2)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H1A⋯O10.93 (2)1.84 (2)2.7576 (18)169 (2)
N1—H1B⋯O2i0.88 (2)1.91 (2)2.7166 (18)152 (2)
N2—H2B⋯O1ii0.86 (3)2.31 (2)2.868 (2)123 (2)
N2—H2A⋯O20.91 (3)2.08 (3)2.976 (2)170 (2)

Symmetry codes: (i) ; (ii) .

  11 in total

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Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

3.  Graph-set analysis of hydrogen-bond patterns in organic crystals.

Authors:  M C Etter; J C MacDonald; J Bernstein
Journal:  Acta Crystallogr B       Date:  1990-04-01

4.  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

5.  Geometry of binding of the benzamidine- and arginine-based inhibitors N alpha-(2-naphthyl-sulphonyl-glycyl)-DL-p-amidinophenylalanyl-pipe ridine (NAPAP) and (2R,4R)-4-methyl-1-[N alpha-(3-methyl-1,2,3,4-tetrahydro-8- quinolinesulphonyl)-L-arginyl]-2-piperidine carboxylic acid (MQPA) to human alpha-thrombin. X-ray crystallographic determination of the NAPAP-trypsin complex and modeling of NAPAP-thrombin and MQPA-thrombin.

Authors:  W Bode; D Turk; J Stürzebecher
Journal:  Eur J Biochem       Date:  1990-10-05

6.  The three-dimensional structure of Asn102 mutant of trypsin: role of Asp102 in serine protease catalysis.

Authors:  S Sprang; T Standing; R J Fletterick; R M Stroud; J Finer-Moore; N H Xuong; R Hamlin; W J Rutter; C S Craik
Journal:  Science       Date:  1987-08-21       Impact factor: 47.728

7.  Substitutions at the P(1) position in BPTI strongly affect the association energy with serine proteinases.

Authors:  A Grzesiak; R Helland; A O Smalås; D Krowarsch; M Dadlez; J Otlewski
Journal:  J Mol Biol       Date:  2000-08-04       Impact factor: 5.469

8.  Benzdiamidine.

Authors:  M Jokić; M Bajić; M Zinić; B Perić; B Kojić-Prodić
Journal:  Acta Crystallogr C       Date:  2001-11-13       Impact factor: 1.172

9.  Benzamidinium tetra-hydro-penta-borate sesquihydrate.

Authors:  Gustavo Portalone
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-06-19

10.  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
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  7 in total

1.  4-Meth-oxy-benzamidinium acetate.

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

2.  4-Meth-oxy-benzamidinium nitrate.

Authors:  Simona Irrera; Gustavo Portalone
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-11-10

3.  4-Meth-oxy-benzamidinium hydrogen oxalate monohydrate.

Authors:  Simona Irrera; Gustavo Portalone
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-11-14

4.  4-Meth-oxy-benzamidinium bromide.

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

5.  4-Meth-oxy-benzamidinium hydrogen sulfate.

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

6.  4-Meth-oxy-benzamidinium chloride monohydrate.

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

7.  Benzamidinium 2-meth-oxy-benzoate.

Authors:  Gustavo Portalone
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2013-06-19
  7 in total

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