Literature DB >> 23284415

4-Meth-oxy-benzamidinium chloride monohydrate.

Simona Irrera1, Gustavo Portalone.   

Abstract

In the cation of the title compound, C(8)H(11)N(2)O(+)·Cl(-)·H(2)O, the C-n class="Chemical">N bonds of the amidinium group are identical within experiemental error [1.305 (2) and 1.304 (2) Å], and its plane forms a dihedral angle of 25.83 (8)° with the phenyl ring. The ionic components are associated in the crystal into polymeric hydrogen-bonded supra-molecular tapes stabilized by N-H(+)⋯Cl(-) and N-H(+)⋯Ow inter-molecular hydrogen bonds, and by Ow-H⋯Cl(-) inter-actions.

Entities:  

Year:  2012        PMID: 23284415      PMCID: PMC3515188          DOI: 10.1107/S1600536812041219

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 structural analysis of proton-transfer adducts containing mol­ecules of biological inter­est, see: Portalone (2011a ▶); n class="Chemical">Portalone & Irrera (2011 ▶). For the supra­molecular association in proton-transfer adducts containing benzamidinium cations, see; Portalone (2010 ▶, 2011b ▶, 2012 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C8H11N2O+·Cl−·H2O M = 204.65 Monoclinic, a = 11.3029 (7) Å b = 9.3142 (5) Å c = 9.9983 (6) Å β = 99.820 (6)° V = 1037.17 (11) Å3 Z = 4 Mo Kα radiation μ = 0.34 mm−1 T = 298 K 0.30 × 0.27 × 0.25 mm

Data collection

Oxford Diffraction Xcalibur S CCD diffractometer Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006 ▶) T min = 0.905, T max = 0.968 7158 measured reflections 2989 independent reflections 1947 reflections with I > 2σ(I) R int = 0.018

Refinement

R[F 2 > 2σ(F 2)] = 0.043 wR(F 2) = 0.113 S = 0.97 2989 reflections 144 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.22 e Å−3 Δρmin = −0.15 e Å−3 Data collection: CrysAlis CCD (Oxford Diffraction, 2006 ▶); cell refinement: CrysAlis n class="Disease">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 for Windows (Farrugia, 1997 ▶); software used to prepare material for publication: WinGX (Farrugia, 1999 ▶). Click here for additional data file. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812041219/qm2085sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812041219/qm2085Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C8H11N2O+·Cl·H2OF(000) = 432
Mr = 204.65Dx = 1.311 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71069 Å
Hall symbol: -P 2ybcCell parameters from 3182 reflections
a = 11.3029 (7) Åθ = 2.8–32.2°
b = 9.3142 (5) ŵ = 0.34 mm1
c = 9.9983 (6) ÅT = 298 K
β = 99.820 (6)°Tablets, colourless
V = 1037.17 (11) Å30.30 × 0.27 × 0.25 mm
Z = 4
Oxford Diffraction Xcalibur S CCD diffractometer2989 independent reflections
Radiation source: Enhance (Mo) X-ray Source1947 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.018
Detector resolution: 16.0696 pixels mm-1θmax = 30.0°, θmin = 2.9°
ω and φ scansh = −15→13
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006)k = −13→13
Tmin = 0.905, Tmax = 0.968l = −14→14
7158 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)] = 0.043Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.113H atoms treated by a mixture of independent and constrained refinement
S = 0.97w = 1/[σ2(Fo2) + (0.0667P)2] where P = (Fo2 + 2Fc2)/3
2989 reflections(Δ/σ)max < 0.001
144 parametersΔρmax = 0.22 e Å3
0 restraintsΔρmin = −0.15 e Å3
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
Cl10.59874 (3)0.29686 (5)0.19860 (4)0.06143 (17)
O10.02187 (9)0.02872 (12)0.72746 (11)0.0585 (3)
N10.37553 (14)0.36637 (18)0.40096 (17)0.0577 (4)
H1A0.4215 (18)0.391 (3)0.351 (2)0.087 (7)*
H1B0.3457 (16)0.424 (2)0.4357 (19)0.070 (7)*
N20.40806 (13)0.1372 (2)0.34687 (16)0.0609 (4)
H2A0.4716 (18)0.167 (2)0.300 (2)0.082 (6)*
H2B0.3898 (16)0.052 (3)0.3475 (19)0.077 (7)*
C10.26509 (11)0.18152 (15)0.49586 (13)0.0400 (3)
C20.17291 (12)0.26955 (17)0.52024 (16)0.0499 (4)
H20.16690.36200.48470.060*
C30.08913 (12)0.22277 (17)0.59666 (16)0.0497 (4)
H30.02730.28320.61200.060*
C40.09816 (11)0.08562 (16)0.64994 (14)0.0425 (3)
C50.19078 (12)−0.00346 (17)0.62752 (15)0.0489 (4)
H50.1974−0.09530.66450.059*
C60.27322 (12)0.04365 (16)0.55054 (14)0.0460 (3)
H60.3348−0.01710.53500.055*
C70.35238 (11)0.22994 (17)0.41160 (14)0.0460 (4)
C8−0.07725 (14)0.1140 (2)0.75071 (19)0.0684 (5)
H8A−0.0482 (3)0.2006 (11)0.7969 (13)0.103*
H8B−0.1241 (9)0.0612 (8)0.8055 (12)0.103*
H8C−0.1263 (8)0.1375 (12)0.6654 (9)0.103*
O2W0.27853 (14)0.61140 (16)0.50438 (18)0.0783 (4)
HWA0.319 (3)0.631 (4)0.579 (3)0.155 (14)*
HWB0.3124 (17)0.667 (2)0.452 (2)0.077 (6)*
U11U22U33U12U13U23
Cl10.0604 (3)0.0699 (3)0.0594 (3)−0.00364 (19)0.02536 (19)0.0085 (2)
O10.0518 (6)0.0581 (7)0.0737 (7)0.0039 (5)0.0337 (5)0.0110 (6)
N10.0595 (8)0.0550 (9)0.0642 (9)−0.0047 (7)0.0267 (7)0.0125 (8)
N20.0583 (8)0.0688 (11)0.0628 (9)−0.0090 (8)0.0311 (7)−0.0027 (8)
C10.0358 (6)0.0472 (8)0.0373 (7)−0.0039 (6)0.0072 (5)0.0001 (6)
C20.0510 (8)0.0403 (8)0.0604 (9)0.0036 (6)0.0156 (7)0.0089 (7)
C30.0437 (7)0.0463 (9)0.0629 (9)0.0077 (6)0.0195 (6)0.0020 (7)
C40.0384 (6)0.0464 (8)0.0443 (7)−0.0017 (6)0.0117 (5)0.0002 (6)
C50.0496 (7)0.0421 (8)0.0584 (9)0.0047 (7)0.0191 (6)0.0082 (7)
C60.0420 (7)0.0449 (8)0.0541 (8)0.0078 (6)0.0167 (6)0.0032 (7)
C70.0405 (7)0.0559 (10)0.0420 (7)−0.0040 (6)0.0084 (6)0.0045 (7)
C80.0503 (8)0.0838 (13)0.0787 (12)0.0101 (8)0.0329 (8)0.0039 (10)
O2W0.1035 (11)0.0605 (8)0.0747 (10)−0.0175 (8)0.0258 (9)0.0015 (7)
O1—C41.3613 (16)C2—H20.9300
O1—C81.4243 (18)C3—C41.381 (2)
N1—C71.305 (2)C3—H30.9300
N1—H1A0.81 (2)C4—C51.3837 (19)
N1—H1B0.75 (2)C5—C61.3776 (19)
N2—C71.304 (2)C5—H50.9300
N2—H2A0.96 (2)C6—H60.9300
N2—H2B0.82 (2)C8—H8A0.9596
C1—C21.3798 (19)C8—H8B0.9596
C1—C61.3926 (19)C8—H8C0.9596
C1—C71.4731 (18)O2W—HWA0.82 (3)
C2—C31.385 (2)O2W—HWB0.87 (2)
C4—O1—C8117.92 (13)C3—C4—C5120.02 (12)
C7—N1—H1A119.0 (17)C6—C5—C4120.14 (14)
C7—N1—H1B123.3 (15)C6—C5—H5119.9
H1A—N1—H1B118 (2)C4—C5—H5119.9
C7—N2—H2A120.7 (11)C5—C6—C1120.49 (12)
C7—N2—H2B119.6 (14)C5—C6—H6119.8
H2A—N2—H2B119.7 (18)C1—C6—H6119.8
C2—C1—C6118.68 (12)N2—C7—N1118.95 (15)
C2—C1—C7121.24 (13)N2—C7—C1120.53 (15)
C6—C1—C7120.07 (12)N1—C7—C1120.52 (15)
C1—C2—C3121.24 (14)O1—C8—H8A109.5
C1—C2—H2119.4O1—C8—H8B109.5
C3—C2—H2119.4H8A—C8—H8B109.5
C4—C3—C2119.43 (13)O1—C8—H8C109.5
C4—C3—H3120.3H8A—C8—H8C109.5
C2—C3—H3120.3H8B—C8—H8C109.5
O1—C4—C3124.57 (12)HWA—O2W—HWB100 (3)
O1—C4—C5115.41 (13)
C6—C1—C2—C3−0.4 (2)C3—C4—C5—C6−0.9 (2)
C7—C1—C2—C3178.39 (14)C4—C5—C6—C10.7 (2)
C1—C2—C3—C40.2 (2)C2—C1—C6—C5−0.1 (2)
C8—O1—C4—C32.8 (2)C7—C1—C6—C5−178.88 (14)
C8—O1—C4—C5−178.22 (14)C2—C1—C7—N2−153.81 (15)
C2—C3—C4—O1179.33 (14)C6—C1—C7—N225.0 (2)
C2—C3—C4—C50.4 (2)C2—C1—C7—N126.4 (2)
O1—C4—C5—C6−179.90 (14)C6—C1—C7—N1−154.78 (15)
D—H···AD—HH···AD···AD—H···A
N1—H1A···Cl10.81 (2)2.85 (2)3.5523 (18)145 (2)
N1—H1B···O2W0.75 (2)2.06 (2)2.805 (2)168 (2)
N2—H2A···Cl10.96 (2)2.25 (2)3.1850 (16)164.4 (16)
N2—H2B···Cl1i0.82 (2)2.43 (2)3.201 (2)157.5 (18)
O2W—HWA···Cl1ii0.82 (3)2.36 (3)3.1731 (18)170 (3)
O2W—HWB···Cl1iii0.87 (2)2.29 (2)3.1603 (17)174.8 (19)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
N1—H1A⋯Cl10.81 (2)2.85 (2)3.5523 (18)145 (2)
N1—H1B⋯O2W 0.75 (2)2.06 (2)2.805 (2)168 (2)
N2—H2A⋯Cl10.96 (2)2.25 (2)3.1850 (16)164.4 (16)
N2—H2B⋯Cl1i 0.82 (2)2.43 (2)3.201 (2)157.5 (18)
O2W—HWA⋯Cl1ii 0.82 (3)2.36 (3)3.1731 (18)170 (3)
O2W—HWB⋯Cl1iii 0.87 (2)2.29 (2)3.1603 (17)174.8 (19)

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

  8 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.  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

4.  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

5.  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

6.  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

7.  4-Meth-oxy-benzamidinium 2,6-dimeth-oxy-benzoate.

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

8.  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
  8 in total
  6 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.  Benzamidinium 2-meth-oxy-benzoate.

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

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