Literature DB >> 23476439

Glycine-phthalic acid (1/1).

T Balakrishnan1, K Ramamurthi, S Thamotharan.   

Abstract

In the title compound, C2H5NO2·C8H6O4, the glycine mol-ecule exists as a zwitterion (2-aza-niumyl-ethano-ate) with a positively charged amino group and a negatively charged carboxyl-ate group. In the crystal, N-H⋯O and O-H⋯O hydrogen bonds link the components into layers parallel to the ab plane. The central part of each layer is composed of hydrogen-bonded glycine zwitterions, while phthalic acid mol-ecules inter-act with the zwitterions in such a way that benzene rings protrude up and down from the layer.

Entities:  

Year:  2012        PMID: 23476439      PMCID: PMC3588298          DOI: 10.1107/S160053681204977X

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


Related literature

For related structures, see: Losev et al. (2011 ▶); Herbstein et al. (1981 ▶). For graph-set motifs, see: Bernstein et al. (1995 ▶). For head-to-tail hydrogen bonds, see: Sharma et al. (2006 ▶); Selvaraj et al. (2007 ▶).

Experimental

Crystal data

C2H5NO2·C8H6O4 M = 241.20 Orthorhombic, a = 7.9657 (5) Å b = 11.3470 (7) Å c = 23.513 (2) Å V = 2125.3 (3) Å3 Z = 8 Mo Kα radiation μ = 0.13 mm−1 T = 173 K 0.53 × 0.46 × 0.30 mm

Data collection

Stoe IPDS diffractometer 15716 measured reflections 2077 independent reflections 1597 reflections with I > 2σ(I) R int = 0.041

Refinement

R[F 2 > 2σ(F 2)] = 0.034 wR(F 2) = 0.090 S = 1.01 2077 reflections 175 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.22 e Å−3 Δρmin = −0.19 e Å−3 Data collection: EXPOSE in IPDS-I Software (Stoe & Cie, 2000 ▶); cell refinement: CELL in IPDS-I Software; data reduction: INTEGRATE in IPDS-I Software; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2009 ▶) and ORTEP-3 for Windows (Farrugia, 2012 ▶); software used to prepare material for publication: SHELXL97. Click here for additional data file. Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S160053681204977X/cv5360sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681204977X/cv5360Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S160053681204977X/cv5360Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C2H5NO2·C8H6O4F(000) = 1008
Mr = 241.20Dx = 1.508 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 8000 reflections
a = 7.9657 (5) Åθ = 2.6–26.1°
b = 11.3470 (7) ŵ = 0.13 mm1
c = 23.513 (2) ÅT = 173 K
V = 2125.3 (3) Å3Block, colourless
Z = 80.53 × 0.46 × 0.30 mm
Stoe IPDS diffractometer1597 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.041
Graphite monochromatorθmax = 26.0°, θmin = 3.1°
Detector resolution: 0.81Å pixels mm-1h = −9→9
phi rotation scansk = −13→13
15716 measured reflectionsl = −29→28
2077 independent reflections
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.034H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.090w = 1/[σ2(Fo2) + (0.064P)2] where P = (Fo2 + 2Fc2)/3
S = 1.01(Δ/σ)max < 0.001
2077 reflectionsΔρmax = 0.22 e Å3
175 parametersΔρmin = −0.19 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0086 (15)
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
O3−0.06389 (12)0.23293 (9)0.08480 (4)0.0293 (3)
O4−0.00401 (15)0.40181 (9)0.12875 (4)0.0374 (3)
H4O−0.058 (3)0.435 (2)0.0959 (11)0.075 (7)*
O50.00354 (13)−0.05643 (9)0.12213 (4)0.0365 (3)
O60.19779 (12)0.05907 (9)0.08314 (4)0.0311 (3)
H6O0.205 (3)−0.008 (2)0.0572 (10)0.072 (6)*
C30.06342 (15)0.22668 (12)0.17621 (5)0.0238 (3)
C40.10175 (15)0.10660 (12)0.17542 (5)0.0242 (3)
C50.15369 (17)0.05214 (13)0.22514 (6)0.0294 (3)
H50.1795−0.02960.22470.035*
C60.16855 (19)0.11483 (14)0.27541 (6)0.0347 (3)
H60.20540.07640.30910.042*
C70.12967 (18)0.23317 (14)0.27639 (6)0.0336 (3)
H70.13870.27650.31080.040*
C80.07751 (17)0.28854 (13)0.22713 (6)0.0278 (3)
H80.05080.37010.22800.033*
C9−0.00603 (16)0.28671 (12)0.12521 (5)0.0249 (3)
C100.09312 (16)0.03014 (11)0.12370 (5)0.0247 (3)
O10.75187 (11)0.11587 (8)−0.01838 (4)0.0269 (2)
O20.65409 (12)−0.01881 (8)0.04157 (4)0.0317 (3)
N10.59761 (16)0.29647 (10)0.03063 (5)0.0258 (3)
H1A0.543 (2)0.3538 (16)0.0511 (8)0.042 (5)*
H1B0.560 (2)0.2998 (17)−0.0061 (9)0.051 (5)*
H1C0.704 (3)0.3178 (16)0.0329 (8)0.043 (5)*
C10.66689 (15)0.08474 (11)0.02398 (5)0.0226 (3)
C20.57097 (16)0.17890 (11)0.05551 (6)0.0249 (3)
H2A0.44970.15990.05460.030*
H2B0.60720.17980.09580.030*
U11U22U33U12U13U23
O30.0348 (5)0.0245 (5)0.0286 (5)−0.0013 (4)−0.0052 (4)−0.0042 (4)
O40.0615 (7)0.0201 (6)0.0307 (6)−0.0003 (5)−0.0090 (5)−0.0012 (4)
O50.0476 (6)0.0296 (6)0.0322 (6)−0.0152 (5)0.0070 (4)−0.0067 (4)
O60.0368 (5)0.0226 (5)0.0338 (5)−0.0036 (4)0.0124 (4)−0.0055 (4)
C30.0231 (6)0.0230 (7)0.0251 (7)−0.0023 (5)0.0022 (5)−0.0020 (5)
C40.0215 (6)0.0229 (7)0.0280 (7)−0.0032 (5)0.0035 (5)−0.0018 (5)
C50.0318 (7)0.0250 (7)0.0315 (7)0.0004 (6)0.0006 (5)0.0024 (6)
C60.0398 (8)0.0363 (9)0.0279 (7)−0.0013 (6)−0.0036 (6)0.0047 (6)
C70.0408 (8)0.0355 (9)0.0245 (7)−0.0047 (7)−0.0017 (6)−0.0044 (6)
C80.0313 (7)0.0239 (7)0.0283 (7)−0.0016 (5)0.0009 (5)−0.0055 (5)
C90.0269 (6)0.0213 (7)0.0266 (7)−0.0011 (5)0.0014 (5)−0.0026 (5)
C100.0278 (6)0.0186 (7)0.0277 (7)−0.0001 (5)0.0021 (5)−0.0004 (5)
O10.0323 (5)0.0227 (5)0.0256 (5)−0.0013 (4)0.0069 (4)−0.0038 (4)
O20.0415 (6)0.0204 (5)0.0332 (5)0.0037 (4)0.0057 (4)0.0041 (4)
N10.0293 (6)0.0192 (6)0.0288 (6)0.0010 (5)0.0024 (5)−0.0043 (5)
C10.0244 (6)0.0211 (7)0.0223 (6)−0.0002 (5)−0.0017 (5)−0.0016 (5)
C20.0283 (7)0.0216 (7)0.0247 (6)−0.0002 (5)0.0040 (5)−0.0012 (5)
O3—C91.2197 (15)C6—H60.9500
O4—C91.3088 (18)C7—C81.382 (2)
O4—H4O0.96 (3)C7—H70.9500
O5—C101.2147 (16)C8—H80.9500
O6—C101.3086 (16)O1—C11.2550 (15)
O6—H6O0.98 (2)O2—C11.2498 (16)
C3—C81.3925 (18)N1—C21.4720 (17)
C3—C41.396 (2)N1—H1A0.917 (19)
C3—C91.4859 (18)N1—H1B0.91 (2)
C4—C51.3855 (19)N1—H1C0.88 (2)
C4—C101.4955 (18)C1—C21.5083 (18)
C5—C61.385 (2)C2—H2A0.9900
C5—H50.9500C2—H2B0.9900
C6—C71.378 (2)
C9—O4—H4O109.8 (14)O3—C9—C3122.68 (13)
C10—O6—H6O107.5 (13)O4—C9—C3113.67 (11)
C8—C3—C4119.06 (12)O5—C10—O6123.72 (12)
C8—C3—C9119.52 (12)O5—C10—C4121.39 (11)
C4—C3—C9121.20 (11)O6—C10—C4114.70 (11)
C5—C4—C3119.29 (12)C2—N1—H1A111.5 (11)
C5—C4—C10116.18 (12)C2—N1—H1B111.5 (12)
C3—C4—C10124.53 (12)H1A—N1—H1B108.2 (16)
C6—C5—C4121.11 (13)C2—N1—H1C111.3 (12)
C6—C5—H5119.4H1A—N1—H1C103.1 (16)
C4—C5—H5119.4H1B—N1—H1C110.9 (17)
C7—C6—C5119.71 (13)O2—C1—O1124.83 (12)
C7—C6—H6120.1O2—C1—C2117.52 (11)
C5—C6—H6120.1O1—C1—C2117.64 (11)
C6—C7—C8119.78 (13)N1—C2—C1111.94 (11)
C6—C7—H7120.1N1—C2—H2A109.2
C8—C7—H7120.1C1—C2—H2A109.2
C7—C8—C3121.05 (13)N1—C2—H2B109.2
C7—C8—H8119.5C1—C2—H2B109.2
C3—C8—H8119.5H2A—C2—H2B107.9
O3—C9—O4123.61 (13)
C8—C3—C4—C5−0.36 (18)C8—C3—C9—O3−159.60 (13)
C9—C3—C4—C5−174.93 (12)C4—C3—C9—O314.95 (19)
C8—C3—C4—C10−179.55 (12)C8—C3—C9—O418.29 (17)
C9—C3—C4—C105.88 (19)C4—C3—C9—O4−167.16 (12)
C3—C4—C5—C6−0.2 (2)C5—C4—C10—O559.45 (18)
C10—C4—C5—C6179.09 (12)C3—C4—C10—O5−121.34 (15)
C4—C5—C6—C70.6 (2)C5—C4—C10—O6−115.59 (13)
C5—C6—C7—C8−0.5 (2)C3—C4—C10—O663.62 (17)
C6—C7—C8—C30.0 (2)O2—C1—C2—N1179.74 (11)
C4—C3—C8—C70.46 (19)O1—C1—C2—N1−1.15 (17)
C9—C3—C8—C7175.12 (12)
D—H···AD—HH···AD···AD—H···A
N1—H1A···O5i0.917 (19)1.992 (19)2.8398 (16)153.0 (16)
N1—H1B···O3ii0.91 (2)2.13 (2)3.0219 (16)164.6 (17)
N1—H1C···O2iii0.88 (2)2.181 (19)2.8934 (16)137.4 (15)
N1—H1C···O3iv0.88 (2)2.416 (19)3.0681 (16)130.9 (15)
O4—H4O···O2i0.96 (3)1.58 (3)2.5383 (14)175 (2)
O6—H6O···O1v0.98 (2)1.56 (2)2.5337 (13)171 (2)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
N1—H1A⋯O5i 0.917 (19)1.992 (19)2.8398 (16)153.0 (16)
N1—H1B⋯O3ii 0.91 (2)2.13 (2)3.0219 (16)164.6 (17)
N1—H1C⋯O2iii 0.88 (2)2.181 (19)2.8934 (16)137.4 (15)
N1—H1C⋯O3iv 0.88 (2)2.416 (19)3.0681 (16)130.9 (15)
O4—H4O⋯O2i 0.96 (3)1.58 (3)2.5383 (14)175 (2)
O6—H6O⋯O1v 0.98 (2)1.56 (2)2.5337 (13)171 (2)

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

  5 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.  Glycinium semi-malonate and a glutaric acid-glycine cocrystal: new structures with short O-H...O hydrogen bonds.

Authors:  Evgeniy A Losev; Boris A Zakharov; Tatiana N Drebushchak; Elena V Boldyreva
Journal:  Acta Crystallogr C       Date:  2011-07-05       Impact factor: 1.172

3.  X-ray studies of crystalline complexes involving amino acids and peptides. XLIII. Adipic acid complexes of L- and DL-lysine.

Authors:  Alok Sharma; S Thamotharan; Siddhartha Roy; M Vijayan
Journal:  Acta Crystallogr C       Date:  2006-02-28       Impact factor: 1.172

4.  X-ray studies of crystalline complexes involving amino acids and peptides. XLIV. Invariant features of supramolecular association and chiral effects in the complexes of arginine and lysine with tartaric acid.

Authors:  M Selvaraj; S Thamotharan; Siddhartha Roy; M Vijayan
Journal:  Acta Crystallogr B       Date:  2007-05-16

5.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  5 in total
  1 in total

1.  Crystal structure and Hirshfeld surface analysis of 1-carb-oxy-2-(3,4-di-hydroxy-phen-yl)ethan-1-aminium chloride 2-ammonio-3-(3,4-di-hydroxy-phen-yl)propano-ate: a new polymorph of l-dopa HCl and isotypic with its bromide counterpart.

Authors:  Perumal Kathiravan; Thangavelu Balakrishnan; Perumal Venkatesan; Kandasamy Ramamurthi; María Judith Percino; Subbiah Thamotharan
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2016-10-25
  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.