organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 65| Part 5| May 2009| Page o1157

(S)-2-(1H-Imidazol-1-yl)succinic acid

aOrdered Matter Science Research Center, College of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, People's Republic of China
*Correspondence e-mail: xjm_cool@163.com

(Received 21 December 2008; accepted 23 April 2009; online 30 April 2009)

The title compound, C7H8N2O4, is a zwitterion, [formal name = (S)-3-carb­oxy-2-(imidazol-3-ium-1-yl)propano­ate], in which the deproton­ated negatively charged carboxyl­ate end shows almost identical C—O bond distances [1.248 (4) and 1.251 (4) Å] due to resonance. The mol­ecules are involved in inter­molecular O—H⋯O and N—H⋯O hydrogen bonds, which define a tightly bound three-dimensional structure.

Related literature

For the use of imidazol-1-ylalkanoic acids as probes to determine the intra­cellular and extracellular pH and cell volume by 1H NMR, see: López et al.(1996[López, P., Zaderenko, P., Balcazar, J. L., Fonseca, I., Cano, F. H. & Ballesteros, P. (1996). J. Mol. Struct. 377, 105-112.]). For the preparation of the title compound, see: Bao et al. (2003[Bao, W., Wang, Z. & Li, Y. (2003). J. Org. Chem. 68, 591-593.]).

[Scheme 1]

Experimental

Crystal data
  • C7H8N2O4

  • Mr = 184.15

  • Orthorhombic, P 21 21 21

  • a = 7.3212 (16) Å

  • b = 7.9193 (16) Å

  • c = 14.254 (3) Å

  • V = 826.4 (3) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.12 mm−1

  • T = 293 K

  • 0.25 × 0.20 × 0.18 mm

Data collection
  • Rigaku Mercury2 diffractometer

  • Absorption correction: multi-scan (CrystalClear; Rigaku, 2005[Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.97, Tmax = 0.98

  • 8489 measured reflections

  • 1110 independent reflections

  • 952 reflections with I > 2σ(I)

  • Rint = 0.053

Refinement
  • R[F2 > 2σ(F2)] = 0.050

  • wR(F2) = 0.151

  • S = 1.12

  • 1110 reflections

  • 118 parameters

  • H-atom parameters constrained

  • Δρmax = 0.19 e Å−3

  • Δρmin = −0.23 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2⋯O2i 0.86 1.91 2.716 (4) 155
O3—H3C⋯O1ii 0.86 1.71 2.572 (3) 177
Symmetry codes: (i) x-1, y, z; (ii) x, y+1, z.

Data collection: CrystalClear (Rigaku, 2005[Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXL97.

Supporting information


Comment top

Imidazol-1-ylalkanoic acids are used as new probes to determine the intracellular and extracellular pH and cell volume by 1H NMR. (López et al., 1996). In this report we present the structure of (S)-2-(1H-imidazol-1-yl)succinic acid. As shown in Fig. 1, the title compound C7H8N2O4 exists in the form of an inner salt where the unprotonated, negatively charged carboxylato end shows almost identical C-O bond distances (1.248 (4) and 1.251 (4)Å respectively) due to resonance.. The molecules are involved in intermolecular O—H···O and N—H···O hydrogen bonds (Table 1) which define a tightly bound 3D structure.

Related literature top

For the use of imidazol-1-ylalkanoic acids as probes to determine the intracellular and extracellular pH and cell volume by 1H NMR, see: López et al.(1996). For the preparation of the lagand, see: Bao et al. (2003).

Experimental top

The ligand was prepared according to a literature method (Bao et al., 2003). A formaldehyde water solution (36%, 1.67 g) and a glyoxal water solution (32%, 3.62 g) were mixed in a 50 ml, three-necked flask provided with a stirrer and a reflux condenser. While the mixture was heated at 50 °C with stirring, a mixture of L-2-aminosuccinic acid (2.66 g, 0.02 mol), ammonia solution (28%, 1.21 g) and sodium hydroxide solution (10%, 8 g) was added in small portions during 0.5 h. After the mixture was stirred for an additional 8 h at 50 °C, the cooled mixture was acidified to pH=3 with concentrated hydrochloric acid. After stirring for 30 min, the suspension was filtered. The resulting solid was washed with H2O and dried in vacuum over P2O5 at room temperature. Colourless crystals suitable for X-ray diffraction were obtained from a solution of 100 mg in 15 ml H2O by slow evaporation after one month.

Refinement top

Positional parameters of all the H atoms except for H3C were calculated geometrically and the H atoms were set to ride on the C and N atoms to which they are bonded, with Uiso(H) = 1.2Ueq(C or N). The carboxyl H3C was initially refined and subsequently allowed to ride with Uiso(H) = 1.5Ueq(O). Due to the abscence of anomalous diffraction effects, Friedel pairs were merged.

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, showing the atomic numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.
(S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate top
Crystal data top
C7H8N2O4F(000) = 384
Mr = 184.15Dx = 1.480 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: p 2ac 2abCell parameters from 2123 reflections
a = 7.3212 (16) Åθ = 2.8–27.4°
b = 7.9193 (16) ŵ = 0.12 mm1
c = 14.254 (3) ÅT = 293 K
V = 826.4 (3) Å3Prism, colorless
Z = 40.25 × 0.20 × 0.18 mm
Data collection top
Rigaku Mercury2
diffractometer
1110 independent reflections
Radiation source: fine-focus sealed tube952 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.053
CCD_Profile_fitting scansθmax = 27.5°, θmin = 2.9°
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
h = 99
Tmin = 0.97, Tmax = 0.98k = 1010
8489 measured reflectionsl = 1818
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.050Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.151H-atom parameters constrained
S = 1.12 w = 1/[σ2(Fo2) + (0.0852P)2 + 0.2196P]
where P = (Fo2 + 2Fc2)/3
1110 reflections(Δ/σ)max < 0.001
118 parametersΔρmax = 0.19 e Å3
0 restraintsΔρmin = 0.23 e Å3
Crystal data top
C7H8N2O4V = 826.4 (3) Å3
Mr = 184.15Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 7.3212 (16) ŵ = 0.12 mm1
b = 7.9193 (16) ÅT = 293 K
c = 14.254 (3) Å0.25 × 0.20 × 0.18 mm
Data collection top
Rigaku Mercury2
diffractometer
1110 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
952 reflections with I > 2σ(I)
Tmin = 0.97, Tmax = 0.98Rint = 0.053
8489 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0500 restraints
wR(F2) = 0.151H-atom parameters constrained
S = 1.12Δρmax = 0.19 e Å3
1110 reflectionsΔρmin = 0.23 e Å3
118 parameters
Special details top

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 > σ(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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.9679 (4)0.2336 (4)0.6099 (2)0.0299 (7)
C20.9073 (4)0.4110 (4)0.6415 (2)0.0309 (7)
H2A0.98460.44500.69430.037*
C30.9360 (5)0.5376 (4)0.5624 (2)0.0367 (7)
H3A1.05540.51970.53460.044*
H3B0.84470.51930.51420.044*
C40.9226 (5)0.7177 (4)0.5977 (2)0.0378 (7)
C50.6549 (5)0.4474 (5)0.7626 (3)0.0493 (10)
H50.72590.48260.81300.059*
C60.4741 (6)0.4230 (7)0.7635 (3)0.0640 (13)
H60.39620.43800.81440.077*
C70.5708 (5)0.3653 (5)0.6236 (3)0.0422 (8)
H70.57190.33330.56080.051*
N10.7172 (3)0.4110 (3)0.67364 (18)0.0314 (6)
N20.4268 (4)0.3725 (4)0.6766 (2)0.0507 (8)
H20.31750.34870.65890.061*
O10.8474 (4)0.1251 (3)0.5944 (2)0.0507 (7)
O21.1355 (3)0.2163 (3)0.59668 (16)0.0409 (6)
O30.9107 (5)0.8279 (3)0.52925 (19)0.0584 (9)
H3C0.89080.92900.54890.070*
O40.9181 (5)0.7543 (4)0.67883 (19)0.0638 (9)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0279 (14)0.0283 (15)0.0334 (15)0.0011 (12)0.0001 (12)0.0036 (13)
C20.0315 (15)0.0274 (15)0.0338 (15)0.0038 (13)0.0014 (13)0.0015 (12)
C30.0455 (18)0.0265 (15)0.0382 (16)0.0006 (15)0.0092 (16)0.0019 (12)
C40.0396 (17)0.0287 (15)0.0452 (18)0.0001 (15)0.0057 (15)0.0020 (14)
C50.0390 (19)0.064 (3)0.045 (2)0.0105 (19)0.0083 (16)0.0169 (19)
C60.055 (2)0.077 (3)0.061 (2)0.014 (2)0.024 (2)0.022 (3)
C70.0345 (16)0.0433 (19)0.0486 (18)0.0050 (17)0.0069 (16)0.0066 (15)
N10.0293 (13)0.0301 (13)0.0349 (14)0.0001 (11)0.0025 (11)0.0032 (11)
N20.0310 (14)0.0487 (18)0.072 (2)0.0010 (15)0.0041 (16)0.0126 (16)
O10.0411 (13)0.0241 (12)0.087 (2)0.0010 (10)0.0034 (14)0.0071 (13)
O20.0350 (12)0.0383 (13)0.0494 (14)0.0044 (10)0.0047 (11)0.0035 (11)
O30.090 (2)0.0294 (13)0.0560 (15)0.0060 (15)0.0122 (16)0.0052 (11)
O40.106 (3)0.0381 (14)0.0472 (15)0.0013 (17)0.0113 (17)0.0097 (12)
Geometric parameters (Å, º) top
C1—O21.249 (4)C5—C61.338 (6)
C1—O11.251 (4)C5—N11.378 (4)
C1—C21.541 (4)C5—H50.9300
C2—N11.465 (4)C6—N21.347 (6)
C2—C31.522 (4)C6—H60.9300
C2—H2A0.9800C7—N21.299 (5)
C3—C41.516 (4)C7—N11.338 (4)
C3—H3A0.9700C7—H70.9300
C3—H3B0.9700N2—H20.8600
C4—O41.193 (4)O3—H3C0.8601
C4—O31.312 (4)
O2—C1—O1126.3 (3)O3—C4—C3112.6 (3)
O2—C1—C2115.3 (3)C6—C5—N1107.9 (4)
O1—C1—C2118.3 (3)C6—C5—H5126.1
N1—C2—C3111.3 (3)N1—C5—H5126.1
N1—C2—C1111.4 (2)C5—C6—N2106.7 (3)
C3—C2—C1110.1 (2)C5—C6—H6126.6
N1—C2—H2A108.0N2—C6—H6126.6
C3—C2—H2A108.0N2—C7—N1109.1 (3)
C1—C2—H2A108.0N2—C7—H7125.4
C4—C3—C2111.4 (3)N1—C7—H7125.4
C4—C3—H3A109.3C7—N1—C5106.4 (3)
C2—C3—H3A109.3C7—N1—C2126.5 (3)
C4—C3—H3B109.3C5—N1—C2127.1 (3)
C2—C3—H3B109.3C7—N2—C6109.9 (3)
H3A—C3—H3B108.0C7—N2—H2125.1
O4—C4—O3123.8 (3)C6—N2—H2125.1
O4—C4—C3123.6 (3)C4—O3—H3C112.9
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O2i0.861.912.716 (4)155
O3—H3C···O1ii0.861.712.572 (3)177
Symmetry codes: (i) x1, y, z; (ii) x, y+1, z.

Experimental details

Crystal data
Chemical formulaC7H8N2O4
Mr184.15
Crystal system, space groupOrthorhombic, P212121
Temperature (K)293
a, b, c (Å)7.3212 (16), 7.9193 (16), 14.254 (3)
V3)826.4 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.25 × 0.20 × 0.18
Data collection
DiffractometerRigaku Mercury2
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku, 2005)
Tmin, Tmax0.97, 0.98
No. of measured, independent and
observed [I > 2σ(I)] reflections
8489, 1110, 952
Rint0.053
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.050, 0.151, 1.12
No. of reflections1110
No. of parameters118
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.19, 0.23

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O2i0.861.912.716 (4)154.7
O3—H3C···O1ii0.861.712.572 (3)176.5
Symmetry codes: (i) x1, y, z; (ii) x, y+1, z.
 

References

First citationBao, W., Wang, Z. & Li, Y. (2003). J. Org. Chem. 68, 591–593.  Web of Science CrossRef PubMed CAS Google Scholar
First citationLópez, P., Zaderenko, P., Balcazar, J. L., Fonseca, I., Cano, F. H. & Ballesteros, P. (1996). J. Mol. Struct. 377, 105–112.  Google Scholar
First citationRigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 65| Part 5| May 2009| Page o1157
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