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

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). For the preparation of the title compound, see: Bao et al. (2003).

Experimental

Crystal data

• C₇H₈N₂O₄

• M_r = 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) ų

• 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) T_min = 0.97, T_max = 0.98

• 8489 measured reflections

• 1110 independent reflections

• 952 reflections with I > 2σ(I)

• R_int = 0.053

Refinement

• R[F² > 2σ(F²)] = 0.050

• wR(F²) = 0.151

• S = 1.12

• 1110 reflections

• 118 parameters

• H-atom parameters constrained

• Δρ_max = 0.19 e Å⁻³

• Δρ_min = −0.23 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2⋯O2^i	0.86	1.91	2.716 (4)	155
O3—H3C⋯O1^ii	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); cell refinement: CrystalClear; data reduction: CrystalClear; 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.

Supporting information

S1. Comment

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

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).

S2. Experimental

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.

S3. Refinement

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

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

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

Crystal data

C7H8N2O4	F(000) = 384
Mr = 184.15	Dx = 1.480 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: p 2ac 2ab	Cell parameters from 2123 reflections
a = 7.3212 (16) Å	θ = 2.8–27.4°
b = 7.9193 (16) Å	µ = 0.12 mm^−1
c = 14.254 (3) Å	T = 293 K
V = 826.4 (3) Å^3	Prism, colorless
Z = 4	0.25 × 0.20 × 0.18 mm

Data collection

Rigaku Mercury2 diffractometer	1110 independent reflections
Radiation source: fine-focus sealed tube	952 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.053
CCD_Profile_fitting scans	θmax = 27.5°, θmin = 2.9°
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	h = −9→9
Tmin = 0.97, Tmax = 0.98	k = −10→10
8489 measured reflections	l = −18→18

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.050	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.151	H-atom parameters constrained
S = 1.12	w = 1/[σ^2(Fo^2) + (0.0852P)^2 + 0.2196P] where P = (Fo^2 + 2Fc^2)/3
1110 reflections	(Δ/σ)max < 0.001
118 parameters	Δρmax = 0.19 e Å^−3
0 restraints	Δρmin = −0.23 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
C1	0.9679 (4)	0.2336 (4)	0.6099 (2)	0.0299 (7)
C2	0.9073 (4)	0.4110 (4)	0.6415 (2)	0.0309 (7)
H2A	0.9846	0.4450	0.6943	0.037*
C3	0.9360 (5)	0.5376 (4)	0.5624 (2)	0.0367 (7)
H3A	1.0554	0.5197	0.5346	0.044*
H3B	0.8447	0.5193	0.5142	0.044*
C4	0.9226 (5)	0.7177 (4)	0.5977 (2)	0.0378 (7)
C5	0.6549 (5)	0.4474 (5)	0.7626 (3)	0.0493 (10)
H5	0.7259	0.4826	0.8130	0.059*
C6	0.4741 (6)	0.4230 (7)	0.7635 (3)	0.0640 (13)
H6	0.3962	0.4380	0.8144	0.077*
C7	0.5708 (5)	0.3653 (5)	0.6236 (3)	0.0422 (8)
H7	0.5719	0.3333	0.5608	0.051*
N1	0.7172 (3)	0.4110 (3)	0.67364 (18)	0.0314 (6)
N2	0.4268 (4)	0.3725 (4)	0.6766 (2)	0.0507 (8)
H2	0.3175	0.3487	0.6589	0.061*
O1	0.8474 (4)	0.1251 (3)	0.5944 (2)	0.0507 (7)
O2	1.1355 (3)	0.2163 (3)	0.59668 (16)	0.0409 (6)
O3	0.9107 (5)	0.8279 (3)	0.52925 (19)	0.0584 (9)
H3C	0.8908	0.9290	0.5489	0.070*
O4	0.9181 (5)	0.7543 (4)	0.67883 (19)	0.0638 (9)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0279 (14)	0.0283 (15)	0.0334 (15)	0.0011 (12)	−0.0001 (12)	0.0036 (13)
C2	0.0315 (15)	0.0274 (15)	0.0338 (15)	−0.0038 (13)	0.0014 (13)	−0.0015 (12)
C3	0.0455 (18)	0.0265 (15)	0.0382 (16)	0.0006 (15)	0.0092 (16)	0.0019 (12)
C4	0.0396 (17)	0.0287 (15)	0.0452 (18)	0.0001 (15)	0.0057 (15)	0.0020 (14)
C5	0.0390 (19)	0.064 (3)	0.045 (2)	−0.0105 (19)	0.0083 (16)	−0.0169 (19)
C6	0.055 (2)	0.077 (3)	0.061 (2)	−0.014 (2)	0.024 (2)	−0.022 (3)
C7	0.0345 (16)	0.0433 (19)	0.0486 (18)	0.0050 (17)	−0.0069 (16)	−0.0066 (15)
N1	0.0293 (13)	0.0301 (13)	0.0349 (14)	−0.0001 (11)	−0.0025 (11)	−0.0032 (11)
N2	0.0310 (14)	0.0487 (18)	0.072 (2)	−0.0010 (15)	−0.0041 (16)	−0.0126 (16)
O1	0.0411 (13)	0.0241 (12)	0.087 (2)	−0.0010 (10)	0.0034 (14)	−0.0071 (13)
O2	0.0350 (12)	0.0383 (13)	0.0494 (14)	0.0044 (10)	0.0047 (11)	−0.0035 (11)
O3	0.090 (2)	0.0294 (13)	0.0560 (15)	0.0060 (15)	0.0122 (16)	0.0052 (11)
O4	0.106 (3)	0.0381 (14)	0.0472 (15)	0.0013 (17)	−0.0113 (17)	−0.0097 (12)

Geometric parameters (Å, º)

C1—O2	1.249 (4)	C5—C6	1.338 (6)
C1—O1	1.251 (4)	C5—N1	1.378 (4)
C1—C2	1.541 (4)	C5—H5	0.9300
C2—N1	1.465 (4)	C6—N2	1.347 (6)
C2—C3	1.522 (4)	C6—H6	0.9300
C2—H2A	0.9800	C7—N2	1.299 (5)
C3—C4	1.516 (4)	C7—N1	1.338 (4)
C3—H3A	0.9700	C7—H7	0.9300
C3—H3B	0.9700	N2—H2	0.8600
C4—O4	1.193 (4)	O3—H3C	0.8601
C4—O3	1.312 (4)
O2—C1—O1	126.3 (3)	O3—C4—C3	112.6 (3)
O2—C1—C2	115.3 (3)	C6—C5—N1	107.9 (4)
O1—C1—C2	118.3 (3)	C6—C5—H5	126.1
N1—C2—C3	111.3 (3)	N1—C5—H5	126.1
N1—C2—C1	111.4 (2)	C5—C6—N2	106.7 (3)
C3—C2—C1	110.1 (2)	C5—C6—H6	126.6
N1—C2—H2A	108.0	N2—C6—H6	126.6
C3—C2—H2A	108.0	N2—C7—N1	109.1 (3)
C1—C2—H2A	108.0	N2—C7—H7	125.4
C4—C3—C2	111.4 (3)	N1—C7—H7	125.4
C4—C3—H3A	109.3	C7—N1—C5	106.4 (3)
C2—C3—H3A	109.3	C7—N1—C2	126.5 (3)
C4—C3—H3B	109.3	C5—N1—C2	127.1 (3)
C2—C3—H3B	109.3	C7—N2—C6	109.9 (3)
H3A—C3—H3B	108.0	C7—N2—H2	125.1
O4—C4—O3	123.8 (3)	C6—N2—H2	125.1
O4—C4—C3	123.6 (3)	C4—O3—H3C	112.9

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···O2^i	0.86	1.91	2.716 (4)	155
O3—H3C···O1^ii	0.86	1.71	2.572 (3)	177

Symmetry codes: (i) x−1, y, z; (ii) x, y+1, z.