d-Glutamic acid hydro­chloride

Fox-Uribe, L.Y.; Hernández-Paredes, J.; Soberanes, Y.; Valenzuela-Chavira, I.; Garcia-Orozco, K.D.; Ochoa-Leyva, A.; Lara, K.O.; Navarro, R.E.; Sotelo-Mundo, R.R.

doi:10.1107/S2414314619004589

organic compounds

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ISSN: 2414-3146

Volume 4| Part 4| April 2019| x190458

https://doi.org/10.1107/S2414314619004589

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D-Glutamic acid hydrochloride

Leonardo Y. Fox-Uribe,^a Javier Hernández-Paredes,^b Yedith Soberanes,^a Ignacio Valenzuela-Chavira,^c Karina D. Garcia-Orozco,^a Adrian Ochoa-Leyva,^d Karen Ochoa Lara,^e Rosa Elena Navarro ^e and Rogerio R. Sotelo-Mundo ^a ^*

^aLaboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A. C., Carretetera Gustavo Enrique Astiazarán Rosas No. 46, Col. La Victoria, Hermosillo 83304, Sonora, Mexico, ^bDepartamento de Física, Universidad de Sonora (UNISON), Edificio 3R (Planta Alta), Blvd. Luis Encinas J. y Rosales s/n, Col. Centro, Hermosillo 83000, Sonora, Mexico, ^cDepartamento de Ciencias Químico Biologicas, Universidad de Sonora (UNISON), Edificio 5A, Blvd. Luis Encinas J. y Rosales s/n, Col. Centro, Hermosillo 83000, Sonora, Mexico, ^dDepartamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62210, Morelos, Mexico, and ^eDepartamento de Investigación en Polímeros y Materiales, Universidad de Sonora (UNISON), Edificio 3G, Blvd. Luis Encinas J. y Rosales s/n, Col. Centro, Hermosillo 83000, Sonora, Mexico
^*Correspondence e-mail: rrs@ciad.mx

Edited by S. Bernès, Benemérita Universidad Autónoma de Puebla, México (Received 6 December 2018; accepted 3 April 2019; online 25 April 2019)

The absolute structure of D-glutamic acid hydrochloride [systematic name: (R)-1,3-dicarboxypropan-1-aminium chloride], C₅H₁₀NO₄⁺·Cl⁻, has been determined by single-crystal X-ray diffraction at room temperature using Cu Kα radiation.

Keywords: crystal structure; amino acids; absolute structure; Flack parameter; Hooft parameter.

CCDC reference: 1515166

Structure description

The asymmetric unit of the title compound (Fig. 1) contains one halide ion (Cl⁻) and one positively charged molecule of glutamic acid. The molecule of glutamic acid (Glu hereafter) is protonated at the γ-COOH group. The carbon chain C1—C2—C3—C4—C5 is almost coplanar. The planes of the α-COOH and the γ-COOH groups form angles of 72.4 (16) and 9.3 (10)°, respectively, to the C1–C5 plane.

Figure 1
ORTEP representation of the asymmetric unit of D-Glu·HCl. Displacement ellipsoids are drawn at the 50% probability level.

In the crystal structures of the α and β forms of pure L-glutamic acid (L-Glu), molecules of the amino acid that are bound to each other by O—H⋯O hydrogen bonds, forming infinite chains (Hirayama et al., 1980 ). In the crystal structure of the title compound reported herein, the Cl⁻ anion disrupts the characteristic head-to-tail self-assembly between Glu molecules, leading to the formation of an O4—H4⋯Cl1 hydrogen bond [3.0436 (13) Å]. Furthermore, the Cl⁻ anion is also bound to two Glu neighbouring molecules by two hydrogen bonds, N1—H1B⋯Cl1 [3.1447 (17) Å] and N1—H1C⋯Cl1 [3.1959 (18) Å]. It is also observed that all the possible hydrogen-bond donors form interactions with all the available hydrogen-bond acceptors in the crystal (Table 1).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯O3ⁱ	0.66	1.98	2.634 (2)	179
N1—H1A⋯O2ⁱⁱ	0.88 (2)	2.11 (2)	2.8904 (18)	146.7 (19)
N1—H1B⋯Cl1ⁱⁱⁱ	0.94 (3)	2.21 (3)	3.1447 (17)	172 (2)
N1—H1C⋯Cl1^iv	0.88 (3)	2.32 (3)	3.1959 (18)	171 (2)
O4—H4⋯Cl1	0.84 (2)	2.21 (2)	3.0436 (13)	169 (2)
Symmetry codes: (i) $[-x+{\script{1\over 2}}, -y+1, z+{\script{1\over 2}}]$ ; (ii) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+2]$ ; (iii) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ ; (iv) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ .

The solution obtained by SHELXT (Sheldrick, 2015a ) was refined to convergence and the resulting absolute structure parameters are listed in Table 2 and R-factors are listed in Table 3. The absolute configuration of C2 in this model is R, which is that expected based on the D-Glu starting material. To confirm this, the structure was inverted (i.e. C2 S configuration) corresponding to L-Glu) and re-refined to give a second set of absolute structure parameters (Table 2), which clearly indicate the wrong absolute structure and significantly higher residuals of R(F) = 0.045 and wR(F²) = 0.1172. We may conclude that this data collection at room temperature has established the absolute structure of the title salt with a high degree of reliability.

Table 2
Comparison of parameters for absolute structures

	Flack (x)	Parsons (z)	Hooft (y)	Hooft (G)
D-Glu·HCl	0.055 (4)	0.057 (6)	0.058 (6)	0.88 (1)
L-Glu·HCl	0.944 (4)	0.944 (6)	0.946 (6)	−0.89 (1)

Table 3
Experimental details

Crystal data
Chemical formula	C₅H₁₀NO₄⁺·Cl⁻
M_r	183.59
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	300
a, b, c (Å)	5.1363 (2), 11.7497 (4), 13.2871 (5)
V (Å³)	801.88 (5)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	4.03
Crystal size (mm)	0.25 × 0.10 × 0.03

Data collection
Diffractometer	Bruker D8 QUEST
Absorption correction	Multi-scan (SADABS; Bruker, 2012 )
T_min, T_max	0.494, 0.754
No. of measured, independent and observed [I > 2σ(I)] reflections	15237, 1630, 1609
R_int	0.034
(sin θ/λ)_max (Å⁻¹)	0.625

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.022, 0.059, 1.07
No. of reflections	1630
No. of parameters	114
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.16, −0.23
Absolute structure	See 'Structure description' section
Absolute structure parameter	0.055 (4)
Computer programs: APEX2 and SAINT (Bruker, 2012 ), SHELXT2014/4 (Sheldrick, 2015a), SHELXL2014/7 (Sheldrick, 2015b ) and ORTEP-3 for Windowsand WinGX (Farrugia, 2012).

Synthesis and crystallization

All materials were purchased from Sigma–Aldrich (Toluca, Mexico) and used without further purification. 50 mmol of (R)-2-aminopentanedioic acid (D-Glu; ≥99% pure) and 50 mmol of CaCl₂ were mixed in a final volume of 1 ml ultrapure water (Milli-Q water, Merck Millipore, Mexico). The solution was left to evaporate at 298 K in a 5 ml glass vial. Good quality crystals of D-Glu·HCl were obtained after four weeks.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3.

Structural data

CCDC reference: 1515166

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314619004589/bh4043sup1.cif

Supporting information file. DOI: https://doi.org/10.1107/S2414314619004589/bh4043Isup3.cdx

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2012); cell refinement: SAINT (Bruker, 2012); data reduction: SAINT (Bruker, 2012); program(s) used to solve structure: SHELXT2014/4 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014/7 (Sheldrick, 2015b); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: WinGX (Farrugia, 2012).

(R)-1,3-Dicarboxypropan-1-aminium chloride top

Crystal data top

C₅H₁₀NO₄⁺·Cl⁻	F(000) = 384
M_r = 183.59	D_x = 1.512 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2ab	Cell parameters from 9897 reflections
a = 5.1363 (2) Å	θ = 5.0–74.4°
b = 11.7497 (4) Å	µ = 4.03 mm⁻¹
c = 13.2871 (5) Å	T = 300 K
V = 801.88 (5) Å³	Plate, colourless
Z = 4	0.25 × 0.10 × 0.03 mm

Data collection top

Bruker D8 QUEST diffractometer	1630 independent reflections
Radiation source: Microfocus sealed tube, Incoatec IµS HB	1609 reflections with I > 2σ(I)
Multiyaler mirrors monochromator	R_int = 0.034
Detector resolution: 102.4 pixels mm^-1	θ_max = 74.4°, θ_min = 5.0°
φ and ω scans	h = −6→6
Absorption correction: multi-scan (SADABS; Bruker, 2012)	k = −14→14
T_min = 0.494, T_max = 0.754	l = −16→16
15237 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.022	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.059	w = 1/[σ²(F_o²) + (0.040P)² + 0.0618P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max < 0.001
1630 reflections	Δρ_max = 0.16 e Å⁻³
114 parameters	Δρ_min = −0.23 e Å⁻³
0 restraints	Absolute structure: See 'Structure description' section
0 constraints	Absolute structure parameter: 0.055 (4)
Primary atom site location: dual

Special details top

Refinement. Hydrogen atoms for CH and CH₂ groups were placed in geometrically calculated positions using the riding model. Hydrogen atom H1 has setting as an idealized OH group, with C1—O1—H1 angle tetrahedral. Hydrogen atoms involved in X—H···Cl interactions (H1A, H1B, H1C and H4) have been located from a difference map and refined with free coordinates. All H atoms were refined with calculated isotropic displacement parameters.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Cl1	0.55328 (8)	0.57267 (4)	0.26144 (3)	0.03036 (14)
O1	0.4381 (4)	0.53718 (11)	0.92637 (12)	0.0451 (4)
H1	0.349 (6)	0.5155 (14)	0.956 (3)	0.068*
N1	0.5594 (4)	0.82112 (12)	0.84223 (10)	0.0251 (3)
C1	0.3874 (3)	0.64434 (14)	0.91039 (11)	0.0245 (4)
H1A	0.572 (5)	0.8424 (17)	0.9058 (16)	0.029*
H1B	0.696 (5)	0.8561 (19)	0.8065 (16)	0.029*
H1C	0.414 (5)	0.8528 (19)	0.8208 (16)	0.029*
O2	0.2122 (3)	0.69746 (11)	0.94905 (10)	0.0347 (3)
C2	0.5687 (4)	0.69496 (13)	0.83245 (11)	0.0213 (3)
H2	0.7466	0.6683	0.8448	0.026*
O3	0.4199 (4)	0.55187 (12)	0.54442 (9)	0.0440 (4)
C3	0.4791 (3)	0.65493 (14)	0.72847 (11)	0.0237 (3)
H3A	0.4571	0.573	0.7302	0.028*
H3B	0.3101	0.6883	0.7145	0.028*
O4	0.6959 (3)	0.66860 (12)	0.46696 (9)	0.0362 (3)
C4	0.6617 (4)	0.68448 (15)	0.64312 (12)	0.0261 (4)
H4A	0.6646	0.7664	0.6338	0.031*
H4B	0.8367	0.66	0.6601	0.031*
H4	0.648 (5)	0.6340 (19)	0.4144 (17)	0.031*
C5	0.5778 (4)	0.62819 (14)	0.54680 (11)	0.0257 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0287 (2)	0.0363 (2)	0.0260 (2)	0.00446 (18)	−0.00205 (16)	−0.00294 (15)
O1	0.0502 (9)	0.0344 (7)	0.0507 (8)	0.0051 (7)	0.0244 (8)	0.0169 (6)
N1	0.0279 (7)	0.0276 (7)	0.0200 (6)	−0.0064 (7)	0.0007 (7)	−0.0023 (5)
C1	0.0256 (9)	0.0307 (8)	0.0171 (7)	−0.0042 (7)	0.0011 (6)	0.0009 (6)
O2	0.0369 (8)	0.0361 (7)	0.0310 (6)	0.0010 (6)	0.0142 (6)	0.0010 (5)
C2	0.0208 (8)	0.0250 (7)	0.0180 (6)	−0.0021 (7)	0.0008 (7)	0.0013 (5)
O3	0.0610 (10)	0.0453 (8)	0.0256 (6)	−0.0267 (8)	−0.0041 (7)	−0.0047 (5)
C3	0.0240 (8)	0.0272 (7)	0.0198 (7)	−0.0051 (6)	−0.0003 (7)	−0.0032 (6)
O4	0.0476 (9)	0.0432 (8)	0.0177 (5)	−0.0119 (7)	0.0048 (6)	−0.0061 (5)
C4	0.0290 (9)	0.0317 (8)	0.0176 (7)	−0.0086 (7)	−0.0008 (7)	−0.0026 (6)
C5	0.0314 (10)	0.0262 (8)	0.0196 (7)	−0.0017 (8)	−0.0013 (7)	−0.0020 (6)

Geometric parameters (Å, º) top

O1—C1	1.303 (2)	O3—C5	1.209 (2)
O1—H1	0.66 (4)	C3—C4	1.512 (2)
N1—C2	1.489 (2)	C3—H3A	0.97
N1—H1A	0.88 (2)	C3—H3B	0.97
N1—H1B	0.94 (3)	O4—C5	1.311 (2)
N1—H1C	0.88 (3)	O4—H4	0.84 (2)
C1—O2	1.210 (2)	C4—C5	1.504 (2)
C1—C2	1.514 (2)	C4—H4A	0.97
C2—C3	1.530 (2)	C4—H4B	0.97
C2—H2	0.98

C1—O1—H1	109.5	C4—C3—C2	114.83 (14)
C2—N1—H1A	111.3 (13)	C4—C3—H3A	108.6
C2—N1—H1B	111.6 (14)	C2—C3—H3A	108.6
H1A—N1—H1B	108 (2)	C4—C3—H3B	108.6
C2—N1—H1C	114.7 (14)	C2—C3—H3B	108.6
H1A—N1—H1C	105 (2)	H3A—C3—H3B	107.5
H1B—N1—H1C	106.5 (18)	C5—O4—H4	111.0 (16)
O2—C1—O1	125.29 (16)	C5—C4—C3	111.06 (14)
O2—C1—C2	123.04 (15)	C5—C4—H4A	109.4
O1—C1—C2	111.61 (15)	C3—C4—H4A	109.4
N1—C2—C1	108.17 (13)	C5—C4—H4B	109.4
N1—C2—C3	112.04 (13)	C3—C4—H4B	109.4
C1—C2—C3	108.18 (14)	H4A—C4—H4B	108
N1—C2—H2	109.5	O3—C5—O4	123.88 (15)
C1—C2—H2	109.5	O3—C5—C4	122.73 (15)
C3—C2—H2	109.5	O4—C5—C4	113.38 (15)

O2—C1—C2—N1	20.8 (2)	C1—C2—C3—C4	−171.82 (14)
O1—C1—C2—N1	−161.84 (16)	C2—C3—C4—C5	172.09 (14)
O2—C1—C2—C3	−100.72 (18)	C3—C4—C5—O3	−14.3 (2)
O1—C1—C2—C3	76.60 (19)	C3—C4—C5—O4	166.94 (16)
N1—C2—C3—C4	69.0 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O3ⁱ	0.66	1.98	2.634 (2)	179
N1—H1A···O2ⁱⁱ	0.88 (2)	2.11 (2)	2.8904 (18)	146.7 (19)
N1—H1A···O3ⁱⁱⁱ	0.88 (2)	2.55 (2)	3.1033 (19)	121.6 (16)
N1—H1B···Cl1^iv	0.94 (3)	2.21 (3)	3.1447 (17)	172 (2)
N1—H1C···Cl1^v	0.88 (3)	2.32 (3)	3.1959 (18)	171 (2)
O4—H4···Cl1	0.84 (2)	2.21 (2)	3.0436 (13)	169 (2)

Symmetry codes: (i) −x+1/2, −y+1, z+1/2; (ii) x+1/2, −y+3/2, −z+2; (iii) −x+1, y+1/2, −z+3/2; (iv) x+1/2, −y+3/2, −z+1; (v) x−1/2, −y+3/2, −z+1.

Comparison of parameters for absolute structures top

	Flack (x)	Parsons (z)	Hooft (y)	Hooft (G)
D-Glu·HCl	0.055 (4)	0.057 (6)	0.058 (6)	0.88 (1)
L-Glu·HCl	0.944 (4)	0.944 (6)	0.946 (6)	-0.89 (1)

Funding information

Funding for this research was provided by: Consejo Nacional de Ciencia y Tecnología (scholarship to L. Y. Fox-Uribe; grant No. CB-2014–237963 to R. R. Sotelo-Mundo; grant No. INFR-2014–01-225455); Red Temática de Química Supramolecular (grant No. 294810); Instituto de Biotecnología-CIC-UNAM and CIAD ; Secretaría de Educación Pública (PRODEP) (grant No. 511–6/18–8537 to J. Hernández-Paredes; grant No. 35986 to I. Valenzuela-Chavira).

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