Revision of the crystal structure of `bis­(glycine) squaric acid'

Seidel, R.W.

doi:10.1107/S241431461801324X

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 3| Part 9| September 2018| x181324

https://doi.org/10.1107/S241431461801324X

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Revision of the crystal structure of `bis(glycine) squaric acid'¹

Rüdiger W. Seidel ^a ^*

^aInstitut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
^*Correspondence e-mail: ruediger.seidel@pharmazie.uni-halle.de

Edited by M. Weil, Vienna University of Technology, Austria (Received 13 August 2018; accepted 17 September 2018; online 21 September 2018)

The crystal structure of `bis(glycine) squaric acid' [Tyagi et al. (2016 ). RSC Adv. 6, 24565–24576], is revised. Re-refinement of the structure against the original X-ray intensity data after correct placement of the donor H atoms proves that the compound is in fact the previously reported diglycinium squarate [systematic name: bis(carboxymethanaminium) 3,4-dioxocyclobut-1-ene-1,2-diolate; Anioła et al. (2014 ). New J. Chem. 38, 3556–3568]. The findings are consistent with the pK_a rule.

Keywords: crystal structure; redetermination; proton-transfer compound; squarate.

CCDC reference: 1832495

Structure description

In a search of the Cambridge Structural Database (CSD Version 5.39 with February 2018 updates; Groom et al., 2016 ) for salts of squaric acid (H₂C₄O₄) and α-amino acids, we stumbled upon CSD entries SIZKIX and SIZKIX01 (additional database identifier VABNUK). SIZKIX is diglycinium squarate, i.e. a 2:1 proton-transfer compound of glycine and squaric acid, and was reported by Anioła et al. (2014). SIZKIX01, however, is reportedly a 2:1 non-ionized acid–base complex of glycine and squaric acid (Tyagi et al., 2016). In the original publication (Tyagi et al., 2016), the compound was designated as ``bis glycine' squarate' whereas in the CSD, `bis(glycine) squaric acid' was assigned as the common name. Since squaric acid is a remarkably strong diprotic acid (Gilli et al., 2001 ), the formation of a non-ionized acid–base complex rather than a salt with a glycinium cation would be very unusual. Considering that incorrect placement of H atoms is a common pitfall in crystal structure refinement (Spek, 2009; Bernal & Watkins, 2013 ; Schwalbe, 2018 ), this prompted us to scrutinize the structure and crystallographic data of SIZKIX01.

First of all, visual inspection of the original structural model for SIZKIX01 revealed that the hydrogen-bonding pattern is not sensible. Moreover, several checkCIF/PLATON (Spek, 2009 ) alerts concerning a strange C—O—H geometry (level A alert), short intra- and intermolecular D—H⋯H—D (D = hydrogen-bond donor) contacts (level B alerts), positive and negative residual electron density at N and O atoms (level C alerts) and a C—O bond without an H atom attached longer than 1.3 Å, indicated incorrectly positioned hydrogen atoms.

It is instructive to inspect the F_obs–F_calc difference electron-density map to identify incorrectly (and correctly) positioned H atoms. From Fig. 1 it is obvious that the positions of the N—H and O—H hydrogen atoms are incorrect, with the exception of that bonded to O6. After re-refinement of the crystal structure with correctly positioned donor H atoms against original diffraction data, R1 [I >2σ(I)] dropped from 0.0589 to 0.0426. It should be noted that the R factors reported in the article by Tyagi et al. (2016) do not agree with those in the corresponding deposited CIF (CCDC 1052856). The residual difference electron densities after re-refinement are 0.35 and −0.28 e Å⁻³ (originally 0.63 and −0.68 e Å⁻³). Fig. 2 depicts the revised and re-refined structural model for SIZKIX01. A detailed description of the crystal structure of diglycinium squarate can be found in the article by Anioła et al. (2014). It is worth noting that the carboxy group of one glycinium ion adopts a syn conformation, whereas the other exhibits an anti conformation. The crystal packing of diglycinium squarate is governed by H bonds of the N—H⋯O and O—H⋯O type (Table 1). For other squarate salts of α-amino acids, see: Seidel & Zareva (2018 ), and references cited therein.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O4	0.89	2.08	2.9148 (15)	156
N1—H1A⋯O11ⁱ	0.89	2.57	3.0297 (16)	113
N1—H1B⋯O3ⁱⁱ	0.89	2.11	2.8933 (15)	146
N1—H1C⋯O4ⁱⁱⁱ	0.89	1.98	2.7890 (15)	151
N2—H2A⋯O3ⁱⁱ	0.89	2.33	3.1075 (19)	146
N2—H2A⋯O11ⁱ	0.89	2.60	3.0591 (18)	113
N2—H2B⋯O3ⁱ	0.89	1.93	2.8064 (17)	167
N2—H2C⋯O1^iv	0.89	2.48	3.1602 (18)	134
N2—H2C⋯O6ⁱⁱ	0.89	2.13	2.8007 (16)	132
O6—H6⋯O2^v	0.82	1.64	2.4406 (16)	167
O9—H9⋯O1	0.82	1.75	2.5629 (15)	169
Symmetry codes: (i) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[x, -y+2, z+{\script{1\over 2}}]$ ; (iii) $[-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iv) $[-x, y, -z+{\script{1\over 2}}]$ ; (v) -x, -y+2, -z.

Figure 1
F_obs – F_calc difference electron density map 1.41 Å around visible atoms for SIZKIX01: 0.11 e⁻ Å⁻³ (green), −0.11 e⁻ Å⁻³ (red), σ = 0.039. Misplaced hydrogen atoms show up as negative density (red), and the correct positions appear as positive density (green).

Figure 2
Revised and re-refined structural model for SIZKIX01, proving that the structure is indeed diglycinium squarate and thus identical with SIZKIX. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented by small spheres of arbitrary radii. Hydrogen bonds are represented by dashed lines.

Considering that for ΔpK_a = pK_a[protonated base] − pK_a[acid] > 4 ionized acid–base proton-transfer compounds were observed exclusively (Cruz-Cabeza, 2012 ), the formation of a non-ionized acid–base complex of glycine and squaric acid appears to be very unlikely. The pK_a value of the amino group in glycine is 9.6 (Dawson et al., 1986 ), and for squaric acid, pK_a₁ values of 0.51±0.02 and 0.55±0.15 were obtained by conductometric determination (Gelb, 1971 ) and potentiometric titration (Schwartz & Howard, 1970 ), respectively, although based on earlier studies pK_a₁ values in the range of 1.2–1.7 were reported (Gilli et al., 2001).

In conclusion, the crystal structure of the compound previously described as `bis(glycine) squaric acid' (CSD refcode: SIZKIX01) is revised. It has been demonstrated that the structure is in fact the known proton-transfer compound diglycinium squarate and, thus, identical with CSD entry SIZKIX. Consequently, the results of Hirshfeld surface analysis in the original report by Tyagi et al. (2016), using the incorrect structure model, must be questioned. It is to be hoped that this contribution helps to avoid such errors in crystal structure refinement in the future.

Synthesis and crystallization

The crystallization of the compound was described by Tyagi et al. (2016).

Refinement

The original data (CCDC 1052856) were retrieved in CIF format from the Cambridge Crystallographic Data Centre (CCDC) via https://www.ccdc.cam.ac.uk/structures. The reflection data (HKL) and the SHELXL instruction file (INS) were extracted from the CIF using the program shredCIF, which is distributed with SHELXL (Sheldrick, 2015b ). A structure factor file (FCF) was generated with SHELXL2018/3 using the LIST 6 command, and the F_obs– F_calc difference electron-density map was visualized as a three-dimensional mesh (Fig. 1), using shelXle (Hübschle et al., 2011 ).

A re-refinement against the original intensity data was carried out with SHELXL2018/3 (Sheldrick, 2015b). For the sake of consistency, the chosen asymmetric unit and atom labels, as shown in Fig. 1, were maintained. The positions of carbon-bound H atoms were calculated geometrically and refined using a riding model with U_iso(H) = 1.2U_eq(C). The C—H bond lengths were set at 0.97 Å. The initial torsion angles of the protonated amino groups and the carboxy O—H groups were determined via difference Fourier syntheses and subsequently refined while maintaining the tetrahedral angles, and with U_iso(H) = 1.5 U_eq(N,O). The N—H bond lengths were set at 0.89 Å and the O—H bond lengths were set at 0.82 Å. Crystal data, data collection and structure refinement details are given in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₄O₄·2C₂H₆NO₂
M_r	264.20
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	293
a, b, c (Å)	16.8050 (16), 8.3008 (8), 15.7976 (13)
β (°)	100.259 (9)
V (Å³)	2168.5 (3)
Z	8
Radiation type	Mo Kα
μ (mm⁻¹)	0.15
Crystal size (mm)	0.50 × 0.50 × 0.50

Data collection
Diffractometer	Rigaku Oxford Diffraction Xcalibur, Sapphire3
Absorption correction	Multi-scan (ABSPACK in CrysAlis PRO; Rigaku OD, 2014 $[Rigaku OD (2014). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ )
T_min, T_max	0.403, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	7067, 2570, 2277
R_int	0.036
(sin θ/λ)_max (Å⁻¹)	0.692

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.043, 0.113, 1.04
No. of reflections	2570
No. of parameters	168
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.35, −0.28
Computer programs: CrysAlis PRO (Rigaku OD, 2014 $[Rigaku OD (2014). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ ), SHELXT2018/3 (Sheldrick, 2015a ), SHELXL2018/3 (Sheldrick, 2015b), shelXle (Hübschle et al., 2011), DIAMOND (Brandenburg, 2014 ), enCIFer (Allen et al., 2004 ) and publCIF (Westrip, 2010 ).

Structural data

CCDC reference: 1832495

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S241431461801324X/wm5461sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S241431461801324X/wm5461Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S241431461801324X/wm5461Isup3.mol

Supporting information file. DOI: https://doi.org/10.1107/S241431461801324X/wm5461Isup4.cml

checkCIF report

Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2014); cell refinement: CrysAlis PRO (Rigaku OD, 2014); data reduction: CrysAlis PRO (Rigaku OD, 2014); program(s) used to solve structure: SHELXT2018/3 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: shelXle (Hübschle et al., 2011) and DIAMOND (Brandenburg, 2014); software used to prepare material for publication: enCIFer (Allen et al., 2004) and publCIF (Westrip, 2010).

Bis(carboxymethanaminium) 3,4-dioxocyclobut-1-ene-1,2-diolate top

Crystal data top

C₄O₄·2C₂H₆NO₂	F(000) = 1104
M_r = 264.20	D_x = 1.619 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 16.8050 (16) Å	Cell parameters from 2994 reflections
b = 8.3008 (8) Å	θ = 3.6–29.4°
c = 15.7976 (13) Å	µ = 0.15 mm⁻¹
β = 100.259 (9)°	T = 293 K
V = 2168.5 (3) Å³	Prism, colourless
Z = 8	0.50 × 0.50 × 0.50 mm

Data collection top

Rigaku Oxford Diffraction Xcalibur, Sapphire3 diffractometer	2570 independent reflections
Radiation source: Enhance (Mo) X-ray Source	2277 reflections with I > 2σ(I)
Detector resolution: 15.9853 pixels mm^-1	R_int = 0.036
ω scans	θ_max = 29.5°, θ_min = 3.6°
Absorption correction: multi-scan (ABSPACK in CrysAlisPro; Rigaku OD, 2014)	h = −21→22
T_min = 0.403, T_max = 1.000	k = −10→11
7067 measured reflections	l = −21→19

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.043	H-atom parameters constrained
wR(F²) = 0.113	w = 1/[σ²(F_o²) + (0.0597P)² + 1.323P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max = 0.001
2570 reflections	Δρ_max = 0.35 e Å⁻³
168 parameters	Δρ_min = −0.28 e Å⁻³
0 restraints	Extinction correction: SHELXL-2018/3 (Sheldrick 2015b), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0281 (16)

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.

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

	x	y	z	U_iso*/U_eq
C1	0.09201 (8)	0.84696 (17)	−0.03393 (8)	0.0264 (3)
C2	0.09470 (9)	0.75825 (17)	0.04588 (8)	0.0277 (3)
C3	0.17481 (8)	0.82723 (16)	0.07796 (8)	0.0232 (3)
C4	0.17066 (8)	0.91641 (17)	−0.00344 (8)	0.0245 (3)
C5	0.10057 (8)	0.62754 (18)	0.28928 (9)	0.0274 (3)
C7	0.15012 (8)	1.19712 (16)	0.15276 (8)	0.0244 (3)
C10	0.11860 (9)	0.53370 (17)	0.37145 (8)	0.0295 (3)
H10A	0.071281	0.472052	0.378862	0.035*
H10B	0.162392	0.458753	0.368893	0.035*
C12	0.12634 (8)	1.10722 (18)	0.22754 (8)	0.0269 (3)
H12A	0.100022	1.180301	0.261757	0.032*
H12B	0.088457	1.022138	0.206253	0.032*
N1	0.19877 (7)	1.03746 (14)	0.28119 (7)	0.0270 (3)
H1A	0.218164	0.958976	0.252287	0.041*
H1B	0.185750	0.997609	0.329215	0.041*
H1C	0.236182	1.113628	0.294491	0.041*
N2	0.14146 (9)	0.64295 (17)	0.44486 (8)	0.0361 (3)
H2A	0.154562	0.738718	0.426043	0.054*
H2B	0.183654	0.602342	0.480560	0.054*
H2C	0.100009	0.654023	0.472474	0.054*
O1	0.04871 (8)	0.66282 (16)	0.07434 (7)	0.0471 (3)
O2	0.04301 (7)	0.85940 (16)	−0.10400 (6)	0.0408 (3)
O3	0.21416 (7)	1.01203 (14)	−0.03532 (6)	0.0353 (3)
O4	0.22470 (6)	0.81538 (12)	0.14578 (6)	0.0297 (3)
O6	0.09122 (6)	1.24195 (15)	0.09348 (6)	0.0366 (3)
H6	0.048364	1.209417	0.105110	0.055*
O9	0.09184 (8)	0.53179 (14)	0.22230 (7)	0.0443 (3)
H9	0.080061	0.585235	0.178194	0.066*
O10	0.09541 (7)	0.77080 (13)	0.28753 (7)	0.0392 (3)
O11	0.22034 (6)	1.22618 (15)	0.15001 (7)	0.0370 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0260 (6)	0.0325 (7)	0.0201 (6)	−0.0021 (6)	0.0021 (5)	0.0027 (5)
C2	0.0307 (7)	0.0320 (7)	0.0188 (6)	−0.0057 (6)	0.0003 (5)	0.0025 (5)
C3	0.0262 (6)	0.0241 (6)	0.0186 (6)	−0.0007 (5)	0.0022 (5)	−0.0012 (4)
C4	0.0274 (6)	0.0275 (7)	0.0182 (6)	−0.0015 (5)	0.0028 (5)	−0.0003 (5)
C5	0.0206 (6)	0.0319 (7)	0.0284 (6)	−0.0028 (6)	0.0006 (5)	0.0048 (5)
C7	0.0277 (6)	0.0255 (6)	0.0200 (6)	−0.0034 (5)	0.0040 (5)	0.0002 (5)
C10	0.0318 (7)	0.0288 (7)	0.0262 (7)	0.0038 (6)	0.0006 (5)	0.0017 (5)
C12	0.0263 (6)	0.0312 (7)	0.0231 (6)	0.0006 (6)	0.0041 (5)	0.0054 (5)
N1	0.0319 (6)	0.0274 (6)	0.0201 (5)	−0.0015 (5)	0.0000 (4)	0.0018 (4)
N2	0.0432 (7)	0.0391 (7)	0.0257 (6)	0.0067 (6)	0.0057 (5)	−0.0018 (5)
O1	0.0467 (7)	0.0612 (8)	0.0289 (6)	−0.0282 (6)	−0.0053 (5)	0.0161 (5)
O2	0.0312 (5)	0.0648 (8)	0.0226 (5)	−0.0073 (5)	−0.0052 (4)	0.0123 (5)
O3	0.0364 (6)	0.0446 (6)	0.0238 (5)	−0.0150 (5)	0.0024 (4)	0.0059 (4)
O4	0.0319 (5)	0.0332 (5)	0.0207 (4)	−0.0029 (4)	−0.0049 (4)	0.0019 (4)
O6	0.0310 (5)	0.0514 (7)	0.0252 (5)	−0.0043 (5)	−0.0005 (4)	0.0130 (4)
O9	0.0659 (8)	0.0400 (6)	0.0237 (5)	−0.0044 (6)	−0.0012 (5)	0.0027 (4)
O10	0.0407 (6)	0.0306 (6)	0.0427 (6)	−0.0029 (5)	−0.0025 (5)	0.0086 (5)
O11	0.0291 (5)	0.0470 (7)	0.0350 (6)	−0.0088 (5)	0.0064 (4)	0.0080 (5)

Geometric parameters (Å, º) top

C1—O2	1.2608 (16)	C10—N2	1.4684 (18)
C1—C4	1.4437 (18)	C10—H10A	0.9700
C1—C2	1.4538 (18)	C10—H10B	0.9700
C2—O1	1.2453 (18)	C12—N1	1.4724 (16)
C2—C3	1.4676 (18)	C12—H12A	0.9700
C3—O4	1.2413 (15)	C12—H12B	0.9700
C3—C4	1.4746 (17)	N1—H1A	0.8900
C4—O3	1.2447 (17)	N1—H1B	0.8900
C5—O10	1.1923 (18)	N1—H1C	0.8900
C5—O9	1.3106 (18)	N2—H2A	0.8900
C5—C10	1.4979 (18)	N2—H2B	0.8900
C7—O11	1.2126 (17)	N2—H2C	0.8900
C7—O6	1.2904 (16)	O6—H6	0.8200
C7—C12	1.5101 (18)	O9—H9	0.8200

O2—C1—C4	132.55 (13)	C5—C10—H10B	109.6
O2—C1—C2	135.85 (13)	H10A—C10—H10B	108.1
C4—C1—C2	91.59 (10)	N1—C12—C7	109.74 (11)
O1—C2—C1	135.23 (13)	N1—C12—H12A	109.7
O1—C2—C3	135.53 (12)	C7—C12—H12A	109.7
C1—C2—C3	89.24 (11)	N1—C12—H12B	109.7
O4—C3—C2	134.77 (12)	C7—C12—H12B	109.7
O4—C3—C4	135.42 (13)	H12A—C12—H12B	108.2
C2—C3—C4	89.81 (10)	C12—N1—H1A	109.5
O3—C4—C1	133.50 (12)	C12—N1—H1B	109.5
O3—C4—C3	137.14 (12)	H1A—N1—H1B	109.5
C1—C4—C3	89.35 (10)	C12—N1—H1C	109.5
O10—C5—O9	126.08 (13)	H1A—N1—H1C	109.5
O10—C5—C10	122.79 (13)	H1B—N1—H1C	109.5
O9—C5—C10	111.13 (12)	C10—N2—H2A	109.5
O11—C7—O6	122.84 (12)	C10—N2—H2B	109.5
O11—C7—C12	121.40 (12)	H2A—N2—H2B	109.5
O6—C7—C12	115.75 (12)	C10—N2—H2C	109.5
N2—C10—C5	110.32 (12)	H2A—N2—H2C	109.5
N2—C10—H10A	109.6	H2B—N2—H2C	109.5
C5—C10—H10A	109.6	C7—O6—H6	109.5
N2—C10—H10B	109.6	C5—O9—H9	109.5

O2—C1—C2—O1	−0.9 (3)	O2—C1—C4—C3	−178.53 (17)
C4—C1—C2—O1	−179.47 (19)	C2—C1—C4—C3	0.14 (11)
O2—C1—C2—C3	178.46 (18)	O4—C3—C4—O3	0.0 (3)
C4—C1—C2—C3	−0.14 (11)	C2—C3—C4—O3	179.65 (18)
O1—C2—C3—O4	−0.9 (3)	O4—C3—C4—C1	−179.79 (16)
C1—C2—C3—O4	179.79 (16)	C2—C3—C4—C1	−0.14 (11)
O1—C2—C3—C4	179.5 (2)	O10—C5—C10—N2	−9.3 (2)
C1—C2—C3—C4	0.14 (11)	O9—C5—C10—N2	170.58 (12)
O2—C1—C4—O3	1.7 (3)	O11—C7—C12—N1	−11.53 (19)
C2—C1—C4—O3	−179.66 (17)	O6—C7—C12—N1	169.34 (12)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O4	0.89	2.08	2.9148 (15)	156
N1—H1A···O11ⁱ	0.89	2.57	3.0297 (16)	113
N1—H1B···O3ⁱⁱ	0.89	2.11	2.8933 (15)	146
N1—H1C···O4ⁱⁱⁱ	0.89	1.98	2.7890 (15)	151
N2—H2A···O3ⁱⁱ	0.89	2.33	3.1075 (19)	146
N2—H2A···O11ⁱ	0.89	2.60	3.0591 (18)	113
N2—H2B···O3ⁱ	0.89	1.93	2.8064 (17)	167
N2—H2C···O1^iv	0.89	2.48	3.1602 (18)	134
N2—H2C···O6ⁱⁱ	0.89	2.13	2.8007 (16)	132
O6—H6···O2^v	0.82	1.64	2.4406 (16)	167
O9—H9···O1	0.82	1.75	2.5629 (15)	169

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

Footnotes

¹In the original publication by Tyagi et al. (2016), the compound was named `bis glycine' squarate.

References

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