Home Crystal structure of di-glycylglycinium squarate dihydrate, C12H22N4O12, at 105 K
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Crystal structure of di-glycylglycinium squarate dihydrate, C12H22N4O12, at 105 K

  • Etelvina de Matos Gomes , Rosa M.F. Baptista and Carl Henrik Görbitz ORCID logo EMAIL logo
Published/Copyright: November 27, 2024

Abstract

C12H22N4O12, triclinic, P 1 (no. 2), a = 6.7126(4) Å, b = 7.7536(5) Å, c = 8.5279(5) Å, α = 89.4803(14)°, β = 86.2595(14)°, γ = 79.4035(14)°, V = 435.35(5) Å3, Z = 2, R gt (F) = 0.0323, wR ref (F 2) = 0.0908, T = 105(2) K.

CCDC no.: 2391129

Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colourless block
Size: 0.50 × 0.37 × 0.25 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.14 mm−1
Diffractometer, scan mode: Bruker D8 Advance, 0.5° ω scans
θ max, completeness: 38.6°, 99 %
N(hkl)measured, N(hkl)unique, R int: 30,177, 4,931, 0.026
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 4,428
N(param)refined: 137
Programs: Bruker 1 , SHELX 2 , 4 , Mercury 3
Table 2:

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

Atom x y z U iso*/U eq
O1A 0.69907 (7) 0.85381 (5) 0.39941 (5) 0.01125 (7)
O2A 0.51197 (7) 0.64261 (6) 0.15892 (5) 0.01292 (8)
H5A 0.4279 (19) 0.6904 (16) 0.0841 (14) 0.019*
O3A 0.73968 (7) 0.69650 (7) −0.03058 (5) 0.01443 (8)
N1A 0.55260 (7) 0.84048 (6) 0.69811 (5) 0.00983 (8)
H1A 0.484619 0.819361 0.790034 0.015*
H2A 0.464275 0.903542 0.633218 0.015*
H3A 0.651114 0.902291 0.717911 0.015*
N2A 0.79888 (7) 0.56010 (6) 0.37172 (5) 0.00914 (7)
H4A 0.812079 0.456353 0.416655 0.011*
C1A 0.64619 (9) 0.67246 (7) 0.62226 (6) 0.01024 (8)
H11A 0.546072 0.593209 0.623768 0.012*
H12A 0.763036 0.615284 0.680798 0.012*
C2A 0.71728 (8) 0.70464 (6) 0.45413 (6) 0.00779 (8)
C3A 0.86521 (8) 0.57538 (7) 0.20843 (6) 0.00978 (8)
H31A 0.934470 0.458231 0.169757 0.012*
H32A 0.966443 0.653716 0.201202 0.012*
C4A 0.69795 (8) 0.64535 (7) 0.10085 (6) 0.00902 (8)
O1B 0.09505 (6) 1.01529 (6) 0.25256 (5) 0.01028 (7)
O2B 0.26898 (6) 0.77560 (6) −0.05380 (5) 0.01128 (7)
C2B 0.12142 (8) 0.89921 (7) −0.02392 (6) 0.00799 (8)
C1B 0.04255 (8) 1.00681 (7) 0.11446 (6) 0.00768 (8)
O1W 0.81913 (7) 0.21149 (6) 0.47676 (5) 0.01323 (8)
H1W 0.8997 (19) 0.1431 (16) 0.4106 (14) 0.020*
H2W 0.8297 (19) 0.1579 (16) 0.5672 (14) 0.020*

1 Source of materials

Glycylglycine (Gly–Gly) and 3,4-dihydroxy-3-cyclobutene-1,2-dione (squaric acid) were purchased from Alfa Aesar chemicals and used without further purification. Crystals of the title salt were prepared by completely dissolving separately, in hot water, 1.0 g of squaric acid and 2.3 g of Gly–Gly, in a 1:2 molecular ratio. After complete dissolution the parts were mixed together. The solution was left to crystallize at room temperature by slow evaporation over a period of several weeks.

2 Experimental details

Singel crystal data collection, cell refinement, data reduction and structure solution was executed with APEX2 1 and structure refinement with SHELXT. 2 The illustration was prepared by Mercury 3 while material for publication was prepared by SHELXL. 4 Coordinates were refined for hydroxyl and water H atoms, other H atoms were positioned with idealized geometry and treated as riding atoms, allowing free rotation for the amino group.

3 Comment

Squaric acid is a planar hydrogen-bonded molecular compound belonging to the class of antiferroelectric crystals at room temperature. 5 , 6 , 7 , 8 It has the ability to crystallize either as a squarate dianion ( C 4 O 4 2 ) or a hydrogen squarate anion ( H C 4 O 4 ) and is of great interest in crystal engineering studies. 9 Non-centrosymmetric crystal structures with chiral amino acid cations have been synthesized and are attractive for non-linear optical and electro-optic applications. 10 , 11 There are no previous crystal structure determinations of dipeptide squarate salts; to the best of our knowledge, only molecular spectroscopic studies of glycylalanine and alanylalanine hydrogen squarate have been reported. 12 This work represents the first effort to study complexes between a dipeptide and squaric acid. In the future, we intend to engineer more salts with acentric structures that could display interesting properties, such as ferroelectricity, similar to diglycine nitrate. 13

The illustration shows the asymmetric unit (with black bonds), a neighbouring glycylglicinium anion (in pale colours) at 1 – x, 2 – y, 1 – z generated by inversion symmetry, and the second half of the squarate dianion (in pale colours) at –x, 2 – y, –z also generated by inversion. Hydrogen bond acceptor atoms appear in pale colours with symmetry operations indicated, while atom labels for donated H atoms appear in grey without symmetry codes. The pertinent centres-of symmetry at (0.5 1 0.5) and (0 1 0), respectively, have been highlighted as green spheres. The grey shade shows the 10-membered ring system associated with formation of the glycylglycinium dimer, involving two amino⋯carbonyl interactions. Formation of similar dimers has been observed for a handful of zwitterionic dipeptides, but is more common when the C-terminal does not carry a negative charge, in which case it is a less attractive acceptor for the amino H atoms. By comparison, out of the 18 distinct structures in the Cambridge Structural Database (CSD) 14 containing the glycylglycine cation, five have similar dimers, but only in the 2,6-naphtalenedisulfonate dihydrate 15 are the two partners related by a centre-of-inversion like here.

Squarate dianions occur in 84 unique metal-free entries in the CSD, 13 in Sohncke space groups, 3 in non-centrosymmetric non-Sohncke space groups and 68 in centrosymmetric space groups. In the latter, the squarate is, like here, located on a centre-of-inversion in 73.5 % of the structures. If only contacts with H⋯O distances shorter than 2.4 Å are included, the number of hydrogen atoms accepted by squarate in the present structure, 10, is also the maximum number encountered in the CSD. Illustrations of the hydrogen bonding pattern are provided as Supplementary Material.

To check for phase transitions, diffraction data were also collected at room temperature, 294 K (CCDC 2391122). The best possible overlay of the refined structures at 105 and 294 K gives a root-mean-square deviation of just 0.028 Å, indicating no major changes with shifting temperature.


Corresponding author: Carl Henrik Görbitz, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, N-0315 Oslo, Norway, E-mail:

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: National funds (OE) through Fundação para a Ciência e a Tecnologia (framework contract under the Decree-Law 57/2016, Law 57/2017) and FEDER (European Fund for Regional Development)-COMPETE-QREN-EU (ref. UID/FIS/04650/2013 and UID/FIS/04650/2019).

  3. Conflict of interest: The authors declare no conflicts of interest regarding this article.

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Supplementary Material

This article contains supplementary material (https://doi.org/10.1515/ncrs-2024-0416).


Received: 2024-10-21
Accepted: 2024-11-14
Published Online: 2024-11-27
Published in Print: 2025-02-25

© 2024 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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