research communications
DL-Piperidinium-2-carboxylate bis(hydrogen peroxide): unusual hydrogen-bonded peroxide chains
aInstitute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russian Federation
*Correspondence e-mail: churakov@igic.ras.ru
The title compound, C6H11NO2·2H2O2, is the richest (by molar ratio) in hydrogen peroxide among the peroxosolvates of aliphatic α-amino acids. The contains a zwitterionic pipecolinic acid molecule and two hydrogen peroxide molecules. The two crystallographically independent hydrogen peroxide molecules form a different number of hydrogen bonds: one forms two as donor and two as acceptor ([2,2] mode) and the other forms two as donor and one as acceptor ([2,1] mode). The latter hydrogen peroxide molecule forms infinite hydrogen-bonded hydroperoxo chains running along the c-axis direction, which is unusual for aliphatic α-amino acid peroxosolvates.
Keywords: peroxosolvates; aliphatic amino acids; charge assisted hydrogen bonds; peroxide H-bonded chains; carboxylate anions; crystal structure.
CCDC reference: 2016846
1. Chemical context
Peroxosolvates are crystalline adducts of hydrogen peroxide with various organic or inorganic compounds. Since they are convenient solid sources of active oxygen, some of them have become widely used commercial bleaching, disinfection and oxidation reagents (Jakob et al., 2012; Cronin et al., 2017). It is well known that their stability is strongly dependent on the hydrogen-bonded motifs formed by hydrogen peroxide (Chernyshov et al., 2017). On other hand, H2O2 is one of the most important signalling molecules in biological systems (Li et al., 2020; To et al., 2020). The structures of amino acid peroxosolvates have been studied intensively as simple models of hydrogen peroxide binding with proteins (Prikhodchenko et al., 2011; Kapustin et al., 2014). Peroxide and water–peroxide clusters are now of special interest since they may simulate cooperative hydrogen-bonded switching in the transportation of hydrogen peroxide species through cell membranes (Grishanov et al., 2017; Varadaraj & Kumari, 2020; Wang et al., 2020). Recently, several structures of organic peroxosolvates with peroxide hydrogen-bonded 1D-aggregates have been reported (Chernyshov et al., 2017; Navasardyan et al., 2017, 2018).
2. Structural commentary
The comprises a pipecolinic acid molecule and two crystallographically independent peroxide molecules (Fig. 1). As expected, the amino acid coformer exhibits the zwitterionic form with almost equal C—O distances [1.2429 (11) and 1.2639 (11) Å]. All bond lengths and angles in the organic coformer are close to those observed in the structures of pure pipecolinic acid [(II); Stapleton & Tiekink, 2001) and pipecolinic acid tetrahydrate [(III); Bhattacharjee & Chacko, 1979; Lyssenko et al., 2006]. As observed for (II) and (III), the pipecolinic acid molecule in (I) adopts a chair conformation with the carboxylate group occupying the equatorial position. It is of interest to note in all three structures (I), (II), and (III), the core amino acid fragments N—C—CO2 are almost planar, with N—C—C—O torsion angles of less than 22°. This is obviously caused by electrostatic interactions between the oppositely charged amino and carboxylic groups.
of the title compound (I)3. Supramolecular features
In the crystal, the organic molecule acts as a donor of two N+—H⋯OHOH, and as an acceptor of three COO−⋯HOOH hydrogen bonds (Table 1, Fig. 2). The O—O bond lengths [1.4600 (9) and 1.4646 (11) Å] are typical for amino acid peroxosolvates (mean value of 1.465 Å according to the latest, March 2020 version of the CSD; Groom et al., 2016). Both crystallographically independent peroxide molecules occupy general positions and adopt skew conformations with H—O—O—H torsion angles of 102.5 (15) and −105.1 (15)°. It is well known that peroxide molecules always form at least two donor hydrogen bonds in the structures of organic peroxosolvates (Chernyshov et al., 2017) and compound (I) is no exception. However, the symmetry-independent peroxide molecules in (I) form a different total number of hydrogen bonds: two donor HOOH⋯−O2C and two acceptor N+—H⋯OHOH for H3—O3—O4—H4 ([2,2] mode; Table 1, Fig. 3) and two donor HOOH⋯−O2C and HOOH⋯OHOH together with one acceptor for H5—O5—O6—H6 ([2,1] mode; Table 1, Fig. 4). The occurrence of interperoxide hydrogen-bonds results in the formation of simple infinite hydrogen-bonded `hydroperoxo'-linked chains (Grishanov et al., 2017), running along the c-axis direction (Fig. 5). It is significant that such chains and HOOH⋯OHOH hydrogen bonds were not observed previously in the structures of aliphatic α-amino acid peroxosolvates. The reason for this is that charge-assisted HOOH⋯−O2C bonds are energetically preferable to HOOH⋯OHOH interactions (Jesus & Redinha, 2011; Zick & Geiger, 2018). For example, in (I) the only interperoxide hydrogen-bond O5—H5⋯O6 is noticeably longer [2.778 (1) Å] than the three HOOH⋯−O2C bonds [2.641 (1)–2.749 (1) Å].
4. Database survey
Aliphatic α-amino acids contain side chains without heteroatoms suitable for hydrogen-bonding. Up to date, six structures of their peroxosolvates are known: monoperoxosolvates of N,N-dimethylglycine (C4H9NO2; Kapustin et al., 2014), N-methylglycine (sarcosine) (C3H7NO2; Navasardyan et al., 2017), isoleucine (C6H13NO2; Prikhodchenko et al., 2011); sesquiperoxosolvates of glycine (C2H5NO2), DL-2-aminobutyric acid (C4H9NO2) and L-phenylalanine (C9H11NO2; Prikhodchenko et al., 2011). In all of these structures, the organic molecules exist as and all peroxide hydrogen atoms are involved in charge-assisted hydrogen-bonds with the carboxylate groups. All peroxide molecules adopt skew conformations with H—O—O—H torsion angles varying between 88.6 and 166.3°.
The carboxylate anions possess four sp2-hybridized lone electron pairs suitable for hydrogen-bond formation (Fig. 6) (Mills & Dean, 1996). It is well known that syn and anti lone pairs exhibit noticeably different basicity (Gandour, 1981; Pal et al., 2018) and hydrogen-bonding properties as a result of electronic and steric effects (Gorbitz & Etter, 1992; Pranata, 1993). Nine hydrogen-bonded linkage modes are theoretically possible in the structures of amino acid peroxosolvates, taking into account that bifurcated HOOH⋯O bonds are not known (Fig. 7). The two simplest modes [0;S] and [0;A] have not been observed in peroxosolvates of α-amino acids, since the peroxide/acid molar ratio is greater than or equal to 1 in each reported structure. The [S;S] linkage was observed in sarcosine monoperoxosolvate. The [S;A] mode was found for the N,N-dimethylglycine and isoleucine monosolvates. Examples of neither the [0;SA] nor the [A;A] case are currently known. As for three hydrogen bonds, both [S;SA] and [SA;A] linkages were found in the sesquiperoxosolvate structures of glycine, DL-2-aminobutyric acid and L-phenylalanine. Following the same logic, we expected to find [SA;SA] in the structure of the title diperoxosolvate (I). However, the triple hydrogen-bonded case [S;SA] occurred, with the fourth donor hydrogen bond HOOH⋯O engaged in forming hydrogen-bonded peroxide chains. It has been shown that the ability of carboxylic anti-orbitals to form hydrogen bonds is strongly affected by caused by β-substituents in the side chains of carboxylic acids (Gorbitz & Etter, 1992). It is clear that in (I) the unfeasibility of the fourth carboxylic hydrogen bond is the result of steric effects caused by the peroxide molecules hydrogen bonded with the ammonium group (Fig. 2). It should be noted that the spatial arrangement of the endocyclic amino group in (I) is predefined by the aforementioned planarity of the N—C—CO2 amino acid fragment.
5. Synthesis and crystallization
96% Hydrogen peroxide was prepared by an extraction method from serine peroxosolvate (Wolanov et al., 2010). Colourless prismatic crystals of the title compound were obtained by cooling a (r.t.) of pipecolinic acid (Aldrich) in 96% hydrogen peroxide to 255 K. Handling procedures for concentrated hydrogen peroxide have been described in detail (danger of explosion!) by Schumb et al. (1955).
6. Refinement
Crystal data, data collection and structure . All hydrogen atoms were found in difference-Fourier maps and were refined with independent positional and isotropic displacement parameters.
details are summarized in Table 2
|
Supporting information
CCDC reference: 2016846
https://doi.org/10.1107/S205698902000972X/fy2147sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S205698902000972X/fy2147Isup2.hkl
Data collection: APEX2 (Bruker, 2008); cell
SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015); molecular graphics: XP in SHELXTL (Sheldrick, 2008).C6H11NO2·2H2O2 | F(000) = 424 |
Mr = 197.19 | Dx = 1.436 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
a = 6.5739 (4) Å | Cell parameters from 5232 reflections |
b = 22.9278 (15) Å | θ = 3.1–30.6° |
c = 6.0647 (4) Å | µ = 0.13 mm−1 |
β = 93.770 (1)° | T = 150 K |
V = 912.12 (10) Å3 | Nugget, colourless |
Z = 4 | 0.50 × 0.50 × 0.50 mm |
Bruker SMART APEXII diffractometer | 2170 reflections with I > 2σ(I) |
ω scans | Rint = 0.018 |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | θmax = 29.0°, θmin = 3.1° |
Tmin = 0.659, Tmax = 0.746 | h = −8→8 |
9809 measured reflections | k = −30→31 |
2418 independent reflections | l = −8→8 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.031 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.084 | All H-atom parameters refined |
S = 1.08 | w = 1/[σ2(Fo2) + (0.0419P)2 + 0.218P] where P = (Fo2 + 2Fc2)/3 |
2418 reflections | (Δ/σ)max = 0.001 |
178 parameters | Δρmax = 0.44 e Å−3 |
0 restraints | Δρmin = −0.19 e Å−3 |
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. |
x | y | z | Uiso*/Ueq | ||
N1 | −0.02450 (12) | 0.57964 (3) | 0.57611 (13) | 0.01528 (16) | |
H1 | −0.093 (2) | 0.5604 (6) | 0.463 (2) | 0.029 (3)* | |
H2 | 0.039 (2) | 0.5538 (6) | 0.661 (2) | 0.025 (3)* | |
O1 | 0.40875 (11) | 0.60608 (3) | 0.25095 (12) | 0.02266 (17) | |
O2 | 0.21298 (11) | 0.52860 (3) | 0.30218 (11) | 0.02005 (16) | |
C1 | −0.17311 (14) | 0.61336 (4) | 0.70359 (15) | 0.01777 (18) | |
H11 | −0.2642 (19) | 0.5851 (6) | 0.759 (2) | 0.021 (3)* | |
H12 | −0.2449 (19) | 0.6384 (6) | 0.597 (2) | 0.024 (3)* | |
C2 | −0.05768 (15) | 0.64708 (4) | 0.88702 (15) | 0.01993 (19) | |
H21 | −0.157 (2) | 0.6679 (6) | 0.968 (2) | 0.029 (3)* | |
H22 | 0.010 (2) | 0.6192 (6) | 0.988 (2) | 0.029 (3)* | |
C3 | 0.10082 (16) | 0.68727 (4) | 0.79508 (17) | 0.0218 (2) | |
H32 | 0.033 (2) | 0.7172 (6) | 0.703 (2) | 0.027 (3)* | |
H31 | 0.179 (2) | 0.7082 (6) | 0.916 (2) | 0.030 (3)* | |
C4 | 0.24769 (14) | 0.65223 (4) | 0.66075 (16) | 0.01923 (19) | |
H41 | 0.343 (2) | 0.6784 (6) | 0.590 (2) | 0.027 (3)* | |
H42 | 0.326 (2) | 0.6256 (6) | 0.759 (2) | 0.027 (3)* | |
C5 | 0.13006 (13) | 0.61800 (4) | 0.47837 (14) | 0.01483 (17) | |
H52 | 0.0520 (18) | 0.6451 (5) | 0.377 (2) | 0.019 (3)* | |
C6 | 0.26188 (13) | 0.58042 (4) | 0.33422 (14) | 0.01570 (18) | |
O3 | 0.74598 (11) | 0.54761 (3) | 0.18291 (11) | 0.01986 (16) | |
O4 | 0.72361 (11) | 0.48529 (3) | 0.13828 (12) | 0.02162 (16) | |
H4 | 0.737 (2) | 0.4839 (7) | −0.003 (3) | 0.040 (4)* | |
H3 | 0.620 (3) | 0.5583 (7) | 0.194 (3) | 0.040 (4)* | |
O5 | 0.67290 (12) | 0.72538 (4) | 0.33260 (14) | 0.02787 (18) | |
O6 | 0.49801 (12) | 0.71623 (3) | 0.17405 (13) | 0.02507 (17) | |
H5 | 0.613 (2) | 0.7454 (7) | 0.434 (3) | 0.041 (4)* | |
H6 | 0.472 (2) | 0.6792 (7) | 0.199 (2) | 0.034 (4)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0163 (3) | 0.0143 (4) | 0.0153 (3) | −0.0005 (3) | 0.0025 (3) | −0.0015 (3) |
O1 | 0.0229 (4) | 0.0170 (3) | 0.0293 (4) | −0.0015 (3) | 0.0110 (3) | −0.0023 (3) |
O2 | 0.0237 (3) | 0.0149 (3) | 0.0221 (3) | −0.0016 (2) | 0.0060 (3) | −0.0044 (2) |
C1 | 0.0169 (4) | 0.0183 (4) | 0.0185 (4) | 0.0023 (3) | 0.0044 (3) | −0.0002 (3) |
C2 | 0.0237 (5) | 0.0202 (4) | 0.0163 (4) | 0.0037 (4) | 0.0042 (3) | −0.0023 (3) |
C3 | 0.0251 (5) | 0.0179 (4) | 0.0225 (5) | −0.0009 (4) | 0.0036 (4) | −0.0074 (4) |
C4 | 0.0186 (4) | 0.0182 (4) | 0.0211 (4) | −0.0024 (3) | 0.0023 (3) | −0.0057 (3) |
C5 | 0.0165 (4) | 0.0132 (4) | 0.0150 (4) | −0.0002 (3) | 0.0028 (3) | −0.0004 (3) |
C6 | 0.0170 (4) | 0.0162 (4) | 0.0140 (4) | 0.0019 (3) | 0.0018 (3) | −0.0012 (3) |
O3 | 0.0193 (3) | 0.0172 (3) | 0.0229 (3) | 0.0006 (3) | 0.0008 (3) | −0.0044 (2) |
O4 | 0.0301 (4) | 0.0158 (3) | 0.0187 (3) | 0.0029 (3) | 0.0003 (3) | −0.0012 (2) |
O5 | 0.0261 (4) | 0.0308 (4) | 0.0265 (4) | −0.0044 (3) | 0.0001 (3) | −0.0053 (3) |
O6 | 0.0308 (4) | 0.0200 (4) | 0.0237 (4) | −0.0027 (3) | −0.0029 (3) | 0.0024 (3) |
N1—C5 | 1.4955 (11) | C3—H32 | 0.974 (14) |
N1—C1 | 1.4996 (11) | C3—H31 | 0.991 (14) |
N1—H1 | 0.912 (15) | C4—C5 | 1.5247 (12) |
N1—H2 | 0.875 (15) | C4—H41 | 0.986 (14) |
O1—C6 | 1.2639 (11) | C4—H42 | 0.975 (14) |
O2—C6 | 1.2429 (11) | C5—C6 | 1.5353 (12) |
C1—C2 | 1.5166 (13) | C5—H52 | 0.991 (12) |
C1—H11 | 0.958 (13) | O3—O4 | 1.4600 (9) |
C1—H12 | 0.966 (13) | O3—H3 | 0.872 (17) |
C2—C3 | 1.5239 (14) | O4—H4 | 0.866 (18) |
C2—H21 | 0.968 (14) | O5—O6 | 1.4646 (11) |
C2—H22 | 0.972 (14) | O5—H5 | 0.883 (17) |
C3—C4 | 1.5313 (13) | O6—H6 | 0.881 (16) |
C5—N1—C1 | 112.57 (7) | C4—C3—H31 | 109.3 (8) |
C5—N1—H1 | 107.6 (9) | H32—C3—H31 | 106.3 (11) |
C1—N1—H1 | 109.2 (9) | C5—C4—C3 | 110.40 (8) |
C5—N1—H2 | 108.7 (9) | C5—C4—H41 | 107.7 (8) |
C1—N1—H2 | 110.4 (9) | C3—C4—H41 | 110.7 (8) |
H1—N1—H2 | 108.2 (12) | C5—C4—H42 | 110.0 (8) |
N1—C1—C2 | 109.24 (7) | C3—C4—H42 | 109.4 (8) |
N1—C1—H11 | 106.0 (8) | H41—C4—H42 | 108.6 (11) |
C2—C1—H11 | 112.4 (8) | N1—C5—C4 | 109.91 (7) |
N1—C1—H12 | 105.4 (8) | N1—C5—C6 | 108.62 (7) |
C2—C1—H12 | 112.9 (8) | C4—C5—C6 | 115.06 (7) |
H11—C1—H12 | 110.4 (11) | N1—C5—H52 | 106.0 (7) |
C1—C2—C3 | 111.17 (8) | C4—C5—H52 | 110.1 (7) |
C1—C2—H21 | 107.6 (8) | C6—C5—H52 | 106.7 (7) |
C3—C2—H21 | 112.8 (8) | O2—C6—O1 | 125.38 (8) |
C1—C2—H22 | 108.3 (8) | O2—C6—C5 | 118.40 (8) |
C3—C2—H22 | 109.6 (8) | O1—C6—C5 | 116.16 (8) |
H21—C2—H22 | 107.3 (11) | O4—O3—H3 | 101.8 (11) |
C2—C3—C4 | 110.34 (8) | O3—O4—H4 | 101.7 (10) |
C2—C3—H32 | 109.7 (8) | O6—O5—H5 | 99.6 (11) |
C4—C3—H32 | 110.2 (8) | O5—O6—H6 | 100.4 (10) |
C2—C3—H31 | 111.0 (8) | ||
C5—N1—C1—C2 | −58.48 (10) | C3—C4—C5—C6 | −179.22 (8) |
N1—C1—C2—C3 | 56.95 (10) | N1—C5—C6—O2 | 6.85 (11) |
C1—C2—C3—C4 | −56.65 (11) | C4—C5—C6—O2 | 130.51 (9) |
C2—C3—C4—C5 | 55.85 (11) | N1—C5—C6—O1 | −175.64 (8) |
C1—N1—C5—C4 | 58.51 (10) | C4—C5—C6—O1 | −51.98 (11) |
C1—N1—C5—C6 | −174.80 (7) | H3—O3—O4—H4 | 102.5 (15) |
C3—C4—C5—N1 | −56.25 (10) | H5—O5—O6—H6 | −105.1 (15) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3···O1 | 0.872 (17) | 1.819 (17) | 2.6463 (10) | 157.8 (15) |
O4—H4···O2i | 0.866 (18) | 1.889 (18) | 2.7490 (10) | 172.2 (15) |
O6—H6···O1 | 0.881 (16) | 1.760 (16) | 2.6412 (10) | 177.4 (14) |
O5—H5···O6ii | 0.883 (17) | 1.898 (18) | 2.7777 (12) | 174.4 (15) |
N1—H1···O3iii | 0.912 (15) | 1.961 (15) | 2.8336 (11) | 159.6 (13) |
N1—H2···O4iv | 0.875 (15) | 2.112 (15) | 2.9459 (11) | 159.1 (12) |
Symmetry codes: (i) −x+1, −y+1, −z; (ii) x, −y+3/2, z+1/2; (iii) x−1, y, z; (iv) −x+1, −y+1, −z+1. |
Acknowledgements
X-ray diffraction studies were performed at the Centre of Shared Equipment of IGIC RAS.
Funding information
Funding for this research was provided by: Russian Foundation for Basic Research (award No. 20-03-00449).
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