research communications
and halogen–hydrogen bonding of a Delépine reaction intermediate
aSchool of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
*Correspondence e-mail: tony.keene@ucd.ie
The reaction of 1,5-dibromopentane with urotropine results in crystals of the title molecular salt, 5-bromourotropinium bromide [systematic name: 1-(5-bromopentyl)-3,5,7-triaza-1-azoniatricyclo[3.3.1.13,7]decane bromide], C11H22BrN4+·Br− (1), crystallizing in P21/n. The packing in compound 1 is directed mainly by H⋯H van der Waals interactions and C—H⋯Br hydrogen bonds, as revealed by Hirshfeld surface analysis. Comparison with literature examples of alkylurotropinium halides shows that the interactions in 1 are consistent with those in other bromides and simple chloride and iodide species.
Keywords: crystal structure; Hirshfeld surface; Delépine reaction; urotropinium.
CCDC reference: 2046576
1. Chemical context
Urotropine, C6H12N4 (also known as hexamethylenetetramine, hmta) and its salts are widely used in chemical organic synthesis (Blažević et al., 1979), as precursors for explosives (Fried et al., 2001) and as pharmaceuticals (Lo et al., 2014).
The Delépine reaction is a classic synthetic route to produce primary , 1897). Alkyl or aryl halides are reacted with hmta to form a quaternary ammonium salt, followed by acid hydrolysis to give a primary amine. A major advantage of this reaction over other routes is that the formation of the quaternary urotropinium cation prevents further alkylation and high yields are possible (Galat & Elion, 1939). We recently made an attempt to find a cost-effective route to synthesize 1,5-diaminopentane (cadaverine) from 1,5-dibromopentane. On an industrial scale, this is produced by bacterial decarboxylation of lysine (Ma et al. 2017; Wang et al., 2018). Attempts to react 1,5-dibromopentane with hmta in the presence of NaI in ethanol (modified from Galat & Elion, 1939) led to the crystallization of a monosubstituted product, 5-bromourotropinium bromide, C11H22BrN4+·Br− (1), the structure and supramolecular features of which are presented here.
(Delépine, 18952. Structural commentary
Compound 1 crystallizes in the centrosymmetric monoclinic P21/n. The of 1 (Fig. 1) contains one C11H22BrN4+ N-(5-bromopentyl)urotropinium cation and one bromide anion. The pentyl chain is in the all-trans configuration, unlike its hexyl relative (Reddy et al., 1994), which displays an anticlinal configuration between C4 and C6 of the hexyl chain (torsion angle = 133°).
3. Supramolecular features
The three-dimensional structure of 1 features C—H⋯Br− and C—H⋯Br—C interactions (Table 1). Hirshfeld surface analysis of the urotropinium cation (see below for further details) reveals that the bromide anion, Br17, accepts C—H⋯Br hydrogen bonds from H12A and H13B [H⋯Br = 2.91 and 2.77 Å, respectively] within the and forms bonds to H6B( + x, − y, − + z, 2.92 Å), H8B ( − x, − + y, − z, 2.82 Å) and H15A(− + x, − y, − + z, 2.86 Å). C—H⋯Br—C bonds are also seen from H5B to Br1(1 − x, 1 − y, −z) at the end of the pentyl chain, linking neighbouring cations into an inversion dimer with an H⋯Br distance of 3.00 Å (Fig. 2).
The overall packing (Fig. 3) is similar to the hexyl compound.
4. Hirshfeld surface analysis and two-dimensional fingerprint plots
The Hirshfeld surface analysis (Spackman & Jayatilaka, 2009) and two-dimensional fingerprint plots (McKinnon et al., 2007) were calculated using Crystal Explorer 17 (Turner et al., 2017). The surface was calculated for the 5-bromopentylurotropinium cation (Fig. 4) in order to differentiate the contribution of the alkylbromine and bromide components to the overall bonding picture. In the dnorm plot (Fig. 5a), white surface areas represent contacts at the sum of van der Waals radii, red is shorter (close contact) and blue is longer (long contact).
The Hirshfeld surface primarily consists of H⋯H van der Waals interactions (59.6%, Fig. 5b) with the next major contributor being H⋯Br (31.0%, Fig. 5c) with a small N⋯H component (9.4%, Fig. 5d). The interaction of H and the alkylbromine residue accounts for 12.6% of the surface (bottom right of Fig. 5c), leaving the remaining 18.4% as H⋯Br− hydrogen bonds to the bromide ions (top left of Fig. 5c), as detailed above.
5. Database survey
Surprisingly few discrete alkylurotropinium salts have been submitted to the Cambridge Structural Database (version 5.41, May 2020 update 2, Groom et al., 2016), given that the salts are reported to crystallize in most cases. There are 48 in total, 17 of which are halide or polyiodide salts. In the remainder, the alkylurotropinium exists as a counter-ion to complex anions or is a bridging species in a coordination polymer. Of the 17, only six are bromide salts (refcode BUXZEZ, Qingchuan et al. 1983; CAQVUO, Aniol et al., 2017; CEXLOG, Mak, 1984; GINHAN, Betz & Klüfers, 2007; YOYWEO and YOYWIS, Reddy et al., 1994).
A close relative to compound 1 is 6-bromohexylurotropinium bromide, C12H24BrN4+·Br− (YOYWIS; Reddy et al., 1994), which is isostructural, also crystallizing in P21/n. As mentioned above, this displays an anticlinal torsion angle in the alkyl chain, but presents very similar H⋯Br− interactions and overall packing. For the purposes of comparison, the in the CSD was completed in OLEX2 to add in the hydrogen atoms present in the original publication, and Hirshfeld surface analysis also undertaken. A potential difficulty in this structure is the presence of a possible disorder in the hexyl chain (atom C10 has a markedly larger Ueq value than its neighbours, plus hydrogen atoms on C10 come into closer than van der Waals contact with hydrogen atoms on neighbouring C10 atoms in the crystal). However, the interactions between hydrogen and bromide account for a similar percentage of the overall Hirshfeld surface (16.6% in YOYWIS versus 18.4% in compound 1).
Direct comparisons with BUXZEZ (Yang et al., 1983) are difficult because of the disorder around the allyl group while the remaining compounds have other significant intermolecular interactions such as hydrogen bonds formed to bromide by a water molecule (CEXLOG, GINHAN) or from a carboxylic acid (YOYWEO). Similar interactions to compound 1 can be seen where chloride is the halide anion: BIDBIZ (Shao et al., 1982) shows hydrogen bonds from the benzylurotropinium cation to the chloride anion, accounting for 12.2% of the interaction surface. Polyiodide compounds appear not to show C—H⋯I interactions in the same manner as the above bromide and chloride compounds, but a methylurotropinium monoiodide compound (VOBCIY; Ribár et al., 1991) displays similar interactions to 1 with H⋯I hydrogen bonds forming 15.5% of the Hirshfeld surface.
6. Synthesis and crystallization
Uroptropine (11.0 mmol, 1.542 g) and NaI (90.95 mmol, 1.648 g) were dissolved in ethanol and 1,5-dibromopentane (5.00 mmol, 0.595 ml) was added. Clear block-like crystals appeared after 8 days, which were found to be a mixture of compound 1 and [Na(H2O)4(hmta)]2Br2·2H2O (Kruszynski et al., 2012), which precluded further analysis, given the instability of hmta adducts to recrystallization.
7. Refinement
Crystal data, data collection and structure . The H atoms were positioned geometrically (C—H = 0.99 Å) and refined as riding atoms with Uiso(H) = 1.2Ueq(C).
details are summarized in Table 2
|
Supporting information
CCDC reference: 2046576
https://doi.org/10.1107/S2056989020015601/hb7951sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989020015601/hb7951Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989020015601/hb7951Isup3.cml
Data collection: CrysAlis PRO (Rigaku OD, 2015); cell
CrysAlis PRO (Rigaku OD, 2015); data reduction: CrysAlis PRO (Rigaku OD, 2015); program(s) used to solve structure: ShelXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Berndt, 1999); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).C11H22BrN4+·Br− | F(000) = 744 |
Mr = 370.14 | Dx = 1.724 Mg m−3 |
Monoclinic, P21/n | Cu Kα radiation, λ = 1.54184 Å |
a = 8.7897 (2) Å | Cell parameters from 10133 reflections |
b = 14.8937 (3) Å | θ = 5.0–76.7° |
c = 11.1294 (2) Å | µ = 7.09 mm−1 |
β = 101.742 (2)° | T = 100 K |
V = 1426.47 (5) Å3 | Block, colourless |
Z = 4 | 0.08 × 0.06 × 0.05 mm |
Rigaku Oxford Diffraction SuperNova, Dual, Cu at zero, Atlas diffractometer | 2652 reflections with I > 2σ(I) |
Detector resolution: 10.3196 pixels mm-1 | Rint = 0.040 |
ω scans | θmax = 76.9°, θmin = 5.0° |
Absorption correction: gaussian (CrysAlisPro; Rigaku OD, 2015) | h = −9→11 |
Tmin = 0.698, Tmax = 0.788 | k = −18→17 |
22370 measured reflections | l = −13→14 |
2992 independent reflections |
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.025 | H-atom parameters constrained |
wR(F2) = 0.063 | w = 1/[σ2(Fo2) + (0.0253P)2 + 1.7861P] where P = (Fo2 + 2Fc2)/3 |
S = 1.04 | (Δ/σ)max = 0.001 |
2992 reflections | Δρmax = 0.53 e Å−3 |
154 parameters | Δρmin = −0.64 e Å−3 |
0 restraints |
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 | ||
Br17 | 0.26207 (3) | 0.11960 (2) | 0.16658 (2) | 0.02528 (8) | |
Br1 | 0.83401 (3) | 0.60049 (2) | 0.02566 (3) | 0.03427 (9) | |
N14 | 0.0484 (2) | 0.32690 (14) | 0.35699 (18) | 0.0220 (4) | |
N9 | 0.1817 (2) | 0.39262 (14) | 0.55095 (18) | 0.0209 (4) | |
N7 | 0.3320 (2) | 0.32645 (13) | 0.41148 (17) | 0.0185 (4) | |
N11 | 0.1807 (2) | 0.23044 (14) | 0.52273 (19) | 0.0233 (4) | |
C13 | 0.1875 (3) | 0.33503 (16) | 0.3076 (2) | 0.0204 (4) | |
H13A | 0.188486 | 0.393964 | 0.266600 | 0.024* | |
H13B | 0.189079 | 0.287431 | 0.245757 | 0.024* | |
C8 | 0.3233 (3) | 0.40058 (15) | 0.5049 (2) | 0.0200 (4) | |
H8A | 0.413960 | 0.396114 | 0.573916 | 0.024* | |
H8B | 0.326628 | 0.459996 | 0.465655 | 0.024* | |
C12 | 0.3222 (3) | 0.23654 (16) | 0.4761 (2) | 0.0222 (5) | |
H12A | 0.325576 | 0.186875 | 0.417548 | 0.027* | |
H12B | 0.412836 | 0.230205 | 0.544750 | 0.027* | |
C4 | 0.6585 (3) | 0.42073 (17) | 0.2631 (2) | 0.0228 (5) | |
H4A | 0.723264 | 0.440004 | 0.342377 | 0.027* | |
H4B | 0.700757 | 0.363271 | 0.239322 | 0.027* | |
C3 | 0.6661 (3) | 0.49142 (17) | 0.1656 (2) | 0.0250 (5) | |
H3A | 0.601900 | 0.471674 | 0.086368 | 0.030* | |
H3B | 0.622209 | 0.548478 | 0.189060 | 0.030* | |
C6 | 0.4807 (3) | 0.32939 (16) | 0.3650 (2) | 0.0216 (5) | |
H6A | 0.491918 | 0.272273 | 0.322120 | 0.026* | |
H6B | 0.568745 | 0.333678 | 0.436101 | 0.026* | |
C2 | 0.8312 (3) | 0.50736 (18) | 0.1499 (2) | 0.0267 (5) | |
H2A | 0.874916 | 0.450893 | 0.124359 | 0.032* | |
H2B | 0.896396 | 0.526437 | 0.229127 | 0.032* | |
C16 | 0.0478 (3) | 0.23966 (17) | 0.4192 (2) | 0.0261 (5) | |
H16A | −0.049980 | 0.233470 | 0.449665 | 0.031* | |
H16B | 0.051124 | 0.190783 | 0.359514 | 0.031* | |
C5 | 0.4915 (3) | 0.40688 (17) | 0.2780 (2) | 0.0241 (5) | |
H5A | 0.453165 | 0.462523 | 0.310466 | 0.029* | |
H5B | 0.424587 | 0.394188 | 0.196898 | 0.029* | |
C15 | 0.0467 (3) | 0.39888 (16) | 0.4473 (2) | 0.0228 (5) | |
H15A | −0.050356 | 0.394968 | 0.479113 | 0.027* | |
H15B | 0.048158 | 0.457856 | 0.406527 | 0.027* | |
C10 | 0.1763 (3) | 0.30439 (16) | 0.6095 (2) | 0.0237 (5) | |
H10A | 0.265689 | 0.298837 | 0.679369 | 0.028* | |
H10B | 0.079868 | 0.299928 | 0.642209 | 0.028* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Br17 | 0.02347 (13) | 0.02523 (14) | 0.02747 (13) | −0.00279 (9) | 0.00593 (9) | −0.00790 (9) |
Br1 | 0.02808 (14) | 0.04267 (18) | 0.03123 (15) | −0.00985 (11) | 0.00409 (11) | 0.00965 (11) |
N14 | 0.0176 (9) | 0.0237 (11) | 0.0244 (10) | −0.0014 (7) | 0.0038 (7) | 0.0001 (8) |
N9 | 0.0214 (9) | 0.0215 (10) | 0.0205 (9) | 0.0016 (7) | 0.0060 (7) | −0.0001 (7) |
N7 | 0.0169 (9) | 0.0173 (9) | 0.0213 (9) | 0.0007 (7) | 0.0039 (7) | −0.0005 (7) |
N11 | 0.0257 (10) | 0.0193 (10) | 0.0264 (10) | −0.0008 (8) | 0.0092 (8) | 0.0013 (8) |
C13 | 0.0169 (10) | 0.0237 (12) | 0.0197 (10) | −0.0002 (8) | 0.0018 (8) | −0.0002 (9) |
C8 | 0.0212 (11) | 0.0167 (11) | 0.0220 (10) | −0.0005 (8) | 0.0045 (8) | −0.0026 (8) |
C12 | 0.0233 (11) | 0.0167 (11) | 0.0269 (12) | 0.0019 (8) | 0.0062 (9) | 0.0013 (9) |
C4 | 0.0191 (11) | 0.0231 (12) | 0.0268 (11) | 0.0003 (9) | 0.0063 (9) | −0.0024 (9) |
C3 | 0.0218 (11) | 0.0274 (13) | 0.0264 (12) | −0.0019 (9) | 0.0060 (9) | 0.0011 (10) |
C6 | 0.0178 (10) | 0.0233 (12) | 0.0248 (11) | 0.0010 (8) | 0.0069 (8) | −0.0023 (9) |
C2 | 0.0248 (12) | 0.0293 (13) | 0.0264 (12) | −0.0019 (10) | 0.0063 (9) | 0.0037 (10) |
C16 | 0.0233 (12) | 0.0246 (13) | 0.0308 (13) | −0.0067 (9) | 0.0062 (10) | −0.0015 (10) |
C5 | 0.0185 (11) | 0.0273 (13) | 0.0266 (12) | −0.0009 (9) | 0.0050 (9) | 0.0019 (9) |
C15 | 0.0199 (11) | 0.0239 (12) | 0.0250 (11) | 0.0049 (9) | 0.0054 (9) | 0.0012 (9) |
C10 | 0.0269 (12) | 0.0224 (12) | 0.0230 (11) | 0.0012 (9) | 0.0077 (9) | 0.0021 (9) |
Br1—C2 | 1.962 (3) | C4—H4A | 0.9900 |
N14—C13 | 1.444 (3) | C4—H4B | 0.9900 |
N14—C16 | 1.473 (3) | C4—C3 | 1.523 (3) |
N14—C15 | 1.472 (3) | C4—C5 | 1.525 (3) |
N9—C8 | 1.444 (3) | C3—H3A | 0.9900 |
N9—C15 | 1.480 (3) | C3—H3B | 0.9900 |
N9—C10 | 1.472 (3) | C3—C2 | 1.515 (3) |
N7—C13 | 1.539 (3) | C6—H6A | 0.9900 |
N7—C8 | 1.529 (3) | C6—H6B | 0.9900 |
N7—C12 | 1.530 (3) | C6—C5 | 1.522 (3) |
N7—C6 | 1.501 (3) | C2—H2A | 0.9900 |
N11—C12 | 1.445 (3) | C2—H2B | 0.9900 |
N11—C16 | 1.471 (3) | C16—H16A | 0.9900 |
N11—C10 | 1.471 (3) | C16—H16B | 0.9900 |
C13—H13A | 0.9900 | C5—H5A | 0.9900 |
C13—H13B | 0.9900 | C5—H5B | 0.9900 |
C8—H8A | 0.9900 | C15—H15A | 0.9900 |
C8—H8B | 0.9900 | C15—H15B | 0.9900 |
C12—H12A | 0.9900 | C10—H10A | 0.9900 |
C12—H12B | 0.9900 | C10—H10B | 0.9900 |
C13—N14—C16 | 109.72 (19) | H3A—C3—H3B | 107.9 |
C13—N14—C15 | 109.01 (18) | C2—C3—C4 | 111.8 (2) |
C15—N14—C16 | 108.66 (19) | C2—C3—H3A | 109.2 |
C8—N9—C15 | 109.30 (18) | C2—C3—H3B | 109.2 |
C8—N9—C10 | 109.79 (18) | N7—C6—H6A | 108.7 |
C10—N9—C15 | 107.96 (19) | N7—C6—H6B | 108.7 |
C8—N7—C13 | 107.64 (17) | N7—C6—C5 | 114.37 (19) |
C8—N7—C12 | 107.27 (17) | H6A—C6—H6B | 107.6 |
C12—N7—C13 | 107.99 (17) | C5—C6—H6A | 108.7 |
C6—N7—C13 | 112.44 (17) | C5—C6—H6B | 108.7 |
C6—N7—C8 | 112.39 (17) | Br1—C2—H2A | 109.7 |
C6—N7—C12 | 108.89 (17) | Br1—C2—H2B | 109.7 |
C12—N11—C16 | 108.50 (19) | C3—C2—Br1 | 109.96 (17) |
C12—N11—C10 | 109.20 (19) | C3—C2—H2A | 109.7 |
C10—N11—C16 | 108.76 (19) | C3—C2—H2B | 109.7 |
N14—C13—N7 | 109.89 (18) | H2A—C2—H2B | 108.2 |
N14—C13—H13A | 109.7 | N14—C16—H16A | 109.2 |
N14—C13—H13B | 109.7 | N14—C16—H16B | 109.2 |
N7—C13—H13A | 109.7 | N11—C16—N14 | 111.85 (19) |
N7—C13—H13B | 109.7 | N11—C16—H16A | 109.2 |
H13A—C13—H13B | 108.2 | N11—C16—H16B | 109.2 |
N9—C8—N7 | 110.37 (18) | H16A—C16—H16B | 107.9 |
N9—C8—H8A | 109.6 | C4—C5—H5A | 109.4 |
N9—C8—H8B | 109.6 | C4—C5—H5B | 109.4 |
N7—C8—H8A | 109.6 | C6—C5—C4 | 111.0 (2) |
N7—C8—H8B | 109.6 | C6—C5—H5A | 109.4 |
H8A—C8—H8B | 108.1 | C6—C5—H5B | 109.4 |
N7—C12—H12A | 109.4 | H5A—C5—H5B | 108.0 |
N7—C12—H12B | 109.4 | N14—C15—N9 | 111.64 (19) |
N11—C12—N7 | 111.02 (18) | N14—C15—H15A | 109.3 |
N11—C12—H12A | 109.4 | N14—C15—H15B | 109.3 |
N11—C12—H12B | 109.4 | N9—C15—H15A | 109.3 |
H12A—C12—H12B | 108.0 | N9—C15—H15B | 109.3 |
H4A—C4—H4B | 108.1 | H15A—C15—H15B | 108.0 |
C3—C4—H4A | 109.5 | N9—C10—H10A | 109.3 |
C3—C4—H4B | 109.5 | N9—C10—H10B | 109.3 |
C3—C4—C5 | 110.7 (2) | N11—C10—N9 | 111.71 (19) |
C5—C4—H4A | 109.5 | N11—C10—H10A | 109.3 |
C5—C4—H4B | 109.5 | N11—C10—H10B | 109.3 |
C4—C3—H3A | 109.2 | H10A—C10—H10B | 107.9 |
C4—C3—H3B | 109.2 | ||
N7—C6—C5—C4 | 164.35 (19) | C3—C4—C5—C6 | 173.8 (2) |
C13—N14—C16—N11 | 61.4 (3) | C6—N7—C13—N14 | 176.92 (19) |
C13—N14—C15—N9 | −61.1 (2) | C6—N7—C8—N9 | −177.46 (18) |
C13—N7—C8—N9 | 58.2 (2) | C6—N7—C12—N11 | 179.94 (19) |
C13—N7—C12—N11 | −57.7 (2) | C16—N14—C13—N7 | −58.7 (2) |
C13—N7—C6—C5 | 49.2 (3) | C16—N14—C15—N9 | 58.4 (2) |
C8—N9—C15—N14 | 60.4 (2) | C16—N11—C12—N7 | 59.3 (2) |
C8—N9—C10—N11 | −60.0 (2) | C16—N11—C10—N9 | −58.7 (2) |
C8—N7—C13—N14 | −58.8 (2) | C5—C4—C3—C2 | 179.3 (2) |
C8—N7—C12—N11 | 58.1 (2) | C15—N14—C13—N7 | 60.2 (2) |
C8—N7—C6—C5 | −72.4 (2) | C15—N14—C16—N11 | −57.7 (2) |
C12—N7—C13—N14 | 56.8 (2) | C15—N9—C8—N7 | −58.9 (2) |
C12—N7—C8—N9 | −57.8 (2) | C15—N9—C10—N11 | 59.0 (2) |
C12—N7—C6—C5 | 168.85 (19) | C10—N9—C8—N7 | 59.3 (2) |
C12—N11—C16—N14 | −60.9 (3) | C10—N9—C15—N14 | −59.0 (2) |
C12—N11—C10—N9 | 59.5 (2) | C10—N11—C12—N7 | −59.1 (2) |
C4—C3—C2—Br1 | −178.93 (17) | C10—N11—C16—N14 | 57.8 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
C12—H12A···Br17 | 0.99 | 2.91 | 3.800 (2) | 150 |
C13—H13B···Br17 | 0.99 | 2.77 | 3.689 (2) | 155 |
C15—H15A···Br17i | 0.99 | 2.92 | 3.844 (3) | 156 |
C8—H8B···Br17ii | 0.99 | 2.82 | 3.777 (2) | 162 |
C6—H6B···Br17iii | 0.99 | 2.86 | 3.819 (2) | 163 |
C5—H5B···Br1iv | 0.99 | 3.00 | 3.960 (3) | 163 |
Symmetry codes: (i) x−1/2, −y+1/2, z+1/2; (ii) −x+1/2, y+1/2, −z+1/2; (iii) x+1/2, −y+1/2, z+1/2; (iv) −x+1, −y+1, −z. |
Funding information
This publication has emanated from research supported in part by funding from Science Foundation Ireland under grant No. 19/FIP/ZE/7567.
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