research communications
A long symmetric N⋯H⋯N hydrogen bond in bis(4-aminopyridinium)(1+) azide(1−): redetermination from the original data
aInstitute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Praha 8, Czech Republic
*Correspondence e-mail: fabry@fzu.cz
The structure of the title molecular salt, C10H13N4+·N3−, has been redetermined from the data published by Qian & Huang [Acta Cryst. (2010), E66, o3086; refcode WACMIY (Groom et al., 2016)]. The improvement of the present redetermination consists in a correction of the site-occupancy parameter of the bridging H atom between the pyridine rings, as well as of its position. The present study has shown that the bridging H atom (site symmetry 2) is involved in a symmetric N⋯H⋯N hydrogen bond, which is one of the longest ever observed [N⋯N = 2.678 (3) Å]. In addition, there are also present weaker Nam—H⋯Naz hydrogen bonds (am = amine and az = azide) of moderate strength and π-electron pyridine⋯π-electron interactions in the structure. All the azide N atoms also lie on a twofold axis.
Keywords: crystal structure; redetermination; hydrogen bonding; symmetric hydrogen bonds; refinement constraints; refinement restraints; Cambridge Structural Database.
CCDC reference: 1566932
1. Chemical context
Structures that contain hydroxyl and secondary and primary amine groups are sometimes determined incorrectly because of an assumed geometry of these groups from which the applied constraints or restraints were inferred. In such cases, the correct geometry is missed as it is not verified by inspection of the difference electron-density maps. Thus, a considerable number of structures could have been determined more accurately – cf. Figs. 1 and 2 in Fábry et al. (2014). The inclusion of such erroneous structures causes bias in crystallographic databases such as the Cambridge Structural Database (Groom et al., 2016).
In the course of recalculation of suspect structures that were retrieved from the Cambridge Structural Database (Groom et al., 2016), the of the title structure by Qian & Huang (2010) with the pertinent CSD refcode WACMIY became a candidate for a checking recalculation. The reason was that both the primary and secondary amine groups were constrained with distance constraints equal to 0.86 Å, with planar conformation and Uiso(H) = 1.2Ueq(N).
Inspection of the publication of the title structure by Qian & Huang (2010) has revealed that the bridging hydrogen atom H2a, lying between two symmetry-equivalent nitrogen atoms related by a crystallographic twofold axis, was modelled by two (undisordered) H atoms both with occupational parameters equal to 1: such a structural motif is impossible. The present article describes the redetermination of bis(4-aminopyridinium)(1+) azide(1−), which was reported by Qian & Huang (2010).
2. Structural commentary
The components of the title molecular salt are shown in Fig. 1. It is seen that the bridging hydrogen atom (H2a) interconnects symmmetry-related 4-aminopyridine molecules; the for atoms with the suffix `a' is the same as symmetry code (i) in Table 1 and Fig. 2, viz. −x + 1, y, −z + . The interplanar angle between the pyridine rings N2/C1–C5 and N2i/C1i–C5i is 87.90 (7) °.
Table 1 lists the hydrogen bonds in the structure. The packing of the ions in the is shown in Fig. 2. Fig. 3 shows the difference electron-density map calculated without the bridging hydrogen atom H2a in the region N2⋯(H2a)⋯N2i. A well-defined, single peak in this map indicates that H2a is situated on a twofold axis, i.e. it is involved in a symmetric hydrogen bond while not being disordered. This hydrogen bond is the strongest hydrogen bond in the structure and is one of the family of long symmetric hydrogen bonds N⋯H⋯N as listed in Table 1. As Tables 1 and 2 show, the title structure contains the second longest known truly symmetric N⋯H⋯N hydrogen bond after CAFHAT01.
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The remaining N—Ham⋯Naz (am = primary amine, az = azide) hydrogen bonds are considerably weaker, though still of moderate strength (Gilli & Gilli, 2009). Atom H1a forms a link to the terminal azide nitrogen atom N3 while H1b bonds to the other terminal azide atom N5. The graph-set motif is described in the Supramolecular features section. In addition to the hydrogen-bonding interactions, there are also π-electron ring⋯π-electron pyridine interactions in the structure. The distance between the ring centroids N2/C1–C5 and N2iv/C1iv–C5iv is 3.7145 (17) Å [symmetry code: (iv) −x + 1, −y + 1, −z + 1].
The primary amine group centered on N1 is almost planar [C3—N1—H1a = 120.0 (9), C3—N1—H1b = 119.1 (9), H1a—N1—H1b = 120.6 (13)°] despite the somewhat lengthened C3—N1 bond [1.345 (2) Å]. The reason may be found in the hydrogen bonds formed by the group with N—H⋯N bond angles being close to 180 °.
Once again, the present redetermination emphasizes the importance of careful examination of the difference electron-density maps during a structure determination.
3. Supramolecular features
In addition to the above-mentioned symmetric hydrogen bond N2⋯H2a⋯N2i [symmetry code: (i) −x + 1, y, −z + ] for which the graph-set motif notation is missing (the donors act simultaneously as acceptors in the title structure; Etter et al., 1990) the principal graph-set motif in which the primary amine group as well the azide atoms are involved is R46(20).
In a detail, the atoms involved in this graph-set motif are as follows (Fig. 2): N3v–H1avi–N1vi–H1bvi–N5ii–N4ii–N3ii–H1a–N1–H1b–N5iii–H1bvii–N1vii–H1avii–N3–N4–N5–H1bviii–N1viii–H1aviii [symmetry codes: (ii) x + 1, y, z; (iii) x + , y − , z; (v) x + , y + , z; (vi) −x + , y + , −z + ; (vii) −x + 1, y, −z + ; (viii) x − , y + , z].
The hydrogen bonds in this graph set motif are directed along the unit-cell parameter b.
4. Synthesis and crystallization
The preparation of the title compound was described by Qian & Huang et al. (2010) in the supporting information of their article.
5. Database survey
The ) has been included into the Cambridge Structural Database (Groom et al., 2016) under the refcode WACMIY.
by Qian & Huang (20106. Refinement
Table 3 lists the details regarding the crystal data, data collection and the The starting structural model was taken from the determination by Qian & Huang (2010). All hydrogen atoms were discernible in the difference electron-density map. The aryl hydrogen atoms were constrained by Caryl—Haryl = 0.93 Å and Uiso(Haryl) = 1.2Ueq(Caryl). The positional parameters of the primary amine hydrogen atoms were refined freely while their displacement parameters were constrained by Uiso(HN2) = 1.2Ueq(N2). The bridging hydrogen atom H2a involved in the symmetric hydrogen bond N2⋯H2a⋯N2i was refined freely. Refinements using JANA2006 and SHELXL (Sheldrick, 2008) with the threshold for observed diffractions I = 2σ(I) led to the same result of the bridging hydrogen atom being located on the twofold axis.
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Supporting information
CCDC reference: 1566932
https://doi.org/10.1107/S2056989017011537/hb7695sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017011537/hb7695Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989017011537/hb7695Isup3.smi
Data collection: SMART (Bruker, 2000); cell
SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: JANA2006 (Petříček et al., 2014); molecular graphics: PLATON (Spek, 2009), DIAMOND (Brandenburg & Putz, 2005) and JANA2006 (Petříček et al., 2014); software used to prepare material for publication: JANA2006 (Petříček et al., 2014).C10H13N4+·N3− | F(000) = 488 |
Mr = 231.27 | Dx = 1.242 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 1359 reflections |
a = 7.507 (3) Å | θ = 3.0–25.4° |
b = 12.247 (5) Å | µ = 0.08 mm−1 |
c = 13.634 (5) Å | T = 291 K |
β = 99.278 (5)° | Block, colourless |
V = 1237.1 (8) Å3 | 0.14 × 0.11 × 0.10 mm |
Z = 4 |
Bruker SMART 1K CCD area-detector diffractometer | 1096 independent reflections |
Radiation source: fine-focus sealed tube | 787 reflections with I > 3σ(I) |
Graphite monochromator | Rint = 0.072 |
φ and ω scans | θmax = 25.0°, θmin = 3.0° |
Absorption correction: multi-scan (SADABS; Bruker, 2000) | h = −8→8 |
Tmin = 0.988, Tmax = 0.992 | k = −12→14 |
3027 measured reflections | l = −16→15 |
Refinement on F2 | 18 constraints |
R[F > 3σ(F)] = 0.034 | H atoms treated by a mixture of independent and constrained refinement |
wR(F) = 0.085 | Weighting scheme based on measured s.u.'s w = 1/(σ2(I) + 0.0004I2) |
S = 1.48 | (Δ/σ)max = 0.004 |
1096 reflections | Δρmax = 0.08 e Å−3 |
87 parameters | Δρmin = −0.07 e Å−3 |
0 restraints |
Experimental. The structure was solved by direct methods (Bruker, 2000) and successive difference Fourier syntheses. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.6719 (2) | 0.44584 (12) | 0.40174 (12) | 0.0889 (6) | |
H1 | 0.732036 | 0.496631 | 0.368331 | 0.1067* | |
C2 | 0.72245 (17) | 0.43524 (10) | 0.50154 (11) | 0.0778 (5) | |
H2 | 0.814514 | 0.478469 | 0.535055 | 0.0934* | |
C3 | 0.63529 (16) | 0.35896 (9) | 0.55351 (10) | 0.0702 (5) | |
C4 | 0.49858 (17) | 0.29730 (11) | 0.49826 (11) | 0.0793 (5) | |
H4 | 0.436698 | 0.245345 | 0.529429 | 0.0952* | |
C5 | 0.4560 (2) | 0.31347 (12) | 0.39842 (12) | 0.0936 (6) | |
H5 | 0.364461 | 0.271568 | 0.362714 | 0.1123* | |
N1 | 0.68183 (18) | 0.34619 (10) | 0.65226 (9) | 0.0859 (5) | |
H1a | 0.776 (2) | 0.3866 (12) | 0.6868 (10) | 0.1031* | |
H1b | 0.631 (2) | 0.2960 (12) | 0.6815 (11) | 0.1031* | |
N2 | 0.54018 (19) | 0.38706 (11) | 0.34930 (8) | 0.0943 (5) | |
N3 | 0 | 0.47492 (16) | 0.75 | 0.1020 (8) | |
N4 | 0 | 0.57130 (18) | 0.75 | 0.0768 (6) | |
N5 | 0 | 0.66663 (17) | 0.75 | 0.1074 (8) | |
H2a | 0.5 | 0.389 (2) | 0.25 | 0.160 (9)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0946 (10) | 0.0866 (10) | 0.0930 (11) | 0.0183 (8) | 0.0376 (9) | 0.0120 (8) |
C2 | 0.0752 (8) | 0.0760 (8) | 0.0853 (10) | 0.0109 (6) | 0.0224 (7) | 0.0054 (7) |
C3 | 0.0685 (7) | 0.0688 (7) | 0.0762 (9) | 0.0166 (6) | 0.0205 (6) | 0.0039 (6) |
C4 | 0.0762 (8) | 0.0795 (8) | 0.0847 (10) | 0.0065 (6) | 0.0205 (7) | 0.0007 (7) |
C5 | 0.0948 (10) | 0.0999 (10) | 0.0854 (11) | 0.0105 (8) | 0.0125 (8) | −0.0094 (8) |
N1 | 0.0909 (8) | 0.0865 (8) | 0.0804 (9) | −0.0012 (5) | 0.0144 (6) | 0.0093 (6) |
N2 | 0.1093 (9) | 0.1039 (9) | 0.0725 (8) | 0.0233 (7) | 0.0229 (7) | 0.0027 (7) |
N3 | 0.0983 (12) | 0.0857 (11) | 0.1212 (15) | 0 | 0.0154 (10) | 0 |
N4 | 0.0625 (8) | 0.1024 (13) | 0.0667 (9) | 0 | 0.0143 (6) | 0 |
N5 | 0.1140 (14) | 0.0918 (12) | 0.1263 (15) | 0 | 0.0495 (12) | 0 |
C1—H1 | 0.93 | C5—H5 | 0.93 |
C1—C2 | 1.359 (2) | C5—N2 | 1.340 (2) |
C1—N2 | 1.334 (2) | N1—H1a | 0.927 (14) |
C2—H2 | 0.93 | N1—H1b | 0.857 (16) |
C2—C3 | 1.397 (2) | H1a—H1b | 1.55 (2) |
C3—C4 | 1.3935 (19) | N2—H2a | 1.3391 (16) |
C3—N1 | 1.345 (2) | N3—N4 | 1.180 (3) |
C4—H4 | 0.93 | N4—N5 | 1.168 (3) |
C4—C5 | 1.362 (2) | ||
H1—C1—C2 | 118.36 | C4—C5—H5 | 118.53 |
H1—C1—N2 | 118.36 | C4—C5—N2 | 122.95 (13) |
C2—C1—N2 | 123.27 (14) | H5—C5—N2 | 118.53 |
C1—C2—H2 | 120.21 | C3—N1—H1a | 120.0 (9) |
C1—C2—C3 | 119.58 (12) | C3—N1—H1b | 119.1 (9) |
H2—C2—C3 | 120.21 | H1a—N1—H1b | 120.6 (13) |
C2—C3—C4 | 116.91 (12) | C1—N2—C5 | 117.61 (13) |
C2—C3—N1 | 121.21 (11) | C1—N2—H2a | 123.9 (8) |
C4—C3—N1 | 121.88 (12) | C5—N2—H2a | 118.2 (9) |
C3—C4—H4 | 120.16 | N3—N4—N5 | 180.0 (5) |
C3—C4—C5 | 119.68 (13) | N2—H2a—N2i | 178 (2) |
H4—C4—C5 | 120.16 |
Symmetry code: (i) −x+1, y, −z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2a···N2i | 1.3391 (16) | 1.3391 (16) | 2.678 (3) | 178 (2) |
N1—H1a···N3ii | 0.927 (14) | 2.067 (14) | 2.990 (2) | 173.6 (13) |
N1—H1b···N5iii | 0.857 (16) | 2.154 (16) | 3.010 (2) | 177.9 (14) |
Symmetry codes: (i) −x+1, y, −z+1/2; (ii) x+1, y, z; (iii) x+1/2, y−1/2, z. |
For the search in the Cambridge Structural Database (Groom et al., 2016), the D—H distance was set in the interval 1.30–1.45 Å and the non-bonding distance between the donor and acceptor nitrogen atoms was set in the interval 2.6–3.0 Å. |
Refcode | D—H | H···A | D···A | D—H···A |
BOTXEOa | 1.322 (3) | 1.515 (3) | 2.829 (4) | 171.09 (16) |
CAFHAT01b | 1.34 | 1.37 | 2.7018 | 169.8 |
CAFHAT01b | 1.35 | 1.35 | 2.7009 | 175.3 |
COFMUF10c | 1.35 (10) | 1.50 (10) | 2.844 (7) | 171 (11) |
DAHGUO01d | 1.33 (6) | 1.38 (6) | 2.690 (8) | 168 (6) |
EFAZOBe | 1.32 (5) | 1.38 (5) | 2.692 (5) | 176 (4) |
EPIWUXf | 1.33 (3) | 1.33 (2) | 2.657 (9) | 172 (8) |
FISROPg | 1.45 (4) | 1.51 (4) | 2.963 (3) | 173 (2) |
FOGKAPh | 1.31 (4) | 1.34 (4) | 2.652 (5) | 175 (4) |
HUJNUWi | 1.341 (15) | 1.414 (16) | 2.68 (2) | 152.7 (8) |
IYEVOXj | 1.33 (7) | 1.37 (7) | 2.691 (6) | 174 (6) |
MIJMUNk | 1.27 (7) | 1.56 (7) | 2.812 (7) | 165 (5) |
MIJMUNk | 1.34 (9) | 1.52 (10) | 2.808 (7) | 159 (8) |
OBUCOEl | 1.33 (3) | 1.43 (3) | 2.736 (2) | 165 (3) |
QUHFEGm | 1.39 (4) | 1.40 (4) | 2.792 (10) | 176 (5) |
SIZSUQn | 1.317 (14) | 1.319 (14) | 2.63 (2) | 176.8 (9) |
WOFGIIo | 1.33 (4) | 1.39 (4) | 2.706 (4) | 167 (3) |
XICRIMp | 1.31 (4) | 1.52 (4) | 2.826 (3) | 164 (3) |
ZEYLIAq | 1.32 (4) | 1.51 (4) | 2.833 (4) | 175 (3) |
Notes: (a) 2-(1,3-Benzoxazol-2-yl)-1-phenylvinyl benzoate (Orozco et al., 2009); (b) hydrogen bis[bis(2-{[(imidazol-4-yl)methylene]amino}ethyl){2-[(imidazolato)methylene]amino}ethyl)amine]cobalt(III) triperchlorate heptahydrate (Marsh & Clemente, 2007); (c) 2,1,3-benzoselenadiazole 2,1,3-benzoselenadiazolium pentaiodide (Gieren et al., 1985); (d) bis{[1,4-diazoniabicyclo(2.2.2)octane][1-aza-4-azoniabicyclo(2.2.2)octane]} tetrakis(tribromide) dibromide (Heravi et al., 2005); (e) bis[(3,5-dimethylpyrazole)(3,5-dimethylpyrazolyl)]platinum(II) (Umakoshi et al., 2008); (f) 4-{2-(pyridin-4-yl)oxy]-1,2-bis(2,3,5,6-tetrafluoro-4-iodophenyl)ethoxy}pyridin-1-ium iodide bis(nitrobenzene) (Martí-Rujas et al., 2012); (g) 5,6:14,15-dibenzo-1,4-dioxa-8-azonia-12-azacyclopentadeca-5,14-diene 5,6:14,15-dibenzo-1,4-dioxa-8,12-diazacyclopentadeca-5,14-diene perchlorate (Tušek-Božić et al., 2005); (h) dioxidotetrakis(4-methylpyridine)rhenium(V) 4-methylpyridinium 4-methylpyridine diodide (Krawczyk et al., 2014); (i) 4-methylpyridinium trans-bis(γ-picoline)tetrakis(thiocyanato)molybdenum 4-methylpyridine (Kitanovski et al., 2009); (j) bis(4,4'-bipyridinium) hexakis(µ2-sulfido)tetragermaniumtetrasulfide 4,4'-bipyridine heptahydrate (Wang et al., 2003); (k) 4,4'-bipyridinium 4-(pyrid-4-yl)pyridinium 4,4'-bipyridine hexakis(isothiocyanato-N)-iron (Wei et al., 2002); (l) tris(2-benzimidazolylmethyl)ammonium 3,5-dinitrobenzoate 3,5-dinitrobenzoic acid clathrate (Ji et al., 2004); (m) (2R,4S,5R)-9-(hydroxyimino)-6'-methoxycinchonan-1-ium (2R,4S,5R)-N-hydroxy-6'-methoxycinchonan-9-imine chloride methanol solvate (Zohri et al., 2015); (n) catena-[bis(µ2-aqua)-(5-cyano-2H-1,2,3-triazole-4-carboxamide)(4-cyano-1,2,3-triazole-5-carboxamide)sodium] (Al-Azmi et al., 2007); (o) (1,1'-hydrogenbis{4-[1'-(4-pyridyl)ferrocen-1-yl]pyridine}) 4-[1'-(4-pyridyl)ferrocen-1-yl]pyridinium tris(5-carboxy-2-thienylcarboxylate) bis(thiophene-2,5-dicarboxylic acid) (Braga et al., 2008); (p) cytosinium 4-amino-2-hydroxybenzoate cytosine monohydrate (Cherukuvada et al., 2013); (q) cytosinium acetylenedicarboxylate cytosine monohydrate (Perumalla et al., 2013). |
Acknowledgements
The support by the grant of the Czech Science Foundation 15–12653S is gratefully acknowledged.
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