A long symmetric N⋯H⋯N hydrogen bond in bis-(4-amino-pyridinium)(1+) azide(1-): redetermination from the original data.

The structure of the title mol-ecular 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 inter-actions in the structure. All the azide N atoms also lie on a twofold axis.

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 ▸).

Figure 1

View of the constituent mol­ecules of the title structure after the improved refinement. The displacement ellipsoids are depicted at the 30% probability level (Spek, 2009 ▸).

Figure 2

A view of the title structure along the unit-cell axis a. Symmetry codes: (i) −x + 1, y, −z + ; (ii) x + 1, y, z; (iii) x + , y − , z. Applied colours for atoms: grey = C and H, blue = N; applied colours for bonds: black = covalent bonds, dashed orange = H⋯hydrogen bonds acceptor (Brandenburg & Putz, 2005 ▸).

In the course of recalculation of suspect structures that were retrieved from the Cambridge Structural Database (Groom et al., 2016 ▸), the structure determination 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 U iso(H) = 1.2U eq(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 ▸).

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 symmetry operation 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

Hydrogen-bond geometry (Å, °)

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) ; (ii) ; (iii) .

Table 1 ▸ lists the hydrogen bonds in the structure. The packing of the ions in the unit cell 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.

Figure 3

A section of the difference electron-density map for the present redetermined title structure, which shows the build up of the electron density between the atoms N and Ni [symmetry code: (i) −x + 1, y, −z + ]. Positive and negative electron densities are indicated by continuous and dashed lines, respectively. The increment of electron density between the neighbouring contours is 0.02 e Å−3 (Petříček et al., 2014 ▸).

Table 2

Structures with long N⋯H⋯N hydrogen bonds (Å, °) with a centred hydrogen

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)
EPIWUX f	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)
IYEVOX j	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)
XICRIM p	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 ▸).

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.

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 (20).

In a detail, the atoms involved in this graph-set motif are as follows (Fig. 2 ▸): N3v–H1a vi–N1vi–H1b vi–N5ii–N4ii–N3ii–H1a–N1–H1b–N5iii–H1b vii–N1vii–H1a vii–N3–N4–N5–H1b viii–N1viii–H1a viii [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.

Synthesis and crystallization

The preparation of the title compound was described by Qian & Huang et al. (2010 ▸) in the supporting information of their article.

Database survey

The structure determination by Qian & Huang (2010 ▸) has been included into the Cambridge Structural Database (Groom et al., 2016 ▸) under the refcode WACMIY.

Refinement

Table 3 ▸ lists the details regarding the crystal data, data collection and the refinement. 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 U iso(Har­yl) = 1.2U eq(Car­yl). The positional parameters of the primary amine hydrogen atoms were refined freely while their displacement parameters were constrained by U iso(HN2) = 1.2U eq(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.

Table 3

Experimental details

Crystal data
Chemical formula	C10H13N4 +·N3 −
M r	231.27
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	291
a, b, c (Å)	7.507 (3), 12.247 (5), 13.634 (5)
β (°)	99.278 (5)
V (Å3)	1237.1 (8)
Z	4
Radiation type	Mo Kα
μ (mm−1)	0.08
Crystal size (mm)	0.14 × 0.11 × 0.10
Data collection
Diffractometer	Bruker SMART 1K CCD area-detector
Absorption correction	Multi-scan (SADABS; Bruker, 2000 ▸)
T min, T max	0.988, 0.992
No. of measured, independent and observed [I > 3σ(I)] reflections	3027, 1096, 787
R int	0.072
(sin θ/λ)max (Å−1)	0.595
Refinement
R[F > 3σ(F)], wR(F), S	0.034, 0.085, 1.48
No. of reflections	1096
No. of parameters	87
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)	0.08, −0.07

Computer programs: SMART and SAINT (Bruker, 2000 ▸), SHELXTL (Sheldrick, 2008 ▸), PLATON (Spek, 2009 ▸), DIAMOND (Brandenburg & Putz, 2005 ▸) and JANA2006 (Petříček et al., 2014 ▸).

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989017011537/hb7695sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989017011537/hb7695Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S2056989017011537/hb7695Isup3.smi

CCDC reference: 1566932

Additional supporting information: crystallographic information; 3D view; checkCIF report

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

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)