Crystal structure and Hirshfeld surface analysis of 4-amino­pyridinium thio­cyanate–4-amino­pyridine (1/1)

Renugadevi, M.; Sinthiya, A.; Poomani, K.; Suresh, S.

doi:10.1107/S2056989020011445

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ISSN: 2056-9890

Volume 76| Part 9| September 2020| Pages 1535-1538

https://doi.org/10.1107/S2056989020011445

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Crystal structure and Hirshfeld surface analysis of 4-aminopyridinium thiocyanate–4-aminopyridine (1/1)

M. Renugadevi,^a A. Sinthiya,^a ^* Kumaradhas Poomani ^b and Suganya Suresh ^b

^aDepartment of Physics, St Josephs College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli 620002, Tamil Nadu, India, and ^bLaboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
^*Correspondence e-mail: r.brightson2010@gmail.com

Edited by A. V. Yatsenko, Moscow State University, Russia (Received 27 July 2020; accepted 20 August 2020; online 28 August 2020)

In the crystals of the title compound, C₅H₇N₂⁺·CNS⁻·C₅H₆N₂, the components are linked by three N—H⋯N and two N—H⋯S hydrogen bonds, resulting in two interpenetrating three-dimensional networks. Hirshfeld surface analysis shows that the most important contributions to the crystal packing are from H⋯H (36.6%), C⋯H/H⋯C (20.4%), S⋯H/H⋯S (19.7%) and N⋯H/H⋯N (13.4%) interactions.

Keywords: crystal structure; 4-aminopyridinium; thiocyanate; 4-aminopyridine; hydrogen bonding.

CCDC reference: 2024317

1. Chemical context

Processes based on metathesis reactions are a greener alternative for the synthesis of organic materials, avoiding hazardous pollution to the environment (Grubbs, 2003 ). A Nobel prize was awarded for the development of metathesis reactions used for the synthesis of organic molecules. Later, new pharmaceuticals and agrochemical materials were developed using this reaction.

In order to access important sulfur-containing compounds, organic thiocyanates play vital role as synthetic intermediates (Castanheiro et al., 2016 ). The versatile thiocyanate ion can join to the reaction centre of a suitable cation or neutral molecule through the S or N atom, resulting in the assembly of supramolecular compounds (Lee et al., 2017 ). For example, the crystal of 2-aminocyclohexan-1-aminium thiocyanate involves N—H⋯S and N—H⋯N interactions between the thiocyanate anion and the amine and aminium groups, leading to the formation of a two-dimensional network (Salem et al., 2012 ). 4-Aminopyridine has many biological applications, especially in treating neurological problems. For example, it acts as a potassium channel blocker (Schwid et al., 1997 ). With this background, the present work is carried out and the results are reported here.

2. Structural commentary

The asymmetric unit of the title compound is composed of one 4-aminopyridine molecule, one 4-aminopyridinium cation and one thiocyanate anion as shown in Fig. 1. The cation forms hydrogen bonds with the neutral molecule and with the anion (Table 1). The bond lengths and angles in neutral 4-aminopyridine are similar to those in a previous report (Anderson et al., 2005 ), but the bond angle at the pyridine N3 atom is increased to 119.47 (14)° due to the hydrogen-bonding interaction. The thiocyanate anion is linear with an N5—C11—S bond of 177.85 (18)°. All bond lengths and angles in the aminopyridinium cation are within the normal ranges (Fun et al., 2010 ).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H4A⋯Sⁱ	0.86	2.58	3.4222 (17)	165
N4—H4B⋯N5	0.86	2.10	2.952 (2)	168
N3—H3⋯N2	0.86	1.83	2.688 (2)	172
N1—H1A⋯Sⁱⁱ	0.86	2.62	3.4498 (18)	162
N1—H1B⋯N5ⁱⁱⁱ	0.86	2.23	3.083 (3)	172
Symmetry codes: (i) $[-x+{\script{3\over 2}}, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) x, y, z-1.

Figure 1
View of the asymmetric unit of the title compound.

3. Supramolecular features

In the crystal, the 4-aminopyridinium cation and 4-aminopyridine molecule are linked by a strong N—H⋯N hydrogen bond (Table 1). The thiocyanate ions act as bridges, each of them forming two N⋯H—N and two S⋯H—N hydrogen bonds (Fig. 2). As a result, two interpenetrating three-dimensional nets of hydrogen bonds are formed, as shown in Fig. 3. The short interplanar distance of 3.3419 (7) Å between the mean planes of two 4-aminopyridine molecules related by an inversion center indicates a π–π interaction [Cg⋯Cg(1 − x, −y, −z) = 3.7635 (13) Å where Cg is the centroid of the N2/C1–C5 ring.

Figure 2
Hydrogen bonds in the crystal of the title compound.

Figure 3
Crystal packing diagram of the title compound showing two interpenetrating 3D nets of hydrogen bonds presented as blue and purple dotted lines.

4. Hirshfeld surface analysis

To quantify the intermolecular contacts in the title structure, the Hirshfeld surface and two-dimensional fingerprint plots were calculated using Crystal Explorer (Turner et al., 2017 ). The Hirshfeld surface mapped over d_norm is depicted in Fig. 4, where the red regions make apparent hydrogen bonds in this structure. The intensity of the red color is higher for N1—H1A⋯S, indicating the strongest interaction as compared to other red spots on the Hirshfeld surface. The fingerprint plots show that the largest contributions are from H⋯H (36.6%), C⋯H/H⋯C (20.4%), S⋯H/H⋯S (19.7%) and N⋯H/H⋯N (13.4%) interactions. Other interactions contributing to the crystal packing are C⋯C (5.8%), N⋯C/C⋯N (2.7%), N⋯N (1.1%), N⋯S/S⋯N (0.2%) and S⋯C/C⋯S (0.2%).

Figure 4
Hirshfeld surface plotted over d_norm and two-dimensional fingerprint plots for the title compound.

5. Database survey

A search of the Cambridge Crystallographic Database (CSD, version 5.40, update of September 19; Groom et al., 2016 ) was undertaken for structures containing 4-aminopyridine and for thiocyanate ions in the salts with organic ammonium cations. The room-temperature structure of 4-aminopyridine was reported by Chao & Schempp (1977 ). Anderson et al. (2005) redetermined the structure at 150 K and reported that pyramidalization occurs at the amino N atom, with the N atom displaced from the plane of the three C/H/H atoms to which it is bonded. An N—H⋯N(pyridine) interaction links the molecules in a head-to-tail manner, forming zigzag chains along the c-axis direction. This is in contrast to the structure of the title compound, where N—H⋯N(pyridine) interactions link the molecules in a tail-to-tail manner. van Rooyan & Boeyens (1975 ) reported the SCH ions in sodium thiocyanate to be linear within experimental error. reported that in 2-aminocyclohexan-1-aminium thiocyanate (Salem et al., 2012), the thiocyanate anion is involved in N—H⋯S and N—H⋯N interactions with both the amine and the aminium N atoms. Bagabas et al. (2015 ) reported that cyclohexyl ammonium thiocyanate has slightly a distorted chair conformation and that the molecules are linked by N—H⋯N and N—H⋯S hydrogen-bonding interactions. In bis[(18-crown-6-κ⁶O)sodium] (18-crown-6-1κ⁶O)-μ-thiocyanato-1:2κ²S:N-pentathiocyanato-2κ⁵N-indate(III)sodium 1,2-dichloroethane sesquisolvate (Kong, 2009 ), the metal atom is in a six-coordinated octahedral environment, bounded to the N atoms of six thiocyanate ions and the crystal packing exhibits no significant short intermolecular contacts. In the title compound the N—H⋯N and N—H⋯S hydrogen bonds link the molecules into centrosymmetric structure and 4-aminopyridine is connected to the SCN ion by N—H⋯N hydrogen bonds.

6. Synthesis and crystallization

4-Aminopyridine and sodium thiocyanate were purchased from Merck. A solution of equimolar amounts of 4-aminopyridine and sodium thiocyanate in double-distilled water was stirred intensively for nearly 4 h, filtered with Whatman filter paper and allowed to evaporate at room temperature. Colourless needle-like crystals of the title compound were obtained after a period of seven days.

7. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. All H atoms were placed in idealized positions (C—H = 0.93 Å, N—H = 0.86 Å) and treated as riding with U_iso(H) = 1.2U_eq(C,N).

Table 2
Experimental details

Crystal data
Chemical formula	C₅H₇N₂⁺·CNS⁻·C₅H₆N₂
M_r	247.32
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	293
a, b, c (Å)	7.9047 (19), 12.138 (2), 13.959 (3)
β (°)	94.670 (8)
V (Å³)	1334.9 (5)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.23
Crystal size (mm)	0.70 × 0.44 × 0.34

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Sheldrick, 2014 )
T_min, T_max	0.86, 0.93
No. of measured, independent and observed [I > 2σ(I)] reflections	15272, 3295, 2604
R_int	0.023
(sin θ/λ)_max (Å⁻¹)	0.667

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.053, 0.148, 1.03
No. of reflections	3295
No. of parameters	154
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.19, −0.27
Computer programs: APEX2 (Bruker, 2005 ), SAINT (Bruker, 2001 ), SHELXT2018/2 (Sheldrick, 2015a ), SHELXL2018/3 (Sheldrick, 2015b ) and ORTEP-3 for Windows and WinGX publication routines (Farrugia, 2012 ).

Supporting information

CCDC reference: 2024317

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2056989020011445/yk2137sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989020011445/yk2137Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989020011445/yk2137Isup4.mol

Supporting information file. DOI: https://doi.org/10.1107/S2056989020011445/yk2137Isup4.cml

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXT2018/2 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: WinGX publication routines (Farrugia, 2012).

4-Aminopyridinium thiocyanate–4-aminopyridine (1/1) top

Crystal data top

C₅H₇N₂⁺·CNS⁻·C₅H₆N₂	F(000) = 520
M_r = 247.32	D_x = 1.231 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71075 Å
a = 7.9047 (19) Å	Cell parameters from 15272 reflections
b = 12.138 (2) Å	θ = 3.0–28.0°
c = 13.959 (3) Å	µ = 0.23 mm⁻¹
β = 94.670 (8)°	T = 293 K
V = 1334.9 (5) Å³	Needle, colourless
Z = 4	0.70 × 0.44 × 0.34 mm

Data collection top

Bruker APEXII CCD diffractometer	2604 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.023
φ and ω scans	θ_max = 28.3°, θ_min = 2.9°
Absorption correction: multi-scan (SADABS; Sheldrick, 2014)	h = −10→10
T_min = 0.86, T_max = 0.93	k = −16→14
15272 measured reflections	l = −18→18
3295 independent reflections

Refinement top

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)] = 0.053	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.148	H-atom parameters constrained
S = 1.03	w = 1/[σ²(F_o²) + (0.0676P)² + 0.2492P] where P = (F_o² + 2F_c²)/3
3295 reflections	(Δ/σ)_max < 0.001
154 parameters	Δρ_max = 0.19 e Å⁻³
0 restraints	Δρ_min = −0.27 e Å⁻³

Special details top

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.

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

	x	y	z	U_iso*/U_eq
S	0.53196 (8)	0.54205 (5)	0.81261 (6)	0.1064 (3)
N4	0.60108 (18)	0.16957 (12)	0.60040 (9)	0.0665 (4)
H4A	0.680133	0.129475	0.628322	0.080*
H4B	0.548015	0.216341	0.633239	0.080*
N3	0.47226 (19)	0.13478 (13)	0.31204 (9)	0.0692 (4)
H3	0.444115	0.126754	0.251630	0.083*
N2	0.4113 (2)	0.11863 (13)	0.12028 (10)	0.0723 (4)
N1	0.3084 (2)	0.15215 (13)	−0.17439 (10)	0.0761 (4)
H1A	0.234378	0.110319	−0.204780	0.091*
H1B	0.360945	0.201212	−0.205073	0.091*
C10	0.56072 (18)	0.15921 (12)	0.50609 (10)	0.0513 (3)
C1	0.34225 (19)	0.14074 (13)	−0.07807 (10)	0.0568 (4)
C7	0.4312 (2)	0.22270 (14)	0.45860 (11)	0.0620 (4)
H7	0.373318	0.274750	0.492303	0.074*
C9	0.6444 (2)	0.08397 (13)	0.45041 (11)	0.0599 (4)
H9	0.731830	0.040635	0.478561	0.072*
N5	0.4673 (3)	0.34464 (16)	0.72012 (13)	0.0982 (6)
C8	0.5971 (2)	0.07464 (15)	0.35512 (12)	0.0649 (4)
H8	0.653756	0.024592	0.318724	0.078*
C2	0.2604 (2)	0.06267 (13)	−0.02580 (12)	0.0650 (4)
H2	0.180504	0.015765	−0.056717	0.078*
C11	0.4971 (2)	0.42600 (16)	0.75820 (12)	0.0656 (4)
C4	0.4626 (2)	0.20694 (14)	−0.02711 (12)	0.0638 (4)
H4	0.521971	0.260152	−0.058647	0.077*
C3	0.2976 (2)	0.05505 (15)	0.07087 (12)	0.0713 (5)
H3A	0.240361	0.002503	0.104414	0.086*
C6	0.3912 (2)	0.20756 (16)	0.36331 (13)	0.0718 (5)
H6	0.304243	0.249325	0.332609	0.086*
C5	0.4917 (2)	0.19239 (16)	0.06949 (13)	0.0712 (5)
H5	0.573045	0.236775	0.102281	0.085*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S	0.0858 (4)	0.0832 (4)	0.1442 (6)	−0.0020 (3)	−0.0260 (4)	−0.0304 (3)
N4	0.0740 (9)	0.0703 (8)	0.0540 (7)	0.0003 (7)	−0.0030 (6)	−0.0093 (6)
N3	0.0759 (9)	0.0846 (10)	0.0466 (7)	−0.0138 (8)	0.0026 (6)	−0.0061 (6)
N2	0.0837 (10)	0.0825 (10)	0.0502 (7)	0.0200 (8)	0.0031 (7)	−0.0076 (7)
N1	0.0919 (10)	0.0808 (10)	0.0546 (8)	−0.0061 (8)	−0.0003 (7)	−0.0010 (7)
C10	0.0518 (7)	0.0510 (7)	0.0513 (7)	−0.0127 (6)	0.0052 (6)	−0.0041 (6)
C1	0.0602 (8)	0.0580 (8)	0.0524 (8)	0.0128 (6)	0.0052 (6)	−0.0065 (6)
C7	0.0575 (8)	0.0665 (9)	0.0620 (9)	0.0026 (7)	0.0052 (7)	−0.0096 (7)
C9	0.0607 (8)	0.0562 (8)	0.0629 (9)	−0.0008 (7)	0.0065 (7)	−0.0045 (7)
N5	0.1254 (16)	0.0796 (12)	0.0945 (13)	−0.0078 (10)	0.0381 (11)	−0.0197 (10)
C8	0.0708 (10)	0.0654 (9)	0.0606 (9)	−0.0094 (8)	0.0180 (7)	−0.0126 (7)
C2	0.0735 (10)	0.0593 (9)	0.0618 (9)	0.0019 (7)	0.0027 (7)	−0.0071 (7)
C11	0.0665 (9)	0.0691 (10)	0.0618 (9)	0.0046 (8)	0.0096 (7)	0.0052 (8)
C4	0.0604 (9)	0.0683 (9)	0.0630 (9)	0.0036 (7)	0.0075 (7)	−0.0066 (7)
C3	0.0853 (12)	0.0663 (10)	0.0635 (10)	0.0089 (9)	0.0133 (9)	0.0021 (8)
C6	0.0666 (10)	0.0843 (12)	0.0631 (10)	0.0041 (9)	−0.0034 (7)	0.0008 (9)
C5	0.0679 (10)	0.0794 (11)	0.0648 (10)	0.0082 (9)	−0.0028 (8)	−0.0180 (9)

Geometric parameters (Å, º) top

S—C11	1.613 (2)	C1—C4	1.395 (2)
N4—C10	1.3351 (19)	C7—C6	1.354 (2)
N4—H4A	0.8600	C7—H7	0.9300
N4—H4B	0.8600	C9—C8	1.357 (2)
N3—C6	1.333 (2)	C9—H9	0.9300
N3—C8	1.331 (2)	N5—C11	1.137 (2)
N3—H3	0.8600	C8—H8	0.9300
N2—C3	1.334 (2)	C2—C3	1.361 (2)
N2—C5	1.335 (2)	C2—H2	0.9300
N1—C1	1.3565 (19)	C4—C5	1.361 (2)
N1—H1A	0.8600	C4—H4	0.9300
N1—H1B	0.8600	C3—H3A	0.9300
C10—C9	1.400 (2)	C6—H6	0.9300
C10—C7	1.404 (2)	C5—H5	0.9300
C1—C2	1.388 (2)

C10—N4—H4A	120.0	C10—C9—H9	120.2
C10—N4—H4B	120.0	N3—C8—C9	122.14 (15)
H4A—N4—H4B	120.0	N3—C8—H8	118.9
C6—N3—C8	119.47 (14)	C9—C8—H8	118.9
C6—N3—H3	120.3	C3—C2—C1	119.71 (16)
C8—N3—H3	120.3	C3—C2—H2	120.1
C3—N2—C5	116.33 (15)	C1—C2—H2	120.1
C1—N1—H1A	120.0	N5—C11—S	177.85 (18)
C1—N1—H1B	120.0	C5—C4—C1	118.94 (17)
H1A—N1—H1B	120.0	C5—C4—H4	120.5
N4—C10—C9	121.56 (14)	C1—C4—H4	120.5
N4—C10—C7	121.36 (14)	N2—C3—C2	123.74 (17)
C9—C10—C7	117.08 (13)	N2—C3—H3A	118.1
N1—C1—C2	121.87 (15)	C2—C3—H3A	118.1
N1—C1—C4	121.19 (16)	N3—C6—C7	122.20 (16)
C2—C1—C4	116.93 (14)	N3—C6—H6	118.9
C6—C7—C10	119.49 (15)	C7—C6—H6	118.9
C6—C7—H7	120.3	N2—C5—C4	124.33 (17)
C10—C7—H7	120.3	N2—C5—H5	117.8
C8—C9—C10	119.61 (15)	C4—C5—H5	117.8
C8—C9—H9	120.2

N4—C10—C7—C6	−178.25 (15)	N1—C1—C4—C5	179.89 (15)
C9—C10—C7—C6	1.2 (2)	C2—C1—C4—C5	−0.6 (2)
N4—C10—C9—C8	178.74 (14)	C5—N2—C3—C2	−0.5 (3)
C7—C10—C9—C8	−0.7 (2)	C1—C2—C3—N2	−0.5 (3)
C6—N3—C8—C9	0.6 (3)	C8—N3—C6—C7	−0.1 (3)
C10—C9—C8—N3	−0.2 (2)	C10—C7—C6—N3	−0.8 (3)
N1—C1—C2—C3	−179.40 (15)	C3—N2—C5—C4	1.1 (3)
C4—C1—C2—C3	1.1 (2)	C1—C4—C5—N2	−0.5 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4A···Sⁱ	0.86	2.58	3.4222 (17)	165
N4—H4B···N5	0.86	2.10	2.952 (2)	168
N3—H3···N2	0.86	1.83	2.688 (2)	172
N1—H1A···Sⁱⁱ	0.86	2.62	3.4498 (18)	162
N1—H1B···N5ⁱⁱⁱ	0.86	2.23	3.083 (3)	172

Symmetry codes: (i) −x+3/2, y−1/2, −z+3/2; (ii) −x+1/2, y−1/2, −z+1/2; (iii) x, y, z−1.

Acknowledgements

We acknowledge the CIMF (Centre for Instrumentation), Periyar University, Tamilnadu, India, for the single crystal X-ray diffraction data collection.

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