1-(2-Amino-6-methyl­pyrimidin-4-yl)-N,N-dimethyl­piperidin-4-aminium chloride

Sreenivasa, S.; ManojKumar, K.E.; Suchetan, P.A.; Srinivasan, T.; Palakshamurthy, B.S.; Velmurgan, D.

doi:10.1107/S1600536812046533

organic compounds

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ISSN: 2056-9890

Volume 68| Part 12| December 2012| Page o3371

doi:10.1107/S1600536812046533

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1-(2-Amino-6-methylpyrimidin-4-yl)-N,N-dimethylpiperidin-4-aminium chloride

S. Sreenivasa,^a ^* K.E. ManojKumar,^a P.A. Suchetan,^b T. Srinivasan,^c B. S. Palakshamurthy ^d and D. Velmurgan ^c

^aDepartment of Studies and Research in Chemistry, Tumkur University, Tumkur, Karnataka 572 103, India, ^bDepartment of Studies and Research in Chemistry, U.C.S., Tumkur University, Tumkur, Karnataka 572 103, India, ^cCentre of Advanced Study in Crystallography and Biophysics, University of Madras Guindy Campus, Chennai 600 025, India, and ^dDepartment of Studies and Research in Physics, U.C.S., Tumkur University, Tumkur, Karnataka 572 103, India
^*Correspondence e-mail: drsreenivasa@yahoo.co.in

(Received 10 November 2012; accepted 11 November 2012; online 17 November 2012)

In the title molecular salt, C₁₂H₂₂N₅⁺·Cl⁻, the cation is protonated at the dimethyl-substituted tertiary N atom. The piperidine ring adopts a chair conformation with the exocyclic N—C bond in an equatorial orientation. The dihedral angle between the piperidine ring (all atoms) and the pyrimidine ring is 14.00 (1)°. In the crystal, the ions are connected by N—H⋯N hydrogen bonds, forming inversion dimers, which are further connected by N—H⋯Cl hydrogen bonds. Aromatic π–π stacking interactions [centroid–centroid separation = 3.4790 (9) Å] are also observed in the structure.

Related literature

For background to pyrimidine derivatives and their biological activity, see: Patel et al. (2003 ).

Experimental

Crystal data

C₁₂H₂₂N₅⁺·Cl⁻
M_r = 271.80
Monoclinic, C 2/c
a = 24.7908 (12) Å
b = 8.2419 (4) Å
c = 13.8764 (6) Å
β = 91.968 (2)°
V = 2833.6 (2) Å³
Z = 8
Mo Kα radiation
μ = 0.26 mm⁻¹
T = 298 K
0.21 × 0.18 × 0.03 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 2004) T_min = 0.947, T_max = 0.994
10807 measured reflections
2502 independent reflections
2266 reflections with I > 2σ(I)
R_int = 0.024

Refinement

R[F² > 2σ(F²)] = 0.036
wR(F²) = 0.107
S = 1.08
2502 reflections
176 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.28 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3NB⋯Cl1	0.84 (2)	2.60 (2)	3.4284 (17)	167.2 (17)
N5—H5N⋯Cl1ⁱ	0.878 (19)	2.20 (2)	3.0785 (14)	177.1 (17)
N3—H3NA⋯N2	0.86 (2)	2.26 (2)	3.114 (2)	175.5 (18)
Symmetry code: (i) x, y-1, z.

Data collection: APEX2 (Bruker, 2004 ); cell refinement: SAINT-Plus (Bruker, 2004); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 2012 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812046533/hb6988sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812046533/hb6988Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812046533/hb6988Isup3.cml

checkCIF report

Comment top

Nitrogen-containing heterocyclic ring such as pyrimidine is a promising structural moiety for drug design. Pyrimidine derivatives form a component in a number of useful drugs and are associated with many biological and therapeutical activities (Patel et al., 2003). In this view, we synthesized the title compound to study its crystal structure. The title compound crystallizes in monoclinic C2/c space group with the piperidine ring in the molecule adopting chair conformation. The dihedral angle between the piperidine ring and the pyrimidine ring in the molecule is 14.00 (1)°. In the crystal structure, the molecules are linked to one another through N—H···N hydrogen bonds generating R₂²(8) ring patterns forming inversion related dimers. These dimers are further connected to one another through N—H···Cl hydrogen bonds and weak π-π interactions.

Related literature top

For background to pyrimidine derivatives and their biological activity, see: Patel et al. (2003).

Experimental top

To a solution of 2-amino-4-chloro-6-methylpyrimidine (1.39 mmol) in acetonitrile (3 ml) was added 4-(dimethylamino)piperidine (1.66 mmol), xantphos (0.0695 mmol), Pd(OAc)₂ (0.139 mmol) and Cs₂CO₃ (2.78 mmol). The reaction mixture was irradiated with microwave radiation at 60° C for 1.5 hrs. The reaction was monitored by TLC. The solvent was removed under reduced pressure and the crude product was purified by column chromatography using MDC/methanol as eluent. Colourless prisms were obtained from slow evaporation of the solution of the compound in dilute alcohol.

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT-Plus (Bruker, 2004); data reduction: SAINT-Plus (Bruker,2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 2012); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. Molecular structure of the title compound, showing displacement ellipsoids drawn at the 50% probability level.
	Fig. 2. Crystal packing of the title compound. Hydrogen bonds and π-π interactions are shown as dashed lines.

1-(2-Amino-6-methylpyrimidin-4-yl)-N,N-dimethylpiperidin- 4-aminium chloride top

Crystal data top

C₁₂H₂₂N₅⁺·Cl⁻	F(000) = 1168
M_r = 271.80	Prism
Monoclinic, C2/c	D_x = 1.274 Mg m⁻³
Hall symbol: -C 2yc	Mo Kα radiation, λ = 0.71073 Å
a = 24.7908 (12) Å	Cell parameters from 2266 reflections
b = 8.2419 (4) Å	θ = 1.6–52°
c = 13.8764 (6) Å	µ = 0.26 mm⁻¹
β = 91.968 (2)°	T = 298 K
V = 2833.6 (2) Å³	Prism, colourless
Z = 8	0.21 × 0.18 × 0.03 mm

Data collection top

Bruker APEXII CCD diffractometer	2502 independent reflections
Radiation source: fine-focus sealed tube	2266 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.024
Detector resolution: 1.20 pixels mm^-1	θ_max = 25.0°, θ_min = 1.6°
ω scans	h = −28→29
Absorption correction: multi-scan (SADABS; Sheldrick, 2004)	k = −9→8
T_min = 0.947, T_max = 0.994	l = −16→16
10807 measured 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)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.107	H atoms treated by a mixture of independent and constrained refinement
S = 1.08	w = 1/[σ²(F_o²) + (0.0623P)² + 1.9022P] where P = (F_o² + 2F_c²)/3
2502 reflections	(Δ/σ)_max = 0.032
176 parameters	Δρ_max = 0.28 e Å⁻³
0 restraints	Δρ_min = −0.24 e Å⁻³
0 constraints

Crystal data top

C₁₂H₂₂N₅⁺·Cl⁻	V = 2833.6 (2) Å³
M_r = 271.80	Z = 8
Monoclinic, C2/c	Mo Kα radiation
a = 24.7908 (12) Å	µ = 0.26 mm⁻¹
b = 8.2419 (4) Å	T = 298 K
c = 13.8764 (6) Å	0.21 × 0.18 × 0.03 mm
β = 91.968 (2)°

Data collection top

Bruker APEXII CCD diffractometer	2502 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 2004)	2266 reflections with I > 2σ(I)
T_min = 0.947, T_max = 0.994	R_int = 0.024
10807 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.036	0 restraints
wR(F²) = 0.107	H atoms treated by a mixture of independent and constrained refinement
S = 1.08	Δρ_max = 0.28 e Å⁻³
2502 reflections	Δρ_min = −0.24 e Å⁻³
176 parameters

Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

	x	y	z	U_iso*/U_eq
Cl1	0.199032 (17)	1.43859 (6)	1.09649 (3)	0.04241 (17)
H5N	0.2006 (7)	0.482 (2)	0.9400 (14)	0.034 (5)*
H3NA	0.0476 (8)	1.470 (3)	1.0540 (14)	0.044 (5)*
H3NB	0.0967 (9)	1.378 (2)	1.0672 (14)	0.038 (5)*
N1	0.07954 (5)	1.14699 (15)	0.96467 (10)	0.0313 (3)
N5	0.20241 (5)	0.49472 (15)	0.87744 (10)	0.0286 (3)
N2	−0.00534 (5)	1.28695 (16)	0.95048 (10)	0.0350 (3)
N4	0.09426 (5)	0.90139 (16)	0.89023 (10)	0.0325 (3)
C4	0.05934 (6)	1.02649 (18)	0.90933 (11)	0.0281 (3)
C3	0.00567 (6)	1.02975 (19)	0.87524 (11)	0.0319 (4)
H3	−0.0092	0.9435	0.8402	0.038*
C7	0.15214 (6)	0.93324 (19)	0.89292 (13)	0.0353 (4)
H7A	0.1605	1.0164	0.9406	0.042*
H7B	0.1625	0.9737	0.8306	0.042*
C6	0.18440 (6)	0.78141 (18)	0.91761 (12)	0.0338 (4)
H6A	0.2226	0.8049	0.9141	0.041*
H6B	0.1774	0.7484	0.9831	0.041*
C10	0.16963 (6)	0.64399 (17)	0.84886 (11)	0.0279 (3)
H10	0.1788	0.6761	0.7834	0.033*
C9	0.10936 (6)	0.6144 (2)	0.85116 (13)	0.0363 (4)
H9A	0.1003	0.5765	0.9147	0.044*
H9B	0.0993	0.5304	0.8050	0.044*
C2	−0.02438 (6)	1.1647 (2)	0.89536 (11)	0.0329 (4)
N3	0.06371 (7)	1.37851 (19)	1.05091 (12)	0.0416 (4)
C8	0.07765 (7)	0.7682 (2)	0.82731 (13)	0.0403 (4)
H8A	0.0832	0.7984	0.7608	0.048*
H8B	0.0395	0.7476	0.8341	0.048*
C1	0.04550 (6)	1.26709 (18)	0.98595 (11)	0.0307 (3)
C12	0.26044 (7)	0.5144 (2)	0.85548 (14)	0.0407 (4)
H12A	0.2740	0.6127	0.8844	0.061*
H12B	0.2641	0.5195	0.7869	0.061*
H12C	0.2806	0.4236	0.8810	0.061*
C11	0.18204 (7)	0.34164 (19)	0.83246 (13)	0.0397 (4)
H11A	0.1446	0.3278	0.8462	0.059*
H11B	0.2024	0.2515	0.8582	0.059*
H11C	0.1860	0.3468	0.7639	0.059*
C5	−0.08123 (8)	1.1816 (3)	0.85504 (15)	0.0527 (5)
H5A	−0.0969	1.2794	0.8792	0.079*
H5B	−0.1022	1.0901	0.8743	0.079*
H5C	−0.0808	1.1862	0.7859	0.079*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0423 (3)	0.0540 (3)	0.0307 (2)	−0.00239 (18)	−0.00195 (18)	0.00571 (17)
N1	0.0286 (7)	0.0259 (7)	0.0397 (7)	0.0011 (5)	0.0026 (5)	−0.0023 (5)
N5	0.0331 (7)	0.0263 (7)	0.0263 (7)	0.0036 (5)	0.0014 (5)	0.0005 (5)
N2	0.0335 (7)	0.0315 (7)	0.0399 (7)	0.0060 (6)	0.0011 (6)	−0.0022 (6)
N4	0.0275 (7)	0.0266 (7)	0.0434 (8)	0.0023 (5)	−0.0001 (6)	−0.0071 (6)
C4	0.0307 (8)	0.0251 (7)	0.0286 (7)	0.0013 (6)	0.0045 (6)	0.0022 (6)
C3	0.0334 (8)	0.0325 (8)	0.0296 (8)	0.0027 (6)	−0.0014 (6)	−0.0032 (6)
C7	0.0287 (8)	0.0255 (8)	0.0518 (10)	−0.0005 (6)	0.0050 (7)	−0.0019 (7)
C6	0.0276 (8)	0.0267 (8)	0.0470 (9)	0.0009 (6)	−0.0017 (7)	−0.0061 (7)
C10	0.0337 (8)	0.0234 (7)	0.0266 (7)	0.0037 (6)	0.0015 (6)	0.0019 (6)
C9	0.0345 (9)	0.0266 (8)	0.0474 (10)	0.0001 (7)	−0.0048 (7)	−0.0086 (7)
C2	0.0319 (8)	0.0370 (9)	0.0299 (8)	0.0052 (7)	0.0010 (6)	0.0007 (7)
N3	0.0348 (8)	0.0326 (8)	0.0571 (9)	0.0052 (7)	−0.0033 (7)	−0.0124 (7)
C8	0.0356 (9)	0.0351 (9)	0.0494 (10)	0.0066 (7)	−0.0094 (7)	−0.0121 (8)
C1	0.0314 (8)	0.0261 (8)	0.0348 (8)	0.0002 (6)	0.0055 (6)	0.0006 (6)
C12	0.0325 (9)	0.0385 (9)	0.0510 (10)	0.0050 (7)	0.0022 (7)	−0.0055 (8)
C11	0.0431 (9)	0.0241 (8)	0.0516 (10)	0.0029 (7)	0.0004 (8)	−0.0036 (7)
C5	0.0419 (10)	0.0593 (12)	0.0559 (12)	0.0167 (9)	−0.0140 (9)	−0.0128 (10)

Geometric parameters (Å, º) top

N1—C1	1.340 (2)	C10—C9	1.515 (2)
N1—C4	1.342 (2)	C10—H10	0.9800
N5—C11	1.488 (2)	C9—C8	1.522 (2)
N5—C12	1.490 (2)	C9—H9A	0.9700
N5—C10	1.5196 (19)	C9—H9B	0.9700
N5—H5N	0.878 (19)	C2—C5	1.505 (2)
N2—C2	1.341 (2)	N3—C1	1.353 (2)
N2—C1	1.347 (2)	N3—H3NA	0.85 (2)
N4—C4	1.378 (2)	N3—H3NB	0.84 (2)
N4—C8	1.453 (2)	C8—H8A	0.9700
N4—C7	1.458 (2)	C8—H8B	0.9700
C4—C3	1.397 (2)	C12—H12A	0.9600
C3—C2	1.373 (2)	C12—H12B	0.9600
C3—H3	0.9300	C12—H12C	0.9600
C7—C6	1.518 (2)	C11—H11A	0.9600
C7—H7A	0.9700	C11—H11B	0.9600
C7—H7B	0.9700	C11—H11C	0.9600
C6—C10	1.518 (2)	C5—H5A	0.9600
C6—H6A	0.9700	C5—H5B	0.9600
C6—H6B	0.9700	C5—H5C	0.9600

C1—N1—C4	116.57 (13)	C8—C9—H9A	109.4
C11—N5—C12	108.81 (12)	C10—C9—H9B	109.4
C11—N5—C10	113.97 (12)	C8—C9—H9B	109.4
C12—N5—C10	111.73 (12)	H9A—C9—H9B	108.0
C11—N5—H5N	106.4 (12)	N2—C2—C3	122.82 (14)
C12—N5—H5N	107.3 (12)	N2—C2—C5	116.69 (14)
C10—N5—H5N	108.3 (12)	C3—C2—C5	120.49 (15)
C2—N2—C1	115.07 (13)	C1—N3—H3NA	119.1 (14)
C4—N4—C8	120.92 (13)	C1—N3—H3NB	118.5 (13)
C4—N4—C7	118.99 (13)	H3NA—N3—H3NB	116.1 (19)
C8—N4—C7	114.18 (13)	N4—C8—C9	111.39 (13)
N1—C4—N4	116.06 (13)	N4—C8—H8A	109.3
N1—C4—C3	120.80 (14)	C9—C8—H8A	109.3
N4—C4—C3	123.14 (14)	N4—C8—H8B	109.3
C2—C3—C4	117.64 (15)	C9—C8—H8B	109.3
C2—C3—H3	121.2	H8A—C8—H8B	108.0
C4—C3—H3	121.2	N1—C1—N2	126.69 (14)
N4—C7—C6	111.57 (13)	N1—C1—N3	116.72 (14)
N4—C7—H7A	109.3	N2—C1—N3	116.58 (14)
C6—C7—H7A	109.3	N5—C12—H12A	109.5
N4—C7—H7B	109.3	N5—C12—H12B	109.5
C6—C7—H7B	109.3	H12A—C12—H12B	109.5
H7A—C7—H7B	108.0	N5—C12—H12C	109.5
C10—C6—C7	111.07 (13)	H12A—C12—H12C	109.5
C10—C6—H6A	109.4	H12B—C12—H12C	109.5
C7—C6—H6A	109.4	N5—C11—H11A	109.5
C10—C6—H6B	109.4	N5—C11—H11B	109.5
C7—C6—H6B	109.4	H11A—C11—H11B	109.5
H6A—C6—H6B	108.0	N5—C11—H11C	109.5
C9—C10—C6	108.89 (12)	H11A—C11—H11C	109.5
C9—C10—N5	112.52 (12)	H11B—C11—H11C	109.5
C6—C10—N5	108.95 (12)	C2—C5—H5A	109.5
C9—C10—H10	108.8	C2—C5—H5B	109.5
C6—C10—H10	108.8	H5A—C5—H5B	109.5
N5—C10—H10	108.8	C2—C5—H5C	109.5
C10—C9—C8	111.32 (14)	H5A—C5—H5C	109.5
C10—C9—H9A	109.4	H5B—C5—H5C	109.5

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3NB···Cl1	0.84 (2)	2.60 (2)	3.4284 (17)	167.2 (17)
N5—H5N···Cl1ⁱ	0.878 (19)	2.20 (2)	3.0785 (14)	177.1 (17)
N3—H3NA···N2	0.86 (2)	2.26 (2)	3.114 (2)	175.5 (18)

Symmetry code: (i) x, y−1, z.

Experimental details

Crystal data
Chemical formula	C₁₂H₂₂N₅⁺·Cl⁻
M_r	271.80
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	298
a, b, c (Å)	24.7908 (12), 8.2419 (4), 13.8764 (6)
β (°)	91.968 (2)
V (Å³)	2833.6 (2)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.26
Crystal size (mm)	0.21 × 0.18 × 0.03

Data collection
Diffractometer	Bruker APEXII CCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 2004)
T_min, T_max	0.947, 0.994
No. of measured, independent and observed [I > 2σ(I)] reflections	10807, 2502, 2266
R_int	0.024
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.036, 0.107, 1.08
No. of reflections	2502
No. of parameters	176
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.28, −0.24

Computer programs: APEX2 (Bruker, 2004), SAINT-Plus (Bruker, 2004), SAINT-Plus (Bruker,2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 2012).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3NB···Cl1	0.84 (2)	2.60 (2)	3.4284 (17)	167.2 (17)
N5—H5N···Cl1ⁱ	0.878 (19)	2.20 (2)	3.0785 (14)	177.1 (17)
N3—H3NA···N2	0.86 (2)	2.26 (2)	3.114 (2)	175.5 (18)

Symmetry code: (i) x, y−1, z.

Acknowledgements

The authors thank Dr S. C. Sharma, Vice Chancellor, Tumkur University, Tumkur, for his constant encouragement. BSPM thanks Dr H. C. Devarajegowda, Department of Physics, Yuvarajas College (constituent), University of Mysore, for his support and guidence.

References

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Sheldrick, G. M. (2004). SADABS. University of Göttingen, Germany. Google Scholar
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