organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

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 ππ 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[Patel, R., Desai, K. & Chikhalia, K. (2003). J. Indian Chem. Soc. 80, 138-145.]).

[Scheme 1]

Experimental

Crystal data
  • C12H22N5+·Cl

  • Mr = 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)[Sheldrick, G. M. (2004). SADABS. University of Göttingen, Germany.] Tmin = 0.947, Tmax = 0.994

  • 10807 measured reflections

  • 2502 independent reflections

  • 2266 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.28 e Å−3

  • Δρmin = −0.24 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Bruker (2004). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT-Plus (Bruker, 2004[Bruker (2004). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]); software used to prepare material for publication: SHELXL97.

Supporting information


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.

Refinement top

The H atoms were positioned with idealized geometry using a riding model with C—H = 0.93- 0.97 Å. All C—H atoms were refined with isotropic displacement parameters (set to 1.2–1.5 times of the Ueq of the parent atom) and N—H atoms were refined freely

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
[Figure 1] Fig. 1. Molecular structure of the title compound, showing displacement ellipsoids drawn at the 50% probability level.
[Figure 2] 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+·ClF(000) = 1168
Mr = 271.80Prism
Monoclinic, C2/cDx = 1.274 Mg m3
Hall symbol: -C 2ycMo Kα radiation, λ = 0.71073 Å
a = 24.7908 (12) ÅCell parameters from 2266 reflections
b = 8.2419 (4) Åθ = 1.6–52°
c = 13.8764 (6) ŵ = 0.26 mm1
β = 91.968 (2)°T = 298 K
V = 2833.6 (2) Å3Prism, colourless
Z = 80.21 × 0.18 × 0.03 mm
Data collection top
Bruker APEXII CCD
diffractometer
2502 independent reflections
Radiation source: fine-focus sealed tube2266 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.024
Detector resolution: 1.20 pixels mm-1θmax = 25.0°, θmin = 1.6°
ω scansh = 2829
Absorption correction: multi-scan
(SADABS; Sheldrick, 2004)
k = 98
Tmin = 0.947, Tmax = 0.994l = 1616
10807 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.107H atoms treated by a mixture of independent and constrained refinement
S = 1.08 w = 1/[σ2(Fo2) + (0.0623P)2 + 1.9022P]
where P = (Fo2 + 2Fc2)/3
2502 reflections(Δ/σ)max = 0.032
176 parametersΔρmax = 0.28 e Å3
0 restraintsΔρmin = 0.24 e Å3
0 constraints
Crystal data top
C12H22N5+·ClV = 2833.6 (2) Å3
Mr = 271.80Z = 8
Monoclinic, C2/cMo Kα radiation
a = 24.7908 (12) ŵ = 0.26 mm1
b = 8.2419 (4) ÅT = 298 K
c = 13.8764 (6) Å0.21 × 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)
Tmin = 0.947, Tmax = 0.994Rint = 0.024
10807 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0360 restraints
wR(F2) = 0.107H atoms treated by a mixture of independent and constrained refinement
S = 1.08Δρmax = 0.28 e Å3
2502 reflectionsΔρmin = 0.24 e Å3
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
xyzUiso*/Ueq
Cl10.199032 (17)1.43859 (6)1.09649 (3)0.04241 (17)
H5N0.2006 (7)0.482 (2)0.9400 (14)0.034 (5)*
H3NA0.0476 (8)1.470 (3)1.0540 (14)0.044 (5)*
H3NB0.0967 (9)1.378 (2)1.0672 (14)0.038 (5)*
N10.07954 (5)1.14699 (15)0.96467 (10)0.0313 (3)
N50.20241 (5)0.49472 (15)0.87744 (10)0.0286 (3)
N20.00534 (5)1.28695 (16)0.95048 (10)0.0350 (3)
N40.09426 (5)0.90139 (16)0.89023 (10)0.0325 (3)
C40.05934 (6)1.02649 (18)0.90933 (11)0.0281 (3)
C30.00567 (6)1.02975 (19)0.87524 (11)0.0319 (4)
H30.00920.94350.84020.038*
C70.15214 (6)0.93324 (19)0.89292 (13)0.0353 (4)
H7A0.16051.01640.94060.042*
H7B0.16250.97370.83060.042*
C60.18440 (6)0.78141 (18)0.91761 (12)0.0338 (4)
H6A0.22260.80490.91410.041*
H6B0.17740.74840.98310.041*
C100.16963 (6)0.64399 (17)0.84886 (11)0.0279 (3)
H100.17880.67610.78340.033*
C90.10936 (6)0.6144 (2)0.85116 (13)0.0363 (4)
H9A0.10030.57650.91470.044*
H9B0.09930.53040.80500.044*
C20.02438 (6)1.1647 (2)0.89536 (11)0.0329 (4)
N30.06371 (7)1.37851 (19)1.05091 (12)0.0416 (4)
C80.07765 (7)0.7682 (2)0.82731 (13)0.0403 (4)
H8A0.08320.79840.76080.048*
H8B0.03950.74760.83410.048*
C10.04550 (6)1.26709 (18)0.98595 (11)0.0307 (3)
C120.26044 (7)0.5144 (2)0.85548 (14)0.0407 (4)
H12A0.27400.61270.88440.061*
H12B0.26410.51950.78690.061*
H12C0.28060.42360.88100.061*
C110.18204 (7)0.34164 (19)0.83246 (13)0.0397 (4)
H11A0.14460.32780.84620.059*
H11B0.20240.25150.85820.059*
H11C0.18600.34680.76390.059*
C50.08123 (8)1.1816 (3)0.85504 (15)0.0527 (5)
H5A0.09691.27940.87920.079*
H5B0.10221.09010.87430.079*
H5C0.08081.18620.78590.079*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0423 (3)0.0540 (3)0.0307 (2)0.00239 (18)0.00195 (18)0.00571 (17)
N10.0286 (7)0.0259 (7)0.0397 (7)0.0011 (5)0.0026 (5)0.0023 (5)
N50.0331 (7)0.0263 (7)0.0263 (7)0.0036 (5)0.0014 (5)0.0005 (5)
N20.0335 (7)0.0315 (7)0.0399 (7)0.0060 (6)0.0011 (6)0.0022 (6)
N40.0275 (7)0.0266 (7)0.0434 (8)0.0023 (5)0.0001 (6)0.0071 (6)
C40.0307 (8)0.0251 (7)0.0286 (7)0.0013 (6)0.0045 (6)0.0022 (6)
C30.0334 (8)0.0325 (8)0.0296 (8)0.0027 (6)0.0014 (6)0.0032 (6)
C70.0287 (8)0.0255 (8)0.0518 (10)0.0005 (6)0.0050 (7)0.0019 (7)
C60.0276 (8)0.0267 (8)0.0470 (9)0.0009 (6)0.0017 (7)0.0061 (7)
C100.0337 (8)0.0234 (7)0.0266 (7)0.0037 (6)0.0015 (6)0.0019 (6)
C90.0345 (9)0.0266 (8)0.0474 (10)0.0001 (7)0.0048 (7)0.0086 (7)
C20.0319 (8)0.0370 (9)0.0299 (8)0.0052 (7)0.0010 (6)0.0007 (7)
N30.0348 (8)0.0326 (8)0.0571 (9)0.0052 (7)0.0033 (7)0.0124 (7)
C80.0356 (9)0.0351 (9)0.0494 (10)0.0066 (7)0.0094 (7)0.0121 (8)
C10.0314 (8)0.0261 (8)0.0348 (8)0.0002 (6)0.0055 (6)0.0006 (6)
C120.0325 (9)0.0385 (9)0.0510 (10)0.0050 (7)0.0022 (7)0.0055 (8)
C110.0431 (9)0.0241 (8)0.0516 (10)0.0029 (7)0.0004 (8)0.0036 (7)
C50.0419 (10)0.0593 (12)0.0559 (12)0.0167 (9)0.0140 (9)0.0128 (10)
Geometric parameters (Å, º) top
N1—C11.340 (2)C10—C91.515 (2)
N1—C41.342 (2)C10—H100.9800
N5—C111.488 (2)C9—C81.522 (2)
N5—C121.490 (2)C9—H9A0.9700
N5—C101.5196 (19)C9—H9B0.9700
N5—H5N0.878 (19)C2—C51.505 (2)
N2—C21.341 (2)N3—C11.353 (2)
N2—C11.347 (2)N3—H3NA0.85 (2)
N4—C41.378 (2)N3—H3NB0.84 (2)
N4—C81.453 (2)C8—H8A0.9700
N4—C71.458 (2)C8—H8B0.9700
C4—C31.397 (2)C12—H12A0.9600
C3—C21.373 (2)C12—H12B0.9600
C3—H30.9300C12—H12C0.9600
C7—C61.518 (2)C11—H11A0.9600
C7—H7A0.9700C11—H11B0.9600
C7—H7B0.9700C11—H11C0.9600
C6—C101.518 (2)C5—H5A0.9600
C6—H6A0.9700C5—H5B0.9600
C6—H6B0.9700C5—H5C0.9600
C1—N1—C4116.57 (13)C8—C9—H9A109.4
C11—N5—C12108.81 (12)C10—C9—H9B109.4
C11—N5—C10113.97 (12)C8—C9—H9B109.4
C12—N5—C10111.73 (12)H9A—C9—H9B108.0
C11—N5—H5N106.4 (12)N2—C2—C3122.82 (14)
C12—N5—H5N107.3 (12)N2—C2—C5116.69 (14)
C10—N5—H5N108.3 (12)C3—C2—C5120.49 (15)
C2—N2—C1115.07 (13)C1—N3—H3NA119.1 (14)
C4—N4—C8120.92 (13)C1—N3—H3NB118.5 (13)
C4—N4—C7118.99 (13)H3NA—N3—H3NB116.1 (19)
C8—N4—C7114.18 (13)N4—C8—C9111.39 (13)
N1—C4—N4116.06 (13)N4—C8—H8A109.3
N1—C4—C3120.80 (14)C9—C8—H8A109.3
N4—C4—C3123.14 (14)N4—C8—H8B109.3
C2—C3—C4117.64 (15)C9—C8—H8B109.3
C2—C3—H3121.2H8A—C8—H8B108.0
C4—C3—H3121.2N1—C1—N2126.69 (14)
N4—C7—C6111.57 (13)N1—C1—N3116.72 (14)
N4—C7—H7A109.3N2—C1—N3116.58 (14)
C6—C7—H7A109.3N5—C12—H12A109.5
N4—C7—H7B109.3N5—C12—H12B109.5
C6—C7—H7B109.3H12A—C12—H12B109.5
H7A—C7—H7B108.0N5—C12—H12C109.5
C10—C6—C7111.07 (13)H12A—C12—H12C109.5
C10—C6—H6A109.4H12B—C12—H12C109.5
C7—C6—H6A109.4N5—C11—H11A109.5
C10—C6—H6B109.4N5—C11—H11B109.5
C7—C6—H6B109.4H11A—C11—H11B109.5
H6A—C6—H6B108.0N5—C11—H11C109.5
C9—C10—C6108.89 (12)H11A—C11—H11C109.5
C9—C10—N5112.52 (12)H11B—C11—H11C109.5
C6—C10—N5108.95 (12)C2—C5—H5A109.5
C9—C10—H10108.8C2—C5—H5B109.5
C6—C10—H10108.8H5A—C5—H5B109.5
N5—C10—H10108.8C2—C5—H5C109.5
C10—C9—C8111.32 (14)H5A—C5—H5C109.5
C10—C9—H9A109.4H5B—C5—H5C109.5
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3NB···Cl10.84 (2)2.60 (2)3.4284 (17)167.2 (17)
N5—H5N···Cl1i0.878 (19)2.20 (2)3.0785 (14)177.1 (17)
N3—H3NA···N20.86 (2)2.26 (2)3.114 (2)175.5 (18)
Symmetry code: (i) x, y1, z.

Experimental details

Crystal data
Chemical formulaC12H22N5+·Cl
Mr271.80
Crystal system, space groupMonoclinic, C2/c
Temperature (K)298
a, b, c (Å)24.7908 (12), 8.2419 (4), 13.8764 (6)
β (°) 91.968 (2)
V3)2833.6 (2)
Z8
Radiation typeMo Kα
µ (mm1)0.26
Crystal size (mm)0.21 × 0.18 × 0.03
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2004)
Tmin, Tmax0.947, 0.994
No. of measured, independent and
observed [I > 2σ(I)] reflections
10807, 2502, 2266
Rint0.024
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.036, 0.107, 1.08
No. of reflections2502
No. of parameters176
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N3—H3NB···Cl10.84 (2)2.60 (2)3.4284 (17)167.2 (17)
N5—H5N···Cl1i0.878 (19)2.20 (2)3.0785 (14)177.1 (17)
N3—H3NA···N20.86 (2)2.26 (2)3.114 (2)175.5 (18)
Symmetry code: (i) x, y1, 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

First citationBruker (2004). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationFarrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.  Web of Science CrossRef CAS IUCr Journals
First citationPatel, R., Desai, K. & Chikhalia, K. (2003). J. Indian Chem. Soc. 80, 138–145.  CAS
First citationSheldrick, G. M. (2004). SADABS. University of Göttingen, Germany.
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals

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