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The title compound, C9H10N4S, has been used as an inter­mediate in the synthesis of potassium channel openers, which show considerable biomolecular current-voltage rectification characteristics. In this crystal form, attractive C—H...N hydrogen bonds between neighboring mol­ecules form a centrosymmetric ten-membered ring. In addition, inter­molecular N—H...N hydrogen bonds form zigzag mol­ecular chains propagating in the b-axis direction.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805042601/gh6032sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536805042601/gh6032Isup2.hkl
Contains datablock I

CCDC reference: 296563

Key indicators

  • Single-crystal X-ray study
  • T = 273 K
  • Mean [sigma](C-C) = 0.003 Å
  • R factor = 0.034
  • wR factor = 0.101
  • Data-to-parameter ratio = 14.1

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical . ? PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given ....... ? PLAT230_ALERT_2_C Hirshfeld Test Diff for N2 - C2 .. 6.55 su PLAT480_ALERT_4_C Long H...A H-Bond Reported H1B .. N1 .. 2.80 Ang. PLAT480_ALERT_4_C Long H...A H-Bond Reported H6A .. N2 .. 2.77 Ang.
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 5 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 1 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 3 ALERT type 4 Improvement, methodology, query or suggestion

Comment top

Methyl N'-cyano-N-(3-pyridinylmethyl)imidothiocarbamate, (I), has been widely used in the synthesis of potassium channel openers (Altenbach et al., 2003, 2002??, 2001), which show considerable biomolecular current-voltage rectification characteristics (Babenko et al., 1998; Nelson & Quayle, 1995).

Fig. 1 depicts the structure of the molecule of (I), and selected bond lengths and angles are given in Table 1. The C2—N1 distance [1.146 (3) Å] shows predominantly triple-bond character, whereas the C2—N2, N2—C3 and C3—N3 distances [1.327 (3), 1.317 (3) and 1.317 (3) Å, respectively] suggest that they are partial double bonds. Together with the quasi-linear N1—C2—N2 angle [173.3 (3)°] of the cyano group, this pattern is typical of the "N C—NC(SCH3)-N" group of methyl N-cyanocarboximidothioate compounds (Lan et al., 2005).

Examination of the crystal structure of (I) reveals the existence of several possible C—H···N and N—H···N interactions (Table 2). A view down the a axis of the unit cell (Fig. 2) reveals hydrogen-bonded centrosymmetric ten-membered rings, which are formed by cyano-N···H7A and cyano-N···H8A intermolecular bonds. This same cyano N atom also accepts a third hydrogen bond that crosslinks neighboring hydrogen-bonded rings via N···H1B bonds. Thus, the terminal cyano N atom is a trifurcated hydrogen-bond acceptor. In addition, intermolecular N3—H3A···N4ii hydrogen bonds [symmetry code: (ii) 3/2 - x, 1/2 + y, 3/2 - z] form zigzag molecular chains propagating along the b axis direction, as shown in Fig. 3.

Experimental top

The title compound was synthesized by the reaction of 3-pyridinemethanamine and dimethyl cyanoimidodithiocarbonate according to the method of Lan et al. (2005). Single crystals of (I) were grown by slow evaporation, in air, of an ethanol solution. Selected analytical data: white solid, yield 91.4%; m.p. 407–409 K; 1H NMR (CDCl3, 500 MHz): δ 7.32–8.61 (m, 4H), 4.58 (d, 2H), 3.52 (br, 1H), 2.54 (s, 3H); IR (KBr) ν: 2997, 2975, 2932, 2181, 1685, 1552, 1427, 1235, 1173, 1019, 869, 767 cm-1

Refinement top

H atoms were included using a riding model, with C—H = 0.93, 0.96 or 0.97 Å, N—H = 0.86 Å and Uiso = 1.2Ueq(C,N) and 1.5Ueq(Cmethyl).

Structure description top

Methyl N'-cyano-N-(3-pyridinylmethyl)imidothiocarbamate, (I), has been widely used in the synthesis of potassium channel openers (Altenbach et al., 2003, 2002??, 2001), which show considerable biomolecular current-voltage rectification characteristics (Babenko et al., 1998; Nelson & Quayle, 1995).

Fig. 1 depicts the structure of the molecule of (I), and selected bond lengths and angles are given in Table 1. The C2—N1 distance [1.146 (3) Å] shows predominantly triple-bond character, whereas the C2—N2, N2—C3 and C3—N3 distances [1.327 (3), 1.317 (3) and 1.317 (3) Å, respectively] suggest that they are partial double bonds. Together with the quasi-linear N1—C2—N2 angle [173.3 (3)°] of the cyano group, this pattern is typical of the "N C—NC(SCH3)-N" group of methyl N-cyanocarboximidothioate compounds (Lan et al., 2005).

Examination of the crystal structure of (I) reveals the existence of several possible C—H···N and N—H···N interactions (Table 2). A view down the a axis of the unit cell (Fig. 2) reveals hydrogen-bonded centrosymmetric ten-membered rings, which are formed by cyano-N···H7A and cyano-N···H8A intermolecular bonds. This same cyano N atom also accepts a third hydrogen bond that crosslinks neighboring hydrogen-bonded rings via N···H1B bonds. Thus, the terminal cyano N atom is a trifurcated hydrogen-bond acceptor. In addition, intermolecular N3—H3A···N4ii hydrogen bonds [symmetry code: (ii) 3/2 - x, 1/2 + y, 3/2 - z] form zigzag molecular chains propagating along the b axis direction, as shown in Fig. 3.

Computing details top

Data collection: SMART (Bruker, 1999); cell refinement: SAINT (Bruker, 1999); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997a); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997a); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXTL (Sheldrick, 1997b).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 2] Fig. 2. The crystal structure of (I); dashed lines indicate C—H···N hydrogen bonds.
[Figure 3] Fig. 3. Zigzag molecular chains propagating in the b-axis direction; dashed lines indicate N3—H3A···N4ii hydrogen bonds. (Symmetry code as in Table 2.)
Methyl N'-cyano-N-(3-pyridinylmethyl)imidothiocarbamate top
Crystal data top
C9H10N4SDx = 1.342 Mg m3
Mr = 206.27Melting point: 409 K
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 11.219 (2) ÅCell parameters from 1019 reflections
b = 7.6960 (16) Åθ = 2.3–20.7°
c = 11.957 (3) ŵ = 0.28 mm1
β = 98.527 (3)°T = 293 K
V = 1021.0 (4) Å3Parallelepiped, colorless
Z = 40.10 × 0.10 × 0.08 mm
F(000) = 432
Data collection top
Bruker SMART CCD area-detector
diffractometer
1793 independent reflections
Radiation source: fine-focus sealed tube1296 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.022
φ and ω scansθmax = 25.0°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1997b)
h = 1313
Tmin = 0.972, Tmax = 0.978k = 95
4341 measured reflectionsl = 1414
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)] = 0.034Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.101H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + 0.2478P]
where P = (Fo2 + 2Fc2)/3
1793 reflections(Δ/σ)max = 0.001
127 parametersΔρmax = 0.15 e Å3
0 restraintsΔρmin = 0.20 e Å3
Crystal data top
C9H10N4SV = 1021.0 (4) Å3
Mr = 206.27Z = 4
Monoclinic, P21/nMo Kα radiation
a = 11.219 (2) ŵ = 0.28 mm1
b = 7.6960 (16) ÅT = 293 K
c = 11.957 (3) Å0.10 × 0.10 × 0.08 mm
β = 98.527 (3)°
Data collection top
Bruker SMART CCD area-detector
diffractometer
1793 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1997b)
1296 reflections with I > 2σ(I)
Tmin = 0.972, Tmax = 0.978Rint = 0.022
4341 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0340 restraints
wR(F2) = 0.101H-atom parameters constrained
S = 1.05Δρmax = 0.15 e Å3
1793 reflectionsΔρmin = 0.20 e Å3
127 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
S11.06402 (5)0.25321 (8)0.49645 (5)0.0621 (2)
C11.1045 (2)0.3244 (4)0.6390 (2)0.0735 (7)
H1A1.19060.33400.65610.110*
H1B1.07620.24180.68920.110*
H1C1.06850.43560.64830.110*
C20.9157 (2)0.1357 (3)0.29804 (19)0.0618 (6)
C30.90709 (17)0.2406 (2)0.47505 (17)0.0483 (5)
C40.71085 (17)0.2680 (3)0.53856 (18)0.0554 (5)
H4A0.67830.29350.46060.067*
H4B0.67800.35210.58620.067*
C50.67237 (15)0.0887 (3)0.56775 (16)0.0488 (5)
C60.65260 (17)0.0436 (3)0.48986 (17)0.0565 (6)
H6A0.66200.02400.41490.068*
C70.61883 (19)0.2054 (3)0.5234 (2)0.0615 (6)
H7A0.60490.29590.47150.074*
C80.60624 (19)0.2306 (3)0.6339 (2)0.0661 (6)
H8A0.58460.34050.65620.079*
C90.65569 (18)0.0507 (3)0.67704 (18)0.0594 (6)
H9A0.66770.13950.73030.071*
N10.9609 (2)0.0882 (3)0.22380 (18)0.0895 (7)
N20.85113 (15)0.1871 (2)0.37640 (14)0.0560 (5)
N30.84227 (14)0.2855 (2)0.55370 (14)0.0522 (4)
H3A0.87860.32670.61650.063*
N40.62347 (16)0.1048 (3)0.71152 (15)0.0678 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0445 (3)0.0725 (4)0.0699 (4)0.0002 (3)0.0105 (2)0.0086 (3)
C10.0567 (13)0.0844 (17)0.0756 (15)0.0073 (13)0.0031 (11)0.0107 (14)
C20.0704 (14)0.0593 (14)0.0555 (13)0.0057 (12)0.0093 (11)0.0110 (11)
C30.0442 (11)0.0463 (11)0.0550 (12)0.0027 (9)0.0093 (9)0.0112 (10)
C40.0449 (11)0.0617 (14)0.0610 (13)0.0072 (10)0.0126 (9)0.0047 (11)
C50.0337 (9)0.0610 (13)0.0522 (11)0.0051 (9)0.0078 (8)0.0011 (11)
C60.0432 (11)0.0737 (15)0.0533 (12)0.0015 (10)0.0099 (9)0.0017 (11)
C70.0464 (12)0.0682 (15)0.0702 (15)0.0023 (11)0.0098 (10)0.0118 (12)
C80.0538 (13)0.0678 (15)0.0759 (16)0.0051 (11)0.0067 (11)0.0092 (14)
C90.0537 (12)0.0700 (15)0.0543 (12)0.0048 (11)0.0072 (10)0.0043 (11)
N10.1114 (18)0.0966 (17)0.0661 (13)0.0194 (14)0.0316 (13)0.0048 (13)
N20.0523 (10)0.0646 (11)0.0514 (10)0.0025 (9)0.0084 (8)0.0039 (9)
N30.0458 (9)0.0590 (11)0.0523 (10)0.0015 (8)0.0090 (8)0.0003 (8)
N40.0644 (12)0.0793 (14)0.0589 (11)0.0097 (10)0.0065 (9)0.0070 (11)
Geometric parameters (Å, º) top
S1—C31.744 (2)C4—H4B0.9700
S1—C11.783 (2)C5—C61.376 (3)
C1—H1A0.9600C5—C91.379 (3)
C1—H1B0.9600C6—C71.378 (3)
C1—H1C0.9600C6—H6A0.9300
C2—N11.146 (3)C7—C81.363 (3)
C2—N21.327 (3)C7—H7A0.9300
C3—N31.317 (3)C8—N41.335 (3)
C3—N21.317 (3)C8—H8A0.9300
C4—N31.465 (2)C9—N41.333 (3)
C4—C51.502 (3)C9—H9A0.9300
C4—H4A0.9700N3—H3A0.8600
C3—S1—C1105.41 (10)C9—C5—C4119.95 (19)
S1—C1—H1A109.5C5—C6—C7119.7 (2)
S1—C1—H1B109.5C5—C6—H6A120.1
H1A—C1—H1B109.5C7—C6—H6A120.1
S1—C1—H1C109.5C8—C7—C6118.8 (2)
H1A—C1—H1C109.5C8—C7—H7A120.6
H1B—C1—H1C109.5C6—C7—H7A120.6
N1—C2—N2173.3 (3)N4—C8—C7123.1 (2)
N3—C3—N2118.74 (18)N4—C8—H8A118.5
N3—C3—S1122.21 (16)C7—C8—H8A118.5
N2—C3—S1119.04 (15)N4—C9—C5124.4 (2)
N3—C4—C5111.99 (16)N4—C9—H9A117.8
N3—C4—H4A109.2C5—C9—H9A117.8
C5—C4—H4A109.2C3—N2—C2119.19 (18)
N3—C4—H4B109.2C3—N3—C4122.67 (17)
C5—C4—H4B109.2C3—N3—H3A118.7
H4A—C4—H4B107.9C4—N3—H3A118.7
C6—C5—C9117.0 (2)C9—N4—C8117.0 (2)
C6—C5—C4123.07 (18)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1B···N1i0.962.803.697 (4)156
N3—H3A···N4ii0.862.132.902 (3)150
C6—H6A···N20.932.773.294 (3)117
C7—H7A···N1iii0.932.513.358 (3)152
C8—H8A···N1iv0.932.563.451 (3)161
Symmetry codes: (i) x+2, y, z+1; (ii) x+3/2, y+1/2, z+3/2; (iii) x+3/2, y1/2, z+1/2; (iv) x1/2, y1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC9H10N4S
Mr206.27
Crystal system, space groupMonoclinic, P21/n
Temperature (K)293
a, b, c (Å)11.219 (2), 7.6960 (16), 11.957 (3)
β (°) 98.527 (3)
V3)1021.0 (4)
Z4
Radiation typeMo Kα
µ (mm1)0.28
Crystal size (mm)0.10 × 0.10 × 0.08
Data collection
DiffractometerBruker SMART CCD area-detector
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1997b)
Tmin, Tmax0.972, 0.978
No. of measured, independent and
observed [I > 2σ(I)] reflections
4341, 1793, 1296
Rint0.022
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.034, 0.101, 1.05
No. of reflections1793
No. of parameters127
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.15, 0.20

Computer programs: SMART (Bruker, 1999), SAINT (Bruker, 1999), SAINT, SHELXS97 (Sheldrick, 1997a), SHELXL97 (Sheldrick, 1997a), ORTEP-3 (Farrugia, 1997), SHELXTL (Sheldrick, 1997b).

Selected geometric parameters (Å, º) top
C2—N11.146 (3)C3—N21.317 (3)
C2—N21.327 (3)C4—N31.465 (2)
C3—N31.317 (3)C8—N41.335 (3)
C3—S1—C1105.41 (10)N3—C4—C5111.99 (16)
N1—C2—N2173.3 (3)C3—N2—C2119.19 (18)
N3—C3—N2118.74 (18)C3—N3—C4122.67 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1B···N1i0.962.803.697 (4)156
N3—H3A···N4ii0.862.132.902 (3)150
C6—H6A···N20.932.773.294 (3)117
C7—H7A···N1iii0.932.513.358 (3)152
C8—H8A···N1iv0.932.563.451 (3)161
Symmetry codes: (i) x+2, y, z+1; (ii) x+3/2, y+1/2, z+3/2; (iii) x+3/2, y1/2, z+1/2; (iv) x1/2, y1/2, z+1/2.
 

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