Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805042601/gh6032sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536805042601/gh6032Isup2.hkl |
CCDC reference: 296563
Key indicators
- Single-crystal X-ray study
- T = 273 K
- Mean (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
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
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).
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—N═C(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.
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).
C9H10N4S | Dx = 1.342 Mg m−3 |
Mr = 206.27 | Melting point: 409 K |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
a = 11.219 (2) Å | Cell parameters from 1019 reflections |
b = 7.6960 (16) Å | θ = 2.3–20.7° |
c = 11.957 (3) Å | µ = 0.28 mm−1 |
β = 98.527 (3)° | T = 293 K |
V = 1021.0 (4) Å3 | Parallelepiped, colorless |
Z = 4 | 0.10 × 0.10 × 0.08 mm |
F(000) = 432 |
Bruker SMART CCD area-detector diffractometer | 1793 independent reflections |
Radiation source: fine-focus sealed tube | 1296 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.022 |
φ and ω scans | θmax = 25.0°, θmin = 2.3° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1997b) | h = −13→13 |
Tmin = 0.972, Tmax = 0.978 | k = −9→5 |
4341 measured reflections | l = −14→14 |
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)] = 0.034 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.101 | H-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 parameters | Δρmax = 0.15 e Å−3 |
0 restraints | Δρmin = −0.20 e Å−3 |
C9H10N4S | V = 1021.0 (4) Å3 |
Mr = 206.27 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 11.219 (2) Å | µ = 0.28 mm−1 |
b = 7.6960 (16) Å | T = 293 K |
c = 11.957 (3) Å | 0.10 × 0.10 × 0.08 mm |
β = 98.527 (3)° |
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 = 0.978 | Rint = 0.022 |
4341 measured reflections |
R[F2 > 2σ(F2)] = 0.034 | 0 restraints |
wR(F2) = 0.101 | H-atom parameters constrained |
S = 1.05 | Δρmax = 0.15 e Å−3 |
1793 reflections | Δρmin = −0.20 e Å−3 |
127 parameters |
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 |
x | y | z | Uiso*/Ueq | ||
S1 | 1.06402 (5) | 0.25321 (8) | 0.49645 (5) | 0.0621 (2) | |
C1 | 1.1045 (2) | 0.3244 (4) | 0.6390 (2) | 0.0735 (7) | |
H1A | 1.1906 | 0.3340 | 0.6561 | 0.110* | |
H1B | 1.0762 | 0.2418 | 0.6892 | 0.110* | |
H1C | 1.0685 | 0.4356 | 0.6483 | 0.110* | |
C2 | 0.9157 (2) | 0.1357 (3) | 0.29804 (19) | 0.0618 (6) | |
C3 | 0.90709 (17) | 0.2406 (2) | 0.47505 (17) | 0.0483 (5) | |
C4 | 0.71085 (17) | 0.2680 (3) | 0.53856 (18) | 0.0554 (5) | |
H4A | 0.6783 | 0.2935 | 0.4606 | 0.067* | |
H4B | 0.6780 | 0.3521 | 0.5862 | 0.067* | |
C5 | 0.67237 (15) | 0.0887 (3) | 0.56775 (16) | 0.0488 (5) | |
C6 | 0.65260 (17) | −0.0436 (3) | 0.48986 (17) | 0.0565 (6) | |
H6A | 0.6620 | −0.0240 | 0.4149 | 0.068* | |
C7 | 0.61883 (19) | −0.2054 (3) | 0.5234 (2) | 0.0615 (6) | |
H7A | 0.6049 | −0.2959 | 0.4715 | 0.074* | |
C8 | 0.60624 (19) | −0.2306 (3) | 0.6339 (2) | 0.0661 (6) | |
H8A | 0.5846 | −0.3405 | 0.6562 | 0.079* | |
C9 | 0.65569 (18) | 0.0507 (3) | 0.67704 (18) | 0.0594 (6) | |
H9A | 0.6677 | 0.1395 | 0.7303 | 0.071* | |
N1 | 0.9609 (2) | 0.0882 (3) | 0.22380 (18) | 0.0895 (7) | |
N2 | 0.85113 (15) | 0.1871 (2) | 0.37640 (14) | 0.0560 (5) | |
N3 | 0.84227 (14) | 0.2855 (2) | 0.55370 (14) | 0.0522 (4) | |
H3A | 0.8786 | 0.3267 | 0.6165 | 0.063* | |
N4 | 0.62347 (16) | −0.1048 (3) | 0.71152 (15) | 0.0678 (5) |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0445 (3) | 0.0725 (4) | 0.0699 (4) | 0.0002 (3) | 0.0105 (2) | 0.0086 (3) |
C1 | 0.0567 (13) | 0.0844 (17) | 0.0756 (15) | −0.0073 (13) | −0.0031 (11) | 0.0107 (14) |
C2 | 0.0704 (14) | 0.0593 (14) | 0.0555 (13) | 0.0057 (12) | 0.0093 (11) | 0.0110 (11) |
C3 | 0.0442 (11) | 0.0463 (11) | 0.0550 (12) | 0.0027 (9) | 0.0093 (9) | 0.0112 (10) |
C4 | 0.0449 (11) | 0.0617 (14) | 0.0610 (13) | 0.0072 (10) | 0.0126 (9) | 0.0047 (11) |
C5 | 0.0337 (9) | 0.0610 (13) | 0.0522 (11) | 0.0051 (9) | 0.0078 (8) | 0.0011 (11) |
C6 | 0.0432 (11) | 0.0737 (15) | 0.0533 (12) | 0.0015 (10) | 0.0099 (9) | −0.0017 (11) |
C7 | 0.0464 (12) | 0.0682 (15) | 0.0702 (15) | −0.0023 (11) | 0.0098 (10) | −0.0118 (12) |
C8 | 0.0538 (13) | 0.0678 (15) | 0.0759 (16) | −0.0051 (11) | 0.0067 (11) | 0.0092 (14) |
C9 | 0.0537 (12) | 0.0700 (15) | 0.0543 (12) | −0.0048 (11) | 0.0072 (10) | −0.0043 (11) |
N1 | 0.1114 (18) | 0.0966 (17) | 0.0661 (13) | 0.0194 (14) | 0.0316 (13) | 0.0048 (13) |
N2 | 0.0523 (10) | 0.0646 (11) | 0.0514 (10) | 0.0025 (9) | 0.0084 (8) | 0.0039 (9) |
N3 | 0.0458 (9) | 0.0590 (11) | 0.0523 (10) | −0.0015 (8) | 0.0090 (8) | −0.0003 (8) |
N4 | 0.0644 (12) | 0.0793 (14) | 0.0589 (11) | −0.0097 (10) | 0.0065 (9) | 0.0070 (11) |
S1—C3 | 1.744 (2) | C4—H4B | 0.9700 |
S1—C1 | 1.783 (2) | C5—C6 | 1.376 (3) |
C1—H1A | 0.9600 | C5—C9 | 1.379 (3) |
C1—H1B | 0.9600 | C6—C7 | 1.378 (3) |
C1—H1C | 0.9600 | C6—H6A | 0.9300 |
C2—N1 | 1.146 (3) | C7—C8 | 1.363 (3) |
C2—N2 | 1.327 (3) | C7—H7A | 0.9300 |
C3—N3 | 1.317 (3) | C8—N4 | 1.335 (3) |
C3—N2 | 1.317 (3) | C8—H8A | 0.9300 |
C4—N3 | 1.465 (2) | C9—N4 | 1.333 (3) |
C4—C5 | 1.502 (3) | C9—H9A | 0.9300 |
C4—H4A | 0.9700 | N3—H3A | 0.8600 |
C3—S1—C1 | 105.41 (10) | C9—C5—C4 | 119.95 (19) |
S1—C1—H1A | 109.5 | C5—C6—C7 | 119.7 (2) |
S1—C1—H1B | 109.5 | C5—C6—H6A | 120.1 |
H1A—C1—H1B | 109.5 | C7—C6—H6A | 120.1 |
S1—C1—H1C | 109.5 | C8—C7—C6 | 118.8 (2) |
H1A—C1—H1C | 109.5 | C8—C7—H7A | 120.6 |
H1B—C1—H1C | 109.5 | C6—C7—H7A | 120.6 |
N1—C2—N2 | 173.3 (3) | N4—C8—C7 | 123.1 (2) |
N3—C3—N2 | 118.74 (18) | N4—C8—H8A | 118.5 |
N3—C3—S1 | 122.21 (16) | C7—C8—H8A | 118.5 |
N2—C3—S1 | 119.04 (15) | N4—C9—C5 | 124.4 (2) |
N3—C4—C5 | 111.99 (16) | N4—C9—H9A | 117.8 |
N3—C4—H4A | 109.2 | C5—C9—H9A | 117.8 |
C5—C4—H4A | 109.2 | C3—N2—C2 | 119.19 (18) |
N3—C4—H4B | 109.2 | C3—N3—C4 | 122.67 (17) |
C5—C4—H4B | 109.2 | C3—N3—H3A | 118.7 |
H4A—C4—H4B | 107.9 | C4—N3—H3A | 118.7 |
C6—C5—C9 | 117.0 (2) | C9—N4—C8 | 117.0 (2) |
C6—C5—C4 | 123.07 (18) |
D—H···A | D—H | H···A | D···A | D—H···A |
C1—H1B···N1i | 0.96 | 2.80 | 3.697 (4) | 156 |
N3—H3A···N4ii | 0.86 | 2.13 | 2.902 (3) | 150 |
C6—H6A···N2 | 0.93 | 2.77 | 3.294 (3) | 117 |
C7—H7A···N1iii | 0.93 | 2.51 | 3.358 (3) | 152 |
C8—H8A···N1iv | 0.93 | 2.56 | 3.451 (3) | 161 |
Symmetry codes: (i) −x+2, −y, −z+1; (ii) −x+3/2, y+1/2, −z+3/2; (iii) −x+3/2, y−1/2, −z+1/2; (iv) x−1/2, −y−1/2, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C9H10N4S |
Mr | 206.27 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 293 |
a, b, c (Å) | 11.219 (2), 7.6960 (16), 11.957 (3) |
β (°) | 98.527 (3) |
V (Å3) | 1021.0 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.28 |
Crystal size (mm) | 0.10 × 0.10 × 0.08 |
Data collection | |
Diffractometer | Bruker SMART CCD area-detector |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1997b) |
Tmin, Tmax | 0.972, 0.978 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4341, 1793, 1296 |
Rint | 0.022 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.034, 0.101, 1.05 |
No. of reflections | 1793 |
No. of parameters | 127 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 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).
C2—N1 | 1.146 (3) | C3—N2 | 1.317 (3) |
C2—N2 | 1.327 (3) | C4—N3 | 1.465 (2) |
C3—N3 | 1.317 (3) | C8—N4 | 1.335 (3) |
C3—S1—C1 | 105.41 (10) | N3—C4—C5 | 111.99 (16) |
N1—C2—N2 | 173.3 (3) | C3—N2—C2 | 119.19 (18) |
N3—C3—N2 | 118.74 (18) | C3—N3—C4 | 122.67 (17) |
D—H···A | D—H | H···A | D···A | D—H···A |
C1—H1B···N1i | 0.96 | 2.80 | 3.697 (4) | 156 |
N3—H3A···N4ii | 0.86 | 2.13 | 2.902 (3) | 150 |
C6—H6A···N2 | 0.93 | 2.77 | 3.294 (3) | 117 |
C7—H7A···N1iii | 0.93 | 2.51 | 3.358 (3) | 152 |
C8—H8A···N1iv | 0.93 | 2.56 | 3.451 (3) | 161 |
Symmetry codes: (i) −x+2, −y, −z+1; (ii) −x+3/2, y+1/2, −z+3/2; (iii) −x+3/2, y−1/2, −z+1/2; (iv) x−1/2, −y−1/2, z+1/2. |
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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—N═C(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.