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Acta Crystallogr Sect E Struct Rep Online. 2009 September 1; 65(Pt 9): o2134–o2135.
Published online 2009 August 12. doi:  10.1107/S1600536809031079
PMCID: PMC2970111

(Z)-2,2,2-Trichloro-N 2-cyano­acetamidine

Abstract

The title compound, C3H2Cl3N3, crystallizes as the Z isomer with respect to the C=N bond. The –C(NH2)=NCN functional group is effectively planar (r.m.s. deviation = 0.016 Å), with only the three Cl atoms out of the mol­ecular plane. A strong network of N—H(...)N hydrogen bonds forms dimers which are associated into ribbons in the crystal structure. Hydrogen bonding is suspected to be the cause of the near-equivalence of the formal C—N and C=N bonds (ΔCN = 0.008 Å)

Related literature

For literature related to characterization, see: Huffman & Schaefer (1963 [triangle]). For comparable structures of N′-cyano­amidines; see Allen (2002 [triangle]). For the crystal structures of N 2-cyano-3-[2-diamino­methyl­eneamino)-4-thia­zolylmethyl­thio]propionamidine­monohydrate, (II) and 3-{2-[amino­(methyl­amino)methyl­eneamino]-4-thia­zolylmethyl­thio}-N 2-cyano­propionamidine, (III), see Ishida et al. (1989 [triangle]). For the crystal structure of (E)-1,2-bis­(1-amino-1-(cyano­imino)-2-methyl­prop-2-yl)diazene-1,2- dioxide, (IV), see: Tretyakov et al. (2006 [triangle]). For the sole other acyclic trichloro­methyl amidine with a reported crystal structure, N-(4-amino-3-furan­zanyl)-2,2,2-trichloro-N-methoxy­acetamidine, (V), see: George & Gilardi (1986 [triangle]). For background to the ΔCN parameter, see: Boeré, et al. (1998 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2134-scheme1.jpg

Experimental

Crystal data

  • C3H2Cl3N3
  • M r = 186.43
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2134-efi1.jpg
  • a = 5.5388 (4) Å
  • b = 6.6127 (4) Å
  • c = 18.4727 (12) Å
  • β = 95.122 (1)°
  • V = 673.89 (8) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 1.26 mm−1
  • T = 173 K
  • 0.41 × 0.27 × 0.21 mm

Data collection

  • Bruker APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2006 [triangle]) T min = 0.616, T max = 0.770
  • 7459 measured reflections
  • 1552 independent reflections
  • 1479 reflections with I > 2σ(I)
  • R int = 0.017

Refinement

  • R[F 2 > 2σ(F 2)] = 0.019
  • wR(F 2) = 0.050
  • S = 1.06
  • 1552 reflections
  • 83 parameters
  • H-atom parameters constrained
  • Δρmax = 0.41 e Å−3
  • Δρmin = −0.27 e Å−3

Data collection: APEX2 (Bruker, 2006 [triangle]); cell refinement: SAINT-Plus (Bruker, 2006 [triangle]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL (Sheldrick, 2008 [triangle]); molecular graphics: Mercury (Macrae et al., 2006 [triangle]); software used to prepare material for publication: publCIF (Westrip, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)
Table 2
Comparative distances (Å) and angles (°) in amidines (I)–(V)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809031079/wn2341sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809031079/wn2341Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The Natural Sciences and Engineering Research Council of Canada (NSERC) is gratefully acknowledged for a Discovery Grant. The diffractometer was purchased with the help of NSERC and the University of Lethbridge. Tracy Burton (formerly of this Department) is acknowledged for the synthesis of the title compound.

supplementary crystallographic information

Comment

The stucture of the title compound, (I), is shown in Fig. 1. Molecular dimensions are available in the archived CIF. Structure (I) crystallizes as the Z isomer with respect to the imino bond (Fig. 1). The structure is essentially planar except for the CCl3 group (r.m.s. mean deviation for the —C(NH2)═NCN group is 0.016 Å), while Cl2 is almost perpendicular to this plane; thus Cl1 deviates by 0.65 and Cl3 by 0.84 Å from the plane. The parameter ΔCN = d(C—N) - d(C═N) has been found to range between 0 and 0.178 Å for many amidines for which the structures are known (Boeré et al., 1998). For (I), ΔCN = 0.008 Å, which is very small for a monomeric amidine with such unsymmetrical substitution. The N2–C3–N3 angle is almost linear, at 172.16 (13)°. There is a network of N—H···N hydrogen bonds (Table 1) linking centrosymmetric pairs of molecules into planar ribbons along the b axis (Fig. 2). Short contacts of 3.203 (1) Å between Cl2 (the upward- and downward-facing chlorine atoms) and N2 (imino nitrogen) link these layers into a 3-D network in the crystal structure. Finally, there are 3.4132 (5) Å short contacts between Cl1 and Cl2 bridging molecules. It is likely that this strong intermolecular hydrogen bonding is responsible for the small value of ΔCN.

Of nine N'-cyanoamidines in the literature, six are E (refcodes HANBAA, ILIPAU, JATLIZ, TAHHOA, TESQAK, WAXXUO; Allen, 2002) and two are Z (refcodes JATMAS, NERKAX; Allen, 2002) with respect to the imino bond; for the last, VOVPUR (Allen, 2002), the isomer is not specified. The most relevant for comparison with (I) are N2-cyano-3-[2-diaminomethyleneamino)-4-thiazolylmethylthio]propionamidinemonohydrate, (II), 3-{2-[amino(methylamino)methyleneamino]-4-thiazolylmethylthio}-N2-cyanopropionamidine, (III) (Ishida et al., 1989) and (E)-1,2-bis(1-amino-1-(cyanoimino)-2-methylprop-2-yl)diazene-1,2- dioxide, (IV) (Tretyakov et al., 2006), which all bear the NH2 group in addition to the nitrile on N'. Each of these structures shares the high degree of planarity of the –C(NH2)═NCN group (r.m.s. deviations for (II) - (IV) are 0.008, 0.025 and 0.069 Å, respectively.) Of these three examples, (II) is E while (III) and (IV) are both Z; note that (II) and (III) differ only in methylation at a very remote amino group. There is only one acyclic trichloromethyl amidine with a crystal structure reported in the literature, viz. N-(4-amino-3-furanzanyl)-2,2,2-trichloro-N-methoxyacetamidine, (V) (George & Gilardi, 1986) and this is the Z isomer. The structure of (IV), which is arguably the most similar structure, electronically and chemically, to (I) also shows a very similar pattern of hydrogen bonding where centrosymetric dimers are linked in ribbons within the crystal structure by additional hydrogen bonds.

Key geometrical parameters for structures (I) - (V) are compared in Table 2, which includes values for ΔCN, all of which fall within the known range. However, (II) and (III) are highly unusual in having the wrong sign for this parameter. That is, the imino bond is actually longer than the amino. We are not aware of other instances of this occurrence; the locations of the NH2 hydrogen atoms in both structures were corroborated by expected hydrogen bonding. It is likely that this powerful hydrogen bonding is responsible for the inversion in expected bond distances, perhaps augmented by the strong electron-withdrawing cyano subsituent on N'.

Experimental

General Procedures: Reagent grade methanol was dried by distillation with Mg and catalytic I2. Sodium methoxide was transferred to the flask within a glove box under nitrogen.

Preparation of methyl trichloroacetimidate: 50 ml of dried methanol and 21.66 g (150 mmol) of trichloroacetonitrile were added to 0.50 g (10 mmol) of sodium methoxide. After stirring for 48 h at room temperature, the solution was saturated with CO2(s) to eliminate remaining sodium methoxide. Methanol was then distilled off at 335–7 K, whereafter the liquid methyl trichloroacetimidate was distilled at 415 K at a reduced pressure. Yield 19.59 g (110 mmol, 74%).

Preparation of 2,2,2-trichloro-N'-cyano-acetamidine: 0.42 g (10 mmol) of cyanamide was dissolved in 5 ml of anhydrous methanol. With stirring, 1.76 g (10 mmol) of methyl trichloroacetimidate was added dropwise. An ice bath may be required to maintain temperature during addition of methyl trichloroacetimidate. The solution was stirred for 3 h at RT. Methanol was removed by rotary evaporation followed by high vacuum. The solid residue was dissolved in a minimum volume (3.5 ml) of hot CH3CN, cooled to room temperature, and placed within the 238 K freezer. The colourless crystals produced were filtered and vacuum dried yielding 0.121 g (0.649 mmol, 6.51% yield), mp 433–7 K (Huffman & Schaefer, 1963).

Refinement

Both H atoms were located in a difference Fourier map. They were refined using a riding model and Uiso(H) was set equal to 1.2Ueq(N1). The highest residual peak has a fraction of the electron density of a single H atom and is located 0.76 Å from Cl1.

Figures

Fig. 1.
A view of (I), plotted with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitrary radius.
Fig. 2.
The network of hydrogen bonds (dashed lines) linking centrosymmetric pairs of molecules into planar ribbons along the b axis. Symmetry equivalents are -x, 1 + y, -z; 2 - x, -y, -x and 2 - x, 1 - y, -x. These ribbons lie parallel to the (207) Miller planes. ...

Crystal data

C3H2Cl3N3F(000) = 368
Mr = 186.43Dx = 1.838 Mg m3
Monoclinic, P21/nMelting point: 441 K
Hall symbol: -P 2ynMo Kα radiation, λ = 0.71073 Å
a = 5.5388 (4) ÅCell parameters from 4497 reflections
b = 6.6127 (4) Åθ = 2.2–27.6°
c = 18.4727 (12) ŵ = 1.26 mm1
β = 95.122 (1)°T = 173 K
V = 673.89 (8) Å3Block, colourless
Z = 40.41 × 0.27 × 0.21 mm

Data collection

Bruker APEXII CCD area-detector diffractometer1552 independent reflections
Radiation source: Molybdenum1479 reflections with I > 2σ(I)
graphiteRint = 0.017
[var phi] and ω scansθmax = 27.5°, θmin = 2.2°
Absorption correction: multi-scan (SADABS; Bruker, 2006)h = −7→7
Tmin = 0.616, Tmax = 0.770k = −8→8
7459 measured reflectionsl = −24→23

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.019H-atom parameters constrained
wR(F2) = 0.050w = 1/[σ2(Fo2) + (0.0247P)2 + 0.2765P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.001
1552 reflectionsΔρmax = 0.41 e Å3
83 parametersΔρmin = −0.27 e Å3
0 restraintsExtinction correction: SHELXTL (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0231 (18)

Special details

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)

xyzUiso*/Ueq
Cl10.23790 (5)0.15285 (5)0.181208 (18)0.02983 (10)
Cl20.66794 (6)0.37010 (5)0.233709 (17)0.02976 (10)
Cl30.33903 (6)0.53919 (5)0.119806 (17)0.02989 (10)
C20.62444 (19)0.20753 (17)0.10178 (6)0.0179 (2)
C30.7632 (2)−0.09854 (17)0.06561 (7)0.0224 (2)
C10.4692 (2)0.31232 (17)0.15584 (6)0.0196 (2)
N20.62859 (18)0.01089 (15)0.10646 (5)0.0229 (2)
N10.74493 (18)0.32334 (15)0.05999 (6)0.0230 (2)
H1A0.84300.26890.03050.028*
H1B0.72770.45550.06140.028*
N30.8680 (2)−0.21297 (17)0.03320 (6)0.0298 (2)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.02508 (16)0.02924 (17)0.03733 (18)−0.00196 (11)0.01472 (13)0.00338 (12)
Cl20.03001 (17)0.03173 (17)0.02701 (16)0.00592 (12)−0.00034 (12)−0.01080 (12)
Cl30.03524 (18)0.02289 (16)0.03307 (17)0.01263 (12)0.01157 (13)0.00600 (11)
C20.0173 (5)0.0184 (5)0.0181 (5)0.0013 (4)0.0022 (4)−0.0011 (4)
C30.0260 (6)0.0158 (5)0.0259 (6)−0.0021 (4)0.0060 (5)0.0019 (4)
C10.0199 (5)0.0175 (5)0.0221 (5)0.0025 (4)0.0054 (4)0.0012 (4)
N20.0269 (5)0.0166 (5)0.0264 (5)0.0015 (4)0.0096 (4)0.0000 (4)
N10.0270 (5)0.0168 (5)0.0270 (5)0.0010 (4)0.0121 (4)0.0001 (4)
N30.0364 (6)0.0194 (5)0.0355 (6)0.0012 (4)0.0136 (5)−0.0025 (4)

Geometric parameters (Å, °)

Cl1—C11.7549 (12)C2—C11.5396 (15)
Cl2—C11.7733 (12)C3—N31.1533 (17)
Cl3—C11.7686 (12)C3—N21.3226 (16)
C2—N21.3032 (15)N1—H1A0.8800
C2—N11.3115 (15)N1—H1B0.8800
N2—C2—N1127.94 (11)C2—C1—Cl2106.31 (7)
N2—C2—C1114.43 (10)Cl1—C1—Cl2109.15 (6)
N1—C2—C1117.52 (10)Cl3—C1—Cl2108.98 (6)
N3—C3—N2172.16 (13)C2—N2—C3121.04 (10)
C2—C1—Cl1111.47 (8)C2—N1—H1A120.0
C2—C1—Cl3111.73 (8)C2—N1—H1B120.0
Cl1—C1—Cl3109.12 (6)H1A—N1—H1B120.0
N2—C2—C1—Cl1−26.28 (12)N2—C2—C1—Cl292.56 (10)
N1—C2—C1—Cl1157.21 (9)N1—C2—C1—Cl2−83.95 (11)
N2—C2—C1—Cl3−148.66 (9)N1—C2—N2—C3−0.9 (2)
N1—C2—C1—Cl334.83 (12)C1—C2—N2—C3−176.95 (10)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1A···N3i0.882.102.9583 (15)164
N1—H1B···N3ii0.882.403.1893 (15)150

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

Table 2 Comparative distances (Å) and angles (°) in amidines (I)–(V)

Value(I)(II)(III)(IV)(V)
C2-N11.3115 (15)1.308 (4)1.308 (3)1.307 (2)1.387 (4)
C2-N21.3032 (15)1.320 (4)1.317 (3)1.306 (2)1.2737 (4)
ΔCN0.008-0.012-0.0090.0010.114
C2-C11.5396 (15)1.520 (4)1.513 (3)1.522 (3)1.525 (5)
C3-N31.1533 (17)1.164 (4)1.1567 (3)1.153 (3)
C3-N21.3226 (16)1.320 (4)1.333 (3)1.322 (3)
N2-C2-N1127.94 (11)118.0 (2)125.9 (2)126.0 (2)127.7 (3)
N2-C2-C1114.43 (10)124.1 (2)116.8 (2)114.9 (1)117.2 (3)
N1-C2-C1117.52 (10)117.9 (2)117.3 (2)118.7 (1)115.0 (3)
C2-N2-C3121.04 (10)119.1 (2)118.7 (1)
N3-C3-N2172.16 (13)173.2 (2)173.9 (3)173.2 (2)

Atom numbering corresponds to that in Fig. 1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: WN2341).

References

  • Allen, F. H. (2002). Acta Cryst. B58, 380–388. [PubMed]
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  • Bruker (2006). APEX2, SAINT-Plus and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • George, C. & Gilardi, R. (1986). Acta Cryst. C42, 1457–1458.
  • Huffman, K. R. & Schaefer, F. C. (1963). J. Org. Chem.28, 1812–1816.
  • Ishida, T., In, Y., Doi, M., Inoue, M. & Yanagisawa, I. (1989). Acta Cryst. B45, 505–512. [PubMed]
  • Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst.39, 453–457.
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  • Westrip, S. J. (2009). publCIF. In preparation.

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