Literature DB >> 21577545

(Z)-2,2,2-Trichloro-N-cyano-acetamidine.

A Elizabeth Baker1, René T Boeré.   

Abstract

The title compound, C(3)H(2)Cl(3)N(3), crystallizes as the Z isomer with respect to the C=N bond. The -C(NH(2))=NCN functional group is effectively planar (r.m.s. deviation = 0.016 Å), with only the three Cl atoms out of the mol-ecular plane. A strong network of N-H⋯N n class="Chemical">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 (Δ(CN) = 0.008 Å).

Entities:  

Year:  2009        PMID: 21577545      PMCID: PMC2970111          DOI: 10.1107/S1600536809031079

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For literature related to characterization, see: Huffman & Schaefer (1963 ▶). For comparable structures of N′-cyano­amidines; see Allen (2002 ▶). For the crystal structures of N 2-cyano-3-[2-diamino­methyl­eneamino)-4-thia­zolylmethyl­thio]propionn class="Chemical">amidine­monohydrate, (II) and 3-{2-[amino­(methyl­amino)methyl­eneamino]-4-thia­zolylmethyl­thio}-N 2-cyano­propionamidine, (III), see Ishida et al. (1989 ▶). 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 ▶). 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 ▶). For background to the ΔCN parameter, see: Boeré, et al. (1998 ▶).

Experimental

Crystal data

C3H2Cl3N3 M = 186.43 Monoclinic, 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 ▶) 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 ▶); cell refinement: SAINT-Plus (Bruker, 2006 ▶); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL (Sheldrick, 2008 ▶); molecular graphics: Mercury (Macrae et al., 2006 ▶); software used to prepare material for publication: publCIF (Westrip, 2009 ▶). 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
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
Bruker APEXII CCD area-detector diffractometer1552 independent reflections
Radiation source: Molybdenum1479 reflections with I > 2σ(I)
graphiteRint = 0.017
φ 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 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)
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.
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)
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)
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)
D—H···AD—HH···AD···AD—H···A
N1—H1A···N3i0.882.102.9583 (15)164
N1—H1B···N3ii0.882.403.1893 (15)150
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)
Table 1

Hydrogen-bond geometry (Å, °)

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

Symmetry codes: (i) ; (ii) .

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)  

Compound (I) corresponds to the title compound and (II)–(V) are defined in the Related Literature section. Atom numbering corresponds to that in Fig. 1 (in Supplementary materials).

  3 in total

1.  The Cambridge Structural Database: a quarter of a million crystal structures and rising.

Authors:  Frank H Allen
Journal:  Acta Crystallogr B       Date:  2002-05-29

2.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

3.  Structural study of histamine H2-receptor antagonists. Five 3-[2-(diamino-methyleneamino)-4-thiazolylmethylthio]propionamidine and -amide derivatives.

Authors:  T Ishida; Y In; M Doi; M Inoue; I Yanagisawa
Journal:  Acta Crystallogr B       Date:  1989-10-01
  3 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.