organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
(Schell & Engels, 1997). Therefore, substituted 1H-imidazole-
4,5-dicarbonitriles were tested as activators for stereoselection
during the synthesis of dinucleoside methyl phosphonates.
Selectivities up to 84/16 (RP/SP) have been reported by Schell
& Engels (1998). Single crystals were obtained for three
different substituted 1H-imidazole-4,5-dicarbonitriles used for
these experiments and the crystal structures of these three
compounds, namely 2-(30,50-dimethylbiphenyl-2-yl)-1H-imid-
azole-4,5-dicarbonitrile, (I), 2-(20,40,60-trimethylbiphenyl-2-yl)-
1H-imidazole-4,5-dicarbonitrile, (II), and 2-[8-(3,5-dimethyl-
phenyl)naphthalen-1-yl]-1H-imidazole-4,5-dicarbonitrile, (III),
are reported here.
ISSN 0108-2701
Biphenyl- and phenylnaphthalenyl-
substituted 1H-imidazole-4,5-dicarbo-
nitrile catalysts for the coupling reac-
tion of nucleoside methyl phosphon-
amidites
Jan W. Bats,* Peter Schell and Joachim W. Engels
Institut fur Organische Chemie und Chemische Biologie, Universitat Frankfurt, Max-
¨
¨
von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
Received 21 March 2013
Accepted 5 April 2013
Crystal structures are reported for three substituted 1H-
imidazole-4,5-dicarbonitrile compounds used as catalysts for
the coupling reaction of nucleoside methyl phosphonamidites,
namely 2-(30,50-dimethylbiphenyl-2-yl)-1H-imidazole-4,5-di-
carbonitrile, C19H14N4, (I), 2-(20,40,60-trimethylbiphenyl-2-yl)-
1H-imidazole-4,5-dicarbonitrile, C20H16N4, (II), and 2-[8-(3,5-
dimethylphenyl)naphthalen-1-yl]-1H-imidazole-4,5-dicarbo-
nitrile, C23H16N4, (III). The asymmetric unit of (I) contains
two independent molecules with similar conformations. There
is steric repulsion between the imidazole group and the
terminal phenyl group in all three compounds, resulting in the
nonplanarity of the molecules. The naphthalene group of (III)
shows significant deviation from planarity. The C—N bond
lengths in the imidazole rings range from 1.325 (2) to
The crystal structure of (I) contains two crystallographically
independent molecules, A and B (Fig. 1), which have very
similar conformations. The angles between the planes of the
six-membered rings of the biphenyl group are 44.91 (6)ꢁ for
molecule A and 42.09 (6)ꢁ for molecule B. The angle between
the plane of the imidazole group and that of the central phenyl
group is 46.02 (7)ꢁ for molecule A and 39.57 (7)ꢁ for molecule
B. There is significant steric repulsion between the dimethyl-
phenyl and imidazole groups [shortest contacts: C5ꢀ ꢀ ꢀC13 =
˚
˚
˚
3.115 (3) A, N5ꢀ ꢀ ꢀC20 = 3.094 (3) A, N5ꢀ ꢀ ꢀC25 = 3.144 (2) A
˚
and C20ꢀ ꢀ ꢀC32 = 3.115 (3) A]. These steric contacts are not
only responsible for the nonplanar conformation of the
biphenyl group, but also result in an out-of-plane distortion of
the dimethylphenyl and imidazole groups with respect to the
plane of the central benzene ring. Consequently, the C6—
C7—C12—C13 and C25—C26—C31—C32 torsion angles are
ꢂ6.6 (3) and ꢂ9.6 (3)ꢁ, respectively. The amino N atoms are
planar, the sums of the three valence angles about atoms N2
and N5 being 359.4 (8) and 360.0 (9)ꢁ, respectively. The mol-
ecules are connected by N—Hꢀ ꢀ ꢀN hydrogen bonds (Fig. 2
and Table 1) between the imidazole groups to form zigzag
chains parallel to the b-axis direction. These chains are
connected by weak intermolecular C—Hꢀ ꢀ ꢀN contacts
(Table 1) to give a three-dimensional structure.
˚
1.377 (2) A. The molecules are connected into zigzag chains
by intermolecular N—Hꢀ ꢀ ꢀNimidazole [for (I)] or N—
Hꢀ ꢀ ꢀꢀNcyano [for (II) and (III)] hydrogen bonds.
Comment
Methyl phosphonate oligonucleotides differ from conven-
tional oligonucleotides by the replacement of a negatively
charged O atom at the phosphonate linkage by a methyl
group. They are more stable to degradation by cellular
nucleases than are conventional oligonucleotides, and they
can be applied in the antisense concept to control gene
expression in mammalian cells (Uhlmann & Peyman, 1990).
The P atoms in methyl phosphonate oligonucleotides are
chiral, and RP-configured molecules bind better to their target
strand than do SP-configured ones (Lebedev & Wickstrom,
1996). The phosphoramidite approach can be used for the
The molecular structure of (II) is shown in Fig. 3. The angle
between the planes of the six-membered rings of the biphenyl
group is 71.20 (4)ꢁ, almost 30ꢁ larger than the corresponding
values in (I), resulting from steric repulsions between the
ortho-methyl groups and the imidazole group on one hand and
the C10—H10A bond on the other [shortest contacts:
˚
˚
C10ꢀ ꢀ ꢀC18 = 3.261 (2) A and C1ꢀ ꢀ ꢀH20C = 2.75 A]. The angle
between the planes of the imidazole ring and the central
benzene ring is 29.39 (6)ꢁ, slightly smaller than the corre-
sponding values observed in (I), despite the short intra-
¨
synthesis of methyl phosphonate oligonucleotides (Jager &
Engels, 1984). The reaction is activated by the use of tetrazole
but no stereocontrol occurs at the P atom. Also, the use of
tetrazoles with a chiral substituent gives only weak selectivity
˚
molecular contact distance of 2.879 (2) A between atoms N1
Acta Cryst. (2013). C69, 529–533
doi:10.1107/S0108270113009293
# 2013 International Union of Crystallography 529