I would think that bond should be the same distance (within hundredths
of an Ångstrom) as the other 5 carbon-carbon bonds in the benzene
ring. That whole molecule is aromatic, by the way.
I can't answer the "how come" question except to say that is most
likely wrong, due to making wrong assumptions about the hybridization
state of the relevant atomic orbitals, I guess.
phenix.elbow will probably do a better job. It even has an option for
using a quantum-mechanics-based geometry optimization.
Your intuition is right: those bonds should be extremely close to the
same distances as those found in benzene and imidazole.
On Sep 24, 2009, at 1:06 AM, Zheng Zhou wrote:
Thanks Bill for clarifying the notion of aromatic bonds
I think the C-C bond shared by the benzene and imidazole ring should
be close to a double bond distance
http://en.wikipedia.org/wiki/Benzimidazole
How come calculation from monomer sketcher and the BZI entry in the
library has a distance close to a single bond?
Joe
On Thu, Sep 24, 2009 at 12:36 PM, William G. Scott
<wgsc...@chemistry.ucsc.edu> wrote:
On Sep 23, 2009, at 5:03 PM, Zheng Zhou wrote:
Is there a clear definition of delocalized bond or armatic bond?
Hi Zheng:
Aromatic bonds only occur in planar cyclic molecules that have 4n
+2 pi
electrons. Aromatic interactions give energetic stabilization
beyond that
observed for delocalized conjugated systems, for example, the
aromatic
stabilization of benzene is the energy difference between real
benzene and a
hypothetical set of resonance structures representing delocalized
1,3,5-cyclohexatriene. Similarly, anti-aromatic interactions occur
in planar
cyclic molecules having 4n pi electrons; they are destabilized
relative to
their hypothetical cycloalkene counterparts. (If you allow for
perpendicular
aromatic interactions, Hoffmann and Goldstein in 1971 demonstrated
that 4n
pi electrons in that case are also stabilizing, due to the different
topology of the pi electron interactions, something that may be of
relevance
to aromatic side chain clusters.)
HTH,
Bill
