Re: [ccp4bb] delocalized bond or aromatic bond

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Rfree in similar data set
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2009-09-24

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Subject: Re: Rfree in similar data set
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-09-24

Subject: Re: delocalized bond or aromatic bond
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2009-09-24

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
> 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
>>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Rfree in similar data set
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2009-09-24

Next message:
Subject: Re: Rfree in similar data set
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-09-24