Subject: Re: CCL:Bond length in solid and gas phase

From: [email-masked] (Per-Ola Norrby)
Date: Thu, 19 Dec 1996 14:03:02 +0100

Hi Gert,

>I would be interested if there is a 'rule of thumb' about differences
>in bond length (and angles) between solid and gase phase organic
>molecules.

        We can actually do better than a rule of thumb.  MM3 (that is,
Allingers original MM3, none of the copies, this is the Mac version) can
calculate the difference between bond lengths from different determination
methods, at least the part that is due to centrifugal distortion and
anharmonic vibration.  I guess this is sufficient?  It still gives nuclear
distances, so it's not appropriate for X-ray hydrogens for example, but the
difference between electron density center and nuclear position shouldn't
be significant for heavy atoms in the X-ray (I'm not entirely sure how much
the nitrogen lone pair will affect the position in the X-ray though).

>Specifically, we are interested in diphenylamine and would
>like to know if one can use the solid state (x-ray) data and somehow
>scale it to a gas phase value.

        One problem here, the usual with MM3.  We don't have all
parameters.  However, using an "amide" (sp2) nitrogen and guessing a single
parameter, I calculated the following table for diphenyl amine:

                VIBRATIONAL AMPLITUDE AND CENTRIFUGAL DISTORTION
                   CONTRIBUTION TO THE BOND LENGTH

           BOND             R(g)      R(z)     R(alp)     R(e)      R(a)
       2( C)-  1( C)       1.3966    1.3926    1.3849    1.3888    1.3951
       3( C)-  2( C)       1.3975    1.3936    1.3825    1.3897    1.3960
       4( C)-  3( C)       1.4009    1.3963    1.3786    1.3930    1.3994
       5( C)-  4( C)       1.3966    1.3926    1.3849    1.3888    1.3951
       6( C)-  1( C)       1.3959    1.3909    1.3731    1.3881    1.3944
       6( C)-  5( C)       1.3960    1.3913    1.3781    1.3883    1.3946
       7( H)-  1( C)       1.1032    1.0855    1.0749    1.0805    1.0978
       8( H)-  2( C)       1.1008    1.0837    1.0711    1.0783    1.0954
       9( H)-  4( C)       1.1029    1.0859    1.0753    1.0802    1.0975
      10( H)-  5( C)       1.1033    1.0852    1.0701    1.0805    1.0979
      11( H)-  6( C)       1.1032    1.0857    1.0787    1.0805    1.0978
      12( N)-  3( C)       1.4247    1.4210    1.4156    1.4167    1.4232
      13( H)- 12( N)       1.0274    1.0106    1.0096    1.0078    1.0224
      14( C)- 12( N)       1.4247    1.4210    1.4156    1.4167    1.4232
      15( C)- 14( C)       1.3974    1.3934    1.3823    1.3896    1.3959
      16( C)- 15( C)       1.3967    1.3927    1.3850    1.3889    1.3952
      17( C)- 16( C)       1.3958    1.3908    1.3730    1.3880    1.3943
      18( C)- 17( C)       1.3961    1.3914    1.3782    1.3884    1.3947
      19( C)- 14( C)       1.4010    1.3964    1.3787    1.3932    1.3995
      19( C)- 18( C)       1.3965    1.3925    1.3848    1.3887    1.3950
      20( H)- 15( C)       1.1008    1.0837    1.0711    1.0783    1.0954
      21( H)- 16( C)       1.1032    1.0855    1.0749    1.0805    1.0978
      22( H)- 17( C)       1.1032    1.0857    1.0787    1.0805    1.0978
      23( H)- 18( C)       1.1033    1.0852    1.0701    1.0805    1.0979
      24( H)- 19( C)       1.1029    1.0859    1.0753    1.0802    1.0975

        The two first columns are gas phase values (expected from electron
diffraction and microwave), then comes expected X-ray values (thermal
averages of nuclear positions at 298 K), minimum energy nuclear positions
(appropriate for ab initio), and one more value I don't know exactly, but I
guess it's gas phase also (thermal average of distance with r-1 weighting).
Take your pick.  Even though absolute values may be off (one guessed
parameter, remember), relative ones should be OK.

        Per-Ola Norrby

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 *  Per-Ola Norrby
 *  The Royal Danish School of Pharmacy, Dept. of Med. Chem.
 *  Universitetsparken 2, DK 2100 Copenhagen, Denmark
 *  tel. +45-35376777-506, +45-35370850    fax +45-35372209
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