Subject: Bonds vs No Bonds in Minimized Structures

From: Gary Breton <[email-masked]>
Date: Wed, 14 Nov 2001 07:16:46 -0500

Hello all,

I have been conducting some geometry minimizations on some
1,2-diazacyclobutane structures using Gaussian98 with the GaussView GUI.
When I minimize the parent compound (1,2-diazacyclobutane with N-H bonds) at
the RHF631G* level, everything looks fine.  If, however, I minimize at the
RB3LYP6311+G** level, a similar structure to the HF minimization results,
but GaussView does NOT SHOW a bond between the two nitrogen atoms.  The bond
has apparently not broken since the molecule adopts a geometry as if its
still there (i.e., in the HF minimization the N-N, C-N and C-C bond lengths
are 1.45405, 1.47272 and 1.53174, respectively, while in the B3LYP they are
1.49052, 1.49351 and 1.53844, respectively).  Furthermore, if I start with
the HF structure and further minimize at the B3LYP level, the bond again
disappears!  If I start with the B3LYP structure and ADD a N-N bond and then
re-minimize, it again eliminates the bond.

Is there any significance to the presence or absence of the bond?  Why would
GaussView not put a bond into the structure?

Thanks and best regards!

Gary W. Breton
Chair and Associate Professor
Department of Chemistry
Berry College
PO Box 495016
Mount Berry, GA 30149

"There's a light at the
end of the tunnel, but it
may be an oncoming train"

---

From: Laurence Cuffe <[email-masked]>
Date: Wed, 14 Nov 2001 14:31:03 +0000

Date sent:      	Wed, 14 Nov 2001 07:16:46 -0500
From:           	Gary Breton <[email-masked]>
Subject:        	CCL:Bonds vs No Bonds in Minimized Structures
To:             	[email-masked]

>GaussView not put a bond into the structure?
GaussView makes the call as to whether a bond exists based on 
the distance between the atoms in the archive entry or failing that 
the last geometry in the log file. Thus if the distance is slightly 
longer than gv expects for such a bond it is not shown.  If you wish 
to present images of the converged structure with the bond present 
you can do this be selecting bond length on the builder panel, 
selecting the two atoms, and then clicking on the bond type button 
in the panel that opens.  I hope this helps
Laurence Cuffe
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From: "Alexandre Hocquet" <[email-masked]>
Date: Wed, 14 Nov 2001 16:18:43 +0100

Looks like the GEOMETRICAL check used by Gaussview for existence or not of a
N-N bond has a threshold between 1.45 and 1.49...

Quantum mechanically, however, add or remove whatever bond you like : as
long as you have the same nuclei in the same geometrical position with the
same number of electrons, it will change nothing : the concept of bond is
useless for the quantum mechanical molecule.

The question "is there a bond between these two atoms" is thus not a
straightforward one, and certainly geometry is a piece of information but
rather incomplete. The analysis of the topology of the electronic density
(AIM or Bader's theory) may also provide clues, but it is not the unique way
either...

We could even say that Molecular Mechanics, on the contrary, is a theory
completely submitted to the concept of "bonding", because "bonding" is
central to the definition of the energy (every energy term is defined with
respect to "bound atoms"), hence the limitations with reactivity : you just
can't break the bonds !

------------------------------------------------------------
Alexandre HOCQUET
Laboratoire de Physicochimie Biomoléculaire et Cellulaire
ESA CNRS 7033
[email-masked]
Fax: 33 1 44277560
LPBC, case courrier 138
4 Place Jussieu, 75252 PARIS Cedex 05 France
------------------------------------------------------------

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From: "C.F. Matta" <[email-masked]>
Date: Wed, 14 Nov 2001 13:20:14 -0500 (EST)

Dear Alexandre

> (AIM or Bader's theory) may also provide clues, but it is not the unique way

I partially agree with you. We have just published a paper which shows
how the bond path, a line of maximum density linking two nuclei mirrored by
a line of maximal stabilization in space (maximlly negative potential
energy density), provides a unique answer to the question of whether
bonding exists or not.

We use an example from experiment where distance alone gives an
ambiguous picture while the bond path provides a clear cut answer
accompagnied by a host of other consequences. For instance, we find
significantly higher electron delocalization between two bonded
atoms (sharing a bond path) than between similar atoms separated by the
same distance but whithout sharing a bond path:

See:
====
Bader, R.F.W.; Matta, C.F. "Bonding to Titanium", Inorg. Chem. (2001), 40,
5603-5611.

Also see:
=========
Bader, R.F.W."A Bond Path: A Universal Indicator of Bonded Interaction",
J. Phys. Chem. A (1998), 102, 7314-7323.

Best wishes,

  Cherif
___________________________________________________________________________

  Cherif F. Matta                         tel. (905) 525-9140 ext. 22502
  Chemistry Department                    fax  (905) 522-2509
  McMaster University
  Hamilton, Ontario, CANADA L8S 4M1.
___________________________________________________________________________

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From: "Stefan Fau" <[email-masked]>
Date: Wed, 14 Nov 2001 11:49:23 -0500

Dear Prof. Breton,

Dr. Robinson is right. Most viewing programs
do not analyze the electronic structure to determine
if there is a bond between two atoms. Instead they
may compare the distance to the sum of covalent
radii or look if the input file specifies the existence
of a bond between the atoms in question (molecular
mechanics).

I assume that GaussView uses the distance criterion.
Since the covalent radius of N is 0.74A, the NN
distances in your molecule are near the critical distance
for drawing a bond or not.

You may analyze the electronic structure of your
molecules with Bader's AIM method or Weinholds
NBO analysis. AIM analyzes the topography of
the electron density and defines a bond as a line
connecting two atoms that is a maximum of the electron
density in the planes orthogonal to each of its points.

The NBO analysis is a series of basis set transformations
that results in the best "Lewis structure". Each NBO
corresponds to a line (or lone pair) in a Lewis structure.
NBO finds the best resonance structure. It does not
necessarily find NBOs that preserve the molecular
symmetry (e.g. benzene).

Stefan
______________________________________________________________________
Dr. Stefan Fau                    |      [email-masked]
Quantum Theory Project     |     (352) 392-6714
University of Florida
Gainesville, FL 32611-8435

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From: Wibke Sudholt <[email-masked]>
Date: Wed, 14 Nov 2001 18:37:04 -0800

Dear all,

first of all I have to excuse that I did not follow the whole discussion.
I only would like to add (if not already done) the ELF (electron
localization function) concept to the methods to analyse chemical bonds.

Best regards,

Wibke Sudholt
University of California, San Diego