Subject: Cyclohexa1,4diene summary : from Boyd and Lipkowitz to us dumb users

From: [email-masked] (Alexandre HOCQUET)
Date: Fri, 10 May 1996 22:10:01 +0200 (MET DST)

Cyclohexa1,4diene summary : from Boyd and Lipkowitz to us dumb users

Dear CCLers, 

Under that title you will find the summary of the answers
 to the message "another dumb question of molecular mechanics".
The initial question is first listed, then the contributions of the cclers.

First, it appears that Cyclohexa1,4diene experimentally exists in the 
two conformations according to experimental results from Xray and NMR
cited in Boyd and Lipkowitz, although the authors comments are brief.
According to Eliel's "Stereochemistry of organic compounds", 
Cyclohexa1,4diene planar form is the most stable but the potential well 
is "shallow". Idid not see further comments. 
The reference cited therein is a book "conformational analysis of
cyclohexadiene..."
from Lipkowitz and Rabideau, which i could not reach.

Although semiempirical methods unambiguously yield planar conformation,
molecular mechanics vary greatly according to the software used ....
even with the (apparently) same forcefields ! In some cases, planar form
 is considered to be the global minimum, in others it is the boat form.
If frequency vibrations are calculed, some find a true minimum, others a
saddle point.

If, as Eliel says, the potentiel well is shallow, then we can imagine that 
according to the force field parameterization, or the minimization technique, 
the PES, as seen by the force field may correspond to a minimum, a saddle point
or even not a minimum at all.

As far as Hyperchem is concerned, a parameterization bug has been enlightened
 and the scientific staff is being resolving it.

Finally, two people gave results and references concerning......
cyclohexa1,3diene, the conjugated one. They are listed at the end of this
summary
_________________________________________________________________
In their molecular mechanics principles review (J. Chem. Ed. , 59, 269-274,
1982) Boyd and Lipkowitz present the conformations of cyclohexa-1,4-diene as
an example of supremacy of molecular mechanics upon hand held molecular
models : the dreiding model predicts boat geometry whereas molecular
mechanics calculate it planar.
I do believe that this example is demonstrative, presenting molecular
mechanics to students as a sophisticated hand held model.
Unfortunately, as i tried to minimize cyclohexa-1,4-diene with the MM+ force
field provided by Hyperchem, the results show that the minimum (9.10
kcal.mol-1) corresponds to a torsion angle between 1,2,3 and 4 carbons of
26°, in a boat conformation. The constrained planar structure corresponds to
9.73 kcal.mol-1 and goes back to the former conformation when constrain is
removed.
Besides, An AM1 semiempirical calculation does find the minimum to be planar.
So my questions are : 
Does the MM+ forcefield, or the parameters provided in Hyperchem, lack the
accuracy needed to perform this calculation ?
Does any references about molecular mechanics calculations of this molecule
exist ?
Does anybody know the references about calculations, Xray and NMR results
that Boyd and Lipkowitz cite with no references (or, to be honnest, the
reference cited was "in press" : Lipkowitz et al. in J. Org. Chem.) ?
Am i doing something wrong ? 

Thanks in advance for any answers (if somebody is interested, i will
summarize the answers)

____________________________________________________________________________
_____

Hi
	I tried this minimization with Hyperchem 4.5 using MM+: I started with the
model builder which gave a boat conformation and then with MM+ and obtained
the non planar structure as a flattened boat and Energy=8.977 Kcal/mol
(Gradient 0.00079). I then took that "optimized" structure and reminimized
it with PCModel for Windows 5.13 where it immediately gave the planar
structure! I went back to Hyperchem redrew the structure "PLANAR" and added
H's WITHOUT using the model builder. I minimized this structure and now I
obtained the planar conformation with Energy= 3.0488 Kcal/mol (Gradient
0,00083), i.e the real minimun.
	I rechecked the "non planar minimun" that HyperChem found, and in both
PCModel AND Hyperchem it has a very high torsion energy component, however
for some strange reason Hyperchem does not reflect that in the Gradient. I
made some other tests and found that Hyperchem reached another boat type
minimun with Energy=10.94!! This structure rapidly converged to the planar
real minimun with PCModel.
	I never found differences between the parameters in Hyperchem and PCModel,
maybe this is a bug in Hyperchem optimizers. As I see it, optimizers are the
weakest point of Hyperchem (an implementation of BFGS would be great!)
	Gerardo

Gerardo Burton
e-mail: [email-masked]
Departamento de Quimica Organica
Facultad de Ciencias Exactas y Naturales
Universidad de Buenos Aires
Tel/FAX 54 1 788-6915

_____________________________________________________________________________

Hola Alexandre
	revisando mis "pruebas" encontre que en aquellas en que Hyperchem dio el
ciclohexadieno plano con energia de aprox 3 kcal/mol estaba usando el
"default parameters", resultado de agregar H sin usar el Model Builder. Sin
embargo si a esa estructura plana se le hace "BUILD/Calculate Types" y se
optimiza normalmente mantiene la conformacion plana usando la opcion de
carga/carga en MM+. Con "bond dipoles" en Hyperchem 4.5 sigue dando plana
pero en Hyperchem 3.0 se curva ligeramente. Te envio el archivo .hin a
continuacion correspondiente a la estructura plana optimizada con MM+ para
que lo pruebes.
	Gerardo

;Cyclohexadiene planar conformer    
;Energy 9.61 kcal/mol  Grad 0.00093  
;MM+     Charge/Charge interaction
forcefield mm+
sys 0
view 40 0.2308208 55 15 0.08100456 -0.02507711 0.9963982 0.7050237 0.7080831
-0.03949571 -0.7045423 0.7056837 0.07503794 -0.1855706 -0.265454 -54.1561
mol 1
atom 1 - C C4 - 0 -0.8421649 1.854515 0.05424488 4 2 s 6 s 7 s 8 s
atom 2 - C C3 - 0 -2.06936 0.9877079 0.01674857 3 1 s 3 d 9 s
atom 3 - C C3 - 0 -2.027517 -0.3502076 -0.04506508 3 2 d 4 s 10 s
atom 4 - C C4 - 0 -0.7485514 -1.138567 -0.08400068 4 3 s 5 s 11 s 12 s
atom 5 - C C3 - 0 0.4786466 -0.2717942 -0.04571453 3 4 s 6 d 13 s
atom 6 - C C3 - 0 0.4368019 1.066121 0.01611715 3 5 d 1 s 14 s
atom 7 - H H - 0 -0.8610181 2.464536 0.9870859 1 1 s
atom 8 - H H - 0 -0.8640453 2.546919 -0.8191209 1 1 s
atom 9 - H H - 0 -3.04832 1.497608 0.04210231 1 2 s
atom 10 - H H - 0 -2.972697 -0.9203283 -0.06959744 1 3 s
atom 11 - H H - 0 -0.7297372 -1.747683 -1.017434 1 4 s
atom 12 - H H - 0 -0.726633 -1.831819 0.7886948 1 4 s
atom 13 - H H - 0 1.457608 -0.7817122 -0.07074484 1 5 s
atom 14 - H H - 0 1.381982 1.636223 0.04099056 1 6 s
endmol 1
_______________________________________________________________________________
Muchas gracias por tu contesta veloz, Gerardo.

Estoy haciendo esfuerzos desperados para alcanzar este minimum plano del 1,4
dihidrobenzeno, pero no puedo conseguirlo. Con metodo semiempirico AM1 o
PM3, la conformacion plana esta imediata, pero incluso con una estructura
inicial obtenida por esta manera, MM+ regresa a una conformacion "boat".
Traté de seguir tu metodo con el "builder" de Hyperchem, pero no funciono :
construi un benzeno para obtener un ciclo plano y , despues de anadir
hidrogenos y cambiar los ordenes de enlace, cambié los tipos de atomos de CA
a C4 y C3.
Finalmente, en el libro "stereochemistry of organic compounds" de Eliel y
Wilen, he leido que "the potential well corresponding to the planar minimum
is very shallow", entonces, parece como una deficiencia del "optimiser"

Saludos

Alexandre Hocquet

Laboratoire de Chimie Analytique
ESPCI
10, Rue Vauquelin
75231 Paris Cedex 05
France

tel : 33 1 40794420
fax : 33 1 40794425
email : [email-masked]
ou [email-masked]
ou [email-masked]

____________________________________________________________________
I just tried 1,4-cyclohexadiene using SPARTAN.  Usint the MM+ force field I
get a strain energy o +1.08. Kcals/mol and an HF (AM1) of 16.998 Kcal/mol.
Does this fit with your calculations?

JIm Macmillan

James G. Macmillan
Department of Chemistry
University of Northern Iowa
Cedar Falls, IA 50614

E-Mail:  [email-masked]
Ph:         (319)273-2476
FAX;     (319)273-7127

==========================================================================
Where good wine flows, so does good conversation.

_________________________________________________________________
Dear Alexandre,

this is not a specific answer to your problem, but illustration of
similar (?) problem.

I tried the MM2 force field in CS Chem3D Pro, which predicts
1,4-cyclohexadiene to be planar.

on the other hand, I also built a carefully-constructed flattened
version of cyclohexane to illustrate how molecular mechanics finds
local energy-minima (eg boat form for cyclohexane if the initail
geometry is not near the global minimum).
 run 1:  CS Chem3D Pro found the boat conformer
 run 2:  I rotated the initial geometry
         (same bond lengths and angles as run 1)
         CS Chem3D Pro then found the chair conformer!

In this case I suspect some numerical round-off instability.  For
research work, I'd recommend (eg) QCPE-type source code.

In your case, do you know if it is MM1 , MM2, or MM3 force field?
These are 3 very similar, but slightly different parameterisations.
Or is MM+ HyperChem's own parameterisation?

Could that be the problem?

Kieran

----------------------------------------------------------
 Dr Kieran F Lim              Biol. and Chemical Sciences
 ph:  + [61] (52) 27-2146     Deakin University
 fax: + [61] (52) 27-1040     Geelong          VIC   3217
 email: [email-masked]     AUSTRALIA
 WWW:   http://www.deakin.edu.au/~lim/

____________________________________________________________________
We had occasion to look at the 1,3-cyclohexadiene problem with AM1
mentioned by Alexandre HOCQUET.  It is really interesting and a fine
pedagocgical example for students.  HOCQUET's conclusion that AM1 gives the
wrong conformation, the planar conformation, is not true.  However, this is
a commonly observed result.  The calculation EASILY FINDS THE WRONG
CONFORMATION.  The wrong conformation is not an energy minimum but rather a
maximum at the transition state.  That is what makes it so interesting.
This is nicely evident by calculating and viewing the IR spectrum, using
for example the CAChe system. The IR spectrum of the planar structure
contains an absorption at a NEGATIVE frequency. Inspection of the nature of
the vibration indicates the distortion necessary to find the proper
nonplanar conformation which is lower in energy.

James E. Gano, Director
Instrumentation Center in Arts and Sciences
Bowman-Oddy Laboratories
University of Toledo
Toledo, Ohio 43606

Instrumentation Center :  http://www.icenter.utoledo.edu
Department of Chemistry:  http://www.chem.utoledo.edu

419-530-7847 (419-530-2104)
419-530-4033 (FAX)

_________________________________________________________________
An obscure bug has been found in the MM+ force field for HyperChem.  The 
effect is that under certain circumstances, HyperChem reads a set of 
parameters for one torsional angle calculation, and uses the same parameters 
for another torsional angle as well, instead of getting new parameters.  
Further details are available on the HyperChem mailing list and on our 
WWW page (http://www.hyper.com).

We would like to thank Alexandre Hocquet for bringing the problem to our 
attention.  We expect to be issuing corrected versions of the MM+ backend to 
all of our users to correct the problem.  Further details will be available 
soon on our mailing list and WWW site.

Joel

------------
Joel Polowin, Ph.D.   Manager, Scientific Support
Email to: [email-masked] 

Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040
Info requests to: [email-masked]    Support questions to: [email-masked]
Email group: Send "subscribe hyperchem" to [email-masked]
WWW: http://www.hyper.com/

____________________________________________________________________
Dear CCLers and Hyperchemers,

Re: Alexandre Hocquet question on the molecular mechanics optimized
structure of 
cyclohexa-1,4-diene

I have had a quick look at this problem using Nemesis (COSMIC MM force field) 
and also found that the pseudo-boat (torsion 25 degrees) is predicted to be
more 
stable than the flat structure by approximately 0.7 kcal/mol.

However if the optimizing is started from a flat structure (modifing 
benzene)than this is not kinked by Nemesis.

/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\
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\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/

_______________________________________________________________
Alexandre Hocquet,

Here is what I have found using SPARTAN.

MM2 with Sybyl FF gives a planar structure of energy 1.081245 Kcal/mol.
AM1 starting from Sybyl geometry is still planar with an energy of 19.733
Kcal/mol.  A frequency calculation gives on imaginary vibration at 191.76 of
B3u symmetry.
AM1 starting from Sybyl geometry has an energy of -229.037790 hartrees and a
frequency calculation does not show and imaginay vibrations although the B3u
vibrationa at 125.97 looks to be the same as the imaginary on from AM1.  

I am not sure why there is a difference between HF ab initio and AM1 semi
empirical.

Jim
==========================================================================
James G. Macmillan
Department of Chemistry
University of Northern Iowa
Cedar Falls, IA 50614

E-Mail:  [email-masked]
Ph:         (319)273-2476
FAX;     (319)273-7127

==========================================================================
Where good wine flows, so does good conversation.

_________________________________________________________________
1996 May 7

  Hello,  There has been a discussion of the conformation of 1,3-cyclohexadiene
as calculated by MM and AM1. I got these results, using Spartan:

MM jobs:
1  C2 (nonplanar ring) input from the builder, opt with MM3-->C2, 9.12 kcal/mol

2  Cs (planar ring) input from the builder, opt with MM3-->C2v, 10.38 kcal/mol

AM1 jobs:
3  C2 input from MM3, opt with AM1--> C2, 17.49 kcal/mol, no imaginary freqs

4  C2v (planar ring) input from MM3, opt with AM1--> C2v, 17.64 kcal/mol,
                                     1 imag. freq, 74i cm-1 ("-74" cm-1)

Now, an MM energy cannot be compared with an AM1 energy, since they refer
to different things, but within each class of computation the C2 (nonplanar
ring) geometry has the lower energy, and the AM1 C2 geom is a relative minimum
on the potential energy surface, since it has no imaginary frequencies. The
"small" value of the imaginary freq of the AM1 C2v structure shows that this AM1
transition state is "flat" (not steeply curved along the reaction coordinate),
as might have been suspected from the very small activation energy, and
animating the vibration reveals that the planar C2v molecule wants to twist
to the C2 geometry.
  This little exercise shows (1) the importance of the _input_ geom; an MM
job can throw an input structure into a higher sym, but a semiempirical
or ab initio calc will keep the input symmetry  (2) the importance of
doing a freq job on an optimized structure, to see if it is a relative
minimum or some kind of saddle point (e.g. a transition state=1st-order
saddle point) ON THAT PARTICULAR PES, which is not necessarily the _true_ PES.
Most MM programs do not yet do freq calcs, altho' I think the latest version of
MM3 does.
  Does any one know what _experiment_ tells us about the shape of 1,3-hexadiene?

E. Lewars  Chemistry Dept Trent U, Ontario, CANADA

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_________________________________________________________________
Hi,

I haven't followed the whole discourse on MM and AM1 calcs on
1,3-cyclohexadiene, so I will be brief.  Microwave and electron
diffraction studies on 1,3-cyclohexadiene are available.
The structure has C2 symmetry and is well represented at the
RHF/6-31G(d) level.  While in the Houk group, I and others looked
at the electrocyclic reactions of substituted 1,3-cyclohexadienes
and at all levels of theory employed (including AM1) these structures
were staggered about the sp3-sp3 single bond.  The microwave and
electron diffraction references are:

Oberhammer, H. ... JACS 1969, 91, 10
Dallinga, G. ... J. Mol. Struc. 1968, 1, 11
Traetteberg, M.  Acta. Chem. Scand. 1968, 22, 2305
Butcher, S. S.  J. Chem. Phys. 1965, 42, 1830

I hope this helps.

Bert

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Alexandre Hocquet

Laboratoire de Chimie Analytique
ESPCI
10, Rue Vauquelin
75231 Paris Cedex 05
France

tel : 33 1 40794420
fax : 33 1 40794425
email : [email-masked]
ou [email-masked]
ou [email-masked]