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Subject: CCL:WORKSHOP: Resonance Phenomena in Chemical Physics
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    Institute of Advanced Studies in Theoretical Chemistry 
                         Technion
 
    -------------------------------------------------------
             Winter-School and Workshop on
       Resonance Phenomena in Chemical Physics
              February 14 - 19, 1999
             Technion City, Haifa, Israel
    -------------------------------------------------------


  
 Program and Registration form: 
 -----------------------------
 http://www.technion.ac.il/technion/chemistry/IASTC/Mo/
 

List of invited speakers:
------------------------

Resonance Definitions and their Fingerprints in Observal Quantities 
(minicourses): 
Vitali Averbukh, Erkki Brandas, Eric Heller, Jürgen Korsch, William Miller, 
Nimrod Moiseyev ,Howard Taylor,Ilya Vorobeichik 

Different Computational Methods and Algorithms for Calculating Resonances:
Claude Leforestier, Vladimir Mandelshtam, Danny Neuhauser, Hans-Dieter Meyer

Theory of Resonance Phenomena in Chemical Physics:
Lorenz Cederbaum, Stavros C. Farantos, R. B. Gerber, Peter Hanggi, Georges 
Jolicard, Pavel Jungwirth, Roland Lefebvre, Claude Leforestier, Evgueni 
Nikitin, Uri Peskin, Eli Pollak, Moshe Shapiro


Experimental Manifestation of Resonance Phenomena:
Eli Kolodney, Ron Naaman, Mark G. Raizen, Hana Reisler, Dan Ritter, Curt 
Wittig, Daniel Zajfman.

Discussion: Theoretical Interpretation of the Experimental Results:
Philip R. Certain


From chemistry-request@www.ccl.net  Mon Nov  2 06:27:01 1998
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From: Michael Nolan <mnolan@nmrc.ucc.ie>
Message-Id: <199811021126.LAA18289@rennes.nmrc.ucc.ie>
Subject: Peptide Rotation Barriers
To: chemistry@www.ccl.net (ccl)
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Hello all,

Thank you to all who amswered my question about rotation about a peptide link.

I had thought that estimating the barrier using only single point calcs would not be valid.
In particular, starting at the trans conformation and stepping along the torsion mentioned below,
at 45^{o} one finds a barrier of over 700kCal/Mol, which indicates a poor geometry (B-LYP/6-31G*).
With PCFF it is even worse......
However that was the only set of calculations I had the resources to carry out (we have one SGI O2 with 
a MIPS R10K 174MHz processor with 128MB RAM and 4GB disk and it runs flat out 24 hours a day)

regards

Michael

**************************************************************************
Mr. Michael Nolan	
Materials Modelling Section, Advanced Materials and Technologies Group
National Microelectronics Research Centre  	
Lee Maltings, Prospect Row				   	
Cork
IRELAND

mail: mnolan@nmrc.ucc.ie

Tel:   + 353 21 90 4113

http://nmrc.ucc.ie/projects/ape/
http://nmrc.ucc.ie/groups/AMT/modellingRes.html

***EMRS Call for papers:***
http://nmrc.ucc.ie/groups/AMT/SympMain.html
****************************************************************************



**************************************************************************************************
Original Question....

Dear all,

I'm studying the link formed between p-aminophenol (AP) and p-hydroxybenzoic acid (HBA). The bond formed between
the two molecules is the peptide link 


		X	    O
		 \	   /
	          \	  /
		   N-----C
		  /	  \
		 /	   \
	        H	    X

Now according to the biochemists the most stable conformation is the trans configuration (steric reasons etc etc)
We computed a rotational barrier (trans->cis for HBA-AP), simply by stepping 15 degree incremenets along the
torsion X-N-C-O and calculating single point energies (our resources are so meagre that we cannot do optimisations
for each structure). We used B-LYP/6-31G* and also the PCFF force-field. B-LYP gave a large barrier (hundreds of
kCal/mol) and the FF gave ridiculous results. At least we could see that the barrier to rotation from trans to cis
is very high, which I guess you would expect. 

I have a couple of questions....

1: Would it be in people's opinion valid to use PCFF for MD simulations of this system? Bearing in mind for HBA
we used the PCFF force-field successfully and I guess we would like to be consistent in our use of force-field.

2: Is it valid to estimate the barrier to rotation around the peptide link only from single point calculations?

3: Has anyone looked at this barrier before? I have looked at a number of databases for AP and only got rubbish
and a chemical abstracts search was none too successful. I would appreciate any refs. at all 


Summary as usual

Thanking you for your time

Michael
****************************************************************************

Answer 1:
From strasner@chem.ucla.edu Thu Oct 29 13:46:56 1998

Dear Micheal,

a couple of years ago I was interested in peptides and computed rotational
barriers. They are only semiempirical and there should be newer ab initio
calculations. But it might give you an idea:

"A semiempirical AM1, MNDO and PM3 study of the rotational barriers 
of various ureas, thioureas, amides and thioamides", 
M. Feigel, T. Strassner, J. Mol. Structure, 283 (1993) 33 - 48.

Additionally concerning your questions:

Single points are not acceptable, because you create unreasonable geometries.
This is also the reason for the high barrier you got. The above mentioned paper
gives you some idea about experimental gas phase NMR data of amides.

The CAS search you mentioned should have provided above mentioned paper.

Thomas


Answer 2:
From spoel@xray.bmc.uu.se Thu Oct 29 15:59:48 1998

Hi Michael,

I've just been busy studying omega angles from MD simulations, and found
in our force field (GROMOS) that the angles are roughly a gaussian 
distribution around 180 (sigma=16), with min and max roughly 120 to 240 
degrees. I think this distribution maybe slightly too wide however.
The transition from trans to cis is possible in the testtube however,
especially for proline, but I think there are also some other examples of
cis peptide bonds in the protein database (Ala?).

Here are some refs:

@Article{Ramachandran68,
  author = 	 {G. N. Ramachandran and V. Sasisekharan},
  title = 	 {Conformation of Polypeptides and Proteins},
  journal = 	 {Advan. Protein Chem.},
  year = 	 1968,
  volume =	 23,
  pages =	 {283-437}
}

@Article{Eggleton85,
  author = 	 {D. S. Eggleton and D. J. Hodgson},
  title = 	 {Intramolecular water bridge and a distorted trans peptide bond in the crystal structure of 
		 {$\alpha$}-{L}-glutamyl-{L}-aspartic acid hydrate},
  journal = 	 {Intern. J. Pept. Prot. Res.},
  year = 	 1985,
  volume =	 26,
  pages =	 {509-517}
}
@Article{HeadGordon91a,
  author = 	 {T. Head-Gordon and M. Head-Gordon and M. J. Frisch and C. L. {Brooks III} and J. A. Pople},
  title = 	 {Theoretical study of blocked glycine and alanine peptide analogues},
  journal = 	 {J.Am. Chem.Soc.},
  year = 	 1991,
  volume =	 113,
  pages =	 {5989-5997}
}
@Article{Burton93a,
  author = 	 {N. A. Burton and S. {S-L}. Chiu and M. M. Davidson and D. V. S. Green and I/ A/ Hillier and J. J. W. 
	         {McD}ouall},
  title = 	 {Rotation about the {C_N} bond in formamide: {A}n ab initio Molecular Oribital study of structure 
		 and Energetics in the gas phase and in solution},
  journal = 	 {J.Chem.Soc.Far.Trans},
  year = 	 1993,
  volume =	 89,
  pages =	 {2631-2635}
}
@Article{MacArthur96a,
  author = 	 {M. W. Mac{A}rthur and J. M. Thornton},
  title = 	 {Deviations from Planarity of the Peptide Bond in Peptides and Proteins},
  journal = 	 {J.Mol.Biol.},
  year = 	 1996,
  volume =	 264,
  pages =	 {1180-1195}
}

Please post your results.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel		Biomedical center, Dept. of Biochemistry
s-mail:	Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: spoel@xray.bmc.uu.se	www: http://zorn.bmc.uu.se/~spoel
phone:	46 18 471 4205		fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Answer 3:
From harrison@physics.phy.uab.edu Thu Oct 29 16:44:36 1998

Mr. Nolan,
I recall having done something similar for peroxynitrite (OONO) some years
back and found that the barrier obtained by just stepping through torsion
angle was much larger (seem to recall an order of magnitude) than what we
finally found by a transition state calculation.  What seemed to be the 
culprit for the misleading result was that as one would go through various
torsion angles, some of the other bond lengths would change when actual 
relaxation of the structure was allowed.  In our case the extremely small
cis-trans barrier was key to understanding some of the kinetics and the
overall role of superoxide dismutase in ALS.  See for example,
J. M. Tsai, et.al. JACS 116, 4145(1994).

Best Regards,

Joe Harrison
Dept. of Physics
Univ. of Alabama at Birmingham



Answer 4:
From asmellie@combichem.com Thu Oct 29 16:57:02 1998

I see one problem immediately with this approach:

As you step the torsions, one might expect internal bond angles to change.
In particular, as VDW interactions rise as 1 / R^12, as two atoms get
closer during the torsion rotation, internal bond angles are likely
to open to relieve the VDW energy. Look at the example of
the central torsion of butane:

C1---C--(T)--C---C2

If T = 180, C1 and C2 are maximally distant and VDW energy in minimized

If T = 0, C1 and C2 are closest and one or more of the internal C-C-C bond
angles opens to relieve the strain.

Hope this helps,

--andrew



Dr. Andrew Smellie,
CombiChem Inc.
1804 Embarcadero Road,
Palo Alto, CA 94303
Phone: (650)-842-0560
FAX: (650-842-0575
email: asmellie@combichem.com



Answer 5:
From soperpd@esvax.email.dupont.com Thu Oct 29 17:08:17 1998

Michael,

Optimizing with PCFF in the trans position gives an energy of -46
kcal/mol and a C-N-C-C dihedral of 179 deg.  Simply changing that
dihedral to 0 deg and reoptimizing gives an energy of -44
kcal/mol and a dihedral of 21 deg.  If the dihedral is
constrained to zero degrees with a 1000 kcal/mol quadratic
restraint the potential energy is still -44 kcal/mol.  The phenyl
rings must be free to rotate relative to the peptide bond.

Paul Soper


Answer 6:
From fau@mailer.uni-marburg.de Fri Oct 30 16:56:24 1998

Dear Michael,

concerning your 2nd question I think that single-point calcs on 
dihedrally modified geometries will lead to poor results. Due to the 
changing interaction of the CO-pi-bond with the N-lone-pair (and the 
NX and NH antibonding orbitals) I expect the molecular geometry to 
change substantially in NC bond length and to a lesser degree in:
* CO bond length
* XNC, HNC, NCO and NCX' bond angles
Therefore I would prefer to do partial optimizations of the 
dihedrally modified geometries, thereby optimizing a few important 
geometry variables.

To my limited knowledge force fields are parametrized against 
(typically experimental) minima and are therefore of limited use for 
non-minimum structures.

To get an idea of the accuracy of your dihedrally modified geometry 
approach, you could compare the geometries and energies of a 
cis-conformer created by dihedral modification of the FF-optimized 
trans-conformer and a FF-optimized cis-conformer.

Just my 0.02$,
              Stefan

Stefan Fau                 <fau@mailer.uni-marburg.de>
Fachbereich Chemie der Philipps-Universität Marburg
35032 Marburg, Deutschland



From chemistry-request@www.ccl.net  Mon Nov  2 09:40:24 1998
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From: "Xianofeng . Duan MLBP CON" <duanx@Picard.ml.wpafb.af.mil>
To: chemistry@www.ccl.net
Subject: controls for x-y diagram?
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Hi, all!
can some one point out where I can find a freeware or shareware of 
active-X or OCX controls (or MFC) which can be integrated in a small VC++ 
program to plot x-y data?
Thanks!  

****************************************
Xiaofeng Duan
WL/MLBP, Bldg. 654
2941 P St. Ste. 1
Wright-Patterson AFB, OH 45433
(937)255-9164
duanx@Picard.ml.wpafb.af.mil
****************************************


From chemistry-request@www.ccl.net  Mon Nov  2 10:32:40 1998
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Message-Id: <199811021513.QAA11285@rs5.csrsrc.mi.cnr.it>
To: CHEMISTRY@www.ccl.net
Subject: Molecular beams review?



Hi all!

Can you suggest a good review (even a web page!)
on molecular beams and/or reactive dynamics?

thanks   Dario Bressanini

From chemistry-request@www.ccl.net  Mon Nov  2 11:54:43 1998
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From: "Gert von Helden" <gertvh@mlfsilly.sci.kun.nl>
Message-Id: <9811021852.ZM2773@mlfsilly.sci.kun.nl>
Date: Mon, 2 Nov 1998 18:52:57 +0000
In-Reply-To: Dario Bressanini <dario@rs5.csrsrc.mi.cnr.it>
        "CCL:Molecular beams review?" (Nov  2,  4:13pm)
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Hello,

R.D. Levine, R.B. Bernstein, "Molecular Reaction Dynamics and Chemical
Reactivity", Oxford University Press.

G. Scoles (ed.), Atomic and Molecular Beam Methods, Oxford University Press
(Vol. 1 and Vol. 2)

Both books are excellent and almost a must have, if you (want to) work
in that field.

Hope that helps,   Gert

On Nov 2,  4:13pm, Dario Bressanini wrote:
> Subject: CCL:Molecular beams review?
>
> Hi all!
>
> Can you suggest a good review (even a web page!)
> on molecular beams and/or reactive dynamics?
>
> thanks   Dario Bressanini
>

-- 

Gert von Helden  
Dept. of molecular and Laser Physics, University of Nijmegen, Netherlands
e-mail: gertvh@sci.kun.nl, phone: (+31) 24 3652179, fax: (+31) 24 3653311


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Date: Mon, 02 Nov 1998 12:08:43 -0600
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Subject: Parameterization
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Hi all,

  Well, my question regarding references for the use of Quantum methods 
to determine valence force field constants was quickly answered.
Many thanks to Joerg Hill, Don Gregory, Matthew F Schlecht, 
David Reichert, and Craig Burkhart.

  Howard



The longest set of references I received was:

_______________________________________________________________________

"Derivation of Force Fields for Molecular Mechanics and Dynamics from ab
initio Energy Surfaces," Maple, J. R.; Dinur, U.; Hagler, A. T. Proc.
Natl. Acad. Sci. USA 1988 85 5350.

"Derivation of Class II Force Fields.  I.  Methdology and Quantum Force
Field for the Alkyl Functional Group and Alkane Molecules," Maple, J.
R.; Hwang, M.-J.; Stockfisch, T. P.; Dinur, U.; Waldman, M.;
Ewig, C. S.; Hagler, A. T. J. Comput. Chem. 1994 15 162.

"Derivation of Class II Force Fields.  2.  Derivation and
Characterization of a Class II Force Field, CFF93, for the Alkyl 
Functional Group and Alkane Molecules," Hwang, M. J.; Stockfisch, T. P.; 
Hagler, A. T. J. Am. Chem. Soc. 1994 116 2515.

"Derivation of Class II Force Fields.  III.  Characterization of a
Quantum Force Field for Alkanes," Maple, J. R.; Hwang, M.-J.; 
Stockfisch, T. P.; Hagler, A. T. Israel J. Chem. 1994 34 195.

"On the Use of Quantum Energy Surfaces in the Derivation of Molecular
Force Fields," Hagler, A. T.; Ewig, C. S. Comput. Phys. Commun. 1994 84 
131.

"Derivation of Class II Force Fields. V. Quantum Force Field for Amides,
Peptides, and Related Compounds," Maple, J. R.; Hwang, M. -J.; Jalkanen,
K. J.; Stockfisch, T. P.; Hagler, A. T. J. Comput. Chem. 1998 19 430.
_______________________________________________________________________


-- 

Howard E. Alper, Ph.D.
Dept. of Chemistry and The Advanced Materials Research Institute
University of New Orleans
New Orleans, LA 70148
504-280-7216

 - Helping molecules find happiness for almost a 5th of a century.

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Subject: Summary: Discover, water ``evaporates``
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Hi,
A few days ago, I ask a question regarding water ``evaporates`` during MD using
Discover. 
I would like to thank Dr. Fiona Case and Dr. Don Gregory for their help (their
responses 
are pasted as follow). First of all, the water didn`t evaperates!  ``As the
water molecules
 wander out of the cell, their images re-enter the opposite side of the cell``.
Since the InsightII
tracks the original molecules only, it would give you a visual effect that some
waters went out 
of the box. Re-imaging is done with Explicit Image model, but it is not done
with Minimum 
Image model.

Thanks a lot,

JianHui Wu

********************************************************************************
******************************
Hi Dr. Wu,
You can find some helpful information on MSI's scientific support,
FAQ web-site.
First go to: 
http://www.msi.com/support/FAQ.html
and select the InsightII Core area.
There you will find a tutorial on creating your own solvent boxes,
and within the "How to Equilibrate the box" portion of that tutorial,
you'll find a discussion on how to treat the 'visual' effect of waters/images
outside the box.
Hope this helps!
Don Gregory
***************************************************************

Hello,

The water didn't evaporate. Its just that the
particular water molecules you are displaying on
the screen (the ones that started in the central
or parent cell of your simulation) diffused
through the bulk material (through the images of
the central cell that you are not displaying 
right now).

If you don't want any diffusion to take place you
could, ofcourse, run the simulation at a very
low temperature - but then nothing else much would
happen either :-)

If you want to see all the atoms within the central
cell there are options to display in this mode.
The commands are a little different depending on
which user interface you use to access Discover.
If you are using Discover from the InsightII user
interface you can use the Assembly/Cell_Display
command to display a "packed cell". If you are using
the Cerius2 user interface you can use change the
display mode using the menus accessed from the
Crystal-Builder menu card. 

Hope this helps


Fiona Case
*********************************************************************
EOF




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Date: Mon, 02 Nov 1998 09:03:09 -0600
From: Steven Bachrach <smb@smb.chem.niu.edu>
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To: computational chemistry list <CHEMISTRY@www.ccl.net>
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The Fifth Computational Chemistry Conference (ECCC-5) is now running.
All articles are available to the public.

There are 71 articles covering a broad range of topics, showing the
great diversity in our discipline.

ECCC5 is free to all. Registration is necessary in order to read the
discussions or to add your own comments or questions, but again,
registration is free.

ECCC5 can be found on the web at

    http:/hackberry.chem.niu.edu/ECCC5/

Full instructions, registration, abstracts, and articles can be found
from this page.

Everyone is invited to participate at their own pace - the conference
runs through November 30, 1998.

Questions and comments can be sent directly to me.

Steve
-- 
Steven Bachrach				
Department of Chemistry and Biochemistry
Northern Illinois University
DeKalb, IL 60115                          Phone: (815)753-6863
smb@smb.chem.niu.edu                      Fax:   (815)753-4802



From chemistry-request@www.ccl.net  Mon Nov  2 20:02:18 1998
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From: Ramon Garduno <ramon@ce.ifisicam.unam.mx>
Subject: MacroDox
To: CHEMISTRY@www.ccl.net (CCL POST MSG)
Date: Mon, 2 Nov 98 18:56:37 CST
Mailer: Elm [revision: 70.85]


Dear netters:

To those that have used MacroDox, does any of you knows what is happening 
with the web site pirn.chem.tntech.edu (home of MacroDox)?.

I have tried to reach it since last week without success.  Any hint will 
be appreciated.

May be someone could tell the webmaster at pirn.chem.tntech.edu of this
problem.

Much obliged.
--

        "...De los 260 musculos que tiene el cuerpo humano, el mas
	dificil de mantener en forma es el corazon...."
___________________________________________________________________________
		  	 Dr. Ramon Garduno-Juarez
                     Research Professor in Biophysics
CENTRO DE CIENCIAS FISICAS          | EMAIL:  ramon@ce.ifisicam.unam.mx
UNIVERSIDAD NAL. AUTONOMA DE MEXICO |
Apdo. Postal 48-3                   | VOICE:  +52(5)6227749 ; +52(73)291749
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MEXICO                              | FAX:    +52(5)6227775 & +52(73)291775
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___________________________________EOF ____________________________________

