From chemistry-request@ccl.net Fri Jul 24 13:41:52 1992
Date: Fri, 24 Jul 92 09:29:17 MDT
From: hogue@sdisu1.den.mmc.com (Pat Hogue)
To: CHEMISTRY@ccl.net
Subject: Surface Interactions
Status: R
I would appreciate hearing from experienced computationalists about the approach I plan to take in trying to use a semiempirical technique (CNDO or MNDO with Burn's coeffecients) to predict reactivities between perfluoropolyether (aka PFPE, with difluoro acetal linkages) and a variety of transition metals and their oxides.
The first approach is to place the PFPE into a cavity lined with the inorganic material. In this case the only important parameter is the inorganic material's dielectric constant.
The second approach (which is more controversial, I think) is to "bond" the "acetal" carbon to the inorganic molecule (e.g., Al of Al2O3) starting at 10 Angstroms and then reduce the bond length at half A increments.
In the third approach I will try to create a Lewis acid site by removing e.g., the onygen from Al2O3 and use dummy atoms to balance the charge, leaving a "naked" Al atom to interact with the acetal link in the stepped manner described above.
My goal is to simply rank the inorganic material's reactivity and then compare this with the reactivities I observed using DSC.
Lastly: since this work forms the basis of my Masters degree thesis I ask that you consider rather the approach outlined above is "good enough". I realize there are more rigerous methods but there is just so much time in the day for a full-time engineer and part-time graduate student. Telephone calls will also be welcomed. Pat Hogue (303) 971-3369
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From chemistry-request@ccl.net Fri Jul 24 15:48:18 1992
Date: Fri, 24 Jul 1992 10:59 MST
From: YAMAMURA@CGF.chem.Arizona.edu
Subject: Summarization of Responses to Interaction Energy and Hydrophobicity
To: chemistry@ccl.net
Status: R
Dear Fellow Netters,
The following is a summary to the net of responses to the query below.
Many thanks to all those who responded. We are very grateful for the
generosity of those who supplied the valuable information summarized below.
Susan Yamamura
***************************************************************************
QUERY
Does anyone know of computational models for calculating interaction
energies between the planar surface of a solid of a known crystal structure
and the surface of an adsorbed protein of known crystal structure? It is
especially desirable for the model to include hydrophobic interactions.
All information received will be summarized to the net. Any information
about references, programs, etc would be very much appreciated.
Thank you.
Susan Yamamura
yamamura@cgf.chem.arizona.edu
RESPONSES
ONE
***************************************************************************
We use a program created by P. Claverie and J. Caillet in the seventies,
this program does not fit exactly with your needs because the proteins
are not parametrized but may be it could work with minors adaptations.
Francois BAYARD | e-mail bayard@chitheo1.univ-lyon1.fr
UNIVERSITE CLAUDE BERNARD LYON 1 | tel (+33) 72 44 82 79
43 Bd du 11 Novembre 1918 | fax (+33) 72 44 08 03
F-69622 VILLEURBANNE - FRANCE |
--------------------------------------------------------------------------
======================================================================
***************************************************
* *
* PROGRAM PCRISTA *
* *
* INTERMOLECULAR ENERGY CALCN. IN A CRYSTAL *
* CALCULATION OF THE PACKING ENERGY *
* AUTHORS : PIERRE CLAVERIE & J.CAILLET *
* ACTA.CRYST A31 P 448-461 1975 *
* ENERGY : DISPERSION REPULSION ELECTROST POLAR*
* *
* SIMULATED ANNEALING - CALCULATION OF THE ENERGY *
* NEAR THE SURFACE OF THE CRYSTAL *
* AUTHORS: BAYARD F. & DECORET C. *
* Mol. Cryst. Liq. Cryst. Inc. Nonlin. Opt *
* vol 161 pp 67-76 1988 *
* *
* VERSION 1992/01 anl *
* ask for registration and update at : *
* *
* UNIVERSITE CLAUDE BERNARD LYON 1 BAT 305 *
* 69622 VILLEURBANNE CEDEX FRANCE *
* tel (+33) 72 44 82 79 *
* e-mail bayard@chitheo1.univ-lyon1.fr *
* *
* draw (Sun Core) and file HPGL in comments *
***************************************************
Package possibilities :
**********************
- Computation of the energy of a crystal which is built around a
central cell.
- Minimization of this energy by the selective variation of the
geometry of the cell and the Euler angles and translation of the
molecules in the central cell (VA10A or Monte-carlo (simulated
annealing).
- Computation of the interaction energy between the cell near the
surface and the bulk.
- Computation of the approach of a ligand near the surface defined
before (and minimisation of energy).
The central cell is built by symetry operations applied to one
molecule or by differents species.
The geometry of the molecule is introduce by :
- cristallographic coordinates
- internal coordinates system (rho theta phi).
Several ways to modifie this geometry are available :
- internal rotations ( e.g. rotation of an acetyl group )
- rotation and translation of the whole molecule :
- rotation defined through Euler angles.
- rotation defined through axes and angles.
Warning : at this moment all molecules are considered fixed and their
internal geometry do not change during the minimisation.
the parametrization concern small organic molecules and is
based on the William's parameters. A work is to be done
to adjust them for proteins.
*************************************************************************
RESPONSE 2
From: SMTP%"hogue@sdisu1.den.mmc.com" 20-JUL-1992 14:31
Date: Mon, 20 Jul 92 15:29:25 MDT
From: hogue@sdisu1.den.mmc.com (Pat Hogue)
Message-Id: <9207202129.AA01776@sdisu1>
To: yamamura@cgf.chem.arizona.edu
Subject: adsorption
I am beginning to study adsorption of polymer chain onto inorganic substrates
and would like to know if you come up with a program to do protein to solid
adsorption. I'm using the semiempirical set of programs called GEOMOS
(QCPE 584). I don't have any results yet. I would appreciate a personal note
if you can. Pat Hogue (303) 971-3369.
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From chemistry-request@ccl.net Fri Jul 24 17:43:51 1992
Date: Fri, 24 Jul 92 16:23:57 -0400
From: jas@medinah.atc.ucarb.com (Jack Smith)
To: chemistry@ccl.net
Subject: Ag Parameters for MOPAC/PM3
Status: R
Does anyone have even a crude set of parameters for Silver to use with
MOPAC 6.0 (PM3)? I realize that there are no d orbitals in MOPAC, but I'm
willing for the moment to assume that d orbitals don't play an important
role.
Jack Smith
Union Carbide
jas@medinah.atc.ucarb.com
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From chemistry-request@ccl.net Fri Jul 24 23:38:55 1992
Date: 24 July 1992 18:45:34 CDT
From: <U22331%UICVM.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU>
To: <CHEMISTRY@ccl.net>
Subject: MOIL
Status: R
Thanks for the 48 computational chemists that picked up MOIL through
the network. For those that still would like to try, unfortunately
our network is down as of thursday noon due to hardware problems in
our gateway. The fix to the problem may take a while. Currently
MOIL is available only via tape (see previous message). If the problem
will not be fixed by middle of next week we shall try to find alternative
ftp site.
Ron Elber
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