From owner-chemistry@ccl.net  Mon Jul 17 02:10:06 1995
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Subject: Rotation rates: confirmation &/or comments
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Dear Colleagues;

     For some work in which I find myself currently engaged, I am interested in
estimating the rate of rotation about the C-C. bond of n-alkyl radicals of the
type

                                   H H
                                   | |
                                 R-C-C.
                                   | |
                                   H H

According to Krusic et al. [Electron spin resonance studies of coformations and
hindered internal rotation in transient free radicals, J. Phys. Chem. 75: 3438-
3453 (1971)], n-alkyl radicals of the type RCH2-CH2. have C-C. rotational bar-
riers of ca. 3.1 kcal/mol.  If the corresponding value of the Arrhenius pre-
exponential factor A is 10^12.5 [Chen et al., Conformations and rotation bar-
riers in allylcarbinyl radicals by electron spin, JACS 95: 7036-7043 (1973)],
then is it proper to estimate the rat of rotation using the equation

                   k(rot) = A exp (-Ea/RT)

where A = 10^12.5 and Ea = 3.1 kcal/mol?  When I make the approriate substitu-
tions and assume that T = 37oC, I get k(rot) = 2 x 10^10/sec, i.e., the C-C.
bond  makes 2 x 10^10 360o rotations per second.  Does this make sense?  Any
confirmations, comments, or criticisms are most welcome.

       A related question: if we assume that the above value of k(rot) was cal-
culated correctly, then k(rot) = 2 x 10^10/sec would represent an _average_
value for the rotation rate constant.  However, I would expect that under "real"
conditions there would be a distribution of rotation rates for a large ensemble
of molecules all at the same "average" temperature (e.g., 37oC), i.e., some
would be rotating faster andother rotating slower.  From the above information
is there a way of calculating the distribution of  k(rot) values for a large
ensemble of molecules?

     Again, all comments, criticisms, and advice are enthusiastically encour-
aged.  Of course, relevant literature references are always welcome.

     Thanks in advance to all responders.


Sincerely,

(Dr.) S. Shapiro
Inst. f. orale Mikrobiol. u. allg. Immunol.
Zent. f. Zahn-, Mund- u. Kieferheilkd. der Univ. ZH
Plattenstr. 11
Postfach
CH-8028 Zuerich 7
Switzerland

Internet: toukie@zui.unizh.ch
FAX-nr: ( ... + 1) 261'56'83

From owner-chemistry@ccl.net  Mon Jul 17 04:40:07 1995
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From: Patrick Bultinck <Patrick.Bultinck@rug.ac.be>
To: "comp. chem. list" <chemistry@ccl.net>
Subject: Machine specs for QC
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Dear CCL-readers,

We have a small budget for a new workstation that will
be used for QC calculations, and will have a 1 person
load.
Our budget is about 30,000 $, and I need some advice.
What do you consider most important specs for QC,

SpecInt values
Specfp
XMark 93
Some Mflops
CPU speed (in MHz)
memory
...

I have nice offerings (thusfar) by two three-letter
hardware producers.
The one machine has all values larger than the first
one, but the first one claims from experience that
allthough the values are smaller, their machines are
equally fast. In short we are already interested in
an IBM RS6k/3AT and a DECAlpha 250 4/266... (still
waiting for other offers) We already have IBM locally.

Any ideas ? (allthough I check CCL every day, please
only replies to my e-address, since I would not want to 
start a commericial better/worse game on CCL, if
interested summaries will be sent to people who asked
for one)

Patrick

From owner-chemistry@ccl.net  Mon Jul 17 09:55:13 1995
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Subject: powermac
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Dear all
Anyone know of a Powermac version of mopac?
Any other programmes for powermac would also be interesting.

Paul Heelis
Heelisp@newi.ac.uk

From owner-chemistry@ccl.net  Mon Jul 17 10:40:16 1995
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From: polowin@hyper.hyper.com (Joel Polowin)
Message-Id: <9507171436.AA20323@hyper.hyper.com>
To: Matt Stahl <matt@synthesis.chem.arizona.edu>
Subject: Re:  CCL:validity of constrained calcs.
Cc: chemistry@ccl.net


> Date: Thu, 13 Jul 1995 13:24:12 -0700 (MST)
> From: Matt Stahl <matt@synthesis.chem.arizona.edu>
> Subject: CCL:validity of constrained calcs.
> 
> 	I am working on a project which involves parameterizing molecular
> mechanics torsion potentials.  We used gaussian to generate energy vs. 
> torsion data by performing constrained optimizations.  One torsion angle was
> held constant while the rest of the coordinates in the molecule were
> optimized.  Someone recently made the comment that constrained optimizations
> with gaussian are not appropriate for such a study because the 
> unconstrained coordinates do not fully optimize.  This suggestion seems 
> odd because the literature seems to be repleat with examples of isolating 
> the energetics of a molecular motions (distances, angles, and torsions) 
> through constrained optimization.  How far off the mark am i in thinking 
> that constrained opts. are appropriate for this type of work. 

If you add a constraint -- say, a torsion angle -- then none of those atoms
have their normal freedom to move; they and their attachments won't be
fully optimized.  Through non-bonding interactions and propagated bonding
interactions, everything else will be slightly distorted as well.  If this
is what you're talking about, it's a problem inherent in the procedure.  In 
my opinion, it is reasonable to use these results as long as one keeps that 
problem in mind; in general I think that the structural distortions are
not serious.

In principle, I suppose it would be possible to get the same results in
other ways.  Most of my work has involved incrementing a constrained
torsion angle to get the barrier to rotation of part of a system with
respect to the rest.  Instead of doing that, I imagine that one could
set up a molecular-dynamics scheme where part of the system was stationary
and the rest was started with initial velocities applied to the atoms
corresponding to the desired rotation.  For sufficiently high velocities,
the barrier would be overcome.  It would be a matter of repeating the
calculations several times with different starting velocities to find out
how much "rotational energy" would be necessary to overcome the barrier.
I'm not sure how effective such calculations would be compared to the
usual procedures.

Joel
polowin@hyper.com


 	The alternative method would be to perform an IRC (internal reaction
> coordinate) calculation to characterize the path between the two minima of
> interest, but as i understand it IRC calculations are dependant on Linear
> Synchronous Transit calculations which ESTIMATE the transition state.  Can
> one perform an IRC from a calculated transition state (opt=ts)?  If not, how
> much more "valid" is an IRC calculation than constrained optimization if at
> any point the IRC has to "guess" the path? 
> 
> thanks,
> matt
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Mr. Matthew Stahl			| 
> Department of Chemistry			| I'd rather be right half of the
> University of Arizona			| time than half right all the
> Tucson, AZ  85721			| time.
> matt@synthesis.chem.arizona.edu		|	-Malcom S. Forbes
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> 
> 
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> 



From owner-chemistry@ccl.net  Mon Jul 17 11:10:15 1995
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Subject: CCL:HOHO
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Netters,

        I need to know if anyone knows anything about the thermochemistry or
excited states of HOHO, a structural isomer of hydrogen peroxide.  In
addition does anyone know anything about the transition state for the
reaction O + H2O yld 2OH.  I would be interested in this for ground and
excited states of O.  References would be appreciated!

                                Thanks much!
                                Sam Abrash
                                Abrash@URVAX.URICH.EDU


From owner-chemistry@ccl.net  Mon Jul 17 13:25:15 1995
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For CCL list--

   A colleague poses the following question that some members of this list
may be able to answer:
> 
> I have some Fortran code we wrote that uses zeta plot library calls. 
> Zeta plotting was very similar to Calcomp plotting routines.  They were
> used heavily in the 60's and part of the 70's, then seem to have been
> superceded by better packages, but many programs still use them.  Our
> computer service here has a package that translates Zeta/Calcomp files
> (*.PLT) to postscript, but it is part of a huge program the manages
> queues and other things and they are not eager to let me have it for
> export to users off site who use our data analysis software.
> 
> So I am looking for a program to translate zeta plot files to postscript
> or any other standard format plot file.  Even a description of zeta plot
> format would be an advance.  Have you run across any such things? 
> Given how common such output was 20 years ago, I imagine lots of
> computer service folks have had to write such things, and many schools
> might have them, perhaps in freeware form.
> 

   If others express interest, I will be happy to compile any useful answers
for the CCL archives.

CJC

-- 

Christopher J. Cramer
University of Minnesota
Department of Chemistry
207 Pleasant St. SE
Minneapolis, MN 55455-0431
--------------------------
Phone:  (612) 624-0859 || FAX:  (612) 626-7541
cramer@maroon.tc.umn.edu
http://dionysus.chem.umn.edu/


From owner-chemistry@ccl.net  Mon Jul 17 13:28:57 1995
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To: CHEMISTRY@ccl.net
From: kfw@lubrizol.com (Kurt F. Wollenberg)
Subject: Re: nmr software


>
>
>*********************************************************************
>
>iX-Sender: adam@cherwell.com
>X-Mailer: Windows Eudora Version 1.4.4
>Date: Fri, 14 Jul 1995 17:40:41 +0100
>To: CHEMISTRY%ccl.net@interlockp.lubrizol.com
>From: adam%cherwell.com@interlockp.lubrizol.com (Adam Hodgkin)
>Subject: CCL:Beta-testers wanted for Windows NMR program
>Sender: Computational Chemistry List
><chemistry-request%ccl.net@interlockp.lubrizol.com>
>Errors-To: ccl%ccl.net@interlockp.lubrizol.com
>Precedence: bulk
>Status: R
>
>
>gNMr is a simulation program aimed at chemists who use NMR analysis and wish
>to obtain immediate results on their desktop. Structures can be imported
>from many drawing programs, real data can be imported from various file
>formats and a range of analysis tools are available. The Mac program was
>beta-tested by members of the CCL and is now published by Cherwell and is
>also being distributed by SoftShell.
>
>Information and demo disks for the Mac version are now available from
>csp@cherwell.com.
>
>We are looking for no more than 10 beta-testers for the Windows version. Our
>ideal beta-tester will work thoroughly with the program within 3 weeks and
>will send us a report itemising any bugs or deficiencies in the program with
>comments on the manual. If you are interested and will be able to test the
>program during early August, please send us an e-mail message with your full
>postal address and mention the facilities available to you (eg whether you
>will be able to test conversions from any experimental file formats - giving
>systems).
>
>We are on a tight schedule and will not be able to consider applications
>received after July 20. If we are unable to include you in the beta-test
>program we will be happy to send you a demo disk in a few months when the
>program is released.
>
>Thanks for your co-operation
>
>---                                                                   ---
>     Adam Hodgkin                    |  e-mail:   adam@cherwell.com
>     Managing Director               |  Phone:    +44 (0)1865 784800
>     Cherwell Scientific Publishing  |  Fax:      +44 (0)1865 784801
>---                                                                   ---
I would be interested in taking a look at the program. Could I get a demo
copy when it becomes available.

Best Regards,
Kurt Wollenberg

Kurt Wollenberg
Research Chemist
NMR Spectroscopy
Lubrizol Corporation
e-mail:kfw@lubrizol.com
ph#:(216)943-1200 ext2026
fax:(216)943-9022



From owner-chemistry@ccl.net  Mon Jul 17 13:40:14 1995
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Date: Mon, 17 Jul 1995 13:43:25 -0500
To: chemistry@ccl.net
From: gmercier@helix.nih.gov (Gustavo A. Mercier, Jr.)
Subject: Molecular Modeling Packages Users Experience?


        Hi!

We are in the process of acquiring a Molecular Modeling Package, such
as Quanta, etc. It would be useful to hear from other users experiences.

We are particularly interested in doing Brownian Dynamic Simulations of
dendrimers tagged with transition metals or lathanides. We recognize that
the available systems are rather poor in handling metals, but we are more
concerned with structure building (including use of symmetry to expedite
model building), interface to quantum mechanical packages (especially
those with DFT implementations), and display of molecular properties and
trajectories.

We would be interested in comments from users of Insight/Discover,
Quanta, Sybyl, Cerius2, and any others.

I will summarize for the net!

Thanks!

Gustavo Mercier, Jr M.D.-Ph.D.
NIH - LDRR
OD OIR LDRR
Building 10 Room B1N256
10 Center Dr MSC 1074
Bethesda, Maryland 20892-1074
phone: 301-402-3586, 301-496-1981
fax:      301-402-3216
e-mail: gmercier@helix.nih.gov




From owner-chemistry@ccl.net  Mon Jul 17 14:55:18 1995
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          High Performance Computational Chemistry Workshop

*************************** Final Announcement ******************************

                          August 13-16, 1995

                          Pleasanton Hilton
                          7050 Johnson Drive
                         Pleasanton, CA 94588

Pacific Northwest Laboratory, The National Institutes of Health, and the
National Energy Research Supercomputer Center are sponsoring a High Performance
Computational Chemistry Workshop in early August 1995.  The workshop will be a
forum for computational chemistry researchers to present and discuss their
current research efforts, algorithms and scientific applications that target
high performance parallel supercomputers.  The goals of the workshop are to
present state-of-the-art developments and applications on parallel
supercomputers and to stimulate research efforts and funding in this area.  Each
of the workshop sessions will comprise invited and contributed talks.  Session
topics include: HF, DFT, ab initio correlated methods, numerical methods, MD,
etc.  Speakers that have accepted this invitation include, Prof. E. Clementi,
Prof. W. Goddard, Prof. R. Kalia, and Dr. M. F. Guest.  A more detailed speaker
list will be provided prior to the meeting.


URL:  http://www.emsl.pnl.gov:2080/docs/tms/workshop_95/workshop.html

Confirmed Speakers:
T. Arias, MIT (tentative)
P. Bagus, National Science Foundation
J. Carpenter, Cray Research Inc.
M. Causa, University of Torino 
E. Clementi, University of Strasbourg, France
R. Friesner, Columbia
J. Gao, SUNY, Buffalo
W. A. Goddard, California Institute of Technology
M. F. Guest, EPSRC, Daresbury Laboratory, England
M. Head-Gordon, University of California, Berkeley
B. Johnson, Q-Chem, Inc. 
R. Kalia, Lousiana State University
T. Kitchens, MICS, Department of Energy
P. Kollman, University of California, San Francisco
H. P. Luthi, ETH, Zurich
L. Mitas, NCSA
J. Nichols, Pacific Northwest Laboratory
I. Nielsen, Sandia National Laboratory, California
R. Pastor, NIH
C. Post, Purdue University
W. Reinhardt, (tentative)
J. Rice, IBM Almaden
B. Roux, University of Montreal
D. Salahub, University of Montreal 
R. Shepard, Arnonne National Laboratory (tentative)
A. St. Amant, University of Ottawa
M A. Thompson, Pacific Northwest Laboratory
T. Truong, University of Utah
S. Wierschke Department of Defense (tentative)
M. Wrinn, Biosym Inc, 

Sponsors:
                Environmental Molecular Sciences Laboratory
                Pacific Northwest Laboratory
                Richland, Washington

                Laboratory of Structural Biology
                Division of Computer Research and Technology (DCRT)
                National Institutes of Health
                Bethesda, Maryland

                National Energy Research Supercomputer Center
                Lawrence Livermore National Laboratory
                Livermore, California


Contact Persons:
        Dr. Ricky A. Kendall
        MSIN K1-90
        Environmental Molecular Sciences Laboratory
        Pacific Northwest Laboratory
        Richland, WA 99352-0999
        FAX:   509-375-6631
        Phone: 509-375-2602
        Email: ra_kendall@pnl.gov

        Dr. Robert J. Harrison
        MSIN K1-90
        Environmental Molecular Sciences Laboratory
        Pacific Northwest Laboratory
        Richland, WA 99352-0999
        FAX:   509-375-6631
        Phone: 509-375-2037
        Email: rj_harrison@pnl.gov

        Dr. Jeffrey A. Nichols
        MSIN K1-96
        Environmental Molecular Sciences Laboratory
        Pacific Northwest Laboratory
        Richland, WA 99352-0999
        FAX:   509-375-6631
        Phone: 509-372-4569
        Email: ja_nichols@pnl.gov

        Dr. Bernard R. Brooks
        NIH/DCRT, LSB
        Bldg. 12A, Rm 2007
        9000 Rockville Pike
        Bethesda, MD 20892
        email:  brbrooks@helix.nih.gov

        Ms. Tammy S. Welcome
        L-561
        National Energy Research Supercomputer Center
        Lawrence Livermore National Laboratory
        Livermore, CA 94550
        Email:  tsw@nersc.gov

Conference Administrator:
        Rebecca R. Wattenburger
        MSIN K1-96
        Environmental Molecular Sciences Laboratory
        Pacific Northwest Laboratory
        Richland, WA 99352-0999
        FAX:   509-375-6631
        Phone: 509-372-4681
        Email: rr_wattenburger@pnl.gov


Organizing Committee:                           Advisory Committee:
        Bernard R. Brooks, NIH                          Thom H. Dunning, Jr.
        Robert A. Eades, PNL                            Ray A. Bair
        Robert J. Harrison, PNL                         David A. Dixon
        Ricky A. Kendall, PNL                           Michel Dupuis
        Jeffrey A. Nichols, PNL                         Bruce C. Garrett
        C. William McCurdy, NERSC                       Martyn F. Guest
        Rebecca R. Wattenburger, PNL


--------------------------------------------------------------------------------
                      HPCC Workshop Registration
                            Form & Payment
                         Due by July 15, 1995

Please print or type:

Full Name: _____________________     __________     ___________________ 
                First                   Middle          Last


Business Address:_______________________________________________________________

________________________________________________________________________________

City:___________________________________  State:______________ Zip:_____________

Country:________________________________

Daytime Phone:  (     )_________________  FAX: (    )___________________________

Email Address:__________________________________________________________________

REGISTRATION FEE:  $100.00                   (Please make checks payable to PNL)

After July 15 and space available: $200.00

Making Presentation: (Yes/No) _________

Title of Poster Presentation:___________________________________________________

________________________________________________________________________________

________________________________________________________________________________
                                                                                                                                                            
Arrival Date:   _________________  Departure Date: _________________

By July 15 please complete this form and mail, email, or Fax to:
        HPCC Workshop
        R. R. Wattenburger
        Environmental Molecular Sciences Laboratory
        Pacific Northwest Laboratory
        PO Box 999 MSIN K1-96
        Richland, WA 99352-0999

        Fax:   509-375-6631
        Phone: 509-372-4681
        Email: rr_wattenburger@pnl.gov

Abstracts: 

Camera Ready Abstracts are due July 7th, 1995 at the above address.  The
abstracts should be one or two pages that clearly describe the presentation and
the presenting author's name should be underlined.


-----------------------------------------------------------------------------------------
                       Hotel Reservation Form:
                         Due by July 15, 1995


          High Performance Computational Chemistry Workshop
                          August 13-16, 1995
                          Pleasanton Hilton
                          7050 Johnson Drive
                         Pleasanton, CA 94588
                        Phone: (510) 463-8000
                        Fax:   (510) 463-3801

Room reservations must be made directly with the Tutorial Hotel.  The
Hotel is approximately 7 miles from LLNL.  Please submit this form
when making your room reservations.  To receive the special rate of
$74.52 (including local taxes) reservations must be made by July 15,
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From owner-chemistry@ccl.net  Mon Jul 17 15:40:18 1995
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	by www.ccl.net (8.6.10/930601.1506) id PAA00255; Mon, 17 Jul 1995 15:28:59 -0400
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Date: Mon, 17 Jul 1995 15:28:48 -0400 (EDT)
From: Shubin Liu <shubin@email.unc.edu>
X-Sender: shubin@isisa.oit.unc.edu
To: chemistry@ccl.net
Subject: CCL: where to ftp Bader's program
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Dear All:
	I need to compute the density, its gradient and Laplacian of a few
molecules lately. I was told that the program by Professor Bader in McMaster 
University does the job. And it is said that it is for free and available 
at some ftp address. Can somebody let me know where I can get one? Thanks 
a lot!

Shubin
.............................................................................
Shubin Liu

Department of Chemistry			    Email: shubin@email.unc.edu
University of North Carolina		           sliu@mulliken.chem.unc.edu
Chapel Hill, NC 27599-3290		    Tel  : (919) 962-0150(O)
USA                                                (919) 914-6923(H)
.............................................................................


From owner-chemistry@ccl.net  Mon Jul 17 18:55:18 1995
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	id AA05284; Mon, 17 Jul 1995 16:45:16 +0600
Date: Mon, 17 Jul 1995 16:45:16 -0600 (CST)
From: Silaghi Dumitrescu Ioan-IQ <ioan@servidor.unam.mx>
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To: chemistry@ccl.net
Subject: coordinates of C70
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Dear netcoleaugues,

I am looking for the coordinates or Z-matrices for C70. These are not in 
the /pub/chemistry/data/fullerenes folder. Can somebody help me?


Ioan Silaghi-Dumitrescu
Universidad Nacional Autonoma de Mexico
Insituto de Quimica
04510 Mexico D.F.
e-mail: ioan@servidor.unam.mx


From owner-chemistry@ccl.net  Mon Jul 17 20:40:21 1995
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Date: Mon, 17 Jul 1995 17:39:54 -0700
From: d3g359@rahman.pnl.gov (John Nicholas)
Subject: point charges in g92/g94
To: CHEMISTRY@ccl.net
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Everyone, we would like to do an optimization of
a molecule in a field of point charges using g92/g94.
So far our attempts have failed. Is this possible,
and if so, would someone please send an example input
deck? Thanks 

John

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