From sling@euclid.chem.washington.edu  Thu Feb 24 02:02:58 1994
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Date: Wed, 23 Feb 1994 22:48:33 -0800
From: sling@euclid.chem.washington.edu (Song Ling)
Message-Id: <9402240648.AA36308@euclid.chem.washington.edu>
To: chemistry@ccl.net, noy@tci002.uibk.ac.at, topper@magnum.cooper.edu
Subject: Re:  CCL:solvation no. from MD & MC


I read Prof. Topper's comments with high interest (honestly I don't 
know where/when the discussion got started.  Just want to mention that
one might want to try several different random number generators in
the Monte Carlo calculations, to my knowledge there are some simple
(not tricky) statistical tests and some random number generators pass
some, others pass some different tests, hardly they pass a "global"
set of tests.  In trajectory calculations, the similar problems may
arise in generating the initial conditions (random number generators
are used).  Whether the initial conditions are chosen on the tori (or
the energy shell, say) only the phase space knows.  If the system is
not that chaotic, it will generally take a rather long to acheive the
so called ergodicity.  I remember what is quoted as said by Arnol'd:
The understanding of 4 dimensional phase space is beyond the present
mathematics.  (Sorry, forget the source, would appreciate if someone
let me know.)
Song Ling

From FLEMMING@dfhvax.nbi.dk  Thu Feb 24 09:03:15 1994
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Date: Thu, 24 Feb 1994 14:28:00 +0100
Subject: Conversion of SHELX output to ORTEP input ?
To: chemistry@ccl.net
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Dear Netters

I'm looking for a program, which convert a 
SHELX (SHELXL-93) output file to an ORTEP 
input file.

We are running SHELX on a SGI workstation
and ORTEP on a Macintosh, so a program on
any of those two platforms would be nice.

Thank you.

Flemming Steen Jorgensen

flemming@dfhvax.nbi.dk



From bob@bob.usuf2.usuhs.nnmc.navy.mil  Thu Feb 24 11:03:23 1994
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Date: Thu, 24 Feb 1994 10:21:15 -0500
From: Bob Williams <bob@bob.usuf2.usuhs.nnmc.navy.mil>
Message-Id: <9402241521.AA18456@bob.usuf2.usuhs.nnmc.navy.mil>
To: chemistry@ccl.net
Subject: Density Functional Theory


Dear Chemistry Net,

We are interested in the relative merits of
Density Functional Theory calculations,
but we do not have access to appropriate software.

What is the relative speed of DFT optimization
and frequency calculations on a large molecule
at modest levels of theory
(compared to a similar RHF/4-31G job).

Also, we would like to know something about
the quality of the force matrix and frequencies
produced by modest level DFT calculations,
and about the transferability of scale factors.
That is: how does the "cancelation of errors" produced by
DFT compare to that from the 4-31G level.
 
Thankyou in advance,
Bob Williams, Dept. of Biochemitry, USUHS


From B.S.Halstead@chemistry.hull.ac.uk  Thu Feb 24 12:03:08 1994
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From: ch4bsh <B.S.Halstead@chemistry.hull.ac.uk>
Date: Thu, 24 Feb 94 16:19:09 GMT
Message-Id: <14840.9402241619@humus.hull.ac.uk>
To: chemistry@ccl.net
Subject: AZT Derivatives



Dear Netters
 
I am attempting to calculate some properties of AZT derivatices using MINDO3.  I
 will therefore be needing structural, thermodyanmic and biological activity
 data for various derivatives.  If anybody has or knows the location of such
 data please let me know - This is only a final year project, if I have to find
 all the data by hand I probably won't have time to run any calculations.
 
Thanks in advance
 
Ben

From mckelvey@Kodak.COM  Thu Feb 24 12:04:42 1994
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To: osc@Kodak.COM
Subject: SAN DIEGO ACS MEETING: SPECIAL TRIBUTE TO QCPE AND RICHARD W. COUNTS






 		       SAN DIEGO, CALIFORNIA
 	         AMERICAN CHEMICAL SOCIETY MEETING 
	      COMPUTERS IN CHEMISTRY SPECIAL SYMPOSIUM

		          THE MORNING OF
 		     WEDNESDAY, MARCH 16, 1994 
			   THE MARRIOTT



			     HONORING 

		THE QUANTUM CHEMISTRY PROGRAM EXCHANGE

				AND 
	
			MR. RICHARD W. COUNTS



		
		     "SOFTWARE SUPPORT DILEMMAS"


	SPEAKERS:


		"THE QCPE EXPERIMENT"

			DR. HARRISON SHULL, PROVOST
			NAVAL GRADUATE SCHOOL
			MONTEREY, CA 93943
			

		"FUNDING COMPUTATIONAL CHEMISTRY IN THE 80'S AND 90'S"

			DR. NORMAN L. ALLINGER
			CHEMISTRY DEPARTMENT
			UNIVERSITY OF GEORGIA
			ATHENS, GA 30602


		"WHYS AND WHY-NOTS OF COMMERCIALLY DISTRIBUTED SOFTWARE"

			DR. MICHAEL C. ZERNER
			QUANTUM THEORY PROJECT
			UNIVERSITY OF FLORIDA
			GAINSVILLE, FL 32606


		"THIRTY YEARS OF THE SOFTWARE SUPPORT PROBLEM"

			MR. RICHARD W. COUNTS
			QUANTUM CHEMISTRY PROGRAM EXCHANGE
			INDIANA UNIVERSITY
			BLOOMINGTON, IN 47405




	CO-SPONSORS: DIGITAL EQUIPMENT CO., FUJITSU COMPUTER SYSTEMS,
		     EASTMAN KODAK CO., STERLING-WINTHROP PHARMACEUTICALS,
		     AND STEWART COMPUTATIONAL CHEMISTRY			

From setlik@acsu.buffalo.edu  Thu Feb 24 13:06:58 1994
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Date: Thu, 24 Feb 1994 12:27:54 -0500
From: "Robert F. Setlik" <setlik@acsu.buffalo.edu>
Message-Id: <199402241727.MAA04295@lictor.acsu.buffalo.edu>
To: CHEMISTRY@ccl.net
Subject: Fe-s charges



Hi Netters,

	Does anyone have charges for a tetrahedral Fe-S complex.  That is,
something like the Iron cysteine complex found in ferredoxin.  Also, has 
anyone done MD simulations on such a protein system.  Any leeds would be
appreciated.

Rob Setlik
..

From 21NBCJ@NPD.UFPE.BR  Thu Feb 24 14:03:09 1994
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 <01H99O6WKF6890NHPS@NPD.UFPE.BR>; Thu, 24 Feb 1994 15:26:49 -0300
Date: Thu, 24 Feb 1994 15:26:49 -0300
From: Nivan Bezerra <21NBCJ@NPD.UFPE.BR>
Subject: He calculation
To: Chemistry@ccl.net
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 Hello netters,
 
 I am interested in CI calculation for He and isoeletronic series with 
 STO basis sets.
 
 Can anyone tell me something about this calculation?

           Thanks in advance.

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
  Nivan Bezerra da Costa Junior                Fone:  (081) 271-8440
  Universidade Federal de Pernambuco           Fax:   (081) 271-8442
  Centro de Ciencias Exatas e da natureza          
  Departamento de Quimica Fundamental          E-mail:
  Cidade Universitaria                         HEPNET:   NPD1(47909)::21nbcj
  50739 - Recife - PE                          INTERNET: nivan@vaxdqf.ufpe.br
                                                         21nbcj@npd1.ufpe.br
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 


From yanke@qtp.ufl.edu Thu Feb 24 11:40:10 1994
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Date: Thu, 24 Feb 94 11:38:49 EST
Message-Id: <9402241638.AA11684@orange.qtp.ufl.edu>
To: jkl@ccl.net
Cc: chemistry@ccl.net
Subject: Applied Molecular Orbital Theory Workshop




    Ninth Florida Workshop on Applied Molecular Orbital Theory

Dear Colleague:

In your research, do many questions about molecular structure, spectra
and reactivity arise? The Florida Quantum Theory Project offers the
ninth edition of their popular one-week short course that will help you
to answer the following questions: 

What is the structure of a proposed novel compound?

What is the activation barrier for a potential reaction mechanism?

How can I predict where to look for the vibrational or electronic
spectra of a molecule to identify it?

What are the structures, spectra and energetics of transient reaction
intermediates?

How can I assess the effect of adding a substituent on the color of a
dye molecule without synthesis?

Can I inexpensively screen functional molecules, such as drug
derivatives, to identify the best prospects for success?

How can computer graphics provide a new perspective on chemistry?

How can I better understand and evaluate the quantum chemical analysis
that accompanies more and more articles in the best chemical journals?

If such questions are important to you, we invite you to attend our
course on molecular orbital theory. The course is designed for
scientists who are active researchers and recognize the potential for
applying molecular orbital theory to molecules in order to provide
information that is otherwise unavailable and for managers, supervisors
and research directors who may be interested in an overview of recent
advances in computational quantum chemistry and how they may be employed
to enhance the productivity of their research unit.

We invite you to learn the current developments in empirical potentials
from Nigel Richards; semiempirical molecular orbital methods, such as
AM1, SAM1, CNDO and INDO, from Michael Zerner; ab initio SCF theory from
Yngve Ohrn; and correlated methods, many-body perturbation theory (MBPT;
also known as MP) and coupled-cluster (CC) theory from Rod Bartlett;
augmented with computer graphics by George Purvis of CAChe Scientific;
and modern density functional theory (DFT). John Watts and Nevin
Oliphant will coordinate the laboratory exercises. The staff's expertise
spans the range from biomolecular applications, through organic
chemistry, to the highest levels of ab initio methods and DFT. 
Applications are brought to life by employing a wide variety of graphics
techniques to visualize the formation of chemical bonds or the
potentials that molecules exert upon each other. 

Computer applications in chemistry are becoming essential. This is an
opportunity for your research group to enhance your computational
capabilities to provide results to complement the other instrumental
techniques at your disposal. In addition to providing lecture material
to assist you to select the right methods and to appreciate their
limitations, the intent of this course is to provide "hands-on"
experience with state-of-the-art computer programs executing on CAChe
Scientific workstations and QTP computers.

To take advantage of inexpensive plane fares that include a Saturday
night stay, the course is scheduled for semester break on the campus of
the University of Florida, with arrival on Sunday, May 1, and
recommended departure on Sunday, May 8, 1994. Lectures are presented in
the morning and early afternoon, with computer lab sessions later in the
afternoon. Optionally, the computers are also available to participants
in the evenings and all day Saturday, May 7, for additional work on
applications. We also devote time to hear about your research problems
and try to assist you in using theoretical methods to help solve them.

Social events include a welcoming reception Sunday evening and dinners
Monday, Wednesday and Friday that are held at the best restaurants in
the area. Tuition, which includes room, dinners, coffee and detailed
lecture notes, is at an inclusive $1250 per person. Enrollment will be
limited to 25 participants, housed in single rooms at the Reitz Union on
campus. Companions are invited to accompany a participant by payment of
an additional $100 to cover the social affairs and room increment.  

Registration plus a check or purchase order payable to the University of
Florida Research Foundation will be required before April 15, 1994, and
should be sent directly to me at the Quantum Theory Project, P.O. Box
118435, University of Florida, Gainesville, FL 32611--8435.  Please send your 
address via e-mail to Mrs. Yanke in my office and she will send you a registration
form by mail or fax if you prefer (yanke@qtp.ufl.edu).   

We hope that you or some of your colleagues will find our course to be
of interest. If we can provide any further information, please call us.

Sincerely,

Rodney J. Bartlett
Graduate Research Professor
of Chemistry and Physics

From pat@mercury.aichem.arizona.edu  Thu Feb 24 15:03:11 1994
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Date: Thu, 24 Feb 1994 12:13:07 -0700 (MST)
From: Pat Walters <pat@mercury.aichem.arizona.edu>
Subject: Re: CCL:Collaborative software development
To: chemistry@ccl.net
In-Reply-To: <Pine.3.89.9402231816.B1949-0100000@ukwbf07>
Message-Id: <Pine.3.05.9402241204.E15884-c100000@mercury>
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Our file conversion program Babel provides another example of collaborative
development via the internet.  We designed the program with an open 
architecture which facilitates the easy inclusion of new file formats.  In
addition we have provided a "Babel Developer's Guide" which provides step
by step instructions on how to add new file formats to the program.  Adding
a new reader or writer routine typically requires less than 50 lines of C 
code.  When we released the program in December it supported 16 file formats.
Now, due to submissions from around the world, Babel supports 35 file formats
and the number is still growing.

In addition to acting as file conversion program Babel can be compiled into 
a library which can provide a variety of routines including :
- assignment of bonds
- assignment of hybridized atom types
- assignment of bond orders
- determination of interatomic distances, bond angles and torsion angles
- conversion between internal, fractional and Cartesian coordinates.
- addition and deletion of hydrogens
- a number of routines for vector manipulation

The program runs under Unix, MS-DOS, and the Mac.  I've heard that there 
are also ports to Atari and Open VMS, but I haven't seen them.

We are currently using the Babel library as the core for our development 
efforts, and we plan to release additions to Babel and the library in the 
coming months.

There will be two presentations on Babel (#36 and #37 in the Division of
Chemical Information) at the San Diego ACS meeting.

For more information on babel finger babel@mercury.aichem.arizona.edu or
send mail to babel@mercury.aichem.arizona.edu
_________________________________________________________________________
Pat Walters                 pat@mercury.aichem.arizona.edu
Graduate Student
Laboratory for Artificial Intelligence in Chemistry    *
Dept of Chemistry                                    * * *  
University of Arizona, Tucson  AZ 85721              * * * 
Voice : 602-621-6334   FAX :  602-621-8407            ***
"At least it's a dry heat"                             * 
_______________________________________________________*__________________



From st-amant@theory.chem.uottawa.ca  Thu Feb 24 16:04:30 1994
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Date: Thu, 24 Feb 1994 15:59:57 -0500
From: st-amant@theory.chem.uottawa.ca (alain st-amant)
Message-Id: <9402242059.AA18394@theory.chem.uottawa.ca>
To: CHEMISTRY@ccl.net
Subject: DFT software



Dear Netters,

As I mentioned a while back, I was working on some DFT code that I'd make
available to other computational chemists free of charge.  Well, it's finally
ready now.  The program, DeFT, can be obtained via ftp.  However, it is NOT
public domain software, and we'd ask you to observe the copyright and license
agreement that come with the source code.  All we ask in return is that all
improvements be sent back to me so that we can make your improvements freely
available to others.  Such contributors will of course be appropriately
recognized.

The code can basically locate local minima, locate transition states,
perform vibrational analyses, with the use of analytic first derivatives.
Sorry, no analytic second derivatives.  DeFT uses gaussian functions and
is therefore quite similar to DGauss.  Both LSDA and NLSDA calculations
can be performed.

The code can be obtained by ftp'ing theory.chem.uottawa.ca (137.122.43.156)
with the username "DeFT_ftp".  The filename is "DeFT_tarfile.Z", and it will
be there in your home directory.  However, to add an extra level of security,
and to help me keep track of how many people are using the code, a password
is required.  People can obtain the password by e-mailing the following
address:

       request@theory.chem.uottawa.ca

I will try to e-mail the password back as promptly as possible (hopefully,
this should be within an hour or two, at worst, overnight if the request
is sent late in the day).  The password will remain valid for several days.

The code, documentation, and sample inputs and outputs, once tar'ed and
compressed, come out to about 800 kilobytes.

Hopefully, the code will be of use to some, and improvements can be added
by its new users.

Alain St-Amant

Department of Chemistry
University of Ottawa

From JFO555F%SMSVMA.BITNET@phem3.acs.ohio-state.edu  Thu Feb 24 17:03:30 1994
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 24 Feb 1994 16:09:17 EST
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Date: Thu, 24 Feb 1994 14:43:35 -0600 (CST)
From: "Jim O'Brien" <JFO555F%SMSVMA.BITNET@phem3.acs.ohio-state.edu>
Subject: Energies in Td Complexes
To: chemistry@ccl.net
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    To read about energies in Td complexes you might try Chapter 9 in the third
edition of F. A. Cotton, Chemical Applications of Group Theory.

From leboeuf@CERCA.UMontreal.CA  Thu Feb 24 17:07:37 1994
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Message-Id: <9402242124.AA12350@pellan.CERCA.UMontreal.CA>
Subject: optimal distribution of charges on sphere
To: chemistry@ccl.net
Date: Thu, 24 Feb 1994 16:24:00 -0500 (EST)
Cc: leboeuf@CERCA.UMontreal.CA (Martin Leboeuf), salahub@ERE.UMontreal.CA
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Dear CCLers,

A computational fluid dynamics friend has asked if we chemists know 
anything about the distribution of points (charges) on a sphere.
(He is interested in bubbles)
I remember seeing some papers on this question but can't place them.
There is some work in theoretical inorganic chemistry and some 
demonstrations of the optimal configurations for quite high N (the
number of points).

Any clues? Please reply to leboeuf@cerca.umontreal.ca and Martin
Leboeuf or I will summarize to the net, if it seems appropriate.

Dennis Salahub

-- 
************************************************************
*   Dennis Salahub               SALAHUB@ERE.UMONTREAL.CA  *
*   Departement de chimie        Tel. (514) 343-6755       *
*   Universite de Montreal       Fax  (514) 343-2468       *
*   C.P. 6128, Succ. A                                     *
*   Montreal, Quebec  H3C 3J7                              *
*   Canada                                                 *
************************************************************                                       




From JSMCM@jazz.ucc.uno.edu  Thu Feb 24 17:12:08 1994
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 <01H99P1IM1KC8X4FIS@jazz.ucc.uno.edu>; Thu, 24 Feb 1994 15:51:40 CST
Date: 24 Feb 1994 15:51:40 -0600 (CST)
From: JORGE <JSMCM@jazz.ucc.uno.edu>
Subject: Density Functional Theory
To: chemistry@ccl.net
Cc: bob@bob.usuf2.usuhs.nnmc.navy.mil
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Here my answers to Bob Williams. Enjoy!

>We are interested in the relative merits of
>Density Functional Theory calculations,
>but we do not have access to appropriate software.

The best merit, as our group is concerned, is that
we can get better energetics (atomization energies)
than MP4SDTQ/6-311+G** or QCISD(T)/6-311G**.
The lowest level of theory that improves the
DFT is MP4SDTQ/6-311(2df,p).
I don't mean by this that we should not continue
developing sophisticated ab initio methods. We 
certainly need then to continue the development
of better functionals.
We used Perdew-Wang functionals for this
particular comparison with a basis set with double
zeta valence plus polarization functions on all
atoms (like 6-31G**).(preprints on request)

>What is the relative speed of DFT optimization
>and frequency calculations on a large molecule
>at modest levels of theory
>(compared to a similar RHF/4-31G job).

The problem (actually advantage) is that DFT
calculations contain almost all of the
correlation portion missing in HF; therefore, it 
requires of polarization functions for its correct
calculation. Calculations without polarization 
functions yield qualitatively wrong results
(similar situation would happen doing MP4/4-31G).
Basically DFT scales as N**3 as opposed to HF who 
scales as N**4. For large systems both exponents
decrease. For small systems, it is commom
that the N**3 is not that advantage because the numerical
integrations involved in DFT codes. When you have ten or
more heavy atoms DFT is the only choice for good energetics.
With respect to second derivatives, until G92/DFT we (in UNO)
did not have an analytical procedure to calculate second 
derivatives. The programs I used have numerical second
derivatives and they were really slow, as they are also
with other ab initio methods using numerical second
derivatives. We hope that analytical second derivatives
for DFT methods became common very soon.

>Also, we would like to know something about
>the quality of the force matrix and frequencies
>produced by modest level DFT calculations,

There is no problem in the quality of results
but the strong limiting fact was that the 
numerical second derivatives were too slow.
(as I told you I have not tried yet G92/DFT for
frequency calculations).
Finally, the modest DFT calculation you want to try
have to use a 6-31G** basis set or equivalent. The
advantage is that you don't need a bigger basis
because the quality of the calculation at that point
is given by the functional you choose any further improvement
would have to done to the functional.

>and about the transferability of scale factors.
>That is: how does the "cancelation of errors" produced by
>DFT compare to that from the 4-31G level.

Being DFT a more precise tool than [HF/]4-31 level,
the errors are much smaller, therefore
DFT do not require of such an (big) error cancellation.
However, I am not very sure to what error
cancellations you referring to.

Hope this help

Jorge M. Seminario
jsmcm@uno.edu

From billys@chmboy.srl.ford.com  Thu Feb 24 19:03:14 1994
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Sorry for replying to the net, but direct mail failed.


There is only one triplet state that arises from the configuration (t2)^2.  It
is 3T_1.  The other states are 1A_1, 1E, and 1T_2.  From Hund's rules the 3T_1
would be the lowest energy.  When coupling two equivalent electrons, you must
use the antisymmetric direct product to obtain the triplet functions, and the
symmetric direct product to obtain the singlet.  Landau and Lifshitz has more
details.

Bill Schneider
Ford Motor Co.

