From PUCHTA@anorganik.chemie.uni-erlangen.de  Wed Dec  6 03:11:10 1995
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From: "Ralph Puchta" <PUCHTA@anorganik.chemie.uni-erlangen.de>
Organization:  Institut fuer Anorganische Chemie
To: chemistry@www.ccl.net
Date:          Wed, 6 Dec 1995 08:57:02 +0100
Subject:       semiempiric
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Dear CCl-Users!

1. Does anyone know free semiempirical calculation program, that are not
     versions of ampac and mopac.
2. Which was the last free version of ampac? 
3. Are there any free forcefield calculating programs?
4. On which ftp-server can I find these programs?

Thank you very much for your help

Ralph Puchta
Puchta@anorganik.chemie.uni-erlangen.de



From mam@atc.atccu.chula.ac.th  Wed Dec  6 04:11:10 1995
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Date: Wed, 6 Dec 95 15:50:35 GMT
From: mam@atc.atccu.chula.ac.th (Thammarat Aree)
Message-Id: <9512061550.AA03950@atc.atccu.chula.ac.th>
To: chemistry@www.ccl.net
Subject: buckyball


Dear CCLs,
	I would like to know the experiment data about the position
of doped particles in the lattice of C60- MnC60. n=1,2,3,4,5,6.
	If anyone know about this please tell me.
	Thank you.
Best regards,
Thammarat
	mam@atc.atccu.chula.ac.th

From michael@argaman.tau.ac.il  Wed Dec  6 04:32:29 1995
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Date: Wed, 6 Dec 1995 11:32:21 +0200 (IST)
From: Michael shoken <michael@argaman.tau.ac.il>
To: CHEMISTRY@www.ccl.net
Subject: Protein 3D from secondary structure ?
Message-ID: <Pine.SGI.3.91-heb-2.05.951206112451.17866A-100000@argaman.tau.ac.il>
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Content-Type: TEXT/PLAIN; charset=US-ASCII


Dear Netters!

I am interested to find the names of some programs which could run via 
PC (486, Pentium etc) and give possibility to reconstruct approximate 3D 
structures of proteins on the basis of their primary sequences and on 
information about secondary structure (alpha and beta sheets etc).

Thank you in advance, 

Michael

*********************************************************

Dr. Michael Shokhen
Senior researcher.
Laboratory of rational drug design

Department of Molecular Microbiology and Biotechnology,
G.S.Wise Faculty of Life Sciences,
Tel-Aviv University,
69978, Tel-Aviv, Israel.
Fax: 972-3-6409407
Email: michael@argaman.tau.ac.il

*********************************************************


From owner-chemistry@ccl.net  Wed Dec  6 05:41:12 1995
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From: rnobes@msicam.co.uk (Ross Nobes)
Message-Id: <199512061033.KAA27163@gaia.msicam.co.uk>
Subject: Re: CCL:G:G94: B3LYP energy and Charge
To: frisch@lorentzian.com (Mike Frisch)
Date: Wed, 6 Dec 1995 10:33:05 +0000 (GMT)
Cc: chemistry@ccl.net
Reply-To: rnobes@msi.com
In-Reply-To: <9512051730.AA14738@mjf> from "Mike Frisch" at Dec 5, 95 12:30:57 pm
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Mike Frisch writes:
  > 
  > > The answer is that both are right!  The Gaussian definition of B3LYP
  > > uses the VWN local correlation functional;  most other programs use
  > > what Gaussian terms VWN5.
  > > 
  > 
  > No, B3LYP was defined to use VWN3.  Using the same name for two different
  > functionals is a disservice to everyone and makes reproducing other peoples
  > results impossible.  This used to be a major problem in the DFT area, and
  > things are finally improving with regard to terminology.  To take a name for
  > something that is specified in the literature and use it for something
  > different is a major step backwards.  Published and in-press tests of B3LYP
  > all use VWN3; an assumption that the same conclusions apply to a different
  > functional just because it has the same name are not valid.
  > 

Point taken.  All that I was implying in my original answer was that there
are no 'numerical' problems here - both programs are giving correct results
within their own definitions of B3LYP.  Most programs (such as Mulliken,
CADPAC, MOLPRO, Turbomole) use the VWN5 functional uniformly as the 
local correlation part of functionals such as SVWN, B3P86 and B3LYP.  It
is unfortunate that Gaussian is alone in using an alternative VWN local
correlation functional and (as Mike says) that the terminology is not 
consistently defined.  The issue is further confused by a bug in the
Gaussian 92/DFT open-shell VWN5 code which leads to small discrepancies
with the other programs even when extremely large quadrature grids are
used.

-- 
+----------------------------------------------------------------+
| Dr Ross Nobes                                                  |
| Senior Scientist, Quantum Mechanics                            !
|                                                                |
| BIOSYM/Molecular Simulations                                   |
| 240/250 The Quorum                 Phone:  + 44 1223 413300    |
| Barnwell Road                      Fax:    + 44 1223 413301    |
| Cambridge CB5 8RE, UK              E-mail: rnobes@msicam.co.uk |
+----------------------------------------------------------------+

From owner-chemistry@ccl.net  Wed Dec  6 08:56:15 1995
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To: chemistry@ccl.net
From: Bruce Wilson <bewilson@eastman.com>
Subject: nmr coupling constants


I asked for info a few days ago about calculations involving coupling
constants.  Several people have asked for a summary.  I will do so,
but I'm working to follow some of the leads and learn something
before I send out that summary.  Thanks.

                          Bruce E. Wilson (bewilson@eastman.com)
                          Information Technology Division
                          Eastman Chemical Company
                          Voice: (423) 229-8886   FAX: (423) 229-4558


From toukie@zui.unizh.ch  Wed Dec  6 10:41:15 1995
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Subject: File conversions for STERIMOL
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Date: Wed, 6 Dec 1995 16:30:01 +0100 (MET)
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Dear Colleagues;

     I would like to know if anyone has, or is aware of, a programme or file
format conversion method, that would allow one to convert from one of the popu-
lar structural file formats (such as one of the file formats included in BABEL)
to a format acceptable for analysis using the programme STERIMOL?  If so, kindly
send details at your earliest convenience.

     Thanks in advance to all responders.


Sincerely,

S. Shapiro
ZH, CH
toukie@zui.unizh.ch

From owner-chemistry@ccl.net  Wed Dec  6 11:11:15 1995
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From: frisch@lorentzian.com (Mike Frisch)
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Subject: Re: CCL:G:G94: B3LYP energy and Charge
To: chemistry@ccl.net
Date: Wed, 6 Dec 1995 09:24:00 -0500 (EST)
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Ross Nobes writes:
> 
> Mike Frisch writes:
>   > 
>   > > The answer is that both are right!  The Gaussian definition of B3LYP
>   > > uses the VWN local correlation functional;  most other programs use
>   > > what Gaussian terms VWN5.
>   > > 
>   > 
>   > No, B3LYP was defined to use VWN3.  Using the same name for two different
>   > functionals is a disservice to everyone and makes reproducing other peoples
>   > results impossible.  This used to be a major problem in the DFT area, and
>   > things are finally improving with regard to terminology.  To take a name for
>   > something that is specified in the literature and use it for something
>   > different is a major step backwards.  Published and in-press tests of B3LYP
>   > all use VWN3; an assumption that the same conclusions apply to a different
>   > functional just because it has the same name are not valid.
>   > 
> 
> Point taken.  All that I was implying in my original answer was that there
> are no 'numerical' problems here - both programs are giving correct results
> within their own definitions of B3LYP.  Most programs (such as Mulliken,
> CADPAC, MOLPRO, Turbomole) use the VWN5 functional uniformly as the 
> local correlation part of functionals such as SVWN, B3P86 and B3LYP.  It
> is unfortunate that Gaussian is alone in using an alternative VWN local
> correlation functional and (as Mike says) that the terminology is not 
> consistently defined.  The issue is further confused by a bug in the
> Gaussian 92/DFT open-shell VWN5 code which leads to small discrepancies
> with the other programs even when extremely large quadrature grids are
> used.

This bug, long since fixed, is not relevent to the question of using terms
consistently.  BLYP, BP, etc. are consistent names for functionals.  This is
a big improvement over "LSDA" which can mean many different things -- not
just VWN3 vs. VWN5 but Perdew 86, the local part of Perdew 91, and other
local correlation functionals as well can be found referred to as LSDA in
the literature.  The confusion over LSDA should not be used to rationalize
adding to the confusion with new functionals.  Things improved more recently
in that, for example, everyone means the same thing by BLYP or BP (=BPW91).
B3LYP numbers were available in the literature for comparison and there
really isn't any excuse for doing something else and claiming ignorance that
the results are different.  The comparisons that Ross mentions having made
between codes for other functionals can be made by anyone implementing
B3LYP, or made using literature results.

Mike Frisch
frisch@lorentzian.com

From owner-chemistry@ccl.net  Wed Dec  6 11:41:15 1995
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From: qfsaulo@usc.es (Saulo Vazquez Rodriguez)
Message-Id: <199512061626.AA06591@uscmail.usc.es>
To: chemistry@ccl.net
Subject: RRKM


Dear netters:
I would want to get the UNIMOL program suite or any similar
program to calculate unimolecular rate constants using the RRKM 
theory (preferably for SGI workstations). Any information about it
is appreciate.
Saulo A. Vazquez (qfsaulo@usc.es)

From owner-chemistry@ccl.net  Wed Dec  6 12:11:20 1995
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From: <qiang@euch4e.chem.emory.edu>
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Date: Wed, 6 Dec 1995 12:03:01 -0500 (EST)
To: CCLink <chemistry@ccl.net>
Subject: non-adiabatic, spin-orbital coupling....
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Hi, CCL members, I've got several basic questions about the Non-adiabatic 
coupling and spin-orbital coupling elements.

1. "selection rule" and Magnitude of the non-adiabatic coupling...
	In principle, non-adiabatic coupling elements are defined as the 
coupling elements of two adiabatic wave function through nuclear momentum 
operator. i.e. <F1(r;R)|P|F2(r;R)>. If we forget about spin-orbital 
coupling, i.e. Fi diagonalize the spin-free Hamiltonian, then the 
"selection rule" of the coupling is fully determined by spatial symmetry. 
If we consider P as the generator of translation, then presumably if 
the direct product of F1 and the displaced F2 (say, along certain 
internal coordinate) has total symmetric component, then the non-adiabatic
coupling is non-zero.( Am I right? ). But how do I get the feeling of 
the magnitude of it? Can I estimate where is the coupling-elements gonna 
be large from the electronic structure before I do the calculation? 
I guess some people will say, it's gonna be large where we have avoided 
crossing. Actually this brings up my another question...=>

2. Avoider vs "perfect" (actually) crossing...
	Again, in principle, the non-crossing rule only holds for diatomic 
systems where one has only one-D. The number of conditions that the system
has to satisfy to acheive a true degeneracy really depends on the behavior
of ur system under time revesal. If one doesn't care about spin-orbital 
coupling, then usually the number of condition is 2 (state of same 
symmetry). Obviously, in poly-atomic systems, the degree-of-freedom is much
larger than 2, namely, one can have actual crossing in polyatomic case, even
between states of same symmetry. Yet, they don't have to, which gives 
avoided crossing. So, after my endless babbling, my question is, in the 
avoided case, the non-adiabtic coupling can be thought to be related to 
the splitting between the two states, which equals to 2 times of the 
diabatic coupling between them (am i right?). What about in the actual 
crossing case? 

3. Rate expression...
	My last question of the day is related to the rate expression of 
radiationless transitions. I've read in many places, where they claim 
that non-adiabatic coupling causes internal conversion, while 
spin-orbital causes intersystem crossing. Of course, this make sense. 
Next what we(they) do is, using Fermi's Golden rule to express the 
transition rate. Obviously, this is the first-order approximation. Let's 
look from another way. To solve spin-forbidden transitions, in principle 
one can go through two ways to solve the Schrodiger's Eq. The first one 
would be using wavefunctions of spin-free Hamiltonian, and treat 
spin-orbital as a perturbation. In this case, the non-adiabatic coupling 
is obviously zero. ( I mean coupling between adiabatic wf. of spin-free 
H). Another way would be, as in many ICN, CH3I studies, solve wave 
function of a Hamiltonian including spin-orbital coupling. In this case,
I guess it's the non-adiabatic coupling between the two states including 
spin-orbital effects that causes the transition. Or, in the dynamic 
calculations, one can diabatrize the potential (wf.) such that the 
off-diagonal elements determines the transition rate. So, which is a 
better, more rigorous approach????

Sorry for such a long message. Thanks VERY MUCH for ur attention...

Please send message directly to: qiang@euch4e.chem.emory.edu

I'll summerize.

Have a nice day, to all of u!!!

______________________________________________________________

Qiang Cui
Dept. of Chem. Emory Univ.         508 Webster Dr. Apt.#2
Atlanta, GA 30322.                 Decatur, GA 30033.
(404)-727-2381                     (404)-636-6149

http://tswww.cc.emory.edu/~qcui
______________________________________________________________



From owner-chemistry@ccl.net  Wed Dec  6 14:56:18 1995
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Date:     Wed, 6 Dec 95 14:24:40 EST
From: George R Famini   <grfamini@cbdcom.apgea.army.mil>
To: chemistry@ccl.net
Subject:  COMP Program for New Orleans
Organization:  International Programs Office
Priority:  Normal
Message-ID:  <9512061424.aa00207@cbdcom.apgea.army.mil>



Enclosed is the first draft of the final program for the 
Division of Computers in Chemistry for the New
Orleans American Chemical Society meeting (end of
March).   The COMP program consists of 168 papers
running from Sunday morning to Thursday afternoon,
with double sessions the entire week and triple 
sessions Sunday and Monday.  

The final program will appear in C&E News in early to
mid February.


The enclosed version has not been "prettied up".  It is
replete with typos and glitches by the program
program I use.  I apologize for the former, complain
to ACS on the latter...


				George Famini
				COMP Program Chair





Division of Computers In Chemistry
G. R. Famini, Program ChairpersonC. J. Cramer, Chairperson

COSPONSORED SYMPOSIA:CINF:  Neural Networks

OTHER SYMPOSIA OF INTEREST:
New Perspectives in Envionmental Chemistry
ANAL
Teaching Chemistry on the Web
CHED
AI Based Techniques for End Users
CINF
Computer Modelng of Polymerization Catalysts
PMSE

SOCIAL EVENTS:
Social Hour  Tues 700PM


SUNDAYMORNING
Section A
ComputationalChemistry Assisted Drug Discovery

J. Damewood, &litalOrganizer, Presiding&rital

9:00--1.Assessment of Structure Based Design. I. D. Kuntz
9:45--2.Moleculr and Brownian dynamics of proteins. J. A. McCammon
10:30--3.Designing nonpeptidal fibronogen receptor antagonists:  theory in collaboration with experiment. A. M. Naylor-Olsen, M. E. Duggan, M. S. Egbertson, R. J. Gould, G. D. Hartman
11:15--4.Quantitative Structure activity relationships of acetlcholinesterase inhibitores ofr teh treatment of memory deficits n Alzheimer's disease:  A comparative molecular field analysis (CoMFA) study. W. J. Welsh, W. Tong, E. R. Collantes, Y. Chen

Section B
MonteCarlo Methods in Chemistry

B. L. Hammond, &litalOrganizer, Presiding&rital

8:50--IntroductoryRemarks
9:00--5.Monte Carlo methods for prediction of phase transitions in fluids. A. Panagiotopoulos
9:30--6.Monte Carlo quantum mechanical calculations of molecular thermodynamic functions. D. G. Truhlar, R. Q. Topper, J. Srinivasan, S. L. Mielke
10:00--7.A smart Monte Carlo technique for free energy simulations.  Direct calculations of conformational free energies. H. Senderowitz, W. C. Still
10:30--8.Using Monte Carlo techniques to explore the space of constitutional isomers. J-L. M. Faulon
11:00--9.A method for free energy calculations using iterative techniques. S. M. Kumar, P. W. Payne, M. Vasquez
11:30--10.Complete search of conformational space for met-enkephalin with the multicanonical method. F. Eisenmenger, U. H. E. Hansmann

SUNDAYAFTERNOON
Section A
ComputationalChemistry Assisted Drug Discovery

J. Damewood, &litalPresiding&rital

1:30--11.The design and synthesis of non peptide peptidomimetic inhibitors of the HIV 1 protease.  Evidence for improved transport. A. B. Smits
2:15--12.RAS farnesyltransferase inhibitors as a new class of antitumor agents:  A chemical approach to controlling cell signaling. Y. Qian, A. Vogt, S. M. Sebti, A. D. Hamilton
3:00--13.Distorted peptides in bioactive structures. M. Goodman
3:45--14.The caveat vector approach for structure based disign and combinatorial chemistry. P. A. Bartlett, G. Lauri
4:30--15.Enlightened screening:  a marriage of computer aided design with combinatorial libraries. M. Kahn

Section B
MonteCarlo Methods in Chemistry

W. A. Lester, &litalPresiding&rital

1:30--IntroductoryRemarks
1:40--16.Recent Progress on QUantum Monte Carlo for Atoms and Molecules. W. A. Lester, R. N. Barnett, C. Greef, B. L. Hammond
2:10--17.QMC Calculation on some positron compounds. N. Jiang, D. M. Schrader
2:40--18.Quantum Monte Carlo Calculations for heavy elements. H-J. Flad, M. Dolg, A. Shulka
3:10--19.Recent Progress in QMC and VMC treatment of molecules. D. Bressanini, J. Reynolds
3:40--20.VQMC Studies of transition metal atoms. D. Young, J. F. Harrison
4:10--21.Quantum Monte Carlo for electronic structure of clusters and solids. L. Mitas, J. C. Grossman
4:40--22.QUantum Monte Carlo evaluation of chemical reaction rate coefficients. A. C. Gentile, D. A. Evensky, J. Chang, U. Schnupf, N. J. Brown, J. L. Durant, M. L. Koszykowski

Section C
Physical/ChemicalProperty Prediction

L. A. Carreira, &litalOrganizer, Presiding&rital

1:30--IntroductoryRemarks
1:35--23.Modeling Solute-Solvent interactions:  an overview. C. J. Cramer, D. G. Truhlar
2:20--24.Using Molecular Orbital  based parameters to predict properties. G. R. Famini, A. H. Lowrey, L. Y. Wilson
3:05--Break
3:20--25.Investigation of solute/solvent characteristics that determine solubilities. P. Politzer, J. S. Murray
4:05--26.Direct ab initio methods for predicting gas phase chemical reaction rates. T. N. Truong

MONDAYMORNING
Section A
ComputationalChemistry Assisted Drug Discovery

J. Damewood, &litalPresiding&rital

8:30--27.Matrix metallopreateases as drub discovery targets:  Insights from a structure based approach. M. F. Browner
9:15--28.Computational tools in structure based drug design. J. J. Wendoloski
10:00--29.Fitting inhibitores into the active site of a metalloprotease. Z. R. Wasserman
10:45--30.Computer asisted search for novel calcineurin inhibitors. A. Tempczyk, C. Kissinger, H. Parge, V. J. Kalish, E. Villafranca
11:30--31.A CoMFA Analysis of FXa inhibitors and subsequent comparison with protein structure for selectivity issues. R. J. Vaz, L. McLean, J. T. Pelton

Section B
MonteCarlo Methods in Chemistry

D. M. Ferguson, &litalPresiding&rital

8:45--32.Application of simulated annealing - optimal histogram methods to the protein folding problem. D. M. Ferguson, D. G. Garret
9:15--33.Monte Carlomethods and protein folding. H. A. Scheraga
9:45--34.A method for the prediction of surface loops/turns and transglobular connections in small proteins. A. Kolinski, J. Skolnick, A. Godzik
10:15--35.Biased probability Monte Carlo as a powerful global energy optimization method for miomolecular structure prediction. R. A. Abagyan, M. M. Totrov
10:45--36.Configurational bias Monte Carlo algorithms for bioactive molecules. J. S. Bader, C. Liang, M. W. Deem
11:15--37.Simulation of peptides and proteins - the multicanonical approach. U. H. E. Hansmann, Y. Okamoto

Section C
Physical/ChemicalProperty Prediction

G. R. Famini, &litalPresiding&rital

9:00--IntroductoryRemarks
9:05--38.The role of hydrogen bonding in solute/solvent interactions. R. W. Taft
9:50--39.SPARC solvation models for ions:  estimation of pKa in the gas phase and non-aqueous solvents. S. H. Hilal, L. A. Carreira, S. W. Karickhoff
10:35--40.Studies of solution properties of organic compounds by quantitative structuer property relationships. P. C. Jurs, J. M. Sutter, H. L. Engelhardt
11:20--41.Deriving QSPR and QSAR from new autocorrelation descriptors. D. Domine, J. Devillers
11:50--Break

MONDAYAFTERNOON
Section A
ComputationalChemistry Assisted Drug Discovery

J. Damewood, &litalPresiding&rital

1:30--42.Degermining Receptor bound conformations of insect neuropeptides. V. A. Robets, R. J. Nachman
2:15--43.A systematic protocol for studying protein ligan interactions. J. Given, M. K. Gilson
3:00--44.CLEW:  Use of a genetic algorithm to determine rules that simplify complex pharmacological data. A. L. Parrill, D. P. Dolata
3:45--45.Directed Diversity@:  an operating system for combinatorial chemistry. D. K. Agrafiotis, E. P. Jaeger
4:30--46.Finding a needle in a haystack:  Using topological similarity to identify biologically active leads. R. Druker, L. B. Pfahler, C. H. Reynolds

Section B
ExperimentalMethods for CHemical Models

K. Rappaport, &litalPresiding&rital

2:00--IntroductoryRemarks
2:10--47.Resin Vehicle Characterization through statistically designed experiments. M. Altekar, A. N. Sacrlatti
2:45--48.Synthesis of starch acetate:  statistically designed experiments to optimize the reaction conditions. B. I. Feuer, S. Lepeniotis
3:20--Break
3:35--49.Development of experimental designs for organic synthetic reactions. W. F. Stansbury
4:10--50.Combining expeimental design and nueral networks:  an empirical chemcial process modeling program. A. J. Owens, M. T. Mocella

Section C
Physical/ChemicalProperty Prediction

L. A. Carreira, &litalPresiding&rital

1:30--51.A general model of solute solvent interactions. R. S. Pearlman, K. M. Smith, J. L. Escobar, R. Balducci, F. Deanda
2:15--52.SAR prediction of Henry's law constant. J. C. Dearden
2:45--Break
3:00--53.Group contribution method for the calculation of solubility properties of molecules. G. Klopman
3:45--54.Origins of medium induced fluorine chemical shifts. E. Y. Lau, J. T. Gerig
4:15--55.A computational model to predict two photon absorption resonances. G. P. Das, A. T. Yeates, D. S. Dudis

MONDAYEVENING

Sci-Mix

G. R. Famini, &litalOrganizer, Presiding&rital

8:00--11:00

56.-- Molecular electronic properties may predict antimalarial activity. A. K. Battacharjee, J. M. Karle
57.-- Calculation of Polarizabilities and hyperpolarizabilities for small carbon-sulfur diffuse systems. X. Duan, A. T. Yates, D. S. Dudis
58.-- Integration of 3D-QSAR and homology modeling in the study of catalytic mechanisms and substrate specificty. W. Zheng, A. Tropsha, C. L. Waller
59.-- Partition Coefficients and phase behavior for nonn-toxic ice inhibitors from quantum mechanical and molecular dynamics simulations. S. Trohalaki, R. Pachter
60.-- Using SAR and QSAR to model the activity and structure of the quinolone/DNA complex. B. Liorente, F. Leclerc
61.-- Predicting Toxicity of chemicals to luminescent bacteria (microtox test) from linear and nonlinear multivariate analysis. J. Devillers, S. bintein, D. Domine
62.-- The prediction of protein loop structure by conformational search. L. Shen, J. Novotny, M. Sippl, R. E. Bruccoleri
63.-- Ab initio calculation of vibtrational circular dichroism spectra using density functional theory. J. R. Cheeseman, M. J. Frisch, F. J. Devlin, P. J. Stephens
64.-- A united-residue potential for protein-structure simulations by analysis of protein crystal data and optimal z-score approach. U. O. G. Liwo, M. R. Pincus, R. J. Wawak, S. R. Rackovsky, S. Oldziej, H. A. Scheraga
65.-- Monte Carlo simulated annealing approach to regional protein folding and conformation. L. Carlacci, S. W. Englander
66.-- Semi-empirical non-linear optical properties:  methods and applications. C. C. Clause
67.-- Modeling Heats of Sublimation and Heats of Formation of Polycyclic Hydrocarbons by Comparative Molecular Field Analysis (CoMFA). W. J. Welsh, W. Tong, E. R. Collantes
68.-- Quantitative structure retention relationships for polycyclic aromatic hydrocarbons from Comparative molecular field analysis (CoMFA). E. R. Collantes, W. J. Welsh, W. Tong

TUESDAYMORNING
Section A
Computersin Chemistry Award Symposium Honoring Norman L. Allinger

K. Lipkowitz, &litalOrganizer, Presiding&rital

8:45--WelcomingRemarks- C. Cramer
8:50--IntroductoryRemarks
9:00--69.MMFF94:  The Merck molecular force field.  Bridging the gap from small organics to proteins. T. A. Halgren, R. B. Nachbar
9:45--70.On the application of molecular mechnaics and dynamics to biological systems:  one of Lou Allinger's legacies. P. A. Kollman
10:30--71.Modeling carbohydrates. A. F. French
11:15--72.Computers in Chemistry Award Address:  Recent Work in Molecular Mechanics. N. L. Allinger

Section B
ExperimentalMethods for Chemical Models

K. Rappaport, &litalPresiding&rital

9:00--IntroductoryRemarks
9:10--73.Statistical Methods for monomer selection in chemical library design. C. M. Cribbs, A. Menius, D. Cummins, S. S. Young
9:45--74.Real time multivariate process monitoring. D. E. Stevens, K. Giese
10:20--Break
10:35--75.Hybridizing linear and nonlinear multivariate analyses for optimal test series design. D. Domine, J. Devillers
11:10--76.Statistical model of systematic errors:  an assessment of the Ba-Cu and Cu-Y phase diagram. E. B. Rudnyi

TUESDAYAFTERNOON
Section A
ComputationalChemistry Assisted Drug Discovery

W. J. Welsh, &litalPresiding&rital

1:30--77.Application of a novel conformatonal bias Monte Carlo method to explore the bioactive conformations of the arginine-glycine-aspartate recognition sequence. X. L. C. Liang, J. S. Bader, M. W. Deem, G. Went
2:15--78.Useof an intercommunicating hybrid system for designing chemical with desired properties. J. Devillers, C. Putavy, D. Domine
3:00--79.Theoretical determination of the solvation free energies of the nucleic acid bases in water and chloroform. J. E. Eksterowicz, J. L. Miller, P. A. Kollman
3:45--80.Les is more:  Improved conformational sampling in molecular dynamics. C. Simmerling, P. A. Kollman
4:30--81.A novel approach to docking flexible molecules - the flash and churn system. M. C. Pitman, I. Rigatousos, D. E. Platt

Section B
MolecularModeling Applications to Environmental Problems

J. Rabinowitz, &litalOrganizer, Presiding&rital

1:30--IntroductoryRemarks
1:45--82.Prediction of the oxidative metabolites by cytochrome P450's with quantum mechanics and molecular dynamics simulations. G. H. Loew, Y-T. Chang
2:15--83.Homology modeling of cytochrome P450 2E1 enzyme. W. Zhang, A. Tropsha, C. L. Waller
2:45--84.Predictive models for cytochrome P450 mediated reactions:  a comparison of expeiment with theory. J. P. Jones, H. Yin, K. R. Korzekwa
3:15--85.Realistic simulations of charged macromolecules. L. G. Pedersen
3:45--Break
4:00--86.Including Solvent Effects in quantum chemistry. M. C. Zerner
4:30--87.Hydrophobic and hydrogen bonding effects on Diels-Alder reactions in aqueous solution. T. R. Furlani, J. Gao
5:00--88.Solvent effects on structure and vibrational spectra of bioloecules in aqueous solution. E. V. Stefanovich, T. N. Truong

Section C
FrugalChemist's Software

C. James, &litalPresiding&rital

1:30--89.Macromodel:  The computational chemists molecular modeling tool. C. A. Parish, W. C. Still
2:00--90.Desktop modeling of metal containing drugs.  Platinum antitumor agents and gadolinium MRI contrast agents. E. W. Moody, T. R. Cundari
2:30--91. MOIL-View:  A program for visualization of structure of biomolecules. C. Simmerling, P. A. Kollman
3:00--92.Dynamic display of structure and stereochemistry in the organic chemistry course. S. W. Slayden
3:30--93.Ab initio quality atomic charges and group electronegativity on a PC. J. Mullay
4:00--94.Ab initio molecular orbital calculations and Visualizations on a PC. J. B. Forseman
4:30--95.Computational chemistry and the nationall HPCC software exchange. J. C. Pool
5:00--96.Kinetic simulations on a budget. S. L. Cooke

TUESDAYEVENING
Section A
PosterSession: General Poster Session

G. R. Famini, &litalOrganizer, Presiding&rital

7:00--10:00

97.-- The electrostatic interactions that determine the rate of pseudorotation torcess in oxyphosphorane intermediates:  implications with respect to the roles of metal ions in the enzymatic cleavage of RNA. T. Uchimaru, M. Uebayasi, T. Hirose, S. Txuzuki, A. Yliniemela, K. Tanabe, K. Taira
98.-- UV Photoelectron and ab initio quantum mechanical characterization of nucleotides:  the valence electronic structures of 5'-dAMP(-).Na(+) and pGpA.2Na(+).4H2o clusters. P. R. LeBreton, H. S. Kim, Q. Jiang
99.-- Ab Initio Studies of Troposhperic Sulfur Chemistry. C. Wilson
100.--  Development of a proton NMR shielding model for the face of a phenyl ring. N. H. Martin, N. W. Allen
101.--  Simulation of internal rotation potential energy curve for serine. K. Zhang, A. Chung-Phillips
56.-- Molecular electronic properties may predict antimalarial activity. A. K. Battacharjee, J. M. Karle
102.--  Modulating force constants of nanosprings. M. Jalaie, K. Lipkowitz
57.-- Calculation of Polarizabilities and hyperpolarizabilities for small carbon-sulfur diffuse systems. X. Duan, A. T. Yates, D. S. Dudis
58.-- Integration of 3D-QSAR and homology modeling in the study of catalytic mechanisms and substrate specificty. W. Zheng, A. Tropsha, C. L. Waller
103.--  Prediction of aromatic amine carcinogenicity:  QSAR calculated lowest unoccupied molecular orbital energy of hypothetical nitrenium ion intermediate. R. Purdy
59.-- Partition Coefficients and phase behavior for nonn-toxic ice inhibitors from quantum mechanical and molecular dynamics simulations. S. Trohalaki, R. Pachter
60.-- Using SAR and QSAR to model the activity and structure of the quinolone/DNA complex. B. Liorente, F. Leclerc
104.--  Single atom doping of clusters. L. S. Perkins
105.--  Ab initio studies of oximide. J. L. Meeks
61.-- Predicting Toxicity of chemicals to luminescent bacteria (microtox test) from linear and nonlinear multivariate analysis. J. Devillers, S. bintein, D. Domine
106.--  An ab initio study of the model thio-wittig reaction PH3CH2 + CH2S =&gt PH3S + C2H5. S. M. Bachrach, L. M. Perriott
107.--  The heuristic potency of art networks for QSAR dat visualization and interpretation. D. Domine, J. Devillers, D. Wienke, L. Buydens
108.--  Application of evolutionary algortihms and a topological index based fitting function in the design of combinatorial chemical libraries. S. J. Cho, W. Zheng, A. Tropsha
109.--  Application of Cluster analysis and monte carlo methods in the design of combinatorial chemcial libraries. W. Zheng, S. J. Cho, A. Tropsha
62.-- The prediction of protein loop structure by conformational search. L. Shen, J. Novotny, M. Sippl, R. E. Bruccoleri
110.--  Molecular dynamics (MD) simulations of transmembrane a-helices in a lipid bilayer:  tryptophan effect. L. Shen, D. Bassolino, T. R. Stouch
63.-- Ab initio calculation of vibtrational circular dichroism spectra using density functional theory. J. R. Cheeseman, M. J. Frisch, F. J. Devlin, P. J. Stephens
64.-- A united-residue potential for protein-structure simulations by analysis of protein crystal data and optimal z-score approach. U. O. G. Liwo, M. R. Pincus, R. J. Wawak, S. R. Rackovsky, S. Oldziej, H. A. Scheraga
65.-- Monte Carlo simulated annealing approach to regional protein folding and conformation. L. Carlacci, S. W. Englander
66.-- Semi-empirical non-linear optical properties:  methods and applications. C. C. Clause
111.--  Study of trichloromethyl radical proton abstraction reaction with ab initio and density functional theory methods. B. S. Jursic
112.--  Theoretical study of borane catalyzed azide anion addition to fluroinated acetonitriles. B. S. Jursic, Z. Zdravkovski
113.--  Estimation  of five membered and benzo fused five membered rings by hybrid DFT computed magnetic properties. B. S. Jursic
114.--  AM1 study of benzo[c]furan as a dienophile for Diels-Alders reactions. B. S. Jursic
115.--  Density functional theory study of ethylene and acetylene addition to oxazole protonated oxazole. B. S. Jursic
116.--  Density functional study of N-methylpyrrole transformation into N-methylisoindole through cycloaddition-extruson reactions. B. S. Jursic
117.--  Theoretical study of thieno[3,4-d]thiepin and furo[2,4-d]thiepin as dienes in the Diels-Alder reaction. B. S. Jursic
118.--  Average deviation from ideal bond order as a measure for aromaticity.  AM1 computed aromatic properties of five membered C4H4X ring systems. B. S. Jursic
119.--  Computation of bond dissociation energies of methyl substituted radicals with density functioal theory methods. B. S. Jursic, J. W. Timberlake, P. S. Engel
120.--  Monte Carlo studies of the ice binding mechanism of the winter-flounder antifreeze proteing (AFP). W. J. Welsh, &lboldW. Tong, R. A. Duta, M. Fagan
67.-- Modeling Heats of Sublimation and Heats of Formation of Polycyclic Hydrocarbons by Comparative Molecular Field Analysis (CoMFA). W. J. Welsh, W. Tong, E. R. Collantes
68.-- Quantitative structure retention relationships for polycyclic aromatic hydrocarbons from Comparative molecular field analysis (CoMFA). E. R. Collantes, W. J. Welsh, W. Tong

WEDNESDAYMORNING
Section A
Semi-EmpiricalMethods:  Is There a Future?

A. Holder, &litalOrganizer, Presiding&rital

8:30--IntroductoryRemarks
8:35--121. A future for semi-empirical MO?  Heck YES! R. S. Pearlman, K. M. Smith
9:05--122. Using semi-empirical molecular orbital methods in linear free energy relationships. G. R. Famini, L. Y. Wilson
9:35--123. Semi-empirical MO methods:  the middle ground in molecular modeling. C. H. Reynolds
10:05--124. Simulations of substrate-enzyme reactions using AM1 reaction coordinate calculations. Y. Lin, G. Duncan, R. King, W. J. Welsh
10:35--Break
10:45--125. The role of semiempirical molecular orbital methods within Dupont. K. D. Dobbs
11:15--126. Quantum Mechanical calculations of partial charges in solution, free energies of solvation, and partition coefficients. D. J. Giesen, C. C. Chambers, Z. Gu, G. D. Hawkins, C. J. Cramer, &lboldD. G. Truhlar
11:45--127. On the rhodanines. D. B. Boyd, R. J. Loncharich, J. S. Nissen

Section B
MolecularModeling Applications to Environmental Problems

W. C. Herndon, &litalPresiding&rital

8:30--128. Molecular surface properties as a tool for investigating and predicting molecular interactions. P. Politzer, J. S. Murray
9:00--129. Ab initio calculation of stabilities and infrared spectra of molecules and ions. D. H. Aue
9:30--130. The effect of crowding in the Bay/Fjord region on the structure and reactivities of diol-epoxides of polycyclic aromatic hydrocarbons. J. Rabinowitz, S. B. Little, L. L. Lewis-Bevan
10:00--131. Computing structures of DNA damaged by environmental polycyclic aromatic carcinogens. B. E. Hingerty, S. Boyde
10:30--Break
10:45--132. Catalytic DNA:  theory and computations. G. R. Pack, G. Lamm
11:15--133. Ab initio quantum mechanical and UV photoelectron  evaluation of nucleotide ionization potentials in water, counterion enviroments:  pi polarization effecs on DNA alkylation by carcinogenic methylating agents. P. R. LeBreton
11:45--134. Energy surfaces on the ethenyl radical. M. Krauss

WEDNESDAYAFTERNOON
Section A
Semi-EmpiricalMethods:  Is There a Future?

A. Holder, &litalPresiding&rital

1:30--IntroductoryRemarks
1:35--135. Calculating the electronic spectra of large molecular systems. M. C. Zerner
2:05--136. NDDO semi-empirical approximation coupled with Green's function technique. D. Danovich
2:35--137. Semi-empirical molecular orbital theory in carcinogenesis. G. P. Ford
3:05--Break
3:20--138. Solvation effects on organic structure and reactivity - semi-empirical calculations with the SMx solvation models. S. E. Barrows, C. C. Chambers, D. J. Giesen, C. J. Cramer, D. G. Truhlar
3:50--139. The future of molecular modeling:  competitive with experiment? D. S. Dudis, A. T. Yeates
4:20--140. Semi-empirical calculation of the electronic structure of proteins. J. J. P. Stewart

Section B
MolecularModeling Applications to Environmental Problems

G. R. Pack, &litalPresiding&rital

1:30--141. Structures and enthalpies of fluorohydrocarbons. W. C. Herndon
2:00--142. Modeling the cytochrome P450 mediated metabolism of chlorinated volatile organic compounds. C. L. Waller, M. V. Evans, J. D. McKinney
2:30--143. Computationally identified reactive intermediates of S-(2,2-dihalo-1,1-difluoroethyl)-L-cysteine conjugates. J-Y. Shim, A. M. Richard
3:00--144. A model for predicting estrogenic activity. R. Purdy
3:30--Break
3:45--145. Ab initio model of slicylate adsorbed onto AL2O3 and illite clay. J. D. Kubicki, M. J. Itoh, S. E. Apitz
4:15--146. Modeling biodegradation from multivariate statsitical tools. J. Devillers
4:45--147. A knowledge rule based expert system for assessing carcinogenic potential of chemcials. Y-T. Woo, D. Y. Lai, J. C. Arcos, M. F. Argus

THURSDAYMORNING
Section A
Semi-EmpiricalMethods:  Is There a Future?

A. J. Holder, &litalPresiding&rital

8:30--IntroductoryRemarks
8:35--148. Use of semi-empirical methods to predict the pKa's of phenols and anilines:  structures, statistics and solvation. Y. C. Martin, J. Wu, J. F. Curley, K. H. Kim
9:05--149. Semi-empirical calculations of O-H N-H and C-H hydrogen bonding interactions.  A comparison with high quality ab initio calculations. J. J. Dannenberg
9:35--150. Theory and experiment in the study of intramolecular O-H''''Pi hydrogen bonding. E. F. Healy, J. D. Lewis
10:05--151. Visualization techniques for locating transition states using semiempirical methods. G. D. Purvis III
10:35--Break
10:50--152. Recent numerical improvements in semi-empirical methods. D. A. Liotard
11:20--153. Use of semi-emipirical quantum chemical molecualr descriptors in QSAR/QSPR. M. Karelson
11:50--154. The use of semi-empirical QM methods in expert systems. G. Klopman

Section B
GeneralOral

G. R. Famini, &litalOrganizer&rital
D. Cronce, &litalPresiding&rital

9:00--155. Studies on the P-N bond. W. E. White
9:30--156. Variable Selection of topological indices for QSAR using genetic algorithms. S. J. Cho, W. Andrews, A. Tropsha
10:00--157. A theoretical of CO and NO interaction with Cu sites in ZSM-5:  Electronic structure and vibrational spectra. R. Ramprasad, K. C. Haas, W. F. Schneider, J. B. Adams
10:30--158. The estimation/prediction of some properties of explosive's stability with the QSPR approach. S. Peshkova, M. Kumskov

THURSDAYAFTERNOON
Section A
Semi-EmpiricalMethods:  Is There a Future?

A. J. Holder, &litalPresiding&rital

2:00--IntroductoryRemarks
2:15--159. Computational enzymology:  chemically accurate models for molecular recognition and catalysis. P. A. Bash
2:35--160. Electron correlation in small clusters:  full CI for model hamiltonians. A. E. Roos, J. A. Pople, M. A. Ratner
2:55--161. The applicability of semi-empirical methods towards the calculations of non-linear optical properties. W. A. Parkinson
3:15--162. Semi-empirical study of small water clusters:  low energy fused cubic structures for (H2O)n, n=8,12,16. P. L. M. Plummer
3:35--Break
3:50--163. AM1 studies of the reaction mechnaism for alkyl transfer from boron to zinc. D. A. Smith, C. W. Ulmer, S. Darling
4:10--164. The ab initio basis of pi electron theory:  highly accurate pi hamiltonians for protonated schiff bases. C. H. Martin
4:30--165. Semi-empirical vs. density functional or ab initio QM/MM methods. P. Lyne, M. Karplus

Section B
GeneralOral

W. E. White, &litalPresiding&rital

2:00--166. Small Angle XRay scattering from oriented single particle systems. B. P. Grady, B. C. McAlister
2:30--167. Ammonium ion interactions in receptor modeling. P-O. Norrby, T. Liljefors
3:00--168. About the aromaticity of dehydro[8]annulenes.  A theoretical study. R. Salcedo, L. E. Sansores


From usdcc2p5@ibmmail.com  Wed Dec  6 16:41:20 1995
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Subject: Reduced coordinates to regular coordinates


Dear colleagues,                                                               
                                                                               
If I have crystallographic coordinates for a molecule (reduced coordinates) and
 I want regular cartesian coordinates, can you recommend a conversion program  
that handles this?                                                             
                                                                               
***************************************************************                
J. Pat Cannady, Ph.D                                                           
Dow Corning Corp.,  Midland, MI       48686-0995                               
usdcc2p5@ibmmail.com                                                           

From chpajt@bath.ac.uk  Wed Dec  6 18:26:21 1995
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From: A J Turner <chpajt@bath.ac.uk>
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cc: I H Williams <chsihw@bath.ac.uk>
Subject: Unit interconversion
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Hi!

Could anyone come up with reasonable accuracy (at least 6 significant 
figures) for

Hartrees to Joules
Calories to Joules
Bohr     to Angstrom

Non of my texts even have the definition of a Hartree.

Thanks in advance

Alex


+--------------------------------------------------+
|Alternate E-mail A.J.Turner@Bath.ac.uk            |
|www home @ http://www.bath.ac.uk/~chpajt/home.html|
+--------------------------------------------------+ 


From nathan@IRIS.mel.dbe.CSIRO.AU  Wed Dec  6 19:26:23 1995
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Subject: Re: CCL:Unit interconversion
To: chpajt@bath.ac.uk (A J Turner)
Date: Thu, 7 Dec 95 11:14:38 EST
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In-Reply-To: <Pine.SOL.3.91.951206232001.22749A-100000@mary.bath.ac.uk>; from "A J Turner" at Dec 6, 95 11:22 pm
X-Mailer: ELM [version 2.3 PL11]


> Could anyone come up with reasonable accuracy (at least 6 significant 
> figures) for
> 
> Hartrees to Joules
> Calories to Joules
> Bohr     to Angstrom
> 
> Non of my texts even have the definition of a Hartree.
> 
> Thanks in advance
> 
> Alex
> 
> 
> +--------------------------------------------------+
> |Alternate E-mail A.J.Turner@Bath.ac.uk            |
> |www home @ http://www.bath.ac.uk/~chpajt/home.html|
> +--------------------------------------------------+ 
> 
> 

Here are the values streight from the Gaussian94 manual

1 Hartree = 4.3597482 E-18 Joules
1 Calorie = 4.184 Joules
1 Bohr = 0.529177249 Angstrom

regards,

Nathan

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                       Nathan Hall

                       PhD Student
     /\       B        Biomolecular  Research Institute
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                       E-mail:    nathan@mel.dbe.csiro.au
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