From rlahana@syntem.eerie.fr  Thu Dec  4 05:39:07 1997
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Dear CCL'ers,

Does anybody know if atomic contributions of lipophilicity are available for
charged atoms - in particular in amino-acids? I will post to the list all
the relevant replies.

Thank you in advance,

Roger
****************************************************************
Dr Roger Lahana                                          Synt:em
Development Director                   Parc Scientifique G.Besse
Molecular Modeling                                   30000 Nimes
email: rlahana@syntem.eerie.fr                            France
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            Discover New Drugs, Discover Synt:em
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From jochen@pc1.uni-duesseldorf.de  Thu Dec  4 05:47:57 1997
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Date: Thu, 4 Dec 1997 11:07:16 +0100
From: Jochen Kuepper <jochen@pc1.uni-duesseldorf.de>
Message-Id: <9712041007.AA00104@bacchus.pc1.uni-duesseldorf.de>
To: 94970459@tolka.dcu.ie, jenninaj@mh.uk.sbphrd.com
Subject: Re: CCL:Re: CCL:HyperChem: Incorrect geometries in amines
Cc: chemistry@www.ccl.net
MIME-version: 1.0
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:> >  I am a user of HyperChem, version 4. Whenever I use molecular =
mechanics
:> > with the MM+ force field, to geometry optimise molecules such as
:> > Phenylamine (C6H5NH2), the geometry about the N atom is planar =
rather than
:> > pyramidal, i.e., an atom type of N2 is used for the nitrogen atom, =
rather
:> > than N3 as would be expected. I get the same result with molecules =
such as
:> > H2C=3DCHNH2 or H2C=3DNNH2. I also get incorrect geometries if I =
initially use
:> > the model builder to obtain an approximate geometry for such =
molecule or
:> > if I use any of the other three force fields available within =
HyperChem.
:> > If I initially set the atom type for the nitrogen atom to be N3, I =
still
:> > get an planar geometry about the nitrogen atom.=20
:> >=20
:> >  However, for molecules such as methylamine and cyclohexamine, =
i.e., where
:> > the atom bonded to the nitrogen atom is saturated, the correct =
geometry
:> > and atom type are obtained for the nitrogen atom.=20
:> >=20
:> >  Has anyone else experienced this problem?
:>=20
:> Unless I'm missing the point here what you see is not a problem - =
simply
:> the correct answer. The nitrogen in these systems WILL be planar due =
to
:> the pi systems delocalising over all conjugated atoms. This forces =
the
:> nitrogen into planarity...something which won't happen with a =
saturated
:> system as there is no opportunity for pi orbital delocalisation. =
Might I
:> suggest reading something like 'A guidebook to mechanism in organic
:> chemistry' by Peter Sykes which has an excellent chapter on atomic
:> orbitals and hybridisation.

Actually Aniline (phenylamine) in _not_ planar !
There is a complete substitution structure determined/published by =
Larson !

But Andy's argumentation is ok at this level of theory (Hyperchem ?-),
MM, ... ?
So, that's why these calculation give 'wrong' results (in any way).

Jochen


PS: To be sure to have calculated something wrong, you need to measure =
it !!!



-----------------------------------------------------------------------
  Jochen K=FCpper

  Heinrich-Heine-Universit=E4t D=FCsseldorf     =
jochen@uni-duesseldorf.de
  Institut f=FCr Physikalische Chemie I
  Universit=E4tsstrasse 1, Geb 26.43.02.19       phone ++49-211-8113681
  40225 D=FCsseldorf                             fax   ++49-211-8115195
  Germany             http://www-public.rz.uni-duesseldorf.de/~jochen
-----------------------------------------------------------------------

From Geoffrey@averell.umh.ac.be  Thu Dec  4 06:39:14 1997
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Dear Ccl'ers,

I' looking for the X-ray data of two inorganic compounds made off
Ruthenium to study
their properties. Unfortunately, my lab has no access to the cambridge
crystallographic
data base.

Is there anyone who could help me?

I would like to have the coordinates concerning the complexes:

(C10H6N4)3Ru(II) = Ru(TAP)3

TAP=1,4,5,8 -tetraazaphenanthrene

(C12H6N6)3Ru(II) = Ru(HAT)3

HAT = 1,4,5,8,9,12-hexaazatriphenylene

Thank you very much for your help.

Geoffrey

--
==================================================
    Geoffrey Pourtois, PhD student - Assistant
 ------------------------------------------------
      University of Mons-Hainaut
      Service de Chimie des Materiaux Nouveaux
      20, Place du parc
      7000 Mons
      Belgium
 ------------------------------------------------
    e-mail : Geoffrey@averell.umh.ac.be
    tel  : +32 65 37 3363
    fax  : +32 65 37 3366
    http://morris.umh.ac.be/

==================================================




From pieter.stouten@dupontmerck.com  Thu Dec  4 09:39:17 1997
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Date: Thu, 04 Dec 1997 09:01:39 -0500
From: Pieter Stouten <pieter.stouten@dupontmerck.com>
Subject: Re: CCL:HyperChem: Incorrect geometries in amines
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On 97/12/04 at 11:07 +0100, Jochen Kuepper wrote:

>Actually Aniline (phenylamine) in _not_ planar !
>There is a complete substitution structure determined/published by
>Larson !
>
>But Andy's argumentation is ok at this level of theory (Hyperchem ?-),
>MM, ... ?
>
There actually is at least one forcefield (MSI's CFF96) that is used in
Molecular Mechancis that does have properly puckered nitrogens. Are there
any other forcefields people know of, that do describe aniline etc.
properly?

Thanks,

Pieter Stouten <pieter.stouten@dupontmerck.com>
DuPont Merck - Computer Aided Drug Design Group
Web: http://www.halcyon.com/stouten/



From bowen@CCMSD.chem.uga.edu  Thu Dec  4 09:47:50 1997
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From: "Dr. J. Phillip Bowen" <bowen@CCMSD.chem.uga.edu>
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To: Willie Cui <info@microsimulations.com>
cc: Armel Le Bail <armel@fluo.univ-lemans.fr>, chemistry@www.ccl.net
Subject: Lists and Noble Prizes
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Hello,

I saw Willie Cui's E-mail message regarding the omission of Professor
Norman L. Allingers name from the list.  This is extremely surprising and
most probably may be due to an inaccurate search.  It would be of interest
to know what search parameters were used to create the list.  In many
cases, Professor Allinger is not listed as the first author on his papers.
This is a practice that I personally use.  From personal experience, I
know that if you are not the first author listed various searchers will
not pick up your name.  Perhaps this is problem.

Professor Allinger has made an extraordinary impact through his pioneering
work in computational chemistry, especially molecular mechanics.  He has
been at the forefront of applications of computational chemistry from the
very beginning of the computer age. It is noteworthy that one of his
publications has been listed in Current Contents as a "Citation Classic"
("Conformational Analysis.  LXIX.  An Improved Force Field for the
Calculation of the Structures and Energies of Hydrocarbons") having been
cited in over 450 publications.  Also, another one of his papers
("Calculation of Molecular Structures and Energy by Force Field Methods
Advances in Physical Organic Chemistry, 13, V. Gold and D. Bethell,
Editors, Academic Press, 1976.) was chosen by the Citation Index  as one
of their most frequently cited papers. He is the founder and editor of the
Journal of Computational Chemistry.  According to the Citation Index, this
is a "core journal" in physical chemistry and chemical physics.  Moreover,
the Burkert and Allinger book "Molecular Mechanics" is widely recognized
as the authoritative treatment of molecular mechanics, and it seems to be
cited in almost every discussion of molecular mechanics.

How many research publications cite MM2 or MM3 or some program that is
based on the Allinger work?  

Lou Allinger is a colleague and friend.  He has been very influential in
my career like so many of us who began using MM1 or MM2.  He is a modest
person who does not court the spotlight -- unlike so many of us in
science.  He has made a significant impact in the field of computational
chemistry in terms of research, teaching, and helping to popularize the
subject.  While there are many theoreticians and computational chemists
that are deserving of significant recognition, Professor Norman L.
Allinger should be at the top of the list for a Noble Prize.  

Phil 
*********************************************************
J. Phillip Bowen, Ph.D.
Professor of Chemistry and Co-Director
Computational Center for Molecular Structure and Design
University of Georgia
Athens, Georgia  30602

Phone:  706-542-2054
FAX:	706-542-2673
EMAIL:	bowen@ccmsd.chem.uga.edu
********************************************************

On Wed, 3 Dec 1997, Willie Cui wrote:

> Armel,
> 
> I took a quick look of the list and surprised to find that Allinger, NL
> is not on the list. I know that his paper on MM2/MM3 are widely cited.
> 
> In my own experience, I found the work of Allinger, Pople J, and Dewar
> have most profound and practical impact on the modern computational
> chemistry. The amount of insight, work, and care that went into the
> three packages, MM2/MM3, Gaussian, and AMPAC/MOPAC, are just tremondous.
> It will be of great excitment that they get Nobel prize.
> It is not too late for Allinger and Pople yet.
> 
> 
> 
> Armel Le Bail wrote:
> > 
> > Willie Cui wrote:
> > 
> > >I share you respect to Prof. Dewar and feel the lost of him passing
> > >away.
> > >
> > >On your message, you raised a very import point that his contribution
> > >to chemistry worthy of the Nobel prize.  I am wondering if computational
> > >chemistry is overlooked by the Nobel prize committee.
> > 
> > You may look at the computational chemists performances and try to guess
> > the next Nobel with the ISI's 1000 Most Cited Chemists list :
> >         http://fluo.univ-lemans.fr:8001/1000chimistes.html
> > 
> > A kind of Pandora box...
> > 
> > Armel Le Bail - Universite du Maine - Laboratoire des Fluorures
> > CNRS UPRESA 6010 - Avenue O. Messiaen - 72085 Le Mans cedex 9 - France
> > Web : http://fluo.univ-lemans.fr:8001/
> > 
> > -------This is added Automatically by the Software--------
> > -- Original Sender Envelope Address: armel@fluo.univ-lemans.fr
> > -- Original Sender From: Address: armel@fluo.univ-lemans.fr
> > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator
> > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73
> > Anon. ftp: www.ccl.net   | CHEMISTRY-SEARCH@www.ccl.net -- archive search
> >              Web: http://www.ccl.net/chemistry.html
> 
> -- 
> Willie Cui			voice: 201-512-0486
> MicroSimulations		fax:   201-512-0489
> 478 Green Mountain Road		email: info@microsimulations.com
> Mahwah, NJ 07430		URL:   http://www.microsimulations.com
> 
> -------This is added Automatically by the Software--------
> -- Original Sender Envelope Address: info@microsimulations.com
> -- Original Sender From: Address: info@microsimulations.com
> CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator
> MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73
> Anon. ftp: www.ccl.net   | CHEMISTRY-SEARCH@www.ccl.net -- archive search
>              Web: http://www.ccl.net/chemistry.html 
> 


From armel@fluo.univ-lemans.fr  Thu Dec  4 10:39:15 1997
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Date: Thu, 04 Dec 1997 16:36:22 +0100
To: chemistry@www.ccl.net
From: Armel Le Bail <armel@fluo.univ-lemans.fr>
Subject: Re: CCL:MJS Dewar died October 10
Cc: <bowen@CCMSD.chem.uga.edu>
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Willie,

>I took a quick look of the list and surprised to find that Allinger, NL
>is not on the list. I know that his paper on MM2/MM3 are widely cited.

Allinger is on the list together with Pople and Dewar :

                           Avrg cite     Total articles    Total citations
  Pople JA          79.80             176                    14044
  Dewar MJS      81.52             119                     9701
  Allinger NL     26.06             138                     3593

Note that Physics journals as defined by ISI are not 
considered (see notes by the analyst, D. Pendlebury).

I have made accessible the complete list of ISI's 10858 Most
Cited Chemists (with the ISI benediction) via a cgi-script motor
search by author name at :
   http://pcb4122.univ-lemans.fr/cgi-bin/perl.exe?chimistes.pl

Don't tell to anybody, shhh (I bought the list 1000 US$ in
association with a group of french chemists :-) otherwise my
small PC server will explode.

Armel


Armel Le Bail - Universite du Maine - Laboratoire des Fluorures
CNRS UPRESA 6010 - Avenue O. Messiaen - 72085 Le Mans cedex 9 - France
Web : http://fluo.univ-lemans.fr:8001/

From ashutosh@ti.com  Thu Dec  4 10:44:56 1997
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To: CHEMISTRY@www.ccl.net, Kharroubi Mohamed <kharroub@cit.enscm.fr>
From: Ashutosh Misra <ashutosh@ti.com>
Subject: re: CCL:Bond Dissociation Energies
Date: Thu, 4 Dec 1997 10:10:14 -0800
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Mohamed,

You may want to look at the following papers dealing with BDE
calculations.

Regards,
Ashutosh
------------------------------------------------------------------
1.	Benson, S. W. J. Chem. Educ. 1965, 42, 502.
2.	Szwarc, M. Chem. Rev. 1950, 47, 75.
3.	Golden, D. M.; Benson, S. W. Chem. Rev. 1969, 69, 125.
4.	Benson, S. W.; O'Neal, H. E. Free Radicals; Wiley: New York, 
	1973; Vol. 2.
5.	Kerr, J. A. In Handbook of Chemistry and Physics; CRC Press: 
	Boca Raton, Fl.; 1981, pp F-222.
6.	Baghal-Vayjooee, M. H.; Colussi, A. J.; Benson, S. W. 
	J. Am. Chem. Soc. 1978, 101, 	3214.
7.	Baghal-Vayjooee, M. H.; Benson, S. W. J. Am. Chem. Soc. 
	1979, 101, 2838.
8.	Baghal-Vayjooee, M. H.; Colussi, A. J.; Benson, S. W. 
	Int. J. Chem. Kinet. 1979, 11, 	147.
9.	Robinson, P. J.; Holbrook, K. A. Unimolecular Reactions; 
	Wiley: New York, 1972.
10.	Bogan, D.; Setser, D., N. Fluorine-Containing Free Radicals: 
	Kinetics and Dynamics of Reactions; Am. Chem. Soc.: Washington, 
	D. C., 1978.
11.	Luo, Y. R.; Holmes, J. L. J. Mol. Struct. (Theochem) 1993, 281, 123.

------------------------------------------------------------------------
>  From: Kharroubi Mohamed <kharroub@cit.enscm.fr>, on 11/26/97 4:18 PM:
>  Hello!
>    
>    I would appreciate if somebody point me to books, reviews or other
>  sources dealing with the calculation of bond dissociation energies (BDE)
>  from theoretical (semi-empirical, ab initio or DFT) and experimental point
>  of view.
>   Thank you in advance.

****************************************************
Ashutosh Misra, Ph.D.		Phone: 972-995-7552
Air Liquide Electronics		Fax  : 972-995-3204
Chemicals & Services, Inc.	Pager: 972-598-1274
13546 N. Central Expressway
M/S 301, Dallas, TX  75243

From leclerc@tammy.harvard.edu  Thu Dec  4 11:39:13 1997
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From: Fabrice Leclerc <leclerc@tammy.harvard.edu>
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To: chemistry@www.ccl.net
In-reply-to: <v03102802b0ac671052ce@[158.117.170.103]> (message from Pieter Stouten on Thu, 04 Dec 1997 09:01:39 -0500)
Subject: Re: CCL:HyperChem: Incorrect geometries in amines



The Merck force field (MMFF94) does have properly puckered nitrogens
as well. It gives a geometry very close to what you get with CFF96
(0.03A).


From shenkin@still3.chem.columbia.edu  Thu Dec  4 11:43:52 1997
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Date: Thu, 4 Dec 1997 11:09:20 -0500
In-Reply-To: Pieter Stouten <pieter.stouten@dupontmerck.com>
        "CCL:HyperChem: Incorrect geometries in amines" (Dec  4,  9:01am)
References: <v03102802b0ac671052ce@[158.117.170.103]>
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Subject: Re: CCL:HyperChem: Incorrect geometries in amines
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On Dec 4,  9:01am, Pieter Stouten wrote:
> Subject: CCL:HyperChem: Incorrect geometries in amines
> On 97/12/04 at 11:07 +0100, Jochen Kuepper wrote:
> 
> >Actually Aniline (phenylamine) in _not_ planar !
 ..
> There actually is at least one forcefield (MSI's CFF96) that is used in
> Molecular Mechancis that does have properly puckered nitrogens. Are there
> any other forcefields people know of, that do describe aniline etc.
> properly?

Hi, Pieter and CCL,

MMFF makes sp2 N's non-planar by default as well;  however, there
is an option to make them planar.  This option might be useful for
comparing computational results to crystal structures for large
molecules, where one would expect either thermal averaging or
the refinement procedure to make these atoms "appear" planar.

The so-called "MMFFs" (s for "static") option was added by Halgren
because of demand by Merck's crystallographic group, if I recall
properly.

	-P.
 

-- 
*********** In memoriam, Stephane Grappelli, 1908 - 1997, RIP *************
* Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 *
** NY, NY  10027;  shenkin@columbia.edu;  (212)854-5143;  FAX: 678-9039 ***
*MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html *

From renate_griffith@uow.edu.au  Thu Dec  4 12:39:14 1997
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Date: Thu, 4 Dec 1997 09:49:10 -0700
To: CHEMISTRY@www.ccl.net
From: Renate Griffith <renate_griffith@uow.edu.au>
Subject: helix axes in proteins


Dear all,

does anybody know of a program (freeware, of course : ) ) which allows me
to calculate and maybe display the axes of alpha helices, the closest
distance and the angle between two helices. I have the cartesian
coordinates of all atoms of the helices and can convert them into most of
the common file formats (pdb, sybylmol2, ...).
I'll summarize, if there is enough interest.

Thank you
Renate

Dr. Renate Griffith
email: renate_griffith@uow.edu.au
CURRENTLY: 	Department of Chemistry and Biochemistry
		University of Colorado at Boulder
		Boulder, Colorado, 80309-0215
		USA
		fax: +1 303 492 5894
		phone: +1 303 492 3597
NORMAL ADDRESS:	Department of Chemistry
		University of Wollongong
		Northfields Ave
		Wollongong, NSW 2522
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		fax: +61 42 214287
		phone: +61 42 213516



From pieter.stouten@dupontmerck.com  Thu Dec  4 12:44:56 1997
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Date: Thu, 04 Dec 1997 11:51:11 -0500
From: Pieter Stouten <pieter.stouten@dupontmerck.com>
Subject: Re: CCL:HyperChem: Incorrect geometries in amines
In-reply-to: <9712041109.ZM8840@still3.chem.columbia.edu>
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References: Pieter Stouten <pieter.stouten@dupontmerck.com>
 <"CCL:HyperChem: Incorrect geometries in amines"@DMPHUB.dmpc.com>
 (Dec 4, 9:01am) <v03102802b0ac671052ce@[158.117.170.103]>


Hello Peter and CCL,

>MMFF makes sp2 N's non-planar by default as well;  however, there
>is an option to make them planar.  This option might be useful for
>comparing computational results to crystal structures for large
>molecules, where one would expect either thermal averaging or
>the refinement procedure to make these atoms "appear" planar.
>
If by "large" you mean proteins, then there is no problem as protons are
not observed (unless the structure is based on neutron diffraction data).
What would the comparison tell you if you knowingly use a "wrong" force
field to make the results look like crystal structures?

>The so-called "MMFFs" (s for "static") option was added by Halgren
>because of demand by Merck's crystallographic group, if I recall
>properly.
>
And again we may come full circle :-). E.g. peptide bonds can to a large
extent be restrained to planarity when solving crystal structures, then
forcefields are fitted ("compared") to these data, the forcefields are used
again in xray refinement and the world is good because all peptide links
are planar. It is concerning that there is even the option to make
forcefields fit the skewed crystallographic perspective <g> (don't flame
me! I was a happy crystallographer in a previous life).

Cheers,

Pieter

*** Note my new e-mail address: pieter.stouten@dupontmerck.com ***

Pieter Stouten                              ||  Nothing shocks me;
Computer Aided Drug Design Group            ||
The DuPont Merck Pharmaceutical Company     ||  I am a scientist!
P.O. Box 80500, Wilmington, DE 19880-0500   ||
Phone: +1 (302) 695 3515                    ||          --
Fax: +1 (302) 695 9090                      ||
Internet: pieter.stouten@dupontmerck.com    ||    Indiana Jones
Web: http://www.halcyon.com/stouten/        ||



From richard@tc.cornell.edu  Thu Dec  4 13:39:14 1997
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        chemistry@www.ccl.net
Subject: Re: CCL:HyperChem: Incorrect geometries in amines
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Peter Shenkin wrote:
> 

> The so-called "MMFFs" (s for "static") option was added by Halgren
> because of demand by Merck's crystallographic group, if I recall
> properly.
> 
>         -P.
> 

Does anyone know if the MMFFs parameter set is published
anywhere?

Also, the original MMFF94 was not paramterized to reproduce liquid
properties as well as say OPLS. Does anyone know if this problem has
been addressed yet?

Richard Gillilan
richard@tc.cornell.edu

From shenkin@still3.chem.columbia.edu  Thu Dec  4 13:43:10 1997
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Date: Thu, 4 Dec 1997 13:17:22 -0500
In-Reply-To: Pieter Stouten <pieter.stouten@dupontmerck.com>
        "Re: CCL:HyperChem: Incorrect geometries in amines" (Dec  4, 11:51am)
References: Pieter Stouten <pieter.stouten@dupontmerck.com> 
	<"CCL:HyperChem: Incorrect geometries in amines"@DMPHUB.dmpc.com> (Dec 4  9:01am) 
	<v03102802b0ac671052ce@[158.117.170.103]> 
	<v03102804b0ac8c4413bd@[158.117.170.103]>
X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail)
To: Pieter Stouten <pieter.stouten@dupontmerck.com>
Subject: Re: CCL:HyperChem: Incorrect geometries in amines
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Mime-Version: 1.0
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Hello again, Pieter and CCL,

Yes, you make several good points.

On Dec 4, 11:51am, Pieter Stouten wrote:
> Subject: Re: CCL:HyperChem: Incorrect geometries in amines
 ...
> >MMFF makes sp2 N's non-planar by default as well;  however, there
> >is an option to make them planar.  This option might be useful for
> >comparing computational results to crystal structures for large
> >molecules, where one would expect either thermal averaging or
> >the refinement procedure to make these atoms "appear" planar.
> >
> If by "large" you mean proteins, then there is no problem as protons are
> not observed (unless the structure is based on neutron diffraction data).

Yup.  It would be interesting to know whether the nonplanarity of
amide N's in proteins can be detected in neutron-diffraction studies.
I suspect that there is still sufficient reliance on force-field
assumptions during refinement that your accusation of circular
reasoning remains valid.

However, there is also the point that protein crystals are very 
floppy, and one might expect these non-planarities, which are
small, to be time-averaged out.

This discussion is similar to the question whether proteins can 
be adequately modeled in torsional space, given reasonable rigid 
values of the bond lengths and angles.  That question has been 
extensively examined, and perhaps this amide-puckering question 
deserves the same kind of examination.

I have personally done some conformational searches on peptides
using both versions of MMFF, and in some situations it did seem 
to make a difference.  What you'd really want to know is whether
two rather different overall conformations can have their relative
energetic stability seriously altered by requiring the sp2 N's to
be planar.

	-P.


-- 
*********** In memoriam, Stephane Grappelli, 1908 - 1997, RIP *************
* Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 *
** NY, NY  10027;  shenkin@columbia.edu;  (212)854-5143;  FAX: 678-9039 ***
*MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html *

From shenkin@still3.chem.columbia.edu  Thu Dec  4 14:39:14 1997
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Date: Thu, 4 Dec 1997 13:54:55 -0500
In-Reply-To: Richard Gillilan <richard@TC.Cornell.EDU>
        "Re: CCL:HyperChem: Incorrect geometries in amines" (Dec  4,  1:31pm)
References: <v03102802b0ac671052ce@[158.117.170.103]> 
	<9712041109.ZM8840@still3.chem.columbia.edu> 
	<3486F709.2847@tc.cornell.edu>
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To: Richard Gillilan <richard@TC.Cornell.EDU>
Subject: MMFF; was: Re: CCL:HyperChem: Incorrect geometries in amines
Cc: Pieter Stouten <pieter.stouten@dupontmerck.com>,
        chemistry@www.ccl.net
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On Dec 4,  1:31pm, Richard Gillilan wrote:
> Subject: Re: CCL:HyperChem: Incorrect geometries in amines
 ...
> Does anyone know if the MMFFs parameter set is published
> anywhere?

J. Comp. Chem, 1996, v.17, five articles covering pages 490-641.
 
> Also, the original MMFF94 was not paramterized to reproduce liquid
> properties as well as say OPLS. Does anyone know if this problem has
> been addressed yet?

I believe not.

	-P.

-- 
*********** In memoriam, Stephane Grappelli, 1908 - 1997, RIP *************
* Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 *
** NY, NY  10027;  shenkin@columbia.edu;  (212)854-5143;  FAX: 678-9039 ***
*MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html *

From youkha@inpharmatics.com  Thu Dec  4 15:39:16 1997
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Date: Thu, 04 Dec 1997 11:54:48 -0800
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Try DeCipher ... you can do all that statically and dynamically, but
it's not freeware ! You can get it from MSI

Renate Griffith wrote:
> 
> Dear all,
> 
> does anybody know of a program (freeware, of course : ) ) which allows me
> to calculate and maybe display the axes of alpha helices, the closest
> distance and the angle between two helices. I have the cartesian
> coordinates of all atoms of the helices and can convert them into most of
> the common file formats (pdb, sybylmol2, ...).
> I'll summarize, if there is enough interest.
> 
> Thank you
> Renate
> 
> Dr. Renate Griffith
> email: renate_griffith@uow.edu.au

=======================================================================
  Philippe Youkharibache, Ph.D.
  InPharmatics Corp.                    e-mail: youkha@inpharmatics.com
  11440 W. Bernardo Court, Suite 300    tel:    (619) 530 8550
  San Diego, CA 92127                   fax:    (619) 530 8555         
=======================================================================

From lavelle@mbi.ucla.edu  Wed Dec  3 21:39:07 1997
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Date: Wed, 03 Dec 1997 18:06:20 -0800
To: chemistry@www.ccl.net, hyperchem@hyper.com
From: Laurence Lavelle <lavelle@mbi.ucla.edu>
Subject: Ab initio computational time.
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Hi,


Not much of a summary as I received one response to my initial posting,
which is listed below. Thanks to Dr. L=E1szl=F3 JICSINSZKY for his=20
comments.


Laurence Lavelle


>>>>=20

Date: Thu, 27 Nov 1997 21:28:42 -0800

To: hyperchem@hyper.com, chemistry@www.ccl.net

From: Laurence Lavelle <<lavelle@mbi.ucla.edu>

Subject: Ab initio computational time.=20


Hi all,


Happy Thanksgiving to those in USA.


I would very much appreciate any estimates (hrs) on the ab initio
computational time of the following system:


single point calculation, 731 basis functions, UHF, MP2, direct SCF


<underline>Hardware:</underline> Dual pentium 200MHz, 256K external
cache, 192MB RAM


<underline>OS:</underline> Windows NT Workstation 4.0 SP3.


<underline>Computational package:</underline> HyperChem 5.02


Although NT uses SMP, HyperChem is not a multithread application so the
"computational system" is a single pentium 200MHz.


I look forward to hearing from you.


Laurence Lavelle

<<<<<<<<



>Date: Mon, 1 Dec 1997 10:26:46 -0500

>From: "CYCLOLAB R&D Lab." <<cyclolab@compuserve.com>

>Subject: Ab initio computational time.

>Sender: "CYCLOLAB R&D Lab." <<cyclolab@compuserve.com>

>To: Laurence Lavelle <<lavelle@mbi.ucla.edu>

>Content-Disposition: inline

>

>Hi Laurence,

>

>>single point calculation, 731 basis functions, UHF, MP2, direct SCF=20

>

> Once I've tried to perform an ab initio single point calculation on

>alfa-cyclodextrin (C36H60O30. 390 basis function with STO-3G, direct
scf,

>grad, P100, HC 4.5). It takes about two weeks, but though the
calculation

>did not finish, because some hw errors (the cooler of CPU went wrong),
I

>was very close to the final step.

>

> The computation time increases in second order, that means, e.g. in=20
my

>computer the calculation on your molecule on bases like above would take
~4

>times more than in case of alpha-cyclodextrin (8 weeks). The UHF+MP2
about

>duplicates the calculation time, i.e. -> ~16 weeks. You are using a
P200

>machine, which approximately halves the calculation time comparing with
my

>machine (->~8 weeks), under Win'95. The HC runs ~70 % speed of HC4.5,
that

>means, your time increases with about three weeks (->11 weeks). Some

>slowing factors are within NT4 (about 60 % slower than Win'95 with a
native

>[32bit] application), i. e. my opinion is that your calculation takes
at

>least 10 weeks but not more than 20 weeks.

>

> Not so inspiring.

>

> I would propose a solution: cut smaller parts your molecule. In that
case

>you may calculate an approximative result, but much more faster (e.g.
you

>may save dielectric integrals, if you have a large HD. As far as I
know,

>the NT can handle larger than 2 GB HD partitions). Otherwise, I do not
know

>any ab initio calculations such a big molecule. It is enough large for
a

>Cray machine, as well.

>

>

> Regards, Laszlo

>

>-----------------------------------------------------------

>Dr. L=E1szl=F3 JICSINSZKY

>Head of Synth. Dept.

>CYCLOLAB R&D Lab. Ltd.

>H-1525 Budapest, P.O. Box: 435

>XI. Domb=F3v=E1ri =FAt 5-7

>email: cyclolab@compuserve.com

>Tel./Fax: (36-1)-206-51-36 or (36-1)-206-51-37

>-----------------------------------------------------------

>

>

<center>


""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""=
""""""""""""""""

Laurence Lavelle, Ph.D.

University of California Los Angeles

Molecular Biology Institute, and Department of Chemistry & Biochemistry=20

Laboratory of Structural Biology & Molecular Medicine

Los Angeles, CA 90095-1570, USA

=20

Email:LAVELLE@MBI.UCLA.EDU

Phone (Lab): (310) 206-8270

Phone (Office): (310) 825-2083

Fax: (310) 267-1957

http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html

""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""=
""""""""""""""""


It will be a great day when schools have all the money they need,

and the military has bake day sales.




In nature's infinite book of secrecy

A little I can read.


</center>


From ccl@www.ccl.net  Wed Dec  3 22:39:03 1997
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Apparently-To: chemistry@ccl.net
Subject: RE: CCL:Re: CCL:HyperChem: Incorrect geometries in amines



        I think the MM+ forcefield is OVERcompensating for the interaction
betwen the nitrogen atom & the pi-system.  If memory serves, the geometry
around the N in aniline is "more planar" than in methyl amine, but not "truly
planar".

        I would recommend checking the literature for structural studies on
aniline, or running ab initio calculations [6-31G(p,d) or DZP at least]
optimizing aniline & cyclohexylamine to check this.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
                           FREDERIC A. VAN-CATLEDGE

Scientific Computing Division         ||   Office: (302) 695-1187 or 529-2076
Central Research & Development Dept.  ||          
The DuPont Company                    ||      FAX: (302) 695-9658
P. O. Box 80320                       ||
Wilmington DE 19880-0320              || Internet: fredvc@esvax.dnet.dupont.com 
--------------------------------------------------------------------------------
Opinions expressed in this electronic message should ***> NOT <*** be taken to 
represent the official position(s) of the DuPont Company.  

*****> ANY OPINIONS EXPRESSED ARE THE PERSONAL VIEWS OF THE AUTHOR ONLY. <*****
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From fgonzale@lauca.usach.cl  Thu Dec  4 16:39:15 1997
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Date: Thu, 4 Dec 1997 18:27:32 -0300 (CDT)
From: Fdo Danilo Gonzalez Nilo <fgonzale@lauca.usach.cl>
To: chemistry@www.ccl.net
Subject: Xmol on O2 SGI
Message-ID: <Pine.SUN.3.91.971204181915.7745B-100000@lauca.usach.cl>
MIME-Version: 1.0
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Hi All!

	I trying to run XMOL on a SGI O2, but when I run it, an error message
"Wrong Architecture" appears.
	Can anybody help me to solve this problem?

Thanks a Lot!!

Fdo. Danilo Gonzalez N.           
University of Santiago de Chile
Faculty of Chemistry and Biology, Computational Chemistry Lab.         
Casilla 40, Correo 33, Santiago, Chile      Fono: (562) 681 2575 Anexo:799
E-mail : fgonzale@lauca.usach.cl            Fax : (562) 681 2108           
URL    : http://quimbio.usach.cl/~danilo/
**************************************************************************


From norge@karin.fmq.uh.edu.cu  Thu Dec  4 16:42:09 1997
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Date: Thu, 4 Dec 1997 14:15:57 -0500 (CST)
From: Norge Cruz Hernández <norge@karin.fmq.uh.edu.cu>
To: CHEMISTRY@www.ccl.net
Subject: Help on bielectronic integrals.
Message-ID: <Pine.LNX.3.91.971204141110.12478A-101000@karin.fmq.uh.edu.cu>
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Dear CCL friends :

I am interesed in solve one of the bielectronic integral, using the 
Laguerre polinomial in the wave function and exponential function.
The exact integral is in the Attchmnt. This is in .doc file.
I would like to solve the problem in analitic hand or in numerical form.

Any of your help will be very importan for me.

Best regard
Norge

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--127467777-66480178-881262957=:12478--

From lavelle@mbi.ucla.edu  Thu Dec  4 22:39:35 1997
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	by www.ccl.net (8.8.3/950822.1) id WAA07425; Thu, 4 Dec 1997 22:30:19 -0500 (EST)
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Date: Thu, 04 Dec 1997 19:38:22 -0800
To: hyperchem@hyper.com, chemistry@www.ccl.net
From: Laurence Lavelle <lavelle@mbi.ucla.edu>
Subject: Gaussian 94 Windows
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Hi,

I have a couple of questions regarding G94W:

Under NT does it use SMP (i.e., is it a multithread application)?

Does it interface with UNIX G94 (i.e., can one use G94W as a front end and
UNIX G94 as a backend for heavy duty computations)?

Since it is over a week since I asked Gaussian Inc. the same questions with
no reply, perhaps someone knows.

Thanks
Laurence Lavelle



