From toukie@zui.unizh.ch  Fri Dec 22 03:20:15 1995
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Date: Fri, 22 Dec 1995 10:19:58 +0100 (MET)
From: "Hr Dr. S. Shapiro" <toukie@zui.unizh.ch>
Sender: toukie@zui.unizh.ch
Reply-To: toukie@zui.unizh.ch
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To: chemistry@www.ccl.net
Subject: ? re STERIMOL notation


Dear Colleagues;

     For those of you who are familiar with the STERIMOL molecular steric
parameter programme:

     is

     HC2(H)RDC2(H)RC(H,H)RC6(X1)RDC6(OH)RDC6(H)RDC6(DC6(H)RDC6(H)RDX1)H*

a proper STERIMOL linear input structure for o-allylphenol?

     If it is indeed correct, please confirm; if it is not, where have I
erred?

     Thanks in advance to all responders.  And schoene Festtage to everyone.


Sincerely,

(Dr.) S. Shapiro
ZH, CH
toukie@zui.unizh.ch

From owner-chemistry@ccl.net  Fri Dec 22 04:35:15 1995
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Date:         Fri, 22 Dec 95 10:11:43 HOE
From: "Dr. Jose Luis Garcia de Paz" <DEPAZ@vm1.sdi.uam.es>
Organization: Native address: <DEPAZ@EMDUAM11.BITNET>
Subject:      mp2 optimization in G94 for big systems
To: CCL list <chemistry@ccl.net>


Dear CCL,
Merry Christmas and a Happy New Year 1996.
I need your help. Because a refree comment, I must perform a
MP2 geometry optimization of a system with 310 basis funcions.
I am using Alpha DEC 3000-600 computer with 128 Mb ram and two scratch
disk, one of 2 GB and the second one of 1Gb. I am using Gaussian 94
rev C2. From Gaussian manual I understand (may be I am wrong) I may
perform a geometry optimization with no disk space restrictions. It is
only a matter of cpu time. I tested three sets of keywords, and all
gives a device full. Allways the 2Gb disk becomes 100% full.
  Can anybody give me a hint to solve the problem?.
  Thank you very much,     Jose

1) first test
%chk=myfile.chk
%mem=14000000
# GEOM=COORD MP2=(VERYSTINGY,DIRECT) SCF=DIRECT 6-31G** OPTCYC=99
# SCFCYC=99 DENSITY=MP2 OPT=CALCHFFC MAXDISK=240MW

  big molecule with 310 basis functions.

0 1
  7   1.235588554   0.601793420   0.000000000
   ----   more atoms  -----

2) second test.
%chk=myfile.chk
%mem=14000000
%rwf=/usr/users/scr/,245MW,/usr/users/tmp/,122MW
# GEOM=COORD MP2=(STINGY,DIRECT) SCF=DIRECT 6-31G** OPTCYC=99 SCFCYC=99
# DENSITY=MP2 OPT=CALCHFFC MAXDISK=367MW

big molecule with 310 basis functions

0 1
  7   1.235588554   0.601793420   0.000000000
    -----   more atoms  -------

3) test
%chk=myfile.chk
%mem=14000000
%rwf=/usr/users/scr/,2GB,/usr/users/tmp/,1GB
# GEOM=COORD MP2=(STINGY,DIRECT) SCF=DIRECT 6-31G** OPTCYC=99 SCFCYC=99
# DENSITY=MP2 OPT=CALCHFFC MAXDISK=3GB

  -- big system with 310 basis functions -----

0 1
  7   1.235588554   0.601793420   0.000000000
   ---- more atoms ----

                                 Dr. Jose Luis Garcia de Paz
                                 (34) (1) 3974957. FAX (34) (1) 3974512.
                                 (34) (1) 3974263.
                                 Departamento de Quimica Fisica Aplicada.
                                 FACULTAD DE CIENCIAS, C-XIV-602.
                                 Universidad Autonoma de MAdrid.
                                 28049-Madrid (Spain).

From smori@utsc.s.u-tokyo.ac.jp  Fri Dec 22 06:05:16 1995
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Date: Fri, 22 Dec 95 19:57:52 JST
From: Seiji Mori <smori@utsc.s.u-tokyo.ac.jp>
Message-Id: <9512221057.AA18852@utsc.s.u-tokyo.ac.jp>
To: chemistry@www.ccl.net
Subject: electron density differences


Dear netters,

 I would like to search the programs of the calculating
the electron density difference(density of whole system
 - sum of densities of two fragments) from the Gaussian
series outputs or checkpoint file to write the Gaussian style output or
checkpoint files,
if one cannot
calculate directly with the Gaussian program.
 I hope that it is the cost free.
Would you tell me an information of the programs?

  Sincerely,
 Seiji Mori

##############################################################
     --Merry X'mas! -- Merry X'mas! --Merry X'mas! --
                             ---------------------------------
          ^                 |    Seiji Mori
        ^  ^                |  Graduate student in Nakamura Laboratory
       ^  ^  ^              |  (Lab. of Physical Organic Chemistry)
      ^ \  ^\  ^            |  Department of Chemistry
    ^ |  ^  ^ & ^           |  The University of Tokyo
   ^ (^-^) ^ ^ \ ^          |  Hongo 7-3-1, Bunkyou-ku, Tokyo 113,
      |   l    |            |  JAPAN.
                            |  email:smori@utsc.s.u-tokyo.ac.jp
                            |
##############################################################


From cwm@proteus.co.uk  Fri Dec 22 07:35:18 1995
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From: Chris Murray <cwm@proteus.co.uk>
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Date: Fri, 22 Dec 1995 11:34:30 +0000
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To: chemistry@www.ccl.net
Subject: Summary synthetic acessibility
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Sorry guys,

I missed some of the responses in the previous message. The rest are here

On Nov 30,  1:18pm, Peter Shenkin wrote:
> Subject: Re: CCL:Synthetic Accessibility
>
> I think that synthetic feasibility is to some extent addressed by
> database-based synthesis programs like SYNLIB.  The larger the
> fragment that SYNLIB succeeds in finding a synthesis for, the
> greater the likelihood, I should think, that the synthesis is
> feasible, since all its synthetic routes come from the literature.
>
> Of course, beyond some fragment size you won't get any hits, but
> by scaling down to the largest fragment sizes that do give hits,
> the number of possibilities that a skilled organic chemist has to
> examine is decreased.  In the end, a skilled organic chemist does
> have to assess feasibility, but a program like SYNLIB might narrow
> down the list of syntheses he needs to examine better than a
> program like LHASA.
>
> Just a thought....
>
> 	-P.
> ******** When somebody says, "It's a matter of principle,"... ********
> *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,*
> *NY, NY  10027;  shenkin@columbia.edu;  (212)854-5143;  FAX: 678-9039*
> ************ ...it's a sure sign he wants the whole pie. *************
>-- End of excerpt from Peter Shenkin


On Nov 30,  2:54pm, MARTIN@cmdb.pprd.abbott.com wrote:
> Subject: Re: CCL:Synthetic Accessibility
> We evaluated Chiron and Peter Johnson's program (forgot its name) vs a panel
> of expert organic chemists. Also looked at similarity searches in Spresi93.
> Bottom line; Spresi searches are sometimes helpful, but the similarity
numbers
> are not especially relevant. Chiron and the other program are OK, but limited
> in reaction types. We concluded that we should just wait a few years and
> maybe the situation will improve. In the meantime, do combinatorial libraries
> , which the chemists say will work!!
>
> Yvonne Martin
>-- End of excerpt from MARTIN@cmdb.pprd.abbott.com


On Dec 1, 12:10pm, Dr. Dave Winkler wrote:
> Subject: Re: CCL:Synthetic Accessibility
> >Hi all,
> >
> >When designing new molecules in drug discovery projects, an important
> >consideration is the synthetic feasibility of the molecules. This is a
somewhat
> >different question than programs like LHASA address since they seem to
> >concentrate on suggesting synthesis routes. Does anybody have information or
> >experience of synthetic feasibility programs? References to papers
describing
> >the programs appear to be few and far between.
> >
> >I will summarise to the net if there is any interest.
> >
> Tripos have an empirical 'synthetic difficulty' measure built into their
> molecular spreadsheet in Sybyl.  I think it is based on the number of
> chiral centres,etc.  I heard they were working on a chemical reaction
> database in Unity too.
>
>
> Cheers,
>
> Dave
>
> Dr. David A. Winkler                            Voice: 61-3-542-2244
> Principal Research Scientist                    Fax:   61-3-543-8160
> CSIRO Division of Chemicals and Polymers        CSIRO: http://www.csiro.au
> Private Bag 10,Rosebank MDC, Clayton, Australia
      http://www.chem.csiro.au
>
>
>-- End of excerpt from Dr. Dave Winkler



-- 

Chris Murray                     | 
Proteus Molecular Design Ltd.,   |  Tel: 01625-500555
Lyme Green Business Park,        |  Fax: 01625-500666
Macclesfield, Cheshire,          |  Email: C.W.Murray@proteus.co.uk
SK11 0JL, UK                     |

From cwm@proteus.co.uk  Fri Dec 22 07:40:38 1995
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To: chemistry@www.ccl.net
Subject: Summary: Synthetic Accesibility
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Here are the summaries of the replies I received about synthetic accessibility.
Apologies for taking so long to get round to them.

The original posting was

On Nov 30,  3:03pm, Chris Murray wrote:
> Subject: CCL:Synthetic Accessibility
>
> Hi all,
>
> When designing new molecules in drug discovery projects, an important
> consideration is the synthetic feasibility of the molecules. This is a
somewhat
> different question than programs like LHASA address since they seem to
> concentrate on suggesting synthesis routes. Does anybody have information or
> experience of synthetic feasibility programs? References to papers describing
> the programs appear to be few and far between.
>
> I will summarise to the net if there is any interest.
>
> chris
>
> --
>
> Chris Murray                     |
> Proteus Molecular Design Ltd.,   |  Tel: 01625-500555
> Lyme Green Business Park,        |  Fax: 01625-500666
> Macclesfield, Cheshire,          |  Email: C.W.Murray@proteus.co.uk
> SK11 0JL, UK                     |
>
> -------This is added Automatically by the Software--------
> -- Original Sender Envelope Address: cwm@proteus.co.uk
> -- Original Sender From: Address: cwm@proteus.co.uk
> CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator
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> Anon. ftp: www.ccl.net   | CHEMISTRY-SEARCH@www.ccl.net -- archive search
>              Web: http://www.ccl.net/chemistry.html
>-- End of excerpt from Chris Murray


On Nov 30,  4:41pm, heelisp@delta.newi.ac.uk wrote:
> Subject: Re: CCL:Synthetic Accessibility
> Dear Dr Murray,
> I would be interested in receiving any response from your query on
> synthetic feasibility programs. I have quite a few modelling projects on the
> go (both post-grad and grad), but this is a new one to me. I suppose that
> you have tried REACCS, but this probably gives the same as LHASA.
> Would not a computed heat of formation, or free energy of formation be a
guide
> to the general likelhood of a compound's formation in a reaction?
> Paul Heelis
> Fac.Science
> North East Wales Institute
> Wrexham
> UK.
>
> ps. we have a project on computer aided design of drugs for phototherapy,
> I would be interested in hearing what your company sells/offers.
>-- End of excerpt from heelisp@delta.newi.ac.uk


On Nov 30,  6:24pm, Leif Norskov wrote:
> Subject: Re: CCL:Synthetic Accessibility
>
> The Peter Johnson group in Leeds have a programme they call CESAR
> (spelling ?) - it looked quite nice a couple of years ago.
> URL http://www.chem.leeds.ac.uk/People/Johnson.html
>
> --
> Leif Norskov
> Novo Nordisk A/S
> Copenhagen
> Denmark
> lnl@novo.dk
>-- End of excerpt from Leif Norskov


On Nov 30, 12:15pm, Steve Bowlus wrote:
> Subject: Synthetic accessibilty
> I would be interested in any responses you receive.
>
> This is among the most common and recurrent problems in drug design.  It is
> one of the biggest and best reasons for moving molecular modeling and
> computational chemistry to the desktop.  It's also the reason that people
> like me (trained and several years on the bench as a synthesis chemist)
> have jobs like mine (modeling wonk for all sorts of things and support for
> the synthesis chemists).
>
> Personally, I doubt that there is a computer program that will give you
> "feasibility".  "Possibility" perhaps; "feasibility" is a judgement
> call on the part of the synthesis chemist working with the modeler.
> "Feasibility" has as much to do with cost, time, and expectation of
> improvement in properties/activity as it does to with one's ability to make
> the material (total synthesis of vitamin B-12 is "feasible," but why would
> you do it?).
>
> Depending on the stage of the project, the chemist may go so far as a
> complete retrosynthetic analysis of the proposed material, if it is very
> dissimilar to lead compounds (I think this is what LHASA does. . .but I
> have no experience with the program).  Beyond this, it is much more common
> for the chemist to concentrate on unit transformations, and problems of
> functional groups compatibility wrt a series of unit transformations.  ORAC
> and REACCS are probably the front runners for addressing this type of
> question.
>
> _BUT_ the information in the last paragraph is best developed and
> interpreted by the synthesis chemist.  Where the modeler can help is to
> suggest alternative targets if (when!) the best-bet analog turns out to be
> _not_ "feasible," and what these alternatives "cost" in terms of lower
> activity or whatever.
>
> sb
>
> ===========================================================================
>   Stephen B. Bowlus, Ph.D.                Computer-Aided Molecular Design
>                                           Research Division
>   e-mail: bowlus@sandoz.com               Sandoz Agro, Inc.
>   Phone:  + 1 415 354 3904                975 California Ave.
>   Fax:    + 1 415 857 1125                Palo Alto, CA 94304
> ===========================================================================
>-- End of excerpt from Steve Bowlus


On Nov 30, 11:10am, Abby Parrill wrote:
> Subject: Re: CCL:Synthetic Accessibility
> Chris,
>
>   This is a problem near and dear to me as it is the subject of one of my
> research proposals I am circulating with my faculty position
> applications.  The closest I have been able to find is a set of
> heuristics used in some de novo design programs.  Following are a few
> references to programs which refer to synthetic accessibility in passing.
>
>  Gehlhaar, D. K.; Moerder, K. E.; Zichi, D.; Sherman, C. J.; Ogden, R.
> C.; Freer, S. T., "De Novo Design of Enzyme Inhibitors by Monte Carlo
> Ligand Generation", J. Med. Chem.  1995, 38, 466-472.
>
>  Pearlman, D. A.; Murcko, M. A., "CONCEPTS:  New Dynamic Algorithm for
> De Novo Drug Suggestion", J. Comp. Chem.  1993, 14, 1184-1193.
>
>  Rotstein, S. H.; Murcko, M. A., "GenStar:  A Method for De Novo Drug
> Design", J. Comp. Aided. Molecular Design  1993, 7, 23-43.
>
> I would appreciate a summary of any other responses you get.
>
> __________________________________________________________
>
>                       Abby Parrill
>                   Chemistry Department
>       Artificial Intelligence in Chemistry Laboratory
>                 The University of Arizona
>              abby@mercury.aichem.arizona.edu
>
> __________________________________________________________
>-- End of excerpt from Abby Parrill



-- 

Chris Murray                     | 
Proteus Molecular Design Ltd.,   |  Tel: 01625-500555
Lyme Green Business Park,        |  Fax: 01625-500666
Macclesfield, Cheshire,          |  Email: C.W.Murray@proteus.co.uk
SK11 0JL, UK                     |

From owner-chemistry@ccl.net  Fri Dec 22 12:20:22 1995
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Date: Fri, 22 Dec 1995 18:17:48 +0100
From: qfsaulo@usc.es (Saulo Vazquez Rodriguez)
Message-Id: <199512221717.AA08477@uscmail.usc.es>
To: chemistry@ccl.net
Subject: SUMMARY:DFT


Some days ago I had posted the following question:

I would like to know the reliability of the DFT methods in 
energy/geometry calculations of hydrogen bonded systems.
Any information about it is appreciated.

Here are the replies. Thanks to all the people who helped me.

Saulo Vazquez (qfsaulo@usc.es)

Reply 1:
Dear Saulo,
we have carried some work on H-bonded complexes and PT reactions:

Chem. Phys. Lett. 231 (1994) 295
J. Chem. Phys. 102 (1995) 364
J. Phys. Chem. 99 (1995) 15062
Int. J. Quantum Chem. 56 (1995) xxx

We have focues our attention on the B3LYP method, but in these papers there 
are also some results regarding more conventional functionals (BLYP and BP)
and some usefull references.  
Ciao 

Carlo

-------------------------------------------------------------------------------
  Dr. Carlo Adamo                  | tel. +39-81-5476504
  Dipartimento di Chimica          | fax  +39-81-5527771
  via Mezzocannone 4               | e-mail ADAMO@CHEMNA.DICHI.UNINA.IT
  I-80134 Napoli                   |
  Italy                            |
________________________________________________________________________________


Reply 2:
Saulo,

See the recent article "Density Functional Theory and Molecular Clusters"
in J. Comp. Chem., 16, 13115-1325 (1995).  Please e-mail me a summary of your
responses.

Regards,
Tom Furlani
-- 
Thomas R. Furlani  
Department of Chemistry
SUNY at Buffalo
Box 603000
Buffalo, NY 14260-3000
furlani@blizzard.chem.buffalo.edu
Office: (716) 645-6800 ext 2120; Fax: (716) 645-6963

                                         Girona 15/12/95
Reply 3:
Estimado Saulo:

              Digamos que en general los metodes DFT para el 
calculo de interacciones debiles (puentes de hidrogeno, complejos
de van der Waals o complejos de transferencia de carga) no son 
especialmente recomendables. En cualquier caso, los mejores resultados
se obtienen con el uso de funcionales hibridos. Te paso algunas
de las referencias mas interesantes sobre el tema.

Puentes de hidrogeno:
(a) Q. Zhang et al. JPC 99 (1995) 592
(b) F. Sim et al. JACS 114 (1992) 4391 
(c) K. Kim and K.D. Jordan, JPC 98 (1994) 10089
(d) J.E. del Bene et al. JPC 99 (1995) 10705
(e) K. Laarsonen et al. CPL 207 (1993) 208
(f) E. Mijoule et al. CPL 208 (1993) 364

Complejos de transferencia de carga:
E. Ruiz et al. JACS 117 (1995) 1141). 

Complejos de van der Waals:
J.M. Perez-Jorda, A.D. Becke, CPL 233 (1995) 134.

     Un abrazo,

                   Miquel 

 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
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Reply 4:
Hi,

I too am interested in the subject of DFT methods on H-bonded systems.  Would
you mind sending me a summary of responces?

What I have found so far (I am a real novice at both ab initio/DFT
calculations) is that the DFT calulations give very similar results to MP2
calculations.  Esp. when looking at differences in energy.  I have done
calculations mostly on  Water/Hydroxide systems using 6-31+G(d,p) basis set and
MP2, HF and B3LYP methods.  As with the ab initio methods the quality of
results with DFT methods depend greatly on basis set.

You may find the following paper helpful:

Del Bene, J.E., Person, W.B., Szczepaniak, K. (1995) "Properties of
Hydrogen-Bonded Complex Obtained from the B3LYP Functional with 6-31G(d,p) and
6-31+G(d,p) Basis Sets:  Comparison with MP2/6-31+G(d,) Results and
Experimental Data."  J. Phys. Chem 99, 10705-10707.

Hope this is helpful.

Hillary

-- 
-----------------------------------------------------------------------
Hillary S. Gilson                                Phone:  (301) 738-6106
Center for Advanced Research in Biotechnology    FAX:    (301) 738-6255
National Institute of Standards and Technology
9600 Gudelsky Drive	    http://indigo15.carb.nist.gov/carb/carb.html
Rockville, MD  20850        e-mail: hillary@indigo15.carb.nist.gov
------------------------------------------------------------------------

Reply 5:
 Dear Saulo;

 As to the reliablity of the hydrogen-bonded systems with 
DFT, please see 
Novoa and Sosa, J. Phys. Chem, 1995, 15837.and
Bene and Szczepaniak, ibid, 1995, 99, 10705.
in this system, 6-31+G(d,p) or triple-zeta basis sets will 
be needed.

 Sincerely,
  Seiji Mori

 Department of Chemistry
 The University of Tokyo

Reply 6:
Tengo algunos ejemplos (mas de tres) en los cuales las interacciones debiles
son muy mal descritas por metodos DFT, aun con todas las correciones y sofisticaciones
que te puedas imaginar. Las distancias son mucho mas largas que las calculadas con
metodos de orbitales con correlacion decentemente incluida y los pozos son mucho mas
debiles. Te recomiendo usar cualquier otra cosa excepto DFT para enlaces de H e
interacciones van der Waals (dipolo-dipolo, ion-dipolo, ion-cuadrupolo) etc.
Hay gente en la Univ. Autonoma Metropolitana-Iztapalapa que esta tratando de
mejorar estas descripciones para interacciones debiles y si quieres te puedo conseguir
sus e-mails al regresar de vacaciones en enero.
Feliz Navidad!
Alejandro Ramirez Solis

Reply 7:
     Hi,

For hydrogen-bonded systems, we have published this
year a paper in which we study it several with density
functional theory.
Here is the reference:

- Y. Jeanvoine, F. Bohr and M.F. Ruiz-Lopez
  Can. J. Chem. 73 (1995) 710.

I know also :

- F. Sim, A. St-Amant, I. Papai and D.R. Salahub
  J. Am. Chem. Soc. 114 (1992) 4391.

- K. Laasonen, M. Parinello, R. Car, C. Lee and D. Vanderbilt
  Chem. Phys. Lett. 207 (1993) 208.

- T. Zhu and W. Yang
  Int. J. Quantum Chem. 49 (1994) 613.

I hope this helps you.

	    Best regards,

		   Frederic Bohr






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Reply 8
Contact Janet DelBene at Youngstown State University.  She has looked at
this problem and found serious deficiencies with the DFT method as I
understand it.

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