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From: "Helder Marques" <HMARQUES@aurum.chem.wits.ac.za>
Organization: Wits Chem
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Date: Mon, 21 Feb 2000 07:06:48 +0200
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Subject: ZINDO/1 estimation of delta E on bond compression
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Dear CCLers,

It is postulated that one of the mechanisms used by the 
coenzyme B12(AdoCbl)-dependent enzymes to catalyse the 
homolysis of the Co-C bond (the first step in the catalytic cycle) 
is mechanochemical triggering where upward flexing of the corrin 
ring by compression of the Co-N axial bond to the base 
benzimidazole in the class II enzymes (or His in the class I 
enzymes) causes weakening of the Co-C bond.  There are two 
possibilities here.  Either the enzyme destabilises the ground state 
by upward flexing of the corrin ring so sterically weakening the 
Co-C bond, or stabilises the transition state.  In the transition 
state version of mechanochemical triggering, the axial Co-N 
bond is sterically compressed in the transition state, to provide 
electronic stabilization through increased ligand-metal orbital 
overlap.

The strain energy consequences of stretching the Co-C bond in 
AdoCbl to simulate the approach to the transition state, and of 
compressing the Co-Nax bond can be determined using 
molecular mechanics methods with a force field that we have 
developed and extensively tested and which accurately and 
reliably reproduces many of the structural features of these 
compounds.

In order to estimate the electronic effect of Co-Nax bond 
shortening in the transition state we proceeded as follows.  I would 
like your comments on our approach.  Are the energy values we 
obtain likely to be reliable?  In particular, I would be grateful if you 
could point me to appropriate references.

To save computational time, AdoCbl was edited to truncate all 
side chains of the corrin ring to methyl groups, and a proton was 
substituted for the ribose at the non-coordinated N of the 
benzimidazole axial base.  Hydrogens were placed in standard 
positions and the structure was energy minimized using the 
molecular mechanics force field. 

The Co-C bond length was then fixed at 2.5, 2.8, or 3.2 A (to 
simulate possible positions of the transition state for Co-C bond 
homolysis), while the Co-Nax bond length was varied from ca. 
2.35 to 1.70 A by changing the strain-free bond length.  Each 
model was energy-minimised using molecular mechanics.  A single 
point calculation was then performed on each model using the 
ZINDO/1 semi-empirical molecular orbital method.  The heat of 
formation of each model was obtained from this calculation and 
normalized against the minimum heat of formation found for the 
series of models with each fixed Co-C bond length.	We find that 
the relative (but not absolute, of course) heats of formation are 
quite insensitive to the Co-C bond distance.  The minimum in the 
potential energy curves is at a Co-Nax bond length of 1.96 A and 
this is also independent of the trans Co-C bond length.  From 
these data, we estimate that compression of the Co-Nax bond 
>from 2.23 (the value in the ground state, obtained from the X-ray
structure) to 1.96 A in the transition state for AdoCbl homolysis 
results in a stabilization of about 10 kcal mol-1  due to improved 
overlap between the metal and the coordinated nitrogen. 

With thanks

Helder Marques



__________________________________________________________
Professor Helder M Marques
Head: Department of Chemistry
University of the Witwatersrand
PO Wits
Johannesburg
2050 South Africa
Tel +27+11+716-2303
Fax +27+11+339-7967
http://www.chem.wits.ac.za

From chemistry-request@server.ccl.net  Mon Feb 21 04:15:17 2000
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To: Y Z <yz0@hotmail.com>
Cc: CHEMISTRY@ccl.net
Subject: CCL:Three dimensional FFT
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 > Are there any way to calculate a (256,256,256) order
 > DOUBLE COMPLEX FFT in FORTRAN77? I tried to do the
 > following subrouitine but cannot pass the compiling.

Nothing on netlib ?
fftw ?

Jochen
--
Heinrich-Heine-Universität
Institut für Physikalische Chemie I
Jochen Küpper
Universitätsstr. 1, Geb. 26.43.02.29
40225 Düsseldorf, Germany
phone ++49-211-8113681, fax ++49-211-8115195
http://www.jochen-kuepper.de


From chemistry-request@server.ccl.net  Mon Feb 21 10:11:19 2000
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From: shinoda@biol2.bio.nagoya-u.ac.jp (Kazuki Shinoda)
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Dear CCLers,

I have performed MD simulations with AMBER param94 and db94. Because my
system has been constituted by only a protein and solvent water, everything
has been O.K.. But now, I must treat a system which includes a heme-protein.
I want to continue using param94 and db94 because I want to use neutral-Asp
and neutral-Glu.

My question is whether can I use the all-atom heme parameter set (heme-all.
in and frcmod.hemall) that is on the AMBER home-page with param94 and
db94 ? If some modifications are required, do someone has any information
about them ?

Any information will be appreciated.

Best regards,
Kazuki


================================================
 Kazuki Shinoda, MC2
 Division of Biological Science, Graduate school of Science
 Nagoya University, Chikusa, Nagoya 464-8602, Japan

 E-mail : shinoda@biol2.bio.nagoya-u.ac.jp
 URL:      http://bio.nagoya-u.ac.jp:8001/~kazuki/kazuki.html
================================================


From chemistry-request@server.ccl.net  Mon Feb 21 11:09:22 2000
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From: "Scheila" <scheila@ifi.unicamp.br>
To: <chemistry@ccl.net>
Subject: X-ray data converter- I need a free software
Date: Mon, 21 Feb 2000 12:53:07 -0300
Message-ID: <NDBBIKCBOLOKJHKEFJDIOELGCAAA.scheila@ifi.unicamp.br>
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I’m a student and I’m working with molecular structure and proprieties in my
doctoral course.
I need a help to convert some x-ray data disposed in a paper. This paper
shows the data group, the a, b and c parameters and the atomic coordinates
in the format:
		x		y		z
C1	     7866(3)    3480(6)	    -1818(4)
C2 	     7641(2)    4107(6)	    -2989(4)
C3 	     7896(2)    5715(6)     -3240(4)
:
:
OMEI	     9490(2)    7341(7)	      3845(4)
CMEI	     9845(5)    5894(15)	3795(10)
W1/2*      9230	      923	      2984
W2/2*      8963        2070         3358


*occupancy factor f=0.5

In fact I don’t know witch format is it and I want to know if there are any
free software that could convert this data to a FDTA format, to be imported
by the Spartan software.
It is important to remember that it is the x-ray atomic coordinates of a
crystallized molecule.
Thanks for any help.

Scheila F. Braga

________________________
Scheila Furtado Braga
IFGW-DFA-UNICAMP
Campinas – Brazil
e-mail : scheila@ifi.unicamp.br
_________________________



From chemistry-request@server.ccl.net  Mon Feb 21 18:30:03 2000
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Date: Mon, 21 Feb 2000 17:21:34 -0500
From: Daquan Gao <dgao@chem.iupui.edu>
To: chemistry@ccl.net
Subject: Re: CCL:Surface and volume calculations (fwd)
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This is the only response I got. Thanks to Yvonne Martin! I believe now
that QCPE is the first place to look for this info. 

Daquan Gao

---------- Forwarded message ----------
Date: Sun, 20 Feb 2000 11:32:03 -0600
From: "Martin,Yvonne" <yvonne.c.martin@abbott.com>
To: dgao@chem.iupui.edu
Subject: Re: CCL:Surface and volume calculations

Try the programs by Robert Pearlman. Savol2 I think is the most recent one.
You can get it from QCPE.

Yvonne Martin




dgao@chem.iupui.edu@INTERNET@ccl.net on 02/18/2000 04:10:34 PM
Sent by: chemistry-request@ccl.net
To: chemistry@ccl.net@INTERNET
cc:
Subject: CCL:Surface and volume calculations


Dear CCLers,

I would like pointers to fast algorithms(preferentially analytical) of
computing the surface areas of molecules? Any idea is also
appreciated.


Yours Truly,

Daquan Gao



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From chemistry-request@server.ccl.net  Mon Feb 21 20:26:11 2000
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From: PEARLMAN@VAX.PHR.UTEXAS.EDU
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To: CHEMISTRY@ccl.net
Message-Id: <000221182002.5ecb@VAX.PHR.UTEXAS.EDU>
Subject: Re: CCL:Surface and volume calculations

Hello from sunny Austin, TX --

Recently, there have been a number of inquiries regarding software
for calculating molecular surface areas, molecular volumes, and atomic
contributions thereto.  The most recent posting (from Daquan Gao) was:

> This is the only response I got. Thanks to Yvonne Martin! I believe
> now that QCPE is the first place to look for this info. 
>
> Daquan Gao
>
> ---------- Forwarded message ----------
> Date: Sun, 20 Feb 2000 11:32:03 -0600
> From: "Martin,Yvonne" <yvonne.c.martin@abbott.com>
> To: dgao@chem.iupui.edu
> Subject: Re: CCL:Surface and volume calculations
>
> Try the programs by Robert Pearlman. Savol2 I think is the most recent
> one.  You can get it from QCPE.

Our community owes a lot to Yvonne Martin, both for her own contributions
and for the frequency with which she replies to such inquiries by offering
pointers to a wide variety of useful software.

In this case, however, the pointer is out-dated.  Please do *NOT* use the
old version of our surface area and volume software from QCPE.  It has not
been updated (or fixed) in many years.  Instead, please send a request to
me (pearlman@vax.phr.utexas.edu) and I will reply with instructions for
down-loading a much newer, much nicer version called "Savol3".  

Savol3 provides extremely rapid, analytic calculation of both surface area
and volume for molecular surfaces and solvent-accessible surfaces.  In
addition to partitioning both the surface area and volume into rationally
defined atomic contributions, Savol3 also partitions the surface area and
volume into polar/non-polar contributions (based either on user-specified
charge thresholds or on the standard but crude hetero/non-hetero basis).

We currently provide Savol3 for use on SGI workstations (but could be
talked into providing it on other platforms if broad-based need exists).
We will soon offer a version which will operate on SMILES or 2D MDL SDfile
input.  Meanwhile, please note that Savol3 currently requires 3D molecular
structures as input.  These can be provided in PDB format or in Tripos' 
mol2 or mol1 format.  I/O can be specified using unix command-line options
or can be provided in response to prompts issued by the program.  
Alternatively, since we provide an object library and source code for an
example calling routine, the 3D structure and other I/O issues could be 
handled via an argument list (without concern for 3D file format).

Best wishes,

  -- Bob Pearlman



From chemistry-request@server.ccl.net  Mon Feb 21 21:25:00 2000
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Also try GEOPOL from QCPE.  It is used in several other programs, including
solvated geometry optimizations.

John McKelvey

Daquan Gao wrote:

> This is the only response I got. Thanks to Yvonne Martin! I believe now
> that QCPE is the first place to look for this info.
>
> Daquan Gao
>
> ---------- Forwarded message ----------
> Date: Sun, 20 Feb 2000 11:32:03 -0600
> From: "Martin,Yvonne" <yvonne.c.martin@abbott.com>
> To: dgao@chem.iupui.edu
> Subject: Re: CCL:Surface and volume calculations
>
> Try the programs by Robert Pearlman. Savol2 I think is the most recent one.
> You can get it from QCPE.
>
> Yvonne Martin
>
> dgao@chem.iupui.edu@INTERNET@ccl.net on 02/18/2000 04:10:34 PM
> Sent by: chemistry-request@ccl.net
> To: chemistry@ccl.net@INTERNET
> cc:
> Subject: CCL:Surface and volume calculations
>
> Dear CCLers,
>
> I would like pointers to fast algorithms(preferentially analytical) of
> computing the surface areas of molecules? Any idea is also
> appreciated.
>
> Yours Truly,
>
> Daquan Gao
>
> CHEMISTRY@ccl.net -- To Everybody    |   CHEMISTRY-REQUEST@ccl.net -- To
> Admins
>
> -= This is automatically added to each message by mailing script =-
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From chemistry-request@server.ccl.net  Mon Feb 21 19:51:55 2000
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To: "'chemistry@ccl.net'" <chemistry@ccl.net>
Cc: "'Guenter Grethe'" <Guenter@mdli.com>
Subject: REMINDER -- REMINDER ------   CALL FOR PAPERS-PACIFICHEM2000
Date: Mon, 21 Feb 2000 15:45:08 -0800

The co-organizers of the symposium 'Use of Chemical Information in Organic
Synthesis' at Pacifichem2000 in Honolulu are asking you again to consider
contributing a paper to this important symposium.  Several eminent
scientists working in this area of reasearch have already accepted an
invitation to present a talk. The original 'Call for Papers' follows below.
We are especially encouraging young scientist to apply for 'Travel Grants
for Young Chemistry Scholars'.  Please check
http://www.acs.org/meetings/pacific2000/tgrants.html for details.

The following Call for Papers has been listed on several servers, I
apologize for any duplication.

CALL FOR PAPERS

The 2000 International Chemical Congress of Pacific Basin Societies will
take place in Honolulu, Hawaii, from December 14 - 19, 2000.  The congress
is cosponsored by the American Chemical Society , the Chemical Society of
Japan, the Canadian Society for Chemistry, the New Zealand Institute of
Chemistry and the Royal Australian Chemical Institute.  Chemical Societies
in the countries that border the Pacific Ocean will be Official
Participating Organizations.  Overall, 6,000 reports on current research and
development will be presented in 179 symposia and in oral and poster general
sessions in 10 topical areas.  If previous congresses are any indication,
this year's program should be highly interesting and attendance should be
very large.

You are invited to submit an abstract for a paper or poster to be considered
for presentation at symposium #175 "Use of Chemical Information in Organic
Synthesis", co-organized  by Prof. Kimito Funatsu, Toyohashi University of
Technology, Japan, Dr. David Winkler, CSRIO Division of Molecular Science,
Australia, and Dr. Guenter Grethe, MDL Information Systems, Inc., USA.
Abstracts of approximately 150 words must be submitted to the Congress
Secretariat at ACS by April 3, 2000, for paper versions, or April 14
electronically.  The congress abstract form is available for electronic
retrieval and submission from the Pacifichem 2000 web site at

				 http://www.acs.org/meetings/pacific2000
      
Paper forms can be obtained by contacting the Congress Secretariat at

			Pacifichem Congress Secretariat 
			American Chemical Society
			1155-16th S., N.W.
			Washington, DC 20036, USA
			e-mail: pacifichem@acs.org

To encourage attendance at the congress by young chemistry professionals
>from developing countries that border the Pacific Ocean, the sponsoring
societies of Pacifichem 2000 are making available up to 40 grants of $1,000
(U.S.) plus complimentary registration to assist with travel and attendance
costs.  Details about the scholarship are to be found on the congress web
site. 

Why is participation in this symposium essential for synthetic chemists and
information specialists?
 
During the last two decades various programs and databases, large
comprehensive and smaller thematic ones, covering a broad range of synthetic
chemistry, have been developed to assist synthetic chemists with their
tasks.  Additionally, these databases have the potential to serve as a rich
source for extracting data into knowledge bases for reaction planning and
reaction prediction programs.  

Speakers at the symposium will address issues important to the various areas
of reaction information management, such as synthesis planning, reaction
retrieval and prediction, reagent selection, integrated web-based
information, information needs in combinatorial chemistry, database
generation and management, and other related topics.  Emphasis of the
symposium will be on the integration of various programs and data from
multiple sources to simulate the working habits of synthetic chemists in
gathering necessary information, thereby generating an environment in which
they will use electronic tools comfortably and efficiently - the synthetic
workbench of the future.  Papers describing the use of the various tools and
information sources available to synthetic chemists and information
specialists alike are solicited.  Presentations for contributed papers will
be restricted to 25 minutes, including 5 minutes for Q & A.

Following is a description of some of the topics we hope to cover in the
symposium: 

Reaction retrieval

	Retrieval of relevant information from existing databases to plan
the synthesis of discrete compounds or libraries and to search for
applicable methodologies and efficient functional group transformations is
the most frequently used and therefore the most important part of any
reaction information system.  Presentations on available systems and
associated applications to facilitate their use, the contents of available
reaction databases, efficient management of large datasets, such as
classification, post-search tools to manage large hitlists and other
retrieval related topics are invited. 
		
Reaction prediction

	Reaction prediction plays an important role in synthesis,
particularly in process development and combinatorial chemistry.
Presentations addressing the use of available programs and the generation of
knowledge bases from reaction databases to assist in the validation of
reaction proposals in the planning process will be part of the symposium.
Other topics for discussion are applications of methodologies to use
physico-chemical parameters in predicting the outcome of reactions and the
importance of functional group perception and their dependency on reaction
conditions as criteria for reagent selection and automated synthesis.

Synthesis planning

	Synthesis planning is experiencing rejuvenation, largely due to
developments in combinatorial chemistry. Emphasis of programs has shifted
>from planning syntheses of complex molecules to generating efficient and
economic preparations of libraries of compounds, frequently involving the
use of solid-phase methodology.  We invite speakers to discuss progress made
in this important area as well as talk about validation procedures used in
the planning process and methods to select viable starting materials. 

Combinatorial chemistry

	Combinatorial synthesis continues to have an immense impact on the
developments in managing chemical information.  Finding the most relevant
methodologies, planning a library, and selecting the most viable reagents
and solid supports are some of the important tasks to be carried out by the
synthetic chemist. Presentations on these topics as well as discussions
about the utilization of available information for automated synthesis and
effective data management are desirable. 

Electronic workbench

	The future and success of using electronic information in synthesis
is heavily dependent on the smooth integration of the required tools in an
electronic workbench through friendly graphical interfaces and smooth
operations. To guarantee good results, the workbench must provide easy
access to large amounts of data in diversified databases - online and
inhouse - and in electronic versions of the primary and secondary
literature.  The electronic labjournal must serve both as an archiving and
registration tool.  We are soliciting papers describing the use of any of
these tools, particularly web-based applications. 

If you have any questions please contact any of the organizers at the
addresses shown below:

Dr. Guenter Grethe
MDL Information Systems, Inc.
14600 Catalina Street
San Leandro, CA 94577
(+1) 510-357-2222, ext. 1430 (voice)
(+1) 510-614-3616 (fax)
guenter@mdli.com

Prof. Kimito Funatsu
Department of Knowledge-Based Information Engineering
Toyohashi University of Technology
Tempaku, Toyohashi 441-8580
Japan
(+81) 532-44-6879 (voice)
(+81) 532-47-9315 (fax)
funatsu@tutkie.tut.ac.jp



Dr. David A. Winkler
CSIRO Molecular Science
Private Bag, Clayton South MDC 3169
Australia
(+61) 3-9545-2477 (voice)
(+61) 3-9545-2446 (fax)
dave.winkler@mo9lsci.csiro.au




