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Date: Tue, 22 Mar 94 00:45:46 +0530
From: "Dr. Mrigank" <mrigank@imtech.ernet.in>
To: chemistry@ccl.net
Subject: bi-furcated [tricentered] h-bonds
X-Vms-Mail-To: CHEM,MRIGANK     


Hi
In some of our MD simulations of DNA we observ bifircated h-bons. some of
therese are seen in crystal or NMR also. Can some pls. help me in what DNA
molecule and what kind of such bonds are seen.

secondly i want to findout are they seen in proteins as well.

Do they have functional meaning

Mrigank

----
Dr. Mrigank                       \/Phone  +91 172 45004 x216
Institute of Microbial Technology /\Email:  mrigank@imtech.ernet.in
P O Box 1304, Sector 39A          \/UUCP:...!uunet!sangam!vikram!imtech!mrigank
Chandigarh 160 014 India.         /\Fax    +91 172 40985 
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-- When I feed the poor, they call me saint. When I ask why the poors do
   not have food, they call me communist - Archbishop Camaran

From cqsimpson@halnet.com  Tue Mar 22 09:43:45 1994
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Date: Tue, 22 Mar 1994 08:42:29 -0600
From: cqsimpson@halnet.com (Charlie Simpson)
Message-Id: <9403221442.AA23362@cre2.duncan.tech.halnet.com>
To: chemistry@ccl.net
Subject: Summary of replys to Fe Basis & Surface


Netters:

Thanks to all who responded to my inquiry.

Respectfully,
Charlie Simpson

**************************
>Original Inquiry
>
>Fellow Netters:
>
>I am interested in the interaction of organic molecules with Fe surfaces using
>a MM/MD approach.  This project requires that the Fe atom charges be as
>realistic as possible.  Currently, my approach is to calculate the
>electrostatic potential of my Fe surface and then fit charges to it.  Three
>questions come to my mind I would like your opinions on:
>
>1)  Can anyone recceommend a suitable Fe basis set for this sort of
>calculation?  My Fe surface could potentially have up 3000 atoms.  Soo,...the
>smallest basis set I could get away with would be great.
>
>2)  What level of theory, beyond HF, would be reasonable to go to considering
>the number of atoms I might be considering?
>
>3)  Finally, has anyone else looked at this type of problem before?  Are there
>Fe surfaces with fitted charges in the literature that any of you know of?
>
>Any comments or suggestions you may have are welcome.  I'll summarize the
>responses early next week.  Many thanks in advance!
>
>
> ************************
> 
> ...
> 1) Basis set:
>    You'll definitely need an ECP basis for the Fe cluster.  I'd recommend
> the model potentials of Huzinaga, rather than the pseudopotentials of Hay.
> Most surface science people I know use these (for good reason).  
> 
> 2) Level of theory:
>    If you are going to include ANY level of electron correlation, it will have
> to be through DFT: for your exchange potential, use the X-alpha approx. for
> starters, then, if possible use something like the 'non-local' exchange 
> correction due to Becke.
> 
> ***********************
> 
> Charlie - 
> 
> I've done some molecular modeling with iron oxide (goethite) using CHARMm 
> and of course, bumped up against the same problem you mention.  Note 
> todays posting about AMPAC 5, parameterized for iron.  Perhaps this would 
> help.  I also have some references on iron modeling, mostly in reference 
> to ions in water, but also for iron complexes.
> 
> Bader, J Phys Chem, v96, p6423 (1992)
> Schilling, JACS, v108, p582 (1986)
> Curtiss, J electrochem Soc, v138, p2032 (1991)
> Curtiss, J Chem Phys, v86, p2319 (1987)
> Halley, Ber Bunsenges Chem, v91, p491 (1987)
> Curtiss, Chem Phys, v133, p89 (1989)
> 
> Hope this helps.
> 
> Regards, 
> Bev
> 
> Beverly Bendiksen
> Research Associate
> Calgon Corporation 
> Pittsburgh, PA 
> (412)7778862 voice    (412)7778714 fax
> 
> ************************
> 
> Dear Netters,
> 
>   Semichem is pleased to announce AMPAC 5.0 with Graphical  User Interface
> to be released May 2, 1994.  AMPAC 5.0 features MJS Dewar's new SAM1 semi-
> empirical method and now includes parameters for iron (Fe).   Our  program
> offers state-of-the-art semiempirical methodology in an easily  accessible
> format, supported by Semichem's expert customer service.   We will  demon-
> strate the  new  version of AMPAC at the American Chemical Society Meeting
> in San Diego next week in Booth 1008.  AMPAC runs on virtually every plat-
> form and our Graphical  User Interface  uses the  popular  X-Windows/Motif
> protocol for compatibility and seamless network access.
> 
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>                            DR. ANDREW HOLDER
>                           President, Semichem
> 
> Semichem, Inc.                 ||  Internet Addr: aholder@vax1.umkc.edu
> 7128 Summitt                   ||  Phone Number:  (913) 268-3271
> Shawnee, KS 66216              ||  FAX Number:    (913) 268-3445
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> 
> *************************
> 
> Charlie, 
> 
> The problem you describe is of great interest to anyone involved in
> modeling surface/interface phenomena, and a lot of time has been and
> is being spent on trying to answer your questions for a variety of
> surfaces.  People working on modeling heterogeneous catalyst
> surfaces are particularly active in this area, and maybe that is
> your area of interest also.
> 
> 	I have personally been involved in modeling metal oxide
> surfaces for a few years and have collected a bunch of references on
> the subject of assigning surface charges.  There is no "right"
> answer, obviously, since the distribution of charge or electron
> density is a continuum phenomenon, so by definition the assignment
> of point charge values to atomic sites on your surface is an
> approximation.  It seems to me therefore, that perhaps the most
> important consideration in assigning charges to model surfaces is
> consistency, especially when surfaces of different composition are
> being compared.  This can lead to problems since there are no
> treatments that I'm aware of that have been comprehensively applied
> and validated for a large enough range of elements and compounds to
> be taken as a "universal" approach.
> 
> 	An alternative to high level theoretical calculations to
> determine charge distribution is experiment, specifically X-ray
> structure determination, the results of which are directly related
> to electron distribution.  One might argue that this approach is the
> most "correct" of all.  The limitation of the absolute correctness
> of this method is that the effective atomic radii used to determine
> the electron population "resident" on a given center are more or
> less arbitrarily chosen introducing a certain amount of subjectivity
> to the ultimate values generated.  You might also consider using the
> results of electronic spectroscopy in determining local electronic
> configurations.
> 
> 	Finally, if you are only considering pure iron surfaces and
> you have a database of experimental results to correlate with your
> calculations, you could take the empirical approach and assign
> arbitrary charges and scale them until the results of your
> simulations are in agreement with the experiments.  
> 
> 	At any rate, here are some references that may be of
> interest to you.
> 
> Structure and Bonding in Crystals, Vols. I and II, O'Keeffe and
> Navrotsky, eds., Academic Press 1981
> 
> Electronic structure of surfaces and of adsorbed species, J.B.
> Pendry, Phil Trans R. Soc. London A(1992) 341,  p 293-300.
> 
> The quantum chemical basis of the catalytic reactivity of transition
> metals, R.A. van Santen et al., ibid (previous ref.) p 269
> 
> There are a bunch of other papers related to the subject in this
> vol. of Phil Trans.
> 
> D.M. Sherman, Phys. Chem. Min. 12,  (3), p 161, (1985)
> (deals with the electronic structure of hematite)
> 
> 
> 
> Let me know if you find something that works really well.
> 
> Michael Sennett
> US Army Research Laboratory
> msennet@watertown-emh1.army.mil
> 
> 
> 
> 

================================================================================
	Charlie Simpson Ph.D.			cqsimpson@halnet.com
	Halliburton Energy Services
	P.O. Box 1431				Phone 405/251-4564
	Duncan, OK 73536-0438			Fax   405/251-3218


    We have staked the whole future of the American civilization, not upon
    the power of government, far from it.  We have staked the future...upon the
    capacity of each and all of us to govern ourselves, to control ourselves,
    to sustain ourselves, according to the Ten Commandments of God.
                                   James Madison

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

From h.rzepa@ic.ac.uk  Tue Mar 22 12:43:47 1994
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From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa)
Subject: TIF Group 4 Fax compression


Some time ago, when ACS introduced this unusual compression format,
there was discussion of good programs to read the format. I can now
add another, the Macintosh
GraphicConverter by Thorsten Lemke, V 1.7.8. Highly
recommended for a huge variety of graphical file types, including the
rarely supported SGI rgb format.


Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY;
rzepa@ic.ac.uk via Eudora 2.02, Tel:+44  71 225 8339, Fax:+44 71 589 3869.
From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804
http://www.ch.ic.ac.uk/rzepa.html




From abby@mercury.aichem.arizona.edu  Tue Mar 22 12:46:25 1994
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From: Abby Parrill <abby@mercury.aichem.arizona.edu>
Subject: computational chemistry experiments
To: chemistry@ccl.net
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It seems that my reply to the request for a computational chemistry
book has elicited some interest.  For those of you who are interested,
it is put out by Wavefunction, Inc.  Their phone number is (714) 955-2120
and their FAX number is (714) 955-2118.  Their is no edition number
listed in the book (copyright 1993).  It was written to be compatible
with the abilities of SPARTAN, though the experiments described within it
are certainly not limited to that software.


__________________________________________________________
                                              
                      Abby Parrill
                  Chemistry Department
      Artificial Intelligence in Chemistry Laboratory                         
                The University of Arizona                    
             abby@mercury.aichem.arizona.edu              
                                           
__________________________________________________________


From wolpert@neon.chem.utk.edu  Tue Mar 22 13:43:52 1994
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From: wolpert@neon.chem.utk.edu (Edward Wolpert)
Message-Id: <9403221746.AA18201@neon.chem.utk.edu>
To: CHEMISTRY@ccl.net
Subject: Tek help with chiron needed...


Netters-
	We've got chiron on a vax cluster going here, and want users to be 
able to log into the vax from a unix system. (esv mips box)  However, the
chiron needs a 41xxtek terminal/emulator to work right.  Our xterm for the
unix box can only handle 4014.  I was wondering if anyone knew of public
domain emulator packages (under X11R4/X11R5) that could work, or other
ideas.  Thanks.
		Virtually,
		Edward Wolpert

---------------------------
wolpert@utk.edu            | System Administrator
wolpert@osti.slip.utk.edu  | Systems Programmer
pa153568@utkvm1.utk.edu	   | Graduate Chemistry Student
---------------------------

From CHE9985@ubvms.cc.buffalo.edu  Tue Mar 22 15:43:47 1994
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 22 Mar 1994 15:09:55 EST
Date: Tue, 22 Mar 1994 15:09:55 -0500 (EST)
Subject: CCL:Does Anyone Have Atomic Wave Functions Data File(s)?
To: chemistry@ccl.net
Message-id: <01HA9ZE9DX7M8Y8L4T@ubvms.cc.buffalo.edu>
Organization: University at Buffalo
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Dear Netter:
	I am looking for Relativistic or Non-relativistic atomic wave functions
that has been input to a data file.   For example, McLean & McLean's
Roothaan-Hartree-Fock Atomic Wave Functions for Z=55-92 are fine.  I understand
it is in printed form  (Atomic Data and Nucl. Data Table 26, 197-381(1981))
but I would appreciate very much if you can save me a lot of time and help
avoid typing errors by giving me the electronic form of it.   Functions 
with Gaussian basis sets are welcome, too.
	Thanks in advance.
Z. Su
Dept. of Chem., SUNY at Buffalo

From KEWISE@aardvark.ucs.uoknor.edu  Tue Mar 22 16:43:45 1994
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From: <KEWISE@aardvark.ucs.uoknor.edu>
Message-Id: <199403222049.PAA24353@www.ccl.net>
Date: Tue, 22 Mar 94 14:50 CST
Subject: Fe parameterization in AMPAC5
To: CHEMISTRY@ccl.net
X-VMS-To: IN%"CHEMISTRY@ccl.net"


     I saw the announcement of AMPAC5 and saw that it is parameterized
for iron.  We are doing calculations on metalloporphyrins in our group
using several different methods, but have been unable to do calculations
on Fe-porphyrin using semi-empirical methods (MNDO) due to the lack of 
Fe parameterization.  Does anyone know if AMPAC5 will be useful for this
sort of application?  We will probably be using LDF methods for final
optimizations and frequency calculations but a speedier method would be
useful for quick jobs.  Any responses on this topic would be appreciated.

Kris Wise   KEWISE@aardvark.ucs.uoknor.edu

From epw@ppco.com  Tue Mar 22 16:48:38 1994
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Date: Tue, 22 Mar 1994 15:37:19 +0000
To: chemistry@ccl.net
From: epw@ppco.com (Dr. Eric P. Wallis)
Subject: Free-Energy Calculations
X-Mailer: <PC Eudora Version 1.4>


Dear Netters,
I am looking for a code which I can use to calculate the free-energy of 
solvation at infinite dilution.  I need it to be flexible enough that I 
could incorporate my potentials into it.  Any help would be appreciated.

Thanks,
Eric
***************************************************************
* Dr. Eric P. Wallis                                          *
* Computational Chemistry                                     *
* Phillips Petroleum Company       Office  (918)-661-7956     *
* 331A PL PRC                      FAX:    (918) 662-1097     *
* Bartlesville, OK 74004           email:   epw@ppco.com      *
***************************************************************


From MARTIN@cmda.abbott.com  Tue Mar 22 18:43:51 1994
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From: MARTIN%CMDA <MARTIN@cmda.abbott.com>
Subject: Molecular Graphics Society Chicago Meeting Abstract Deadline Extended
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=======================================================
                    ANNOUNCEMENT

       "MOLECULAR GRAPHICS AT THE FRONTIER"
13TH ANNUAL CONFERENCE OF THE MOLECULAR GRAPHICS SOCIETY
     NORTHWESTERN UNIVERSITY, EVANSTON IL JULY 9-13
         
      REVISED ABSTRACT DEADLINE - APRIL 15TH, 1994

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

Due to mailing delays many members did not receive the 
meeting registration packet and information on abstract
submission until after the March 15th deadline had passed.

The deadline has been extended to April 15th, 1994.

Abstracts can be mailed to:

		Dr. Arthur Olson
		Molecular Biology, MB5 (room MB112)
		The Scripps Research Institute
		10666 N. Torrey Pines Road
		La Jolla, CA 92037
 
		*FAX (619) 554 6860

		e-mail to: olson@scripps.edu

If you need a copy of the registration packet, or
instructions on submitting an abstract, contact:

Peggy Graber (619) 554-2526; e-mail graber@scripps.edu
 

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

From elewars@alchemy.chem.utoronto.ca  Tue Mar 22 18:48:46 1994
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Date: Tue, 22 Mar 1994 18:00:48 -0500
From: "E. Lewars" <elewars@alchemy.chem.utoronto.ca>
Message-Id: <199403222300.SAA07003@alchemy.chem.utoronto.ca>
To: chemistry@ccl.net
Subject: Books for teaching computational chem


"Experiments in Computational Orgenic Chemistry", by Hehre, Burke, Shusterman
and Pietro, which has recently been recommended on the net, is an excellent
book for showing the capabilities of computational chem in hands-on work.
It works most naturally with Wavefunction's SPARTAN program, but should be
adaptable to, e.g. Gaussian with some success.
"Exploring Chemistry With Electronic Structure Methods" by Foresman and 
A. Frisch of Gaussian Inc is a very instructive book for those getting into
comp chem.  Unlike the Wavefunction book, it is devoted essentially entirely
to ab initio calculations ("Experiments.." deals with mechanics, semiemp and 
ab initio), and input is limited to the Z-matrix (with a nod at cartesians),
while results must be interpreted by poring over the printed output, unless
you are lucky enough to have a program that will create Gaussian input from
mousedrawn structures, and bring wavefunctions to life, animate normal modes,
etc etc.  But "Exploring...." has plenty of valuanble information, and is well
worth reading [students read studying].
As for software, the only integrated MM, semiempirical, ab initio cum 
supergraphics comp chem program I know of is SPARTAN.
=====

From jle@world.std.com  Tue Mar 22 19:43:47 1994
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From: jle@world.std.com (Joe M Leonard)
Message-Id: <199403222358.AA04953@world.std.com>
To: chemistry@ccl.net
Subject: Moment of inertia from G92


Stupid question here...

How can one get the moment of inertia (or, moments of intertia?) from
G92.  I've found the rotational constants, but can't see anything obvious
for anything else...  

Thanks in advance,

Joe Leonard
jle@world.std.com

From sling@euclid.chem.washington.edu  Tue Mar 22 20:43:51 1994
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From: sling@euclid.chem.washington.edu (Song Ling)
Message-Id: <9403230124.AA30473@euclid.chem.washington.edu>
To: CHEMISTRY@ccl.net
Subject: NuBus


Stupid question about Apple MacIntosh:
What is NuBus?  Is it going to be outdated?
Thanks!
		Song Ling

From TANG@Kitten.Chem.uh.edu  Tue Mar 22 21:43:50 1994
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Date: Tue, 22 Mar 1994 20:26:01 -0600 (CST)
From: "Tang, Huang (UH-Chem)" <TANG@Kitten.Chem.uh.edu>
To: chemistry@ccl.net
Message-Id: <940322202601.23a0295e@Kitten.Chem.uh.edu>
Subject: info for GAMESS-UK needed


Dear Netters:

I remember not long ago someone posted a summary about GAMESS-UK package.
Could anyone please tell me again how to contact the person(s) in charge
of releasing this package?  Is GAMESS-UK version capable of doing MP2
optimization and frequency (via conventional, direct, or semidirect etc
methods)?  Thanks in advance.

--------                
   _         Huang TANG
 _| ~-       Chem. Dept, U. of Houston
 \,  _}      Houston, Texas 77204-5641
   \(        e-mail:  tang@kitten.chem.uh.edu
             phone:   (713) 743-3269  

From jkl@ccl.net  Tue Mar 22 22:43:49 1994
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From: Jan Labanowski <jkl@ccl.net>
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Date: Tue, 22 Mar 1994 22:07:34 -0500
Message-Id: <199403230307.WAA23266@hawkeye.ccl.net>
To: chemistry@ccl.net
Subject: Your coordinator's grievances
In-Reply-To: Mail from '"Tang, Huang (UH-Chem)" <TANG@Kitten.Chem.uh.edu>'
      dated: Tue, 22 Mar 1994 20:26:01 -0600 (CST)
Cc: jkl@ccl.net


Dear Netters, it is your "coordinator" speaking...

I see lately some messages which may appear to be useless to most of the
2000+ subscribers on the list. I see also many very useful ones...
I am not posting this to damp the discussions. I am just asking for more
interesting discussions. I may be wrong ("the beauty is in the eye of
the beholder", and you can always think that this message does not
concern you personally...).  Please review the help file for the list
(it can be obtained by sending:
     help chemistry
to MAILSERV@ccl.net)
and try to understand that if you are the only person who may be interested
in the answer to your question, your question was not worth asking (unless
you are better than all of us humans...).
Also remember that this list is on Computational Chemistry.
There are many newsgroups and lists for specific topics outside Comp.Chem.
I provided fairly recent overview of electronic lists in
the ./info/electronic-lists subdirectory of the CCL ftp/gopher on
www.ccl.net.

Also, before you ask your question, try to review the past discussions
on the topic. The archives of the list can be thoroughly searched for
keywords and topics. Please send a message:
   help search
to MAILSERV@ccl.net to find out more about searching the list.
Learning the regular expressions and logic never hurts...
Some questions have been asked before and answered. Do not start from scratch,
since you have better ways to get where eagles dare...

Sorry if my pH and LUMO was low today, but I am trying to do my job...

Jan Labanowski
Ohio Supercomputer Center
jkl@ccl.net





