From owner-chemistry@ccl.net Sun Jun 19 00:51:00 2011 From: "Neeraj Naithani neerajnaithani/./gmail.com" To: CCL Subject: CCL: Editing of forcefield in Material Studio Message-Id: <-44927-110619005018-23724-jmeW+r7UxV3mQ+3l9g1ExQ_-_server.ccl.net> X-Original-From: "Neeraj Naithani" Date: Sun, 19 Jun 2011 00:50:16 -0400 Sent to CCL by: "Neeraj Naithani" [neerajnaithani---gmail.com] Dear Members, i want to model perchlorate and azide ions but the parameters are not available in forcefield in Material Studio (Discover). I want to modify the forcefield, but no idea how to do that. Please help me in this. Thank You Neeraj Naithani, Ph.D. From owner-chemistry@ccl.net Sun Jun 19 10:15:00 2011 From: "Mehdi Esrafili m_esrafili]~[yahoo.com" To: CCL Subject: CCL: Non-covalent vs Covalent bond Message-Id: <-44928-110619101218-1423-7+eGSb5nZGMLSTxgrPCiXA[#]server.ccl.net> X-Original-From: Mehdi Esrafili Content-Type: multipart/alternative; boundary="0-2080867817-1308492729=:56006" Date: Sun, 19 Jun 2011 07:12:09 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Mehdi Esrafili [m_esrafili : yahoo.com] --0-2080867817-1308492729=:56006 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi;=0AYou may use energy decomposition analysis (EDA) scheme. This approach= is =0Aimplemented in GAMESS package.=0A=A0=0Asincerely=0A=A0=0AMehdi=A0=0A= =A0=0A---------------------------------------------------------------------= ---------------------------------------------------------=A0=A0=0A=0A`The m= an who makes no mistakes does not usually make anything.'=0A=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 Edward John Phelps (1822-1900)=0A--------------------------------= ---------------------------------------------------------------------------= -------------------=0A =0AMehdi D. Esrafili=0AAssistant Professor of Physic= al Chemistry=A0=0ACurrent address:=A0Department of Chemistry, =0AFaculty of= Basic Sciences,University of=0AMargheh, Iran. =0AE-mail 1:m_esrafili(a)yahoo= .com=0AE-mail 2: esrafili(a)maragheh.ac.ir=0A--------------------------------= ---------------------------------------------------------------------------= -------------------=0A =0A=0A=0A=0A=0A________________________________=0AFr= om: Ron Cook cookrl:tda.com =0ATo: "Esrafili, Mehd= i D " =0ASent: Thu, June 16, 2011 8:24:15 PM= =0ASubject: CCL: Non-covalent vs Covalent bond=0A=0A=0ASent to CCL by: "Ron= Cook" [cookrl^^^tda.com]=0AHi=0A=0AUsing the information provided by Atoms= in Molecules software (e.g. AIMALL=0Aor AIMPAC) specifically information p= rovided on the bond critical points=0Awill answer your questions=0A=0ARonal= d Cook=0APrincipal Scientist=0ATDA Research, Inc.=0A=0A-----Original Messag= e-----=0A> From: owner-chemistry+cookrl=3D=3Dtda.com.:.ccl.net=0A[mailto:ow= ner-chemistry+cookrl=3D=3Dtda.com.:.ccl.net] On Behalf Of Eliac Brown=0AEli= acbrown-x-yahoo.com=0ASent: Thursday, June 16, 2011 7:28 AM=0ATo: Cook, Ron= ald L =0ASubject: CCL: Non-covalent vs Covalent bond=0A=0A=0ASent to CCL by= : "Eliac=A0 Brown" [Eliacbrown-,-yahoo.com]=0ADear All=0AFirst of all, than= ks for your help over my last post (especial thanks to=0ANicho =0ADemus and= Serghei Glinca)=0AI have a fundamental question here, I have searched for = its answer but=A0 =0Acouldn't find one.=0A* Is there a relation/equation ca= n be used to distinguish a bond as a non-=0Acovalent bond or Covalent bond?= =0Athe problem is that I used a software to get contact between two atoms i= n =0Acrystal structures (inter-molecular contact), but I found some of the= =0Aresults =0Ahave distance very short compared to the vdw radii. I think i= t is a=0Atechnical =0Aerror, so I need to clean the data. what can I do?=0A= In addition, what is the scientific difference between Contact, bond, and = =0Ainteraction? A lot of papers using contact in the position of bond, is t= hat =0Aright scientifically?=0AThanks in advance and forgive me if my quest= ions were not at the same level=0Aof =0Athe mailing list.=0AEliachttp://www= .ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub= .shtmlhttp://www.ccl.net/spammers.txt=0A=0A=0A=0A-=3D This is automatically= added to each message by the mailing script =3D-=0ATo recover the email ad= dress of the author of the message, please change=0Athe strange characters = on the top line to the (a) sign. You can also=0Alook up the X-Original-From: = line in the mail header.=0A=0AE-mail to subscribers: CHEMISTRY(a)ccl.netor us= e:=0A=A0 =A0 =A0=0A=0AE-mai= l to administrators: CHEMISTRY-REQUEST(a)ccl.netor use=0A=A0 =A0 =A0 http://w= ww.ccl.net/cgi-bin/ccl/send_ccl_message=0A=0A=0A=A0 = =A0 =A0=0A=0ABefore posting, c= heck wait time at: http://www.ccl.net=0A=0A=0A==0A= =0A=0A= =0A=0A=A0 =A0 =A0 htt= p://www.ccl.net/spammers.txt=0A=0ARTFI: http://www.ccl.net/chemistry/aboutc= cl/instructions/ --0-2080867817-1308492729=:56006 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A

Hi;

=0A

You may use energy decomposition analysis (EDA) scheme. This approach= is implemented in GAMESS package.

=0A

 

=0A

sincerely

=0A=

 

= =0A
Mehdi <= /FONT>
=0A
=  
=0A
--------------------------------------------------------------------= ----------------------------------------------------------  
=0A
`The= man who makes no mistakes does not usually make anything.'
=0A=
  &nb= sp;            =             &nb= sp;      Edward John Phelps (1822-1900)=0A
----------= ---------------------------------------------------------------------------= -----------------------------------------
Mehdi D. Esrafili
=0A
Assistant P= rofessor of Physical Chemistry 
Current address:&n= bsp;Department of Chemistry,
=0A
Faculty of Basic Sciences,University of
=0A
Margh= eh, Iran.
=0A
E-mail 1: m_e= srafili(a)yahoo.com
E-mail 2:
= = esra= fili(a)maragheh.ac.ir
=0A
---------------------------------------------------= ---------------------------------------------------------------------------=
=0A

=0A
=0A
=0AFrom: Ron Cook cookrl:tda.com <owner-chemistry(a)ccl.ne= t>
To: "Esrafili, Meh= di D " <m_esrafili(a)yahoo.com>
Sent: Thu, June 16, 2011 8:24:15 PM
Subject: CCL: Non-covalent vs Covalent bo= nd


Sent to CCL by: "Ron Cook" [cookrl^^^tda.com]
Hi

Us= ing the information provided by Atoms in Molecules software (e.g. AIMALLor AIMPAC) specifically information provided on the bond critical pointswill answer your questions

Ronald Cook
Principal Scientist
T= DA Research, Inc.

-----Original Message-----
> From: owner-che= mistry+cookrl=3D=3Dtda.com.:.
ccl.ne= t
[mailto:owner-chemistry+cookrl=3D=3Dtda.com.:.ccl.net] On = Behalf Of Eliac Brown
Eliacbrown-x-yahoo.com
Sent: Thursday, June 16, 2011 7:28 AM
To:= Cook, Ronald L
Subject: CCL: Non-covalent vs Covalent bond


= Sent to CCL by: "Eliac  Brown" [Eliacbrown-,-yahoo.com]
Dear AllFirst of all, thanks for your help over my last post (especial thanks toNicho
Demus and Serghei Glinca)
I have a fundamental question here= , I have searched for its answer but 
couldn't find one.
* Is t= here a relation/equation can be used to distinguish a bond as a non-
cov= alent bond or Covalent bond?
the problem is that I used a software to ge= t contact between two atoms in
crystal structures (inter-molecular cont= act), but I found some of the
results
have distance very short compared to the = vdw radii. I think it is a
technical
error, so I need to clean the d= ata. what can I do?
In addition, what is the scientific difference betwe= en Contact, bond, and
interaction? A lot of papers using contact in the= position of bond, is that
right scientifically?
Thanks in advance a= nd forgive me if my questions were not at the same level
of
the mail= ing list.
Eliachttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www= .ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

-=3D This is automatically added to each message by the mailing script = =3D-
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