From owner-chemistry@ccl.net Fri Mar 18 03:58:00 2011
From: "Hans De Winter hans.dewinter(_)silicos.com" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: Converting sybyl line notation to smiles or sdf
Message-Id: <-44155-110318035250-32756-AwP2KVe/uAAM4OonLZGooA(_)server.ccl.net>
X-Original-From: Hans De Winter <hans.dewinter-*-silicos.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Date: Fri, 18 Mar 2011 08:52:34 +0100
Mime-Version: 1.0 (Apple Message framework v936)


Sent to CCL by: Hans De Winter [hans.dewinter[#]silicos.com]
Dear,

I have a library of ~60,000 structures defined in SLN (sybyl line  
notation) and I need to convert these in smiles or sdf format. I don't  
believe that Open Babel can help me on that (unless I missed it), so  
are there any other tools (preferably on Mac OS X) that can do this?

Thx in advance.

Hans De Winter
Silicos NV


From owner-chemistry@ccl.net Fri Mar 18 07:52:00 2011
From: "Kacper Druzbicki kacper.druzbicki * uj.edu.pl" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: IR intensities from VASP
Message-Id: <-44156-110318053802-31024-Q/A/JbvyybFHtaAGmt45jg*server.ccl.net>
X-Original-From: "Kacper  Druzbicki" <kacper.druzbicki%x%uj.edu.pl>
Date: Fri, 18 Mar 2011 05:36:49 -0400


Sent to CCL by: "Kacper  Druzbicki" [kacper.druzbicki%uj.edu.pl]
Hello,

It is not directly possible to get the vibrational intensities for crystals, and as I know there is no way to compute the Raman activities at the moment (but please correct me, if I am wrong)

There is a freely available python module, called ASE, which gets infrared intensities for VASP and SIESTA programs:

https://wiki.fysik.dtu.dk/ase/ase/infrared.html

I have not used it yet, but as I remember, the method arises from the Born charges (as in Crystal program), which has the advantage that is somehow theoretically adjustable. 

In contrast, i.e. when using DMOL3, there is only a script written by Mr. George Fidgerald from Accelrys, which base on the so called differential dipole method.

https://community.accelrys.com/message/8221#8221

The method was proposed by Damian G. Allis et.al. from the Syracuse University, and base on Mulliken or Hirschfield charges. Thus, it is as reliable as the population analyses are. Moreover it is only an approximation. I suppose that it will fail for inorganic ionic compounds, but it may be found that the method works extremely well for molecular organic crystals. 

See for example Damians brilliant THz papers:

http://www.somewhereville.com/?category_name=dmol3

Greetings!
Casper

Kacper Drubicki,                  
Faculty of Chemistry,
Department of Chemical Physics, 
Jagiellonian University, 
Ingardena Street 3, 30-060 Krakw, Poland
phone: +48 12 6632265

> "Alfred Gil Arranz agil ~ cesca.cat"  wrote:
> 
> Sent to CCL by: Alfred Gil Arranz [agil|a|cesca.cat]
> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
> <html>
>   <head>
>     <meta content="text/html; charset=ISO-8859-15"
>       http-equiv="Content-Type">
>   </head>
>   <body text="#000000" bgcolor="#ffffff">
>     Dear Ralf,<br>
>     <br>
>     Sorry for the delay in the answer. I must check where the code would
>     be right now (so many years have passed...). Hope this week I can
>     have a look at my older files.<br>
>     <br>
>     But answering your mail, yes, essentially the IR intensities are
>     calculated taking into account two topics:<br>
>     <br>
>     - Intensities are directly related to the square of the derivative
>     of dipole moment with respect to the normal mode.<br>
>     - The surface selection rule: only normal modes of adsorbed species
>     giving rise to a dynamic dipole moment perpendicular to the surface
>     are seen in IR spectra. Therefore, I only payed attention to the
>     changes of dipole moment in the z direction.<br>
>     <br>
>     Best regards,<br>
>     <br>
>     Alfred.<br>
>     <br>
>     <br>
>     Al 14/03/11 11:22, En/na Ralf Tonner ha escrit:
>     <blockquote cite="mid:4D7DEC4D.6020206{:}chemie.uni-marburg.de"
>       type="cite">Dear Alfred,
>       <br>
>       <br>
>       thank you very much for your answer.
>       <br>
>       I would indeed be interested in IR intensities of adsorbed
>       molecules in a later stage of my research.
>       <br>
>       Do I understand correctly, that your program uses the dipolmoment
>       changes in one direction for the intensity calculations?
>       <br>
>       <br>
>       If it is not too much hassle for you, I would be interested in
>       obtaining the code and give it a go. I have access to VASP4, so I
>       could start with these calculations first to test the program.
>       <br>
>       I might need Google translate from time to time, but that should
>       be possible :)
>       <br>
>       <br>
>       Kind regards,
>       <br>
>       Ralf.
>       <br>
>       <br>
>       Am 11.03.2011 09:03, schrieb Alfred Gil Arranz agil^^^cesca.cat:
>       <br>
>       <blockquote type="cite">Sent to CCL by: Alfred Gil Arranz
>         [agil!A!cesca.cat] Dear Ralf,
>         <br>
>         <br>
>         Some years ago, I did a graphical tool to analyze the output of
>         vasp, which
>         <br>
>         included infrared intensities. The point is that there are two
>         important
>         <br>
>         limitations. First, it only works for 4.5 version, so a revision
>         of the code is
>         <br>
>         needed. And second, I was only interested in adsorption of
>         molecules on
>         <br>
>         surfaces, in the adsorbate vibrational modes perpendicular to
>         surface to be
>         <br>
>         precise. Therefore, several approximations were applied to
>         obtain the relative
>         <br>
>         intensities of the modes. You can see how it looks at chapter 10
>         of my doctoral
>         <br>
>         thesis (in Spanish, sorry :-( )
>         (<a class="moz-txt-link-freetext" href="http://www.tesisenxarxa.net/index.html">http://www.tesisenxarxa.net/index.html</a> and
>         <br>
>         search by Author).
>         <br>
>         <br>
>         To be honest, I need to recover the code to remember the
>         algorithm that
>         <br>
>         calculates the intensities. So, if that limitations are ok to
>         you, please let me
>         <br>
>         know and I'll try to find out the information.
>         <br>
>         <br>
>         Best regards,
>         <br>
>         <br>
>         Alfred Gil
>         <br>
>         <br>
>         Al 10/03/11 16:15, En/na Ralf Tonner ralf.tonner%googlemail.com
>         ha escrit:
>         <br>
>         <blockquote type="cite">
>           <br>
>           Sent to CCL by: Ralf Tonner [ralf.tonner(!)googlemail.com]
>           <br>
>           Dear CCL-members,
>           <br>
>           <br>
>           in moving from molecular quantum chemistry to surface and
>           solid state problems
>           <br>
>           I am investigating vibrational properties of molecular
>           crystals with VASP.
>           <br>
>           Now I would like to extract the infrared intensities of the
>           respective modes
>           <br>
>           but this is unfortunately not given directly.
>           <br>
>           <br>
>           Is anyone out there with experience in extracting IR
>           intensities from VASP
>           <br>
>           calculations ?
>           <br>
>           <br>
>           Thank you in advance,
>           <br>
>           Ralf.
>           <br>
>           <br>
>           <br>
>         </blockquoteTo
>         <br>
>         recover the email address of the author of the message, please
>         change the
>         <br>
>         strange characters on the top line to the {:} sign. You can also
>         look up the
>         <br>
>         X-Original-From: line in the mail header. E-mail to subscribers:
>         <br>
>         <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY{:}ccl.net">CHEMISTRY{:}ccl.net</a> or use:
>         <a class="moz-txt-link-freetext" href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a> E-mail
>         <br>
>         to administrators: <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY-REQUEST{:}ccl.net">CHEMISTRY-REQUEST{:}ccl.net</a> or use
>         <br>
>         <a class="moz-txt-link-freetext" href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a<br>
>         <a class="moz-txt-link-freetext" href="http://www.ccl.net/chemistry/sub_unsub.shtml">http://www.ccl.net/chemistry/sub_unsub.shtml</a> Before posting,
>         check wait time at:
>         <br>
>         <a class="moz-txt-link-freetext" href="http://www.ccl.net">http://www.ccl.net</a> Job: <a class="moz-txt-link-freetext" href="http://www.ccl.net/jobs">http://www.ccl.net/jobs</a> Conferences:
>         <br>
>         <a class="moz-txt-link-freetext" href="http://server.ccl.net/chemistry/announcements/conferences/">http://server.ccl.net/chemistry/announcements/conferences/</a>
>         Search Messages:
>         <br>
>         <a class="moz-txt-link-freetext" href="http://www.ccl.net/chemistry/searchccl/index.shtml">http://www.ccl.net/chemistry/searchccl/index.shtml</a> If your mail
>         bounces from CCL
>         <br>
>         with 5.7.1 error, check: <a class="moz-txt-link-freetext" href="http://www.ccl.net/spammers.txt">http://www.ccl.net/spammers.txt</a> RTFI:
>         <br>
>         <a class="moz-txt-link-freetext" href="http://www.ccl.net/chemistry/aboutccl/instructions/">http://www.ccl.net/chemistry/aboutccl/instructions/</a>
>         <br>
>       </blockquote>
>       <br>
>       <br>
>     </blockquote>
>     <br>
>     <br>
>     <pre class="moz-signature" cols="72">-- 
> ......................................................................
>        __
>       / /           Alfred Gil i Arranz
> C E / S / C A       Tcnic d'Aplicacions
>     /_/             Centre de Supercomputaci de Catalunya
> 
> Gran Capit, 2-4 (Edifici Nexus)  08034 Barcelona
> T. 93 205 6464 (ext 201)  F. 93 205 6979  <a class="moz-txt-link-abbreviated" href="mailto:agil{:}cesca.cat">agil{:}cesca.cat</a>
> ...................................................................... 
> </pre>
>   </body>
> </html>
> 
>


From owner-chemistry@ccl.net Fri Mar 18 08:30:00 2011
From: "Wolf Ihlenfeldt wdi ~ xemistry.com" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: Converting sybyl line notation to smiles or sdf
Message-Id: <-44157-110318080006-9024-pMUmdF+K05594+/FXDvQWw(!)server.ccl.net>
X-Original-From: Wolf Ihlenfeldt <wdi:-:xemistry.com>
Content-Type: multipart/alternative; boundary=000e0cd47b4247a8d3049ec084fb
Date: Fri, 18 Mar 2011 12:59:57 +0100
MIME-Version: 1.0


Sent to CCL by: Wolf Ihlenfeldt [wdi(0)xemistry.com]
--000e0cd47b4247a8d3049ec084fb
Content-Type: text/plain; charset=UTF-8

The Cactvs toolkit (www.xemistry.com) can perform both conversions, in both
directions.


On Fri, Mar 18, 2011 at 8:52 AM, Hans De Winter hans.dewinter(_)silicos.com
<owner-chemistry-,-ccl.net> wrote:

>
> Sent to CCL by: Hans De Winter [hans.dewinter[#]silicos.com]
> Dear,
>
> I have a library of ~60,000 structures defined in SLN (sybyl line notation)
> and I need to convert these in smiles or sdf format. I don't believe that
> Open Babel can help me on that (unless I missed it), so are there any other
> tools (preferably on Mac OS X) that can do this?
>
> Thx in advance.
>
> Hans De Winter
> Silicos NVhttp://www.ccl.net/chemistry/sub_unsub.shtml>
> Job: http://www.ccl.net/jobsConferences:
> http://server.ccl.net/chemistry/announcements/conferences/>
>
>


-- 
Wolf-D. Ihlenfeldt, Xemistry GmbH
www.xemistry.com

--000e0cd47b4247a8d3049ec084fb
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<br>The Cactvs toolkit (<a href=3D"http://www.xemistry.com">www.xemistry.co=
m</a>) can perform both conversions, in both directions.<br><br><br><div cl=
ass=3D"gmail_quote">On Fri, Mar 18, 2011 at 8:52 AM, Hans De Winter hans.de=
winter(_)<a href=3D"http://silicos.com">silicos.com</a> <span dir=3D"ltr">&=
lt;<a href=3D"mailto:owner-chemistry-,-ccl.net">owner-chemistry-,-ccl.net</a>&g=
t;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; borde=
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
Sent to CCL by: Hans De Winter [hans.dewinter[#]<a href=3D"http://silicos.c=
om" target=3D"_blank">silicos.com</a>]<br>
Dear,<br>
<br>
I have a library of ~60,000 structures defined in SLN (sybyl line notation)=
 and I need to convert these in smiles or sdf format. I don&#39;t believe t=
hat Open Babel can help me on that (unless I missed it), so are there any o=
ther tools (preferably on Mac OS X) that can do this?<br>

<br>
Thx in advance.<br>
<br>
Hans De Winter<br>
Silicos NV<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br<br=<br<br>
<br>
E-mail to subscribers: <a href=3D"mailto:CHEMISTRY-,-ccl.net" target=3D"_blan=
k">CHEMISTRY-,-ccl.net</a> or use:<br>
 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" =
target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br>
E-mail to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST-,-ccl.net" targ=
et=3D"_blank">CHEMISTRY-REQUEST-,-ccl.net</a> or use<br>
 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" =
target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br=C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/chemistr=
y/sub_unsub.shtml" target=3D"_blank">http://www.ccl.net/chemistry/sub_unsub=
.shtml</a><br>
<br>
Before posting, check wait time at: <a href=3D"http://www.ccl.net" target=
=3D"_blank">http://www.ccl.net</a><br>
<br>
Job: <a href=3D"http://www.ccl.net/jobsConferences" target=3D"_blank">http:=
//www.ccl.net/jobsConferences</a>: <a href=3D"http://server.ccl.net/chemist=
ry/announcements/conferences/" target=3D"_blank">http://server.ccl.net/chem=
istry/announcements/conferences/</a><br>

<br>
Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh=
tml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</=
a><br>
<br<br>
 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank=
">http://www.ccl.net/spammers.txt</a><br>
<br>
RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" targe=
t=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>
<br>
<br>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Wolf-D. Ihlenfeldt, Xem=
istry GmbH<br><a href=3D"http://www.xemistry.com" target=3D"_blank">www.xem=
istry.com</a><br><br>

--000e0cd47b4247a8d3049ec084fb--


From owner-chemistry@ccl.net Fri Mar 18 10:40:00 2011
From: "Dario Fernando Coral ferchocoralg16**gmail.com" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: lower energies for transition states
Message-Id: <-44158-110318103314-21592-zx+w+ZUe5URv62Rqd1oWAg+*+server.ccl.net>
X-Original-From: "Dario Fernando Coral" <ferchocoralg16(~)gmail.com>
Date: Fri, 18 Mar 2011 10:33:12 -0400


Sent to CCL by: "Dario Fernando Coral" [ferchocoralg16.!A!.gmail.com]
Henry martinez,

I made the calculations of IRC and this confirms that the transition states connecting the desired reactants and products. The problem occurs when calculating the electronic energy including the ZPVE.

I suspect the problem stems from the use of harmonic approximation. However, do not know how to fix it.


From owner-chemistry@ccl.net Fri Mar 18 11:31:00 2011
From: "Ben Ellingson ben:+:eyesopen.com" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL: lower energies for transition states
Message-Id: <-44159-110318112856-13125-zDU53HmRoc2DGpL46zK8/A(a)server.ccl.net>
X-Original-From: Ben Ellingson <ben%%eyesopen.com>
Content-Language: en
Content-Type: multipart/alternative;
	boundary="_000_C9A8D64DC932beneyesopencom_"
Date: Fri, 18 Mar 2011 08:28:45 -0700
MIME-Version: 1.0


Sent to CCL by: Ben Ellingson [ben-$-eyesopen.com]
--_000_C9A8D64DC932beneyesopencom_
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Dear Dario,

This is unusual but not impossible.  The important thing to remember is tha=
t the bottleneck is at the maximum of free energy for the reaction, which i=
s usually close to the saddle point but it can vary widely for nearly flat =
surfaces.  Have you tried using a variational transition state program like=
 POLYRATE?  The problem could be that you are not using a high enough level=
 of theory for either electronic structure or vibrations, but it's also pos=
sible that what you are seeing is actually a good model for the reaction an=
d you just to vary the location of the dividing surface.

Best,
Ben


On 3/17/11 5:59 PM, "Dario Fernando Coral ferchocoralg16(a)gmail.com" <owne=
r-chemistry]~[ccl.net> wrote:



Sent to CCL by: "Dario Fernando Coral" [ferchocoralg16%gmail.com]
Greetings

Modeling Azepines fragmentations, I have found that the relative energies o=
f some transition states are found to be lower than the corresponding reage=
nt. The modeling of the reactions I've been doing with the B3LYP 6-31G(d)me=
thod.

Analyzing the output files I noticed that the electronic energy of these tr=
ansition states is higher than the reactants, the problem occurs when the e=
lectron energy is added with the zero point vibrational energy (ZPVE). Mayb=
e some of you know the solution to this problem.

Sorry for my very bad english and thanks in advance.

Dario Fernando Coral Obando
Chemistry Student
Universidad de Nario
Pasto - Colombia



-=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_C9A8D64DC932beneyesopencom_
Content-Type: text/html; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<HTML>
<HEAD>
<TITLE>Re: CCL: lower energies for transition states</TITLE>
</HEAD>
<BODY>
<FONT FACE=3D"Calibri, Verdana, Helvetica, Arial"><SPAN STYLE=3D'font-size:=
11pt'>Dear Dario,<BR>
&nbsp;<BR>
This is unusual but not impossible. &nbsp;The important thing to remember i=
s that the bottleneck is at the maximum of free energy for the reaction, wh=
ich is usually close to the saddle point but it can vary widely for nearly =
flat surfaces. &nbsp;Have you tried using a variational transition state pr=
ogram like POLYRATE? &nbsp;The problem could be that you are not using a hi=
gh enough level of theory for either electronic structure or vibrations, bu=
t it&#8217;s also possible that what you are seeing is actually a good mode=
l for the reaction and you just to vary the location of the dividing surfac=
e.<BR>
<BR>
Best,<BR>
Ben<BR>
<BR>
<BR>
On 3/17/11 5:59 PM, &quot;Dario Fernando Coral ferchocoralg16(a)gmail.com&q=
uot; &lt;<a href=3D"owner-chemistry]~[ccl.net">owner-chemistry]~[ccl.net</a>&gt=
; wrote:<BR>
<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE=3D"Calibri, Verdana, Helvetica, Arial"=
><SPAN STYLE=3D'font-size:11pt'><BR>
<BR>
Sent to CCL by: &quot;Dario Fernando Coral&quot; [ferchocoralg16%gmail.com]=
<BR>
Greetings<BR>
<BR>
Modeling Azepines fragmentations, I have found that the relative energies o=
f some transition states are found to be lower than the corresponding reage=
nt. The modeling of the reactions I've been doing with the B3LYP 6-31G(d)me=
thod.<BR>
<BR>
Analyzing the output files I noticed that the electronic energy of these tr=
ansition states is higher than the reactants, the problem occurs when the e=
lectron energy is added with the zero point vibrational energy (ZPVE). Mayb=
e some of you know the solution to this problem.<BR>
<BR>
Sorry for my very bad english and thanks in advance.<BR>
<BR>
Dario Fernando Coral Obando<BR>
Chemistry Student<BR>
Universidad de Nario<BR>
Pasto - Colombia<BR>
<BR>
<BR>
<BR>
-=3D This is automatically added to each message by the mailing script =3D-=
<BR<BR=<BR<BR>
<BR>
E-mail to subscribers: <a href=3D"CHEMISTRY]~[ccl.net">CHEMISTRY]~[ccl.net</a> =
or use:<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=3D"http://www.ccl.net/cgi-bin/c=
cl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><BR=
>
<BR>
E-mail to administrators: <a href=3D"CHEMISTRY-REQUEST]~[ccl.net">CHEMISTRY-R=
EQUEST]~[ccl.net</a> or use<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=3D"http://www.ccl.net/cgi-bin/c=
cl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><BR=
>
<BR>
Subscribe/Unsubscribe:<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=3D"http://www.ccl.net/chemistry=
/sub_unsub.shtml">http://www.ccl.net/chemistry/sub_unsub.shtml</a><BR>
<BR>
Before posting, check wait time at: <a href=3D"http://www.ccl.net">http://w=
ww.ccl.net</a><BR>
<BR>
Job: <a href=3D"http://www.ccl.net/jobs">http://www.ccl.net/jobs</a><BR>
Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/confe=
rences/">http://server.ccl.net/chemistry/announcements/conferences/</a><BR>
<BR>
Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh=
tml">http://www.ccl.net/chemistry/searchccl/index.shtml</a><BR>
<BR<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=3D"http://www.ccl.net/spammers.=
txt">http://www.ccl.net/spammers.txt</a><BR>
<BR>
RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/">http:=
//www.ccl.net/chemistry/aboutccl/instructions/</a><BR>
<BR>
<BR>
<BR>
</SPAN></FONT></BLOCKQUOTE>
</BODY>
</HTML>


--_000_C9A8D64DC932beneyesopencom_--


From owner-chemistry@ccl.net Fri Mar 18 13:19:01 2011
From: "Shirley Peng speng/a\chemcomp.com" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: Chemical Computing Group Announces Winners of the CCG Excellence Award
Message-Id: <-44160-110318124341-17169-RhV1HDCWQaLw7vKHD6EGkw.@.server.ccl.net>
X-Original-From: "Shirley  Peng" <speng*chemcomp.com>
Date: Fri, 18 Mar 2011 12:43:32 -0400


Sent to CCL by: "Shirley  Peng" [speng() chemcomp.com]
Chemical Computing Group Announces Winners of the CCG Excellence Award for the Spring 2011 ACS National Meeting 

MONTREAL, Canada - March 4, 2011 - Chemical Computing Group (CCG) and the American Chemical Society's (ACS) Division of Computers in Chemistry (COMP) congratulate the winners of the CCG Excellence Awards for the Fall 2010 ACS National Meeting in Anaheim. 

The award winners' research will be recognized at the award presentation ceremony during the COMP Division Poster Session on Tuesday, March 29, 2011. Each winner will receive a one-year license for the latest version of the Molecular Operating Environment (MOE), as well as financial support to cover their travel costs to Anaheim. 

The winners are: 

Bin Zhang, Department of Chemistry and Chemical Engineering, California Institute of Technology
Hydrophobically stabilized open state for the lateral gate of the Sec translocon 

Christina Bergonzo, Department of Chemistry, Stony Brook University
Selective destabilization of lesions leads to divergent base flipping pathways by a DNA glycosylase 

Justin M Spiriti, Department of Chemistry and Biochemistry and Center for Biological Physics, Arizona State University
Intrinsic bending flexibility of bare and protein-bound DNA by adaptive umbrella sampling on roll angles 

Ramu Anandakrishnan, Department of Computer Science, Virginia Polytechnic Institute and State University
N Log N generalized Born approximation 

Sudipto Mukherjee, Department of Applied Mathematics & Statistics, Stony Brook University
Development of the SB2010 testset to evaluate docking 

About CCG Excellence Award 

The Chemical Computing Group (CCG) Excellence Awards have been created to recognize and promote excellence in scientific research, and reflect CCG's belief in the importance of encouraging new researchers. The awards are granted semi-annually based on the quality and significance of the work, supporting graduate students who have used computational chemistry to further their research. For more information about the CCG Excellence Awards and eligibility criteria, please visit: www.chemcomp.com/ssupport-academic.htm 

About Chemical Computing Group 

Chemical Computing Group (CCG) is a leading supplier of software solutions for life sciences. From its inception in 1994, CCG has provided state of the art drug discovery applications for pharmaceutical, biotech, and academic research. CCG has a proven track record in scientific innovation, consistently producing releases and upgrades for all their products. CCG's products and services are used by biologists, medicinal chemists and computational chemists throughout the world today. CCG is known for its strong collaborative scientific support, maintaining support offices in both Europe and North America. CCG headquarter is in Montreal, Canada. For more information visit: www.chemcomp.com 

For additional information please contact: 

Raul Alvarez
Senior Marketing Manager
(514) 393-1055
info%chemcomp.com


From owner-chemistry@ccl.net Fri Mar 18 14:08:00 2011
From: "tcorrera!=!iq.usp.br" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: lower energies for transition states
Message-Id: <-44161-110318135747-24268-rQYIQSi8imYFWOIGX7I61g*_*server.ccl.net>
X-Original-From: tcorrera++iq.usp.br
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
	charset=ISO-8859-1;
	DelSp="Yes";
	format="flowed"
Date: Fri, 18 Mar 2011 14:57:24 -0300
MIME-Version: 1.0


Sent to CCL by: tcorrera**iq.usp.br

I had the same problem studing SN2 reaction in alkyl nitrates.
(http://pubs.acs.org/doi/abs/10.1021/jp107500s Table 3)

More extended basis sets make the TS energy higher than reactant complex.
The TS E+ZPVE requires a larger basis set to become higher than  
reactants than E(electronic energy) does.
Based on this, I would suggest you to try extended basis sets (an why  
not other methodologies?).

I'm not used to the reactions you are studying, but sometimes, when  
the reaction involves breaking a light atom bond (like H), the TS  
loses a high freq mode that can lower the ZPVE enough to make its  
energy lower than reactants.
That usually happens when you have a flat potential well, where you  
need high computational level, anyway.

You could also try to correct the BSSE and check what happens. Let me  
know the results if you try that.

Best Regards

Thiago Correra
Instituto de Qu�mica, Universidade de S�o Paulo - Brasil.
Av. Prof. Lineu Prestes, 748 - Butant� - S�o Paulo - SP
Sala 450 - B4S - Cep:05508-900 - tel. 3091-3852

Citando "Dario Fernando Coral ferchocoralg16(a)gmail.com"  
<owner-chemistry() ccl.net>:

>
> Sent to CCL by: "Dario Fernando Coral" [ferchocoralg16%gmail.com]
> Greetings
>
> Modeling Azepines fragmentations, I have found that the relative  
> energies of some transition states are found to be lower than the  
> corresponding reagent. The modeling of the reactions I've been doing  
> with the B3LYP 6-31G(d)method.
>
> Analyzing the output files I noticed that the electronic energy of  
> these transition states is higher than the reactants, the problem  
> occurs when the electron energy is added with the zero point  
> vibrational energy (ZPVE). Maybe some of you know the solution to  
> this problem.
>
> Sorry for my very bad english and thanks in advance.
>
> Dario Fernando Coral Obando
> Chemistry Student
> Universidad de Nario
> Pasto - Colombia>
>
>


From owner-chemistry@ccl.net Fri Mar 18 15:07:00 2011
From: "Phil Hasnip phil.hasnip^york.ac.uk" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: IR intensities from VASP
Message-Id: <-44162-110318141754-10164-/ws2SSRqiP65exaQvvo08w[a]server.ccl.net>
X-Original-From: Phil Hasnip <phil.hasnip(0)york.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Fri, 18 Mar 2011 18:32:18 +0000 (GMT)
MIME-Version: 1.0


Sent to CCL by: Phil Hasnip [phil.hasnip!^!york.ac.uk]
Hello everyone,

> It is not directly possible to get the vibrational intensities for 
> crystals, and as I know there is no way to compute the Raman activities 
> at the moment (but please correct me, if I am wrong)

CASTEP is capable of calculating IR intensities including those for 
crystals, as well as Raman activity (although this is a more intensive 
calculation). See

http://www.castep.org/documentation.html

for more details, in particular the "User Guide for Phonons and Related 
Calculations".

Yours,

Phil Hasnip

-------------------------------------------------------
Dr Phil Hasnip            Email: phil.hasnip##york.ac.uk
Dept of Physics
University of York        Tel:  +44 (0)1904 324624
York YO10 5DD


From owner-chemistry@ccl.net Fri Mar 18 22:54:00 2011
From: "Edroaldo Lummertz da Rocha edroaldo##gmail.com" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: Force Field Nanomaterials and Biomembranes
Message-Id: <-44163-110318181336-11885-EYqXH5q29MT+r7VVkf+EGQ _ server.ccl.net>
X-Original-From: Edroaldo Lummertz da Rocha <edroaldo . gmail.com>
Content-Type: multipart/alternative; boundary=485b3979db462769c8049ec91658
Date: Fri, 18 Mar 2011 19:13:24 -0300
MIME-Version: 1.0


Sent to CCL by: Edroaldo Lummertz da Rocha [edroaldo~~gmail.com]
--485b3979db462769c8049ec91658
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Hi, I am starting a setup to simulate nanomaterials in biological media but
I have a doubt about how I can perform the force field parametrization. I
have gold nanoparticles and lipid bilayers. I am thinking about using the
MARTINI force field because I want to do a coarse-grained simulation. Can
you help me providing directions about how I represent correctly my
nanoparticles and the biological media to execute a coarse-grained molecula=
r
dynamics simulations? Any directions are useful.

Best regards.

--=20
Edroaldo Lummertz da Rocha
Doutorando em Ci=EAncia e Engenharia de Materiais
GruDE - EEL - CTC - UFSC
Phn. ----
http://www.grude.ufsc.br
Mude Sua Vida, Mude o Mundo

--485b3979db462769c8049ec91658
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Hi, I am starting a setup to simulate nanomaterials in biological media but=
 I have a doubt about how I can perform the force field parametrization. I =
have gold nanoparticles and lipid bilayers. I am thinking about using the M=
ARTINI force field because I want to do a coarse-grained simulation. Can yo=
u help me providing directions about how I represent correctly my nanoparti=
cles and the biological media to execute a coarse-grained molecular dynamic=
s simulations? Any directions are useful.<br>
<br>Best regards.<br clear=3D"all"><br>-- <br>Edroaldo Lummertz da Rocha<br=
>Doutorando em Ci=EAncia e Engenharia de Materiais<br>GruDE - EEL - CTC - U=
FSC<br>Phn. ----<br><a href=3D"http://www.grude.ufsc.br" target=3D"_blank">=
http://www.grude.ufsc.br</a><br>
Mude Sua Vida, Mude o Mundo<br>

--485b3979db462769c8049ec91658--