From owner-chemistry@ccl.net Mon Dec 21 07:33:01 2015 From: "Alcides Simao alsimao]|[gmail.com" To: CCL Subject: CCL: Trans azo benzene Message-Id: <-51942-151221031331-8574-iA0gUcbe9Ggzkc2J7w6ojg[]server.ccl.net> X-Original-From: Alcides Simao Content-Type: multipart/alternative; boundary=001a11c313062403eb0527641005 Date: Mon, 21 Dec 2015 08:13:14 +0000 MIME-Version: 1.0 Sent to CCL by: Alcides Simao [alsimao(!)gmail.com] --001a11c313062403eb0527641005 Content-Type: text/plain; charset=UTF-8 A collegue of mine published some quantum and experimental works on this: 10.1039/C4CP00240G , 10.1021/jp405061b Best, Alcides A seg, 21/12/2015, 06:29, Visvaldas K. coyote_v2002=-=yahoo.com < owner-chemistry*ccl.net> escreveu: > A quick search on QCLDB showed a paper in Chem Phys Lett, 501, 379, but > it's geared towards adsorption on solids, I am not sure how useful it is. > > Best wishes, > > Vis Kairys > > > > ------------------------------ > *From:* John McKelvey jmmckel^gmail.com > *To:* "Kairys, Visvaldas " > *Sent:* Sunday, December 20, 2015 7:54 PM > *Subject:* CCL: Trans azo benzene > > Henry, > > Thank for the torsion data in the graphs. Could you provide the color code > for the entries in the two graphs? Info on substituted azobenzenes is also > relevant. > > For the moment the issue is constrained to computed geometries in vacuum, > XRAY, and neutron diffraction structures. > > Best regards, > > John > > > > On Sun, Dec 20, 2015 at 4:20 AM, Rzepa, Henry S h.rzepa::imperial.ac.uk < > owner-chemistry++ccl.net> wrote: > > John, > > Here is a possible answer: > http://www.ch.imperial.ac.uk/rzepa/blog/?p=15141 (Sorry, it contains > images which I would rather not post as attachments here). > > Sadly, there is no generally accepted database of computed molecular > geometries, only for experimental structures. But I would add that an > organisation called DataCite collects metadata about computed results that > have been published in a data repository supporting DataCite, and it > should be possible to mine such repositories for metadata relating to > azobenzene and the computational methods, retrieve the coordinates, and > establish the required dihedral. This is part of the aspects of RDM > (Research data management) about which there will be a two day session at > the ACS meeting in San Diego in March 2016. Do come along if you want to > contribute suggestions for general solutions to questions such as John > posed here. > > On 18 Dec 2015, at 21:06, John McKelvey jmmckel*gmail.com a ccl.net> wrote: > > Hello, > > Could anyone comment on any recent calculated results on the planarity, or > lack thereof, of azobenzene? > > Thanks! > > John > -- > John McKelvey > 545 Legacy Pointe Dr > O'Fallon, MO 63376 > 636-294-5203 > jmmckel-$-gmail.com > > > > > > -- > John McKelvey > 545 Legacy Pointe Dr > O'Fallon, MO 63376 > 636-294-5203 > jmmckel++gmail.com > > > --001a11c313062403eb0527641005 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

A collegue of mine published some quantum and experimental w= orks on this: 10.1039/C4CP00240G , 10.1021/jp405061b
Best,

Alcides


A seg, 21/12/2015, 06:29,= =C2=A0Visvaldas K. coyote_v2002=3D-=3Dyahoo.co= m <owner-chemistry*ccl.ne= t> escreveu:
A quick se= arch on QCLDB showed a paper in Chem Phys Lett, 501, 379, but it's gear= ed towards adsorption on solids, I am not sure how useful it is.
=
Best wishes,

Vis Kairys



=
From: John McKelvey jmmckel^gmail.com <owner-chemistry= ,+,ccl.net>
To: "Kairys, Visvaldas " = <coyote_v2002,+,yahoo.com= >
Sent: Sunday, = December 20, 2015 7:54 PM
Subject:<= /span> CCL: Trans azo benzene

Henry,

Thank for the torsion data in the graphs. C= ould you provide the color code for the entries in the two graphs?=C2=A0 In= fo on substituted azobenzenes is also relevant.

For the moment the= issue is=C2=A0 constrained to computed geometries in vacuum, XRAY, and neu= tron diffraction structures.

Best regards,

John<= br>

=C2=A0

On Sun, Dec 20, = 2015 at 4:20 AM, Rzepa, Henry S h.rzepa::imperial.ac.uk &l= t;owner-chemistry++ccl.net> wrote:
John,

Here is a possible answer:=C2=A0http://www.ch.i= mperial.ac.uk/rzepa/blog/?p=3D15141=C2=A0=C2=A0(Sorry, it contains imag= es which =C2=A0I would rather not post as attachments here).

Sadly, there is no generally accepted database of computed molecular g= eometries, only for experimental structures. But =C2=A0I would add that an = organisation called =C2=A0DataCite collects metadata about computed results= that have been published in a data repository supporting =C2=A0DataCite, and it should be possible to mine su= ch repositories for metadata relating to azobenzene and the computational m= ethods, retrieve the coordinates, and establish the required dihedral.=C2= =A0 This is part of the aspects of =C2=A0RDM (Research data management) about which there will be a two day session at the =C2=A0= ACS meeting in =C2=A0San Diego in March 2016.=C2=A0 Do come along if you wa= nt to contribute suggestions for general solutions to questions such as =C2= =A0John posed here.

On 18 Dec 2015, at 21:06, John McKelvey jmmckel*gmail.com <owner-che= mistry a ccl.net> wrote:

Hello,

Could anyone comment on any recent calculated results on the planarity, or = lack thereof, of azobenzene?

Thanks!

John
--
John McKelvey
545 Legacy Pointe Dr




--
<= div>
John McKelvey
545 Legacy Pointe Dr
O= 'Fallon, MO 63376
636-294-5203
jmmckel++gmail.com


--001a11c313062403eb0527641005-- From owner-chemistry@ccl.net Mon Dec 21 08:07:00 2015 From: "vijay s chinthusukumar(_)gmail.com" To: CCL Subject: CCL: tinker Message-Id: <-51943-151221035248-3257-IwfayYlrblGNboM+Qls+ag::server.ccl.net> X-Original-From: "vijay s" Date: Mon, 21 Dec 2015 03:52:47 -0500 Sent to CCL by: "vijay s" [chinthusukumar^gmail.com] dear sir i have some doubts while preparing the input file for a molecule for which different conformations has to be obtained . doubt is with assigning the atom types. for example, for a carbon attached to both COOH group and NH2 group, which atom type has to be assigned?- carbon attached to COOH or as a carbon attached to NH2? which is to be preferred?