Dear All,

Stefan, Cina, Mikael and others that have contributed t= o my post in the forum thank you very much.

I am already implementing your suggestions appropriately as they= apply to the work I am doing currently.

Hoping to get more contributions from= you when necessary.

= Best Regards.

&= nbsp;

Lukman Olawale= Olasunkanmi

Current Address:Department of Chemistry,
Faculty of Agricul= ture, Science and Technology,
North West University (Mafike= ng Campus),
South Africa.
Cell: +2771015625= 2 OR +27747614116

Permanent Address:
= Department of Chemistry,
Obafemi Awolowo Unive= rsity,
Ile-Ife,
Nigeria.
Ce= ll: +234 805 240 1564

From: Mikael Johansson mikael.johansson+/-ik= i.fi <owner-chemistry]-[ccl.net>
To: "Olasunkanmi, Olawale Lukman " <walecomuk]-[yah= oo.co.uk>
Sent: Sa= turday, 14 February 2015, 13:29
S= ubject: CCL: QTAIM or else

Hello Lukman and All,

There is quite a debate o= n whether bond critical points always correspond
to a stabilising inter= action or not, and H...H bonds are an often
discussed case in the liter= ature. I doubt you will get an answer using
QTAIM that would satisfy ev= eryone ;-)

You could try out the non-covalent interactions (NCI) ana= lysis by Johnson
and co-workers:
http://pubs.acs.org/doi/ab= s/10.1021/ja100936w
http://pubs.acs.org/doi/abs/10.1021/ct1= 00641a

It's, in my opinion, a rather beautiful method, and is al= ready implemented
in quite many programs. Look up NCIplot and Multiwfn,= for example.

Then there's of course a plethora of other analysis me= thods, like electron
sharing numbers and various energy partititoning s= chemes that you could
use, but I'd start out with the NCI analysis.
=
Good luck,
Mikael J.
http://www.iki.fi/~mpjohans/

On Fri, 13 Feb 2015, Olasunkanmi Lukman Olawale walecomuk]~[y= ahoo.co.uk wrote:

> Dear CClers,
> Kindly assist.
>> I made DFT calculations on a nitrogen heterocycle which was ordinari= ly
> expected to be a D2h molecule but was found to be otherwise. It= was
> found out that a pair of hydrogen atoms in the molecule seems= to exhibit
> intramolecular interaction. I have a vague idea that Q= TAIM analysis
> could be used to justify whether the interaction bet= ween the two
> hydrogen atoms is stabilizing (H-H attraction) or des= tabilizing
> (repulsion) but I am not very sure of what (QTAIM) para= meters will be
> used for the findings. Your suggestions will be app= reciated.
>
> Thank you.
>
> Lukman Olawale = Olasunkanmi
>
> Current Address:
> Department of Chemist= ry,
> Faculty of Agriculture, Science and Technology,
> North W= est University (Mafikeng Campus),
> South Africa.
> Cell: +2771= 0156252 OR +27747614116
>
> Permanent Address:
> Departm= ent of Chemistry,
> Obafemi Awolowo University,
> Ile-Ife,
&= gt; Nigeria.
> Cell: +234 805 240 1564
>
>

Dear Lukma= n,

As it was told before, there is a heated debat= e on QTAIM and chemi= cal bond. I recommend you to read Bader=C2=B4s seminal paper in 2009 (JPCA, 113, 10391). I also= would like to add that:

1)The atomic interaction = lines can only be considered as bond path when it is mirrored by its corres= ponding virial path.= Then we=C2=B4d rather work with the virial graph than its molecular graph mainly for the analy= sis of intermolecular/intramolecular interactions;

2) The virial graph and molecular = graph depend on the quality of the wave function previously calculated. The= n, bad molecular graph (or = virial graph) can come from bad wave function.

3) For some cases, in order to = have a reliable molecular graph (or virial graph), you=C2=B4d better obtain molecular graph (or= virial graph) from = different critical point searching methods.

Not al= ways these steps are taken into account.=C2=A0

I a= lso recommend you to read our following paper:

http://pubs.acs.org/do= i/citedby/10.= 1021/jp500131z

Where we showed that H-H bond i= s indeed a stabilizing interaction for alkanes (highly branched alkanes and alkane complexes) and we also found correlation between num= ber of H-H bond in alkane complexes and their corresponding boiling points. We also used ELF to= show the existence of the critical point between hydrogen atoms from diffe= rent molecules in alkane complexes. Ab initio optimizations also indicated the tendency of alignment between hydrog= en atoms from different molecules in alkane complexes.

Caio

Feder= al University of Rio Grande= do Norte

Natal, Brazil.

2015-02-14 8:29 GMT-03:00 Mikael Johansson mikael.johan= sson+/-iki.fi &= lt;owner-chemi= stry-*-ccl.net>= :

Hello Lukman and All,

There is quite a debate on whether bond critical points always correspond t= o a stabilising interaction or not, and H...H bonds are an often discussed = case in the literature. I doubt you will get an answer using QTAIM that wou= ld satisfy everyone ;-)

You could try out the non-covalent interactions (NCI) analysis by Johnson a= nd co-workers:
=C2=A0 http://pubs.acs.org/doi/abs/10.1021/ja100936w
=C2=A0 http://pubs.acs.org/doi/abs/10.1021/ct100641a

It's, in my opinion, a rather beautiful method, and is already implemen= ted in quite many programs. Look up NCIplot and Multiwfn, for example.

Then there's of course a plethora of other analysis methods, like elect= ron sharing numbers and various energy partititoning schemes that you could= use, but I'd start out with the NCI analysis.

Good luck,
=C2=A0 =C2=A0 Mikael J.
=C2=A0 =C2=A0 ht= tp://www.iki.fi/~mpjohans/

On Fri, 13 Feb 2015, Olasunkanmi Lukman Olawale walecomuk]~[yahoo.co.uk wrote:

Dear CClers,
Kindly assist.

I made DFT calculations on a nitrogen heterocycle which was ordinarily expe= cted to be a D2h molecule but was found to be otherwise. It was found out t= hat a pair of hydrogen atoms in the molecule seems to exhibit intramolecula= r interaction. I have a vague idea that QTAIM analysis could be used to jus= tify whether the interaction between the two hydrogen atoms is stabilizing = (H-H attraction) or destabilizing (repulsion) but I am not very sure of wha= t (QTAIM) parameters will be used for the findings. Your suggestions will b= e appreciated.

Thank you.
=C2=A0
Lukman Olawale Olasunkanmi

Current Address:
Department of Chemistry,
Faculty of Agriculture, Science and Technology,
North West University (Mafikeng Campus),
South Africa.
Cell: +27710156252 OR +27747614116

Permanent Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife,
Nigeria.
Cell: +234 805 240 1564

--001a11c383626c0b24050f38b116-- From owner-chemistry@ccl.net Mon Feb 16 14:11:00 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor=fluor.quimica.uniovi.es" To: CCL Subject: CCL: strain energy Message-Id: <-51039-150216131230-13128-kByFHehVPA68v9MnNtWxIg|*|server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Mon, 16 Feb 2015 19:07:06 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor=-=fluor.quimica.uniovi.es] On Mon, Feb 16, 2015 at 07:31:04AM -0500, satya p singh satyapiit(~)gmail.com wrote: > > Sent to CCL by: "satya p singh" [satyapiit{:}gmail.com] > Dear All, > > is there any software package available to calculate directly the strain > energy of a ring system or any code available? Satya, 1) Please: strain energy. Do a calculation in your molecule, Change the geometry appropriately. Do again the calculation. If required use a fitting scheme to derive the thermodynamical parameters desired. 2) Are you asking for a slave to do your homework? 3) If you need a textbook I recommend you Duane C. Wallace, "Statistical Physics of Crystals and Liquids", (WorldSci,2002) ISBN 9812381139 4) Remember that a quantum mechanical calculation provides basically the internal energy, U, of your system. Regards, Dr. V�ctor Lua�a -- \|/a "The hardest part in solving a problem is being |^.^| able to formulate the significative question" +-!OO--\_/--OO!------------------------------+----------------------- ! Dr.V�ctor Lua�a ! ! Departamento de Qu�mica F�sica y Anal�tica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor(_)fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +----------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Mon Feb 16 16:15:01 2015 From: "Lela Vukovic Lvukov1]*[illinois.edu" To: CCL Subject: CCL: "Hands-On" Workshop on Computational Biophysics (Apr 6-10, 2015) Message-Id: <-51040-150216155711-781-mdSF9abtDXjKO2AwyqcpEQ(0)server.ccl.net> X-Original-From: "Lela Vukovic" Date: Mon, 16 Feb 2015 15:57:10 -0500 Sent to CCL by: "Lela Vukovic" [Lvukov1- -illinois.edu] The Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu) at the University of Illinois at Urbana- Champaign (www.uiuc.edu), announces a "Hands-On" Workshop on Computational Biophysics http://www.ks.uiuc.edu/Training/Workshop/Urbana2015/ to be held April 6-10, 2015 at the Beckman Institute on the University of Illinois at Urbana- Champaign campus in Urbana, Illinois, USA. Application, selection, and notification of participants is on-going through March 24, 2015. The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes and membrane proteins, trafficking in the living cell through water and ion channels, and signaling pathways. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and parameterizing new molecules, simulating membrane proteins and ion channels, modeling nucleic acid systems, computational nano-bio, free energy calculations, evolutionary algorithms and network dynamics. The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. Enrollment limited to 24 participants. The workshop will be held April 6-10, 2015. All participants are required to bring their own laptop, prepared for use in workshop tutorial sessions. Course materials will be provided. The workshop is sponsored by the National Institute of General Medical Sciences (www.nigms.nih.gov), and the NIH Center for Macromolecular Modeling and Bioinformatics. We look forward to receiving your application! TCBG Workshop Organizers Email: workshop+urbana2015~~ks.uiuc.edu From owner-chemistry@ccl.net Mon Feb 16 21:17:00 2015 From: "Geoffrey Hutchison geoffh=-=pitt.edu" To: CCL Subject: CCL:G: Field Message-Id: <-51041-150216211608-14611-Q6UvJ+YqjsiEB0bIjY13Nw^-^server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Type: multipart/alternative; boundary="Apple-Mail=_6E5E8392-8A8F-4106-8652-CE2618D38BDE" Date: Mon, 16 Feb 2015 21:15:58 -0500 Mime-Version: 1.0 (Mac OS X Mail 8.2 $2081$) Sent to CCL by: Geoffrey Hutchison [geoffh-$-pitt.edu] --Apple-Mail=_6E5E8392-8A8F-4106-8652-CE2618D38BDE Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Gaussian doesn't allow fractional fields though the field keyword. The = smallest field would be Field=3DX+1, corresponding to 1 x 1e-4 atomic = units of field. Other programs (e.g., Q-Chem) do allow arbitrary decimal field values. = So if you'd like to see the effect of a smaller field, you will need to = use a different program. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh!^!pitt.edu web: http://hutchison.chem.pitt.edu/ > On Feb 13, 2015, at 1:44 PM, Partha Sengupta anapspsmo__gmail.com = wrote: >=20 > friends I want to use a field equivalent to 1microVolt (muV/ = 10**-6)) for a Gaussian calculation. I use field=3Dx+0.0002 polar test = with other key words. But the Gaussian fails with=20 > " QPErr --- A syntax error was detected in the input line. > lyp/6-31+g(d) field=3Dx+0.0002 polar test > , > How can I use 1microVolt as the field? > Partha > --=20 > Dr. Partha Sarathi Sengupta > Associate Professor > Vivekananda Mahavidyalaya, Burdwan --Apple-Mail=_6E5E8392-8A8F-4106-8652-CE2618D38BDE Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii

Gaussian doesn't allow fractional fields though the field keyword. The smallest field would be Field=X+1, corresponding to 1 x 1e-4 atomic units of field.

Other programs (e.g., Q-Chem) do allow arbitrary decimal field values. So if you'd like to see the effect of a smaller field, you will need to use a different program.

Hope that helps,

-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoffh!^!pitt.edu
web: http://hutchison.chem.pitt.edu/

On Feb 13, 2015, at 1:44 PM, Partha Sengupta anapspsmo__gmail.com <owner-chemistry!^!ccl.net> wrote:

friends I want to use a field equivalent to 1microVolt (muV/ 10**-6)) for a Gaussian calculation. I use field=x+0.0002 polar test with other key words. But the Gaussian fails with
" QPErr --- A syntax error was detected in the input line.
lyp/6-31+g(d) field=x+0.0002 polar test
,
How can I use 1microVolt as the field?
Partha
--
Dr. Partha Sarathi Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan

--Apple-Mail=_6E5E8392-8A8F-4106-8652-CE2618D38BDE--