From owner-chemistry@ccl.net Tue Nov 3 07:09:01 2015 From: "Partha Sengupta anapspsmo::gmail.com" To: CCL Subject: CCL: wiberg bond index Message-Id: <-51847-151103034212-338-nM9HDi7z4eLaYBu6Rd7UMw^^server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=047d7bacb8c40cfabc05239ede68 Date: Tue, 3 Nov 2015 14:12:00 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo(!)gmail.com] --047d7bacb8c40cfabc05239ede68 Content-Type: text/plain; charset=UTF-8 Thank you for your important comments. Partha On Mon, Nov 2, 2015 at 10:16 PM, Tymofii Nikolaienko tim_mail(a)ukr.net < owner-chemistry .. ccl.net> wrote: > I'd like just to add that a freeware program JANPA ( > http://janpa.sourceforge.net/ , see Comput. Theor. Chem. (2014), V.1050, > P.15-22 - open access) > is also capable of calculating Wiberg bond index in the NAO basis and this > program is compatible with a number > of freeware quantum chemical packages. > > Regards, > Tymofii > > > > On 02.11.2015 17:38, Thomas Manz thomasamanz**gmail.com wrote: > > Hi Partha, > > If you compute the Wiberg bond index in the NAO basis using the NBO > program (NBO keyword BNDIDX), it gives a reasonable quantification of bond > order in many cases > (for hydrogen or other kinds of bonds, whether intermolecular or > intramolecular). > > For spin polarized systems, you have to add twice the sum of the spin-up > (alpha) and spin-down (beta) Wiberg bond indices to get the approximate > bond order. > For spin unpolarized systems, the Wiberg bond indices of the total > electron density matrix is used, with no multiplication by two. > > Effective bond orders quantify the approximate number of electrons > exchanged between two atoms. > > Tom > > On Sun, Nov 1, 2015 at 10:23 PM, Partha Sengupta anapspsmo%%gmail.com < > owner-chemistry-x-ccl.net> wrote: > >> Friends, I have a question "how Wiberg bond index is related to >> intramolecular hydrogen bond ?" >> Partha >> >> -- >> >> >> *Dr. Partha Sarathi Sengupta Associate Professor Vivekananda >> Mahavidyalaya, Burdwan* >> > > > -- *Dr. Partha Sarathi SenguptaAssociate ProfessorVivekananda Mahavidyalaya, Burdwan* --047d7bacb8c40cfabc05239ede68 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thank you for your important comments.
Partha

On Mon, Nov 2,= 2015 at 10:16 PM, Tymofii Nikolaienko tim_mail(a)ukr.net <owner-chemistry .. ccl.net> wrote:
=20 =20 =20
I'd like just to add that a freeware program JANPA ( http://janp= a.sourceforge.net/=C2=A0 , see Comput. Theor. Chem. (2014), V.1050, P.15-22 - open access)
is also capable of calculating Wiberg bond index in the NAO basis and this program is compatible with a number
of freeware quantum chemical packages.

Regards,
Tymofii



On 02.11.2015 17:38, Thomas Manz thomasamanz**gmail.com= wrote:
Hi Partha,

If you compute the Wiberg bond index in the NAO basis using the NBO program (NBO keyword BNDIDX), it gives a reasonable quantification of bond order in many cases
(for hydrogen or other kinds of bonds, whether intermolecular or intramolecular).

For spin polarized systems, you have to add twice the sum of the spin-up (alpha) and spin-down (beta) Wiberg bond indices to get the approximate bond order.
For spin unpolarized systems, the Wiberg bond indices of the total electron density matrix is used, with no multiplication by two.

Effective bond orders quantify the approximate number of electrons exchanged between two atoms.

Tom

On Sun, Nov 1, 2015 at 10:23 PM, Partha Sengupta anapspsmo%%gmail.com <owner-chemistry-x-ccl.net> wrote:
Friends, I have a question "how Wiberg bond index =C2=A0is related to intramolecular =C2=A0 hydrogen bond ?= "
Partha

--
Dr. Partha Sarathi Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan=





--
Dr. Partha Sarathi Sen= gupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan
--047d7bacb8c40cfabc05239ede68-- From owner-chemistry@ccl.net Tue Nov 3 07:44:01 2015 From: "Partha Sengupta anapspsmo]|[gmail.com" To: CCL Subject: CCL: wiberg bond index Message-Id: <-51848-151102130349-18969-nQ4x/dPAAMz9i77JT9yEYw]=[server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=047d7bf0bf98193feb0523929915 Date: Mon, 2 Nov 2015 23:33:44 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo^-^gmail.com] --047d7bf0bf98193feb0523929915 Content-Type: text/plain; charset=UTF-8 Sir, How can I quantitatively infer the existence of intramolecular hydrogen bond from the data obtained? Partha On Mon, Nov 2, 2015 at 9:08 PM, Thomas Manz thomasamanz**gmail.com < owner-chemistry]![ccl.net> wrote: > Hi Partha, > > If you compute the Wiberg bond index in the NAO basis using the NBO > program (NBO keyword BNDIDX), it gives a reasonable quantification of bond > order in many cases > (for hydrogen or other kinds of bonds, whether intermolecular or > intramolecular). > > For spin polarized systems, you have to add twice the sum of the spin-up > (alpha) and spin-down (beta) Wiberg bond indices to get the approximate > bond order. > For spin unpolarized systems, the Wiberg bond indices of the total > electron density matrix is used, with no multiplication by two. > > Effective bond orders quantify the approximate number of electrons > exchanged between two atoms. > > Tom > > On Sun, Nov 1, 2015 at 10:23 PM, Partha Sengupta anapspsmo%%gmail.com < > owner-chemistry-x-ccl.net> wrote: > >> Friends, I have a question "how Wiberg bond index is related to >> intramolecular hydrogen bond ?" >> Partha >> >> -- >> >> >> *Dr. Partha Sarathi SenguptaAssociate ProfessorVivekananda Mahavidyalaya, >> Burdwan* >> > > -- *Dr. Partha Sarathi SenguptaAssociate ProfessorVivekananda Mahavidyalaya, Burdwan* --047d7bf0bf98193feb0523929915 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Sir, How can I quantitatively infer the existence =C2=A0of= intramolecular hydrogen bond from the data obtained?
Partha

On Mon, Nov 2, 2= 015 at 9:08 PM, Thomas Manz thomasamanz**gmail= .com <owner-chemistry]![ccl.net> wrote:
Hi Partha,

If you= compute the Wiberg bond index in the NAO basis using the NBO program (NBO = keyword BNDIDX), it gives a reasonable quantification of bond order in many= cases
(for hydrogen or other kinds of bonds, whether intermolecu= lar or intramolecular).

For spin polarized systems= , you have to add twice the sum of the spin-up (alpha) and spin-down (beta)= Wiberg bond indices to get the approximate bond order.
For spin = unpolarized systems, the Wiberg bond indices of the total electron density = matrix is used, with no multiplication by two.

Eff= ective bond orders quantify the approximate number of electrons exchanged b= etween two atoms.

Tom
=

On Sun, Nov 1, 20= 15 at 10:23 PM, Partha Sengupta anapspsmo%%gmail.com <owner-chemistry-x-ccl.net> wrote:
Friends= , I have a question "how Wiberg bond index =C2=A0is related to intramo= lecular =C2=A0 hydrogen bond ?"
Partha
<= div>
--
Dr. Partha Sarath= i Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan




--
Dr. Partha Sarathi Sen= gupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan
--047d7bf0bf98193feb0523929915-- From owner-chemistry@ccl.net Tue Nov 3 08:18:01 2015 From: "Fedor Goumans goumans(0)scm.com" To: CCL Subject: CCL: Transition state location for reaction include three reactants Message-Id: <-51849-151103033928-32659-PvGgqO7L8yCUPoaohBCZ6g[a]server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 03 Nov 2015 09:39:19 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans^scm.com] Dear Saied, There are very few three-body reactions, i.e. where the transition state involves three products having to come together at the same time. Statistically the frequency that three molecules are at the same place at the same time (in the right orientation) is very low. Therefore reactions involving three reactant indeed typically go through an intermediate as you suggest: 1. A + B => I 2. I + C => P You would still need to map out the reaction profile to make sure what is the rate-determining /regio-selectivity determining step. I presume I could already exist in two regio-isomers. If A + B and I are in equilibrium and their interconversion is faster than the reaction with C, step 2. determines regioselectivity. In that case the transition state for the two regio-isomers I reacting with C determines overall regioselectivity (Curtin-Hammett conditions). If on the other hand A + B => I is irreversible and I rapidly reacts with C, step 1. determines the regioselectivity as it is already locked in there. There are quite a few good lecture notes and books on physical organic chemistry that explain these principles. There are also many research papers where they have applied computational chemistry to back up experimental results on observed regio- and stereo-selectivity. I hope this helps, Best wishes, Fedor On 11/2/2015 10:13 PM, Saied Mohammed Soliman saied1soliman .. yahoo.com wrote: > Sent to CCL by: "Saied Mohammed Soliman" [saied1soliman]-[yahoo.com] > Sorry,I was posted an e-mail regarding the transition state location for > reaction involve three reactants so may be it was not clear? > I have reaction between three reactants > A+B+C------Product > > the suggested mechanism is: > > 1- A+B-----intermediate > then > > 2- intermediate + C-------final product(regioselective cycloaddition > reaction) > > We expected two products but actually the cycloadditon goes > regioselectively to give only one product. I want to explain why? > > My problem is, how to work on these two steps? > or Should I consider only the second step to locate the transition state > of the second step only? > > How can work on the intermediate, is it considered as reactant or > considered as a transition state? I mean is the structure of the > intermediate should be optimized to an energy minimum or to a transition > state > > Thank you > Saied> > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 https://www.scm.com https://twitter.com/SCM_Amsterdam From owner-chemistry@ccl.net Tue Nov 3 10:54:01 2015 From: "Mikael Johansson mikael.johansson a iki.fi" To: CCL Subject: CCL: Winter School in Theoretical Chemistry: Computational Biochemistry Message-Id: <-51850-151103104535-31375-QUMMMr75MM7wzm02Pim1ig**server.ccl.net> X-Original-From: Mikael Johansson Content-Type: text/plain; charset=US-ASCII Date: Tue, 3 Nov 2015 17:45:24 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson]_[iki.fi] Dear All, It is soon time again for the annual Winter School in Theoretical Chemistry, traditionally held at the University of Helsinki, Finland. The topic of this year's edition of the School is "Computational Biochemistry"; the venue, Department of Chemistry, University of Helsinki, Finland; the dates, 14-17 Dec 2015. For full information, see: http://www.chem.helsinki.fi/Info/WinterSchool/ws2015.html Speakers include: Jochen Blumberger, University College London, United Kingdom Carles Curutchet, University of Barcelona, Spain Fahmi Himo, University of Stockholm, Sweden Gerhard Hummer, Max Planck Institute of Biophysics, Germany Ville R. I. Kaila, Technical University of Munich, Germany Lynn Kamerlin, Uppsala University, Sweden Edina Rosta, King's College London, United Kingdom Ulf Ryde, Lund University, Sweden Ilpo Vattulainen, Tampere University of Technology, Finland Adrian Goldman, University of Leeds, United Kingdom / University of Helsinki, Finland Participants are requested to register by December 1st, 2015. Questions can be sent to winterschool[-]chem.helsinki.fi Welcome! Ville Kaila, Technical University of Munich, Germany Dage Sundholm, University of Helsinki, Finland Mikael Johansson, University of Helsinki, Finland From owner-chemistry@ccl.net Tue Nov 3 17:46:01 2015 From: "rayen mahi mahi.rayen-$-gmail.com" To: CCL Subject: CCL:G: DOS calculations with G09 Message-Id: <-51851-151103174151-32410-rwbWIatBll1nH9WbQnS8bA---server.ccl.net> X-Original-From: rayen mahi Content-Type: multipart/alternative; boundary=001a1138f8641d60aa0523aa992d Date: Tue, 3 Nov 2015 23:41:43 +0100 MIME-Version: 1.0 Sent to CCL by: rayen mahi [mahi.rayen ~ gmail.com] --001a1138f8641d60aa0523aa992d Content-Type: text/plain; charset=UTF-8 Hello everyone, Does anyone know how to get density of states with Gaussian09 ? I need the command for the input file . I appreciate your help --001a1138f8641d60aa0523aa992d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Hello everyone,


Does any= one know how to get density of states wi= th Gaussian09 ? I need the command for the =C2= =A0input file .


I appreciate your help

--001a1138f8641d60aa0523aa992d--