From owner-chemistry@ccl.net Sun Nov 10 05:09:00 2013 From: "Hamid Shojaei shojaei81^gmail.com" To: CCL Subject: CCL: Differences between theoretical and experimental torsion angles Message-Id: <-49327-131110050808-12412-RfXnB0r2drVyhZfpbeaQWA(!)server.ccl.net> X-Original-From: "Hamid Shojaei" Date: Sun, 10 Nov 2013 05:08:07 -0500 Sent to CCL by: "Hamid Shojaei" [shojaei81**gmail.com] Dear Dr. Hugo Alejandro Jimnez Vzquez, Thank you very much for your comment on my question in CCL. in some of torsional angles we have differences in a negative sign. How can I ignore this sign. Regards, shojaei > "Hugo Alejandro Jimenez Vazquez hjimenez[*]woodward.encb.ipn.mx" wrote: > > Sent to CCL by: Hugo Alejandro Jimenez Vazquez [hjimenez^_^woodward.encb.ipn.mx] > This message is in MIME format. The first part should be readable text, > while the remaining parts are likely unreadable without MIME-aware tools. > > ---862666845-1686960974-1384055120=:5311 > Content-Type: TEXT/PLAIN; CHARSET=ISO-8859-1; format=flowed > Content-Transfer-Encoding: QUOTED-PRINTABLE > Content-ID: > > > To be sincere, I do not see those "big differences" you mention. If you=20 > take into account that the negative angles can be converted to positive by= > =20 > adding 360, what you have is: > > 175.1 vs. 184.0 > 178.9 vs. 183.0 > 177.0 vs. 179.8 > 178.7 vs. 182.2 > 174.2 vs. 169.7 > 91.0 vs. 138.2 > > At least for me, only the values for the last angle differ by a more than= > =20 > reasonable amount; out of all the others, the first one differs the most,= > =20 > by less than 10=B0. > > I have no idea about what your molecule looks like. In addition, you do=20 > not mention how you got the experimental values, but I would assume they=20 > came from an X-ray diffraction structure. You should be aware that the=20 > gas phase structure (from the calculations) does not necessarily have to=20 > be exactly the same as the structure in the crystal. In the solid phase=20 > the geometry is influenced by nonbonded interactions with all the=20 > neighbouring molecues which might lead to a slight or severe changes with= > =20 > respect to the gas phase structure, particularly in floppy molecules. > > The gas phase geometry obtained through calculation also depends on the=20 > level of theory employed, something that you do not mention either. > > Regards, > > --- > Hugo A. Jimenez Vazquez > hjimenez(a)woodward.encb.ipn.mx > Departamento de Quimica Organica > ENCB-IPN > Mexico > > > On Sat, 9 Nov 2013, Hamid Shojaei Shojaei81..gmail.com wrote: > > > > > Sent to CCL by: "Hamid Shojaei" [Shojaei81-#-gmail.com] > > Dear All, > > > > I do some structural calculations but I see big differences between theor= > etical > > and experimental torsion angles. > > > > Torsion angle=09 Experimental=09Theoretical > > N(2)C(2)C(3)C(8)=09 175.1=09 -175.965 > > O(1)C(2)C(3)C(4)=09 178.94=09 -177.005 > > C(8)C(3)C(4)N(3)=09177.0 179.837 > > C(2)C(3)C(4)C(5)=09 178.73=09 -177.808 > > C(31)N(3)C(4)C(3)=09 174.2=09 169.686 > > C(4)N(3)C(31)C(32)=09 91.0=09 138.193 > > > > > > Any idea explaining such a differences is highly appreciated. > > > > > > > ---862666845-1686960974-1384055120=:5311-- > > From owner-chemistry@ccl.net Sun Nov 10 07:16:00 2013 From: "Michel Petitjean petitjean.chiral*o*gmail.com" To: CCL Subject: CCL: Differences between theoretical and experimental torsion angles Message-Id: <-49328-131110071341-17149-C85t6km/arj/+S/oavk9/g^server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 10 Nov 2013 13:13:34 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral .. gmail.com] Dear Shojaei, Usually torsion angles are expected to fall in the range -180...+180 degrees. A sign change could mean either a reverse ordering in the 4-tuple of involved atoms, or a mirror inversion done by the modeling software ? Regarding the 91.0 vs 138.2, could it be due to a rotation of the fourth atom (or of the first atom) at very low energy cost so that the difference between observed and predicted values could be unimportant ? May be you should provide more information about the structures, the modeling software, etc. Best regards, Michel. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral|gmail.com (preferred), michel.petitjean|univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html >Sent to CCL by: "Hamid Shojaei" [Shojaei81-#-gmail.com] >Dear All, > >I do some structural calculations but I see big differences between theoretical and experimental torsion angles. > >Torsion angle Experimental Theoretical >N(2)C(2)C(3)C(8) 175.1 -175.965 >O(1)C(2)C(3)C(4) 178.94 -177.005 >C(8)C(3)C(4)N(3) 177.0 179.837 >C(2)C(3)C(4)C(5) 178.73 -177.808 >C(31)N(3)C(4)C(3) 174.2 169.686 >C(4)N(3)C(31)C(32) 91.0 138.193 > > >Any idea explaining such a differences is highly appreciated. > From owner-chemistry@ccl.net Sun Nov 10 08:20:00 2013 From: "Olasunkanmi Lukman Olawale walecomuk .. yahoo.co.uk" To: CCL Subject: CCL: DFT for reactivity indices Message-Id: <-49329-131110080635-6896-+Jz+BZrWVeGatbrXdvS2mQ/a\server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Sun, 10 Nov 2013 13:06:26 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk^^yahoo.co.uk] Dear fellow subscribers, I have used conceptual DFT to calculate some global reactivity indices and fukui indices of some compounds. Is it reasonable to use the values obtained to compare chemical reactivity of two different compounds with the same functional groups? Previous articles I came across have only used these parameters to compare reactivity of isomeric compounds.