From owner-chemistry@ccl.net Fri Oct 25 05:24:00 2013 From: "Dr. Vitaly Chaban vvchaban###gmail.com" To: CCL Subject: CCL:G: DFT Simulation of Ionic bonding in GaussView and Gaussian09 software Message-Id: <-49276-131025052217-16605-0DuxoG6Ps6N+0SEu3wbymg],[server.ccl.net> X-Original-From: "Dr. Vitaly Chaban" Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 25 Oct 2013 11:21:29 +0200 MIME-Version: 1.0 Sent to CCL by: "Dr. Vitaly Chaban" [vvchaban!A!gmail.com] You ought to provide the most reliable input structure possible and then optimize the geometry. You need not to explicitly connect the particles though. Dr. Vitaly V. Chaban On Thu, Oct 24, 2013 at 10:52 AM, Shaumik Ray rayshaumik*gmail.com wrote: > > Sent to CCL by: "Shaumik Ray" [rayshaumik===gmail.com] > I have a background o f simulating organic molecules in GaussView and > Gaussian09 software package. > > However, when I am trying to do DFT simulations (Frequency and Optimisation) > with B3LYP and 6-31G (d) basis set combinations (giving an overall charge of 0 > and Spin - Singlet) OF Ionic Bond structures like Calcium Silicate, Calcium > Hydroxide etc, I am getting an error message. > > For Calcium Silicate, I am connecting SO4 and keeing 2 Ca atoms on either side. > > Can someone help me to simulate ionic bonds in Gaussian software. Do I have to > connect all the molecules in some way? > > Please help.> > From owner-chemistry@ccl.net Fri Oct 25 08:38:01 2013 From: "mohan maruthi sena maruthi.sena:-:gmail.com" To: CCL Subject: CCL:G: Frequency calculations in gaussian09 at different temperatures Message-Id: <-49277-131025013315-11403-bc2gnNhguOl/f2xFqn4yQw:-:server.ccl.net> X-Original-From: "mohan maruthi sena" Date: Fri, 25 Oct 2013 01:33:14 -0400 Sent to CCL by: "mohan maruthi sena" [maruthi.sena===gmail.com] Hi all, I am new to gaussian09 and I want to perform frequency calculations for a organic molecule at different temperature and pressure. I used g09 keyword temperature , pressure in input file. I hesitant about this, can we do like this. Thanks, Mohan From owner-chemistry@ccl.net Fri Oct 25 09:13:01 2013 From: "huixiaokang328 15940870616|163.com" To: CCL Subject: CCL: DFT Simulation of Ionic bonding in GaussView and Gaussian09 software Message-Id: <-49278-131025064707-8320-I7FamLqNVrMKDXxvZSjveg.@.server.ccl.net> X-Original-From: huixiaokang328 <15940870616,+,163.com> Content-Type: multipart/alternative; boundary="----=_Part_233277_1059695068.1382698013978" Date: Fri, 25 Oct 2013 18:46:53 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: huixiaokang328 [15940870616###163.com] ------=_Part_233277_1059695068.1382698013978 Content-Type: text/plain; charset=GBK Content-Transfer-Encoding: base64 Y2FuIHlvdSBzaG93IHVzIHlvdXIgZXJyb3IgaW5mb3JtYXRpb24gcGFydD8KIApEci4gS2FuZwoK CgoKCgoKCkF0IDIwMTMtMTAtMjUgMTc6MjE6MjksIkRyLiBWaXRhbHkgQ2hhYmFuIHZ2Y2hhYmFu IyMjZ21haWwuY29tIiA8b3duZXItY2hlbWlzdHJ5QGNjbC5uZXQ+IHdyb3RlOgo+Cj5TZW50IHRv IENDTCBieTogIkRyLiBWaXRhbHkgQ2hhYmFuIiBbdnZjaGFiYW4hQSFnbWFpbC5jb21dCj5Zb3Ug 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all, I have some doubts regarding the theoretical identification of biradicals. I have read in the literature that a value of between 0.4 and 1 indicates biradical character. However, to this end we should look at before or after spin annihilation? I am asking because I have tried to replicate a study in which the authors claim that they have found a biradical structure. Having performed the calculations, I have found that before annihilation was near 1, while after annihilation was ~0.03. So, this is a biradical or a calculation with high spin contamination? From owner-chemistry@ccl.net Fri Oct 25 12:02:00 2013 From: "Dr. Vitaly Chaban vvchaban-#-gmail.com" To: CCL Subject: CCL: Comparison of qm-derived force fields Message-Id: <-49280-131025103742-24477-KTXAtkF0z8L3tkHfOzIdJQ a server.ccl.net> X-Original-From: "Dr. Vitaly Chaban" Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 25 Oct 2013 16:36:55 +0200 MIME-Version: 1.0 Sent to CCL by: "Dr. Vitaly Chaban" [vvchaban+*+gmail.com] I do not have references at hand, but the things are not as easy as -- use better electronic structure method, get better classical force field. Even if you compute something very straightforward, such as ionization potential, and plot it as a function from basis set, there is sometimes no clear "convergence" towards an experimental value. Such phenomena as [ignored] many-particle interactions normally play a larger role than the profit (even if it is) from the more advanced electronic structure approach. In some of my papers, I tried to make such comparisons (very sporadically though) and the undoubted verdict is above. Dr. Vitaly V. Chaban On Fri, Oct 25, 2013 at 12:04 AM, Joseph Leonard jleonard42- -gmail.com wrote: > Folks, does anybody have references where people have compared "old" force > fields derived from HF/6-31g* (maybe mp2) with "new" force fields derived > from larger-basis DFT calculations? I'm interested in learning how the > state of the art has progressed and lack a better lit searching engine than > google. Given the qm experience in ccl's readership I hope some ff > developers are reading. Thanks in advance for pointers! > > Joe Leonard > > > -- > I live in a science fiction fantasy, except it's all real now. You guys > grew up with computers. Computers grew up with me. > > From owner-chemistry@ccl.net Fri Oct 25 12:37:00 2013 From: "Dr. Vitaly Chaban vvchaban|,|gmail.com" To: CCL Subject: CCL: Comparison of qm-derived force fields Message-Id: <-49281-131025104517-28936-3UE551MwkRUeIjB+TLQleQ^_^server.ccl.net> X-Original-From: "Dr. Vitaly Chaban" Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 25 Oct 2013 16:44:30 +0200 MIME-Version: 1.0 Sent to CCL by: "Dr. Vitaly Chaban" [vvchaban*gmail.com] I do not have references at hand, but the things are not as easy as -- use better electronic structure method, get better classical force field. Even if you compute something very straightforward, such as ionization potential, and plot it as a function from basis set, there is sometimes no clear "convergence" towards an experimental value. Such phenomena as [ignored] many-particle interactions normally play a larger role than the profit (even if it is) from the more advanced electronic structure approach. In some of my papers, I tried to make such comparisons (very sporadically though) and the undoubted verdict is above. Dr. Vitaly V. Chaban On Fri, Oct 25, 2013 at 12:04 AM, Joseph Leonard jleonard42- > Folks, does anybody have references where people have compared "old" force > fields derived from HF/6-31g* (maybe mp2) with "new" force fields derived > from larger-basis DFT calculations? I'm interested in learning how the > state of the art has progressed and lack a better lit searching engine than > google. Given the qm experience in ccl's readership I hope some ff > developers are reading. Thanks in advance for pointers! > > Joe Leonard > From owner-chemistry@ccl.net Fri Oct 25 14:00:01 2013 From: "Nuno Alexandre Guerreiro Bandeira nuno.bandeira\a/ist.utl.pt" To: CCL Subject: CCL: Doubts about biradicals Message-Id: <-49282-131025115156-18013-W/XDt2QhANvMs54im7plXw---server.ccl.net> X-Original-From: Nuno Alexandre Guerreiro Bandeira Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Fri, 25 Oct 2013 15:51:47 +0000 MIME-Version: 1.0 Sent to CCL by: Nuno Alexandre Guerreiro Bandeira [nuno.bandeira[A]ist.utl.pt] Em 2013-10-25 13:39, Luis Pinto da Silva LuisPdSilva%gmail.com escreveu: > Sent to CCL by: "Luis Pinto da Silva" [LuisPdSilva*o*gmail.com] > Hi all, > > I have some doubts regarding the theoretical identification of > biradicals. I > have read in the literature that a value of between 0.4 and 1 > indicates > biradical character. However, to this end we should look at > before or > after spin annihilation? I am asking because I have tried to > replicate a study > in which the authors claim that they have found a biradical > structure. Having > performed the calculations, I have found that before > annihilation was > near 1, while after annihilation was ~0.03. > > So, this is a biradical or a calculation with high spin > contamination? First of all what kind of method are you referring to here ? I presume single determinant methods like DFT or HF. From your text you seem to be referring to an open-shell singlet biradical in which case your only solution is to get a broken (spin) symmetry solution and that is always a mixture of two spin states and after that you apply a spin projection technique (J. Comput. Chem. 1999, 20, 1391) to calculate the energy gap for spin exchange. Spin annihilation is in fact counter-productive since you do not want to resolve the wavefunction into the closed shell solution. Another possible solution to a biradical is the triplet which should be degenerate with the open-shell singlet (you should check this). Triplets in biradical systems can be obtained trivially and should be one-determinantal. Best wishes, -- Nuno A. G. Bandeira, AMRSC Institut Català d'Investigació Química 16, Av. Països Catalans 43007 Tarragona, SPAIN http://www.researcherid.com/rid/B-6399-2012 http://pt.linkedin.com/pub/nuno-a-g-bandeira/47/55a/2aa --