From owner-chemistry@ccl.net Tue Mar 24 02:23:00 2015 From: "berger%chem.helsinki.fi" To: CCL Subject: CCL:G: Gaussian IR frequency calculation Message-Id: <-51182-150324021856-27972-L3MT4BASE3yHumMMyj18rQ ~ server.ccl.net> X-Original-From: berger++chem.helsinki.fi Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 24 Mar 2015 08:18:24 +0200 MIME-Version: 1.0 Sent to CCL by: berger[a]chem.helsinki.fi Hello, 300-400 cm-1 in the whole range also in my eyes seems much too large. Are you calculating the correct molecule? Is the experimental data correct? Are there impurities in the compound / solvens, ...? Is there a overall similarity between computed and experimental spectrum? Cheers B > Sent to CCL by: Robert Molt [r.molt.chemical.physics]![gmail.com] > I respectfully disagree with the claim that KS-DFT functionals get 97% > accuracy of the correct value, and the remaining 3% is mostly > anharmonic. That assumes that KS-DFT functionals are describing electron > correlation perfectly, as opposed to it being an approximate method > varying in semi-empirical character from none to high. > > The mean absolute error over the G2 set of vibrational frequencies of > B3LYP is 31 wavenumbers (see the 1998 paper from Adamo and Barone), > obviously weighted more heavily for the higher values frequencies > statistically. The RMS error can be as high as 42 wavenumbers (1993 > Pople paper). > > The first harmonic mode of many molecules is often small, and the > percent error is much higher on this first mode (independent of harmonic > vs. anharmonic). > > On 3/23/15 8:51 PM, Abrash, Samuel sabrash%a%richmond.edu wrote: >> Sent to CCL by: "Abrash, Samuel" [sabrash|a|richmond.edu] >> With an appropriate functional with a good basis set, dft should get you >> to within about 97% of the correct value. The remainder of the error >> will be due to the harmonic approximation. Adding an anharmonic >> correction can get you to within 99%. >> >> Sent from my iPhone >> >>> On Mar 23, 2015, at 8:45 PM, zborowsk zborowsk^chemia.uj.edu.pl >>> wrote: >>> >>> >>> Sent to CCL by: zborowsk [zborowsk^chemia.uj.edu.pl] >>> W dniu 2015-03-23 19:26, ggotelli()kaliumtech.com napisaÅ‚(a): >>>> Sent to CCL by: [ggotelli[]kaliumtech.com] >>>> Thank you all for your help! >>>> I'll condense all my notes in the same mail. >>>> >>>> Krzysztof , yes I observed the difference in the whole spectrum. >>> Well, something strange. 300-400 cm-1 difference between theory and >>> experiment around 3000 cm-1 and also around 100 cm-1?? By the way, do >>> you have positive or negative (imaginary) frequencies around 100??? >>> >>> >>>> Serdar, the molecule that I 'm trying to calculate and where I have >>>> the >>>> differences is a dimer derived from dilactide. To estimate a scaling >>>> factor >>>> my reference molecule is dilactide in itself, which in turn has little >>>> differences between the calculated spectrum and the real one, >>>> depending on >>>> the peaks. >>>> >>>> André, thanks for the scaling factor reference. >>>> >>>> Stent, the polymer spectrum was made with an ATR device and without >>>> solvent. >>>> Because of this all calculations have done in vacuum. >>>> >>>> Robert, thanks for all your comments, they made me realize that my >>>> error was >>>> trying to adjust a dimer spectrum to a polymer spectrum, what are, of >>>> course, very different things. Although the dimer peaks are displaced >>>> with >>>> respect to those of the polymer, it can be seen from the GView >>>> animation >>>> that they correspond to what is expected, beyond the displacement >>>> involved. >>>> >>>> Regards! >>>> Gustavo Gotelli >>>> Polymer Synthesis >>>> Pharmaceutical Technology Department >>>> Faculty of Pharmacy and Biochemistry >>>> Buenos Aires University >>>> Argentina >>>> >>>> -----Mensaje original----- >>>> De: owner-chemistry+ggotelli==kaliumtech.com a ccl.net >>>> [mailto:owner-chemistry+ggotelli==kaliumtech.com a ccl.net] En nombre >>>> de >>>> Víctor Luaña Cabal victor^^fluor.quimica.uniovi.es >>>> Enviado el: sábado, 21 de marzo de 2015 21:16 >>>> Para: Gotelli, Gustavo A >>>> Asunto: CCL: Gaussian IR frequency calculation >>>> >>>> >>>> Sent to CCL by: Víctor Luaña Cabal >>>> [victor]|[fluor.quimica.uniovi.es] >>>> On Sat, Mar 21, 2015 at 05:56:44PM -0400, Robert Molt >>>> r.molt.chemical.physics],[gmail.com wrote: >>>>> Sent to CCL by: Robert Molt [r.molt.chemical.physics---gmail.com] >>>>> Moreover, you are using the B3LYP functional. It has limited >>>>> accuracy, >>>>> depending on the system specifics. If it is a multi-reference >>>>> problem, >>>>> great care is necessary. >>>>> >>>>> Also note that you can only compare the TOTAL spectrum, not any one >>>>> peak. >>>> Robert, >>>> >>>> 1) Let me take your highly correct advise to remember to the newest >>>> generations that the role on computational chemistry is not being >>>> able to reproduce the number of the experiment. >>>> >>>> 2) The experiment helps in modulating our calculations, and the final >>>> objective is a perfect reprodution of the experiment. >>>> >>>> 3) But the reason is not substituting experiments. The reason is that >>>> in the processs of mimicking it we learn the rules that govern >>>> Nature. >>>> >>>> 4) There are too many questions in this forum that tend to ignore >>>> this rule and it is important to remember it again and again. >>>> >>>> Best regards, >>>> Dr. Víctor Luaña >>>> -- >>>> . . "The hardest part in solving a problem is recognizing >>>> / `' \ its existence. Learning the causes CAN be the road to >>>> /(o)(o)\ the solution." >>>> /`. \/ .'\ -- ¿? >>>> / '`'` \ "Lo mediocre es peor que lo bueno, pero también es peor >>>> | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es una >>>> | >>>> |'`'`| | actitud" >>>> \/`'`'`'\/ -- Jorge Wasenberg, 2015 >>>> ===(((==)))==================================+========================= >>>> ! Dr.Víctor Luaña ! Mediocre is worse >>>> than >>>> ! Departamento de Química Física y Analítica ! good, but it is also >>>> ! >>>> Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because >>>> ! e-mail: victor-#-fluor.quimica.uniovi.es ! mediocrity is not a >>>> grade, >>>> ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude >>>> +--------------------------------------------+ >>>> GroupPage : http://azufre.quimica.uniovi.es/ (being >>>> reworked)http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- >>> https://www.youtube.com/watch?v=IGyfx3Pmeyk >>> Krzysztof K. Zborowski >>> Faculty of Chemistry >>> Jagiellonian University >>> 3 Ingardena Street >>> 30-060 Krakow >>> Poland >>> phone: +48(12)663-2067 >>> email: zborowsk(~)chemia.uj.edu.pl >>> gg 3817259 >>> skype kzys70 >>> www.chemia.uj.edu.pl/~zborowskhttp://www.ccl.net/chemistry/sub_unsub.shtml> >> > > -- > Dr. Robert Molt Jr. > r.molt.chemical.physics=-=gmail.com > Nigel Richards Research Group > Department of Chemistry & Chemical Biology > Indiana University-Purdue University Indianapolis > LD 326 > 402 N. Blackford St. > Indianapolis, IN 46202> > >