From owner-chemistry@ccl.net Mon Mar 23 13:31:01 2015 From: "ggotelli()kaliumtech.com" To: CCL Subject: CCL:G: Gaussian IR frequency calculation Message-Id: <-51176-150323132627-19765-iO8cLnG6ux/9JuowSpJXoQ]![server.ccl.net> X-Original-From: Content-Language: es Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 23 Mar 2015 14:26:20 -0400 MIME-Version: 1.0 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. 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(~)ccl.net [mailto:owner-chemistry+ggotelli==kaliumtech.com(~)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: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= 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 From owner-chemistry@ccl.net Mon Mar 23 19:29:00 2015 From: "zborowsk zborowsk^chemia.uj.edu.pl" To: CCL Subject: CCL:G: Gaussian IR frequency calculation Message-Id: <-51177-150323183440-29086-gvYzmRPICXn7A6GVaHdnhA,server.ccl.net> X-Original-From: zborowsk Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 23 Mar 2015 23:34:30 +0100 MIME-Version: 1.0 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: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= 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 > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/-- 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/~zborowsk From owner-chemistry@ccl.net Mon Mar 23 20:53:01 2015 From: "Abrash, Samuel sabrash%a%richmond.edu" To: CCL Subject: CCL:G: Gaussian IR frequency calculation Message-Id: <-51178-150323205149-9832-Usu0dEtqcuEEaU8x86m3Dw]^[server.ccl.net> X-Original-From: "Abrash, Samuel" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Tue, 24 Mar 2015 00:51:40 +0000 MIME-Version: 1.0 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: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= 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> > From owner-chemistry@ccl.net Mon Mar 23 23:00:00 2015 From: "Robert Molt r.molt.chemical.physics ~ gmail.com" To: CCL Subject: CCL:G: Gaussian IR frequency calculation Message-Id: <-51179-150323225757-21093-rMB+yqMGV6BYrA0SoY1TGA[a]server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Mon, 23 Mar 2015 22:57:49 -0400 MIME-Version: 1.0 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: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= 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 From owner-chemistry@ccl.net Mon Mar 23 23:34:01 2015 From: "Mohamed Abdulhameed mabdulhameed-*-bhsai.org" To: CCL Subject: CCL: Call for abstracts - Computational Toxicology symposium Message-Id: <-51180-150323222335-15902-a2w7CLyZGNSYvIJ4aplLeg^^^server.ccl.net> X-Original-From: "Mohamed Abdulhameed" Date: Mon, 23 Mar 2015 22:23:33 -0400 Sent to CCL by: "Mohamed Abdulhameed" [mabdulhameed[*]bhsai.org] Hello, I am organizing a symposium on "Computational Toxicology - QSAR models to Adverse Outcome Pathways" under the Division of Chemical Information (CINF) at the 250th American Chemical Society (ACS) National Meeting, Boston, MA (Aug 16- 20 2015). The symposium aims to cover recent trends in computational toxicology. The abstract submission deadline is March 29, 2015. Abstract submission link: http://www.acs.org/content/acs/en/meetings/abstract- submissions/acsnm250/division-of-chemical-information.html Call for abstracts can be found at: https://www.linkedin.com/pulse/call-abstracts-computational-toxicology-from- qsar-abdulhameed Thanks Mohamed