From owner-chemistry@ccl.net Sun May 15 12:03:00 2011 From: "Arne Dieckmann adieckma . googlemail.com" To: CCL Subject: CCL:G: What's the appropriate method? Message-Id: <-44634-110515120226-1839-UtyzUR6SapzlwoxqiAFInA|,|server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Sun, 15 May 2011 18:02:09 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Arne Dieckmann [adieckma]^[googlemail.com] Thanks a lot for your help. Unfortunately, my systems are too large for DFT - it would have been my method of choice. On May 13, 2011, at 2:41 PM, Sergio Emanuel Galembeck segalemb!=!usp.br wrote: > > Sent to CCL by: Sergio Emanuel Galembeck [segalemb*o*usp.br] > Dear Arne, > > If molecules are not so large, I suggest the use of DFT methods. They > are fast and some are reliable. If you could use other programs, I suggest > GAMESS, because there are several funcionals, and the EFP2 method for solvation. > I only remain that MOPAC2000 is free for academics. > > Best regards, > > Sergio > > > > > Citando "Arne Dieckmann adieckma+*+googlemail.com" : > >> >> Sent to CCL by: Arne Dieckmann [adieckma++googlemail.com] >> Thanks, Sergio. Unfortunately, I will have to use Gaussian03 for the calculations. How about PM3MM then? >> >> >> On May 12, 2011, at 6:00 PM, Sergio Emanuel Galembeck segalemb~~usp.br wrote: >> >>> >>> Sent to CCL by: Sergio Emanuel Galembeck [segalemb-$-usp.br] >>> Arne, >>> >>> I suggest PM6-DH2, present in MOPAC2000. Another option is >>> RM1. >>> >>> Best regards, >>> >>> Sergio >>> >>> >>> >>> >>> Citando "Arne Dieckmann adieckma*|*googlemail.com" : >>> >>>> >>>> Sent to CCL by: "Arne Dieckmann" [adieckma]*[googlemail.com] >>>> Dear all, >>>> >>>> I would like to optimize some structures containing nucleobases (and base-pairing) as well as peptide-bonds. Furthermore, potentials and barriers for some conformational changes and isomerizations should be determined. I would like to go beyond force fields as the molecules are small enough for e.g. semiempirical methods and use implicit solvation. What semiempirical method (AM1, PM3,...) - if any - would you recommend? >>>> >>>> >>>> Cheers, >>>> Arnehttp://www.ccl.net/chemistry/sub_unsub.shtml> >>> Job: http://www.ccl.net/jobshttp://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobs> > From owner-chemistry@ccl.net Sun May 15 12:38:00 2011 From: "Dr. Bhargav Trivedi bhargavatrivedi*gmail.com" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44635-110515032627-21482-RpW1TXXOhVhPF5hZTHDWGg_._server.ccl.net> X-Original-From: "Dr. Bhargav Trivedi" Content-Type: multipart/alternative; boundary=bcaec517a9422ec51104a34b747c Date: Sun, 15 May 2011 12:56:13 +0530 MIME-Version: 1.0 Sent to CCL by: "Dr. Bhargav Trivedi" [bhargavatrivedi{:}gmail.com] --bcaec517a9422ec51104a34b747c Content-Type: text/plain; charset=ISO-8859-1 For your kind attention, the site was Indonesian and not Indian. On Sat, May 7, 2011 at 2:42 AM, David A Mannock dmannock]*[ualberta.ca < owner-chemistry,+,ccl.net> wrote: > Anurikta, Put your moral indignation aside for the moment. Yes, piracy > happens everywhere, but we are not talking about soccer games here, but text > books and software. Many of the major computer chemistry software programs > come from Western companies and texts relevant to that software generally > cost more money than is available to a student in a third world country. If > I borrow something from the internet as a trial or an illegal copy, I try > out the software or book and if it is useful, I go ahead with a personal > purchase (Yes, out of my own pocket!!) or get something through my > institution. Incidentally, I have purchased lower priced texts of interest > to me from publishers in India and they are similar in price to the Dover > classics available on Amazon. The difference in price is an order of > magnitude. My focus on China and India is simply that there have been many > news items here over the past 10 years about exactly this type of piracy and > the reluctance of the respective institutions and governments to take > positive steps to eliminate it. What I am saying is that I understand the > need for students in non-western countries to get what they need to have an > education. Research and higher education is expensive and even in countries > like Canada, money for such things is very tight. > > Part of the piracy problem is that some publishing houses are trying to cut > costs by outsourcing the printing of the books, presumably through the > transfer of electronic media to those countries. One of the arguments that I > have made here is for proper assertion of the rights of authorship through > the universities commercial offices and publishing houses to stamp out > institutional piracy. It was pointed out on this forum that the web site on > which Prof Cramer's book was stored was at an Indian institution. I suspect > that a blind eye is turned to such practices by both the institution and the > local government. Here it is feasible for the publishing or software company > or the author to make the accusation of plagiarism or piracy in the civil > court and sue. This is not easily done in other countries and the amount of > any settlement may itself be dictated by the local market rather than the > market where the product was developed. If you feel strongly that this > practice should be stamped out in your own institution, try approaching your > VP research and see if you can accomplish this. My guess is that you will > receive nothing more than lip-service from the senior administration and > that no one will want to touch this issue with a barge pole. > > Here on my lab computers, I am not permitted to install illegal copies of > software and as a general rule, I do not download textbooks that I do not > consider for purchase. When my responsibilities for writing up manuscripts > ends here and I have to find a job elsewhere, all university licensed > software will need to be uninstalled from my lab and home computers. In > fact, I was reminded of this by our IT support person this week. Today, > everyone wants their buck. There is no escaping this. Dave > > > -- Dr. Bhargav Trivedi, Associate Professor Of Chemistry, J & J College Of Science, Nadiad, Gujarat. India. Phone: +919825654872 --bcaec517a9422ec51104a34b747c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable For your kind attention, the site was Indonesian and not Indian.

On Sat, May 7, 2011 at 2:42 AM, David A Mannock dm= annock]*[ualberta.ca &= lt;owner-chemistry,+,ccl.net&g= t; wrote:
Anurikta, Put you= r moral indignation aside for the moment. Yes, piracy happens everywhere, b= ut we are not talking about soccer games here, but text books and software.= Many of the major computer chemistry software programs come from Western c= ompanies and texts relevant to that software generally cost more money than= is available to a student in a third world country. If I borrow something = > from the internet as a trial or an illegal copy, I try out the software or = book and if it is useful, I go ahead with a personal purchase (Yes, out of = my own pocket!!) or get something through my institution. Incidentally, I h= ave purchased lower priced texts of interest to me from publishers in India= and they are similar in price to the Dover classics available on Amazon. T= he difference in price is an order of magnitude. My focus on China and Indi= a is simply that there have been many news items here over the past 10 year= s about exactly this type of piracy and the reluctance of the respective in= stitutions and governments to take positive steps to eliminate it. What I a= m saying is that I understand the need for students in non-western countrie= s to get what they need to have an education. Research and higher education= is expensive and even in countries like Canada, money for such things is v= ery tight.

Part of the piracy problem is that some publishing houses are trying to= cut costs by outsourcing the printing of the books, presumably through the= transfer of electronic media to those countries. One of the arguments that= I have made here is for proper assertion of the rights of authorship throu= gh the universities commercial offices and publishing houses to stamp out i= nstitutional piracy. It was pointed out on this forum that the web site on = which Prof Cramer's book was stored was at an Indian institution. I sus= pect that a blind eye is turned to such practices by both the institution a= nd the local government. Here it is feasible for the publishing or software= company or the author to make the accusation of plagiarism or piracy in th= e civil court and sue. This is not easily done in other countries and the a= mount of any settlement may itself be dictated by the local market rather t= han the market where the product was developed. If you feel strongly that t= his practice should be stamped out in your own institution, try approaching= your VP research and see if you can accomplish this. My guess is that you = will receive nothing more than lip-service from the senior administration a= nd that no one will want to touch this issue with a barge pole.

Here on my lab computers, I am not permitted to install illegal copies = of software and as a general rule, I do not download textbooks that I do no= t consider for purchase. When my responsibilities for writing up manuscript= s ends here and I have to find a job elsewhere, all university licensed sof= tware will need to be uninstalled from my lab and home computers. In fact, = I was reminded of this by our IT support person this week. Today, everyone = wants their buck. There is no escaping this. Dave





--
Dr. Bhargav Trivedi,Associate Professor Of Chemistry,
J & J College Of Science,
Nadi= ad, Gujarat.
India.
Phone: +919825654872

--bcaec517a9422ec51104a34b747c-- From owner-chemistry@ccl.net Sun May 15 14:25:00 2011 From: "Jim Kress ccl_nospam*kressworks.com" To: CCL Subject: CCL:G: What's the appropriate method? Message-Id: <-44636-110515132713-7128-XnHnDmaKnB/kXR+85E3e3w*server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 15 May 2011 13:26:38 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam#%#kressworks.com] Have you tried Firefly, ORCA, Turbomole, or ADF? They are all high performance QM codes that can handle quite large polypeptide systems. Firefly and ORCA are free. Firefly: http://classic.chem.msu.su/gran/gamess/index.html ORCA: http://www.thch.uni-bonn.de/tc/orca/ Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com[A]ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com[A]ccl.net] On Behalf Of Arne > Dieckmann adieckma . googlemail.com > Sent: Sunday, May 15, 2011 12:02 PM > To: Kress, Jim > Subject: CCL:G: What's the appropriate method? > > > Sent to CCL by: Arne Dieckmann [adieckma]^[googlemail.com] > Thanks a lot for your help. Unfortunately, my systems are too large for > DFT - it would have been my method of choice. > > > On May 13, 2011, at 2:41 PM, Sergio Emanuel Galembeck segalemb!=!usp.br > wrote: > > > > > Sent to CCL by: Sergio Emanuel Galembeck [segalemb*o*usp.br] > > Dear Arne, > > > > If molecules are not so large, I suggest the use of DFT methods. > They > > are fast and some are reliable. If you could use other programs, I > suggest > > GAMESS, because there are several funcionals, and the EFP2 method for > solvation. > > I only remain that MOPAC2000 is free for academics. > > > > Best regards, > > > > Sergio > > > > > > > > > > Citando "Arne Dieckmann adieckma+*+googlemail.com" chemistry\a/ccl.net>: > > > >> > >> Sent to CCL by: Arne Dieckmann [adieckma++googlemail.com] > >> Thanks, Sergio. Unfortunately, I will have to use Gaussian03 for the > calculations. How about PM3MM then? > >> > >> > >> On May 12, 2011, at 6:00 PM, Sergio Emanuel Galembeck > segalemb~~usp.br wrote: > >> > >>> > >>> Sent to CCL by: Sergio Emanuel Galembeck [segalemb-$-usp.br] > >>> Arne, > >>> > >>> I suggest PM6-DH2, present in MOPAC2000. Another option is > >>> RM1. > >>> > >>> Best regards, > >>> > >>> Sergio > >>> > >>> > >>> > >>> > >>> Citando "Arne Dieckmann adieckma*|*googlemail.com" chemistry%ccl.net>: > >>> > >>>> > >>>> Sent to CCL by: "Arne Dieckmann" [adieckma]*[googlemail.com] > >>>> Dear all, > >>>> > >>>> I would like to optimize some structures containing nucleobases > (and base-pairing) as well as peptide-bonds. Furthermore, potentials > and barriers for some conformational changes and isomerizations should > be determined. I would like to go beyond force fields as the molecules > are small enough for e.g. semiempirical methods and use implicit > solvation. What semiempirical method (AM1, PM3,...) - if any - would > you recommend? > >>>> > >>>> > >>>> Cheers, > >>>> Arnehttp://www.ccl.net/chemistry/sub_unsub.shtml> > >>> Job: > http://www.ccl.net/jobshttp://www.ccl.net/chemistry/sub_unsub.shtml> > > Job: http://www.ccl.net/jobs> To recover the email address of the author of the message, please > change> From owner-chemistry@ccl.net Sun May 15 17:23:01 2011 From: "Sergio Emanuel Galembeck segalemb###usp.br" To: CCL Subject: CCL:G: What's the appropriate method? Message-Id: <-44637-110515171413-2588-SvKToa1BbSGTxsA/R4cw1g,+,server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sun, 15 May 2011 18:13:58 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb%%usp.br] Dear Arne, An alternative for your problem is to use ONIOM method, if it is possible. But, as you need to use G03, and DFT are very expensive for the size of your system, even local functionals, you have few alternatives, or AM1 or PM3. Best regards, Sergio Citando "Arne Dieckmann adieckma . googlemail.com" : > > Sent to CCL by: Arne Dieckmann [adieckma]^[googlemail.com] > Thanks a lot for your help. Unfortunately, my systems are too large > for DFT - it would have been my method of choice. > > > On May 13, 2011, at 2:41 PM, Sergio Emanuel Galembeck > segalemb!=!usp.br wrote: > >> >> Sent to CCL by: Sergio Emanuel Galembeck [segalemb*o*usp.br] >> Dear Arne, >> >> If molecules are not so large, I suggest the use of DFT methods. They >> are fast and some are reliable. If you could use other programs, I suggest >> GAMESS, because there are several funcionals, and the EFP2 method >> for solvation. >> I only remain that MOPAC2000 is free for academics. >> >> Best regards, >> >> Sergio >> >> >> >> >> Citando "Arne Dieckmann adieckma+*+googlemail.com" >> : >> >>> >>> Sent to CCL by: Arne Dieckmann [adieckma++googlemail.com] >>> Thanks, Sergio. Unfortunately, I will have to use Gaussian03 for >>> the calculations. How about PM3MM then? >>> >>> >>> On May 12, 2011, at 6:00 PM, Sergio Emanuel Galembeck >>> segalemb~~usp.br wrote: >>> >>>> >>>> Sent to CCL by: Sergio Emanuel Galembeck [segalemb-$-usp.br] >>>> Arne, >>>> >>>> I suggest PM6-DH2, present in MOPAC2000. Another option is >>>> RM1. >>>> >>>> Best regards, >>>> >>>> Sergio >>>> >>>> >>>> >>>> >>>> Citando "Arne Dieckmann adieckma*|*googlemail.com" >>>> : >>>> >>>>> >>>>> Sent to CCL by: "Arne Dieckmann" [adieckma]*[googlemail.com] >>>>> Dear all, >>>>> >>>>> I would like to optimize some structures containing nucleobases >>>>> (and base-pairing) as well as peptide-bonds. Furthermore, >>>>> potentials and barriers for some conformational changes and >>>>> isomerizations should be determined. I would like to go beyond >>>>> force fields as the molecules are small enough for e.g. >>>>> semiempirical methods and use implicit solvation. What >>>>> semiempirical method (AM1, PM3,...) - if any - would you >>>>> recommend? >>>>> >>>>> >>>>> Cheers, >>>>> Arnehttp://www.ccl.net/chemistry/sub_unsub.shtml> >>>> Job: http://www.ccl.net/jobshttp://www.ccl.net/chemistry/sub_unsub.shtml> >> Job: http://www.ccl.net/jobs> > > From owner-chemistry@ccl.net Sun May 15 17:58:00 2011 From: "Sergio Emanuel Galembeck segalemb\a/usp.br" To: CCL Subject: CCL:G: van-der-Waals-complex vs. weak forces Message-Id: <-44638-110515174651-26652-VO6HFctWMWUmiQg+fOhkLg##server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sun, 15 May 2011 18:46:40 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb/a\usp.br] Dear Gutram, There are some methods to analyze the electron density and to obtain informations about the nature of the intra or intermolecular interactions. Some of them are Natural Bond Orbitals (NBO) Atoms in Molecules (AIM), Electron Localization Function (ELF), and the several energetic decomposition methods of analysis, as Morokuma's and EDA. A very interesting review that contains a classification of the chemical interactions is SJ Grabowski, Chem. Rev., 2011, 111, 2597. However, you need to remember that there is no consensus about criteria for the distinction between types of interactions. Hope this help you, Sergio Citando "Guntram Schmidt guntram.schmidt]=[chemie.uni-halle.de" : > > Sent to CCL by: "Guntram Schmidt" [guntram.schmidt(-)chemie.uni-halle.de] > Hello together! > > I want to exam some (mainly organic) crystal structures, which seem > to be mainly held together by weak forces like Phenyl-H---O hydrogen > bonds, Phenly-H---Phenyl hydrogen bonds or Pi-Pi-stacking. > > I cut out the corresponding dimers of the crystal structure and > subjected them to geometry optimisation, using gaussian 09 with the > input line > > #T opt freq b97d/6-31g(d,p)/auto=all > > which works quite well, resulting in minima for expected bonding, > but striding away molecules for dimers which are not supposed to > interact in a "bonding" way. > > Now having some optimized structures, is there anything to do to > prove the nature of the "bonding"? > How can I distinguish the "van-der-Waals complex" from a dispersion > interaction or some kind of hydrogen bonding? > > > Thanks a lot for suggestions on how to treat this problem, > Guntram> > >