From owner-chemistry@ccl.net Sat Dec 10 00:22:00 2005 From: "Telkuni Tsuru telkuni++venus.dti.ne.jp" To: CCL Subject: CCL:G: Summary) TDDFT calculation in water solvent ... else Message-Id: <-30264-051210001815-22626-SrDyitp2sii3Q6yep9sacA=-=server.ccl.net> X-Original-From: "Telkuni Tsuru" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-2022-jp" Date: Sat, 10 Dec 2005 14:18:09 +0900 MIME-Version: 1.0 Sent to CCL by: "Telkuni Tsuru" [telkuni^^venus.dti.ne.jp] Hello, CCLers and Brazil, Croatia, Australia people. Let's meet in Germany 2006WC. I've sent following question a few days ago. And I've received good replies for it. Thank you very much Massimo Ottonelli and Douglas J. Fox. In summary, although G98 can't do TDDFT-IPCM calculation, G03 can do it by IEFPCM model ----- Original Question ----- Sent: Tuesday, December 06, 2005 11:22 PM Subject: CCL: TDDFT calculation in water solvent > Hello, CCLers. > > I'm trying to do TDDFT calculation in water solvent using Gaussian98W_A7. > I wrote following GJF of which molecular CO2 coordination was optimized > by HF/STO-3G. > . . . > . . . > . . . > Although the first job step(optimization) was succeed, second job step(TDDFT) > was failed with following error massage: > -------------------------------------------------- > Reaction Field using a Density IsoSurface Boundary > -------------------------------------------------- > Epsi= 78.4000 Cont = 0.0010 > Will Allow IsoSurface To Relax Throughout > Convergence set to 1.00D-06 > 40 Phi and 20 Theta Values Per Atom > NABMO STP ISTEP RAD NUMR CUTOFF DStMX0 MoBas? > 4 5.00E-02 5 1.0E-01 20 1.0E-10 1.0E+01 F > Using single center to handle rho isosurface. > Density number -1 is not available. > Error termination via Lnk1e in C:\G98W\l117.exe. > Job cpu time: 0 days 0 hours 6 minutes 17.0 seconds. > File lengths (MBytes): RWF= 10 Int= 0 D2E= 0 Chk= 3 Scr= 1 > ============ end of error massage ============ > > I guess that the problem depends on Link117, but I don't have any idea to > know the reason. If you have any advice or example input, please send me > (or send to this ML). > All responses I'll appreciate. I'll summarize them and upload to ML. ================ Summary ================ 1) from Massimo ---- Hi, on my knowledge from the G98W manual " The IPCM model is available for HF, DFT, MP2, MP3, MP4(SDQ), QCISD, CCD, CID, and CISD energies only" so seems that TD calculations with the IPCM model are not possible. Regards Massimo 2) from Douglas ---- Dr. Tsuru, G98 did not have TD implemented to use solvated ground states. In G03 it is the IEFPCM model, not IPCM or CPCM, which can handle this. Douglas J. Fox Technical Support Gaussian, Inc. ================ end of Summary ================ . . . And I add one reply which I missed to upload. It is what I've asked the problem concerning the interpretation of excited states of G98 output. Thank you very much Noel. O. Boyle. ================ The Reply ================ Sent to CCL by: "Noel O'Boyle" [no228{=}cam.ac.uk] > Question1) Symmetry of orbital No.12 is A1G. Can electron excite > gerade representation to gerade representation? (A1G to E1G ?) Question (1) As far as I know, electronic transitions between orbitals of the same symmetry are forbidden. That is why excited state 7, which is 'G' (i.e. involves a transition between orbitals of the same symmetry), has oscillator strength of 0. > Question2) Each value of right side of orbital number is wave-function > coefficients. Does the plus/minus sign of these coefficients have any > quantum meaning for excitaion? > If one should pay attention to plus values, "13 -> 47 0.00297" is > the most effective component of these four relation? Or, when one > takes absolute value, "13 -> 22 -0.02923" is the most effective > component? I think you should take the absolute value, or the square of the value. Note that the square of the values does not add to exactly 100% but should be in the neighbourhood of 100%. Noel Sincerely yours, ---------------------------------------------------- Telkuni Tsuru telkuni_+_venus.dti.ne.jp Bunshi Gijyutu From owner-chemistry@ccl.net Sat Dec 10 08:39:00 2005 From: "Faisal Rahman s101alif~!~mail.chem.itb.ac.id" To: CCL Subject: CCL:G: How to Calculate Proton afinities using gaussian Message-Id: <-30265-051210044816-22542-+ZNCp63P/cMHP7ayn6iiqw%%server.ccl.net> X-Original-From: "Faisal Rahman" Sent to CCL by: "Faisal Rahman" [s101alif{}mail.chem.itb.ac.id] Hi... It's Really Great to join this Forum Thank's before I'am Faisal, an undergraduate student of Bandung Institute of Technology. I'am doing my final project about hydrogen bonding in transfer proton of DNA bases molecules with chloride acid. Could anyone tell me how to use gaussian to calculate proton affinities of molecules such as adenine or guanine? and .. do anyone know where to find proton afinities exprimental data of molecules such as adenine or guanine,... I'll very appreciate your help ... -Faisal Rahman- From owner-chemistry@ccl.net Sat Dec 10 13:20:00 2005 From: "Steve Bowlus chezbowlus]^[goldrush.com" To: CCL Subject: CCL: Is there non-comercial software for doing QSAR/QSAR-3D? Message-Id: <-30266-051210112139-15941-mEypIQRgvnl2g5g8Zp1PKA^_^server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 10 Dec 2005 07:43:42 -0800 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus!A!goldrush.com] For 3D-QSAR, look at SOMFA from the Richards group http://bellatrix.pcl.ox.ac.uk/ Descriptors for conventional QSAR can be developed from a number of sources; statistics can be done for free by R, or more conveniently (and not too expensively) by just about any of the common statistical packages. I prefer SAS/JMP for this purpose. sb D.BIO- Gerard Pujadas gerard.pujadas() urv.net wrote: > Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas*urv.net] > > Dear CCL list members, > > I would like to know if there is non-comercial > software for doing QSAR and also for doing > QSAR-3D. I would also appreciate a lot your > critical comments about how this non-comercial > software compares with commercial ones. > > With many thanks in advances for your help > > Yours sincerely > > Gerard > From owner-chemistry@ccl.net Sat Dec 10 13:55:01 2005 From: "errol lewars elewars:+:trentu.ca" To: CCL Subject: CCL:G: How to Calculate Proton afinities using gaussian Message-Id: <-30267-051210124405-28301-bpIXV2T4DnZqxEt+U50tGw.:.server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Sat, 10 Dec 2005 12:44:07 -0500 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars::trentu.ca] 2005 Dec 10 Hello, 1 This paper explains how to account for the enthalpy of the proton in the calculation: E. I. von Nagy-Felsobuki, K. Kimura, J Phys Chem, 1990, 94, 8041. 2 Proton affinity of polyguanides: Z. B. Maksic, B. Kovacevic, J Org Chem, 2000, 65, 3303. 3 Usinn AM1 (useful for very big molecules): M. J. S. Dewar, K. M. Dieter, J Am Chem Soc., 1986, 108, 8075. 4 R. Notario et al. (points out proton affinity is deltaH, basicity is delta G): Chemistry, a European Journal, 2001, 7, 342. 5 Z. B. Maksic et al., J Phys Chem, 1997, 101, 7445. - E. Lewars ===== Faisal Rahman s101alif~!~mail.chem.itb.ac.id wrote: >Sent to CCL by: "Faisal Rahman" [s101alif{}mail.chem.itb.ac.id] >Hi... >It's Really Great to join this Forum >Thank's before > >I'am Faisal, an undergraduate student of Bandung Institute of Technology. >I'am doing my final project about hydrogen bonding in transfer proton of DNA bases molecules with chloride acid. Could anyone tell me how to use gaussian to calculate proton affinities of molecules such as adenine or guanine? >and .. do anyone know where to find proton afinities exprimental data of molecules such as adenine or guanine,... > >I'll very appreciate your help ... > >-Faisal Rahman-> > > > > > > From owner-chemistry@ccl.net Sat Dec 10 17:48:01 2005 From: "Sengen Sun sengensun\a/yahoo.com" To: CCL Subject: CCL: Advice to Prof. Avijit Ghosh Message-Id: <-30268-051210173812-8859-QifFECbARPJ6iHCzbGr76Q/./server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 10 Dec 2005 14:38:02 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun],[yahoo.com] Dear Professor Ghosh, Please say something safe and responsible about history! (This message is also for some friendly new CCLers who requested for references and some background information.) Professor Ghosh arbitrarily fabricated and distorted the history by saying: ["Incidentally, it is somewhat amusing to me that this thread actually has not only been part of the CCL list for ages, but I remember a variation of this exact thread made by many of the same players on a "philosophy of chemistry" listserv when I was a 2nd year graduate student (I think some 10 years ago at this point)."] My story of the history: Chapter 1 I had a long-standing interest in computational studies of reaction mechanisms including cycloadditions. That drove me to CCL and Philchem list, where I learned a philosophy that orbitals cannot possibly be observed. Actually, I was not quite interested in philosophy but wished to learn something about mechanisms. But a Professor from Germany on Philchem List wrote on Mon, 25 Nov 2002 14:09:51 +0100 ["it reminds me of the 19th century, when there was a common argument: atoms are too small to be ever seen, therefore they do not exist really, they are only a useful hypothetical concept. there is one difference: that statement was made before atoms became visible. you make the statement after wavefunctions had been measured........You can find descriptions in the literature how to measure their wave functions. an especially nice example is the complex wavefunction of the valence electron of Cs in a nonstationary excited state, see the first page of http://www.tc.chemie.uni-siegen.de/mess_wellenfkt.pdf original reference is Weihnacht et al., Phys Rev Let 1998, 80:5508, and Nature 1999, 397:233 "] These remarks remained in the Philchem list for MORE THAN A YEAR without being addressed or commented by any one else! Any true and solid experimental results can refute any opposite theoretical perceptions and philosophical views. Therefere, if the remarks above could hold true, all kinds of notions of orbital unobservability would be trashed. This Germany professor also claimed that Max Born was incorrect. With the confusion in my mind, I traced back all references from Weihnacht's papers. Based on my thorough and months analyses of their cited mathemetical approaches, I concluded that the two papers by Weihnacht et al are no more than fabrications of science. In about Feb 04, I exchanged extensively my opinions with the Germany Professor in the Philchem list. He is a very nice person, while I behaved very rude. Even now I still regret about my offensive languages. I learned a lesson. We met once and we are still good friends of opposite opinions. In my arguments against Weihnacht's papers, I stated that their mathematical approaches are arbitrary. They assumed that laser pulse WF can interfere with a single electron WF. Therefore an electron WF was derived (observed, or measured) from a source laser pulse and a consequently altered pulse received in the detector. I argued that there is not a physical basis to do the hybridized interference. Such an assumption just serves as your need to make pictures of orbitals. I can design a mathematical approach to make a picture of a ghost from the same information. That does not mean that a ghost is observed. I compared the hybridized interference as a marriage between a human and a ghost. I have the confidence in myself to make such a scientific judgement. I did my PhD (89-94) in org chem at McMaster U of Canada, postdoc at U of Chicago (94-97) and Johnson&Johnson (97-99). I have been very productive whereever I have worked. To my best knowledge, no body else has done something like what I did to refute the claims in Weihnacht's papers. But I am not a judge of myself. If I am wrong and if the claims in Weihnacht's papers can be justified, all notions of orbital unobservability are just garbage! Either way, I have positively contributed to science. I am proud of myself! Chapter 2. On Dec. 20, 2004, Dr. Mikael Johansson had a CCL post, which was also forwarded to Philchem List. See references: [1] http://www.ccl.net/cgi-bin/ccl/message-new?2004+12+20+002 [2] J. Itatani et al., "Tomographic imaging of molecular orbitals", Nature 432 (2004) 867-871. [3] Single N2 Bonding Orbital Imaged, Chem & En News, December 20, 2004 Volume 82, Number 51, p. 10 Evidently to me, these references are about wrong and bad science. To me,[2] and [3] are also about suppresion, refusal, or ignorance of opposite opinions in our textbooks of QM. I wished that some else could have had come forward to address the issues while I wanted to watch. But I was absolutely stunned that thousands of CCLers remained silent! I then stood up and screemed again and again in Jan 05. Finally, we had a very hot one. See examples: http://www.ccl.net/cgi-bin/ccl/day-index.cgi?2005+01+20 Subject: RE: orbitals and reality Chapter 3. Every one is equal to me. I am not fair if I just criticize wrong sciences from ordinary people, while ignoring a statement by a Nobel Laureate that is evidently wrong to me. Again, I am competent enough with a solid scientific background to make a scientific judgement. I do not need to ask any one else. I do not force any one else to agree with me. But I must fight for my right of free expression of my scientific opinions. To me, the worst thing in science is to ignore a wrong statement by a high profile Nobel Laureate. If his statement is wrong, its negative impact on science is simply too huge. It is his responsibility to act as a model in the scientific community and to clarify or correct his statement. Chapter 4 I did not post anything anywhere in the Internet until mid 2001. I was also learning by posting in CCL in 2001-2. My posts were not more than many other CCLers until 2005. Conclusions: I am amazed that a university professor in science does not devote his energy to tackle wrong sciences, but instead is engaged in arbitrary fabrications and distortions. I have been seriously insulted by a university professor who made irresponsible remarks on historical facts. Sengen __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Sat Dec 10 18:22:01 2005 From: "janl]![speakeasy.net" To: CCL Subject: CCL:G: How to Calculate Proton afinities using gaussian Message-Id: <-30269-051210175953-16635-sPFEEi2AzN259x+gsXAKzg . server.ccl.net> X-Original-From: janl__speakeasy.net Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Sat, 10 Dec 2005 22:59:44 +0000 MIME-Version: 1.0 Sent to CCL by: janl%speakeasy.net Faisal, I linked an unfinished paper from about dozen years ago to CCL archives that we were considered publishing, but never got to it. It is available from the documents page on the CCL: http://www.ccl.net/chemistry/resources/overview/ under "Unfinished paper on proton affinities", namely: http://www.ccl.net/cca/documents/proton-affinity/ You can also get to it via anon. FTP: ftp://ftp.ccl.net/pub/chemistry/documents/proton-affinity It has quite extensive methods part, and it may be useful, if you want to run the calculations yourself. Also, there are some results (comp and exp) for smaller molecules that you can use for testing. Both PDF and LaTeX is given, though the formatting sucks big way... Jan Labanowski (without unmoderator hat). > -----Original Message----- > From: Faisal Rahman s101alif~!~mail.chem.itb.ac.id [mailto:owner-chemistry*o*ccl.net] > Sent: Saturday, December 10, 2005 01:52 PM > To: 'Labanowski, Jan ' > Subject: CCL:G: How to Calculate Proton afinities using gaussian > > Sent to CCL by: "Faisal Rahman" [s101alif{}mail.chem.itb.ac.id] > Hi... > It's Really Great to join this Forum > Thank's before > > I'am Faisal, an undergraduate student of Bandung Institute of Technology. > I'am doing my final project about hydrogen bonding in transfer proton of DNA bases molecules with chloride acid. Could anyone tell me how to use gaussian to calculate proton affinities of molecules such as adenine or guanine? > and .. do anyone know where to find proton afinities exprimental data of molecules such as adenine or guanine,... > > I'll very appreciate your help ... > > -Faisal Rahman- From owner-chemistry@ccl.net Sat Dec 10 23:46:01 2005 From: "Charlie Bradley chemicalbond001]_[yahoo.com" To: CCL Subject: CCL: To Dr's Sun's recent post Message-Id: <-30270-051210234346-17584-MlJUHAopw/DOkg6TREUnHQ-$-server.ccl.net> X-Original-From: "Charlie Bradley" Sent to CCL by: "Charlie Bradley" [chemicalbond001[A]yahoo.com] Never assume most peolpe on this list do not understand as much QM as you. I guess most people including myself are just tired of those discussions, which are mostly about one's philosophy, and a little far away from science itself. Also it would be nice to other listers by not sending so many emails. It's a free speech world, but we all receive respect by doing things properly. CCL.net is a place for discussion, but not for rigorous publications of scientific research. To deliver really research professionally, the best approach is to publish your research in peer-reviewed scientific journals, not simply shouting at other fellow scientists at a place like this. This is the way to respect others and receive respect. If you really believe you have big claims or statements over some fundmental science, while many others including Nobel prize winner, Nature, PRL, Science (many more) magazine editors have been all completely wrong on that special topic, please write something professionally, ie, try to publish it to get your history made, and get scientific history remade! Would not that be wonderful?