From owner-chemistry@ccl.net Fri Oct 10 00:16:00 2008 From: "Melissa melchem{:}gmail.com" To: CCL Subject: CCL:G: fluorescence spectra Message-Id: <-37886-081009162138-999-JlOA4M4wJZnnt4F7XuOKdg[#]server.ccl.net> X-Original-From: "Melissa" Content-Type: multipart/alternative; boundary="----=_NextPart_000_009A_01C92A33.6E22E890" Date: Thu, 9 Oct 2008 17:21:13 -0300 MIME-Version: 1.0 Sent to CCL by: "Melissa" [melchem^_^gmail.com] Esta i uma mensagem em varias partes no formato MIME. ------=_NextPart_000_009A_01C92A33.6E22E890 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCL readers, I would like to know how to calculate fluorescence spectra of organic = molecules using g03? Could anyone please help me. Thanks in advance, Melissa ------=_NextPart_000_009A_01C92A33.6E22E890 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCL readers,
 
I would like to know how to calculate = fluorescence=20 spectra of organic molecules using g03? Could = anyone=20 please help me.
 
Thanks in advance,
Melissa
------=_NextPart_000_009A_01C92A33.6E22E890-- From owner-chemistry@ccl.net Fri Oct 10 01:37:01 2008 From: "Sengen Sun sengensun.:.yahoo.com" To: CCL Subject: CCL: Why conceptual DFT fails conceptually? Message-Id: <-37887-081010013424-21157-0+JoP4+mMH46tBI8hzVvvw{}server.ccl.net> X-Original-From: Sengen Sun Content-Type: text/plain; charset=us-ascii Date: Thu, 9 Oct 2008 22:34:07 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun_-_yahoo.com] > Quote: > "Still Sun's > argument that DFT is just a computational tool does not > hold water. > Admittedly this is how the majority of people use it and > this is why they > awarded Kohn the Nobel prize with Pople (purely > computational tool > there), but there have been significant chemical insights > from conceptual > DFT due to Parr and coworkers which are on par (pun > intended) with those > of Bader." > > This is a part of the first of 4 messages I received on 10-08-2008. All 4 questioned about my remarks on DFT. I must address this issue after nearly a decade hesitation (I may hurt too many!). DFT starts with good physics, and ends with contradictory "conceptual". In the nature, there are electron density and electrostatic forces, but not Fukui functions derived from HOMO and LUMO. By the end of 2007 and early 2008, I was asked twice by 2 Editors to review 2 papers from 2 different groups, which were about use of conceptual DFT in prediction and understanding of regiochemistry of cycloadditions. In the end of my review, I said something like this: "I don't mind publishing this paper as there have been many papers of this kind in the literature any way, and there will be more. But I must express my strong personal opinion that this is not what scientific theory is about." I asked the editors to release my identity to the authors as I welcome the authors to argue with me directly in order to be fair. They did not contact me afterward and I have not seen their papers out yet. Simply for the known 1,3-dipolar cycloadditions in the literature, prediction using conceptual DFT may fail as much as 30-40% (my very rough estimate)! A simple Diels-Alder reaction it cannot address is acrolein dimerization. I would like to challenge any one in this community, you come forward to rationalize its regioselectivity based on matching the nucleophilicity and electrophilicity indexes. If you claim you have a conceptual theory, you must be able, within your theoretical frame, to address these "exceptions" and draw a boundary to use your theory. Otherwise, prediction and understanding are meaningless! Who else understands this "conceptual"? Please look at the back-to-back debate (JPC A, 2001, 10943-10948). How do you understand the "conceptual DFT" there, my friends? ...... By the way, 2 people said that I was not accurate in describing Bader's theory in my last post. I have not be convinced. At least, I think I am close. They are just my own words to say it after I digested the literature. Somewhere in the literature, it says something like that the computed ED from AIM can be closely compared with that from X-rays crystallogrophy. I interpreted this to my own words in my last e-mail. Bader is my hero in science, and is in the right direction of theoretical chemistry to me. If you use physics to explain chemistry, chemistry can be easily understood. Theoretical chemistry is about connections between physics and chemistry. If you use chemistry to explain chemistry, it is just like you ask me "why" and my answer is "because why". Further, no one is perfect, and our theory is far from being perfect. There are some particular things, on which I don't agree or others don't agree with Bader. There is no way that two people can think exactly the same. I encourage open and fair discussions. Regards to every one. Sengen From owner-chemistry@ccl.net Fri Oct 10 03:48:00 2008 From: "VITORGE Pierre 094605 Pierre.VITORGE[A]cea.fr" To: CCL Subject: CCL:G: Visualization of NBOs Message-Id: <-37888-081009121011-23663-8CX0RGQvf8cy6p3//4wn+w a server.ccl.net> X-Original-From: "VITORGE Pierre 094605" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01C92A29.78CA9E50" Date: Thu, 9 Oct 2008 18:09:56 +0200 MIME-Version: 1.0 Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE%cea.fr] This is a multi-part message in MIME format. ------_=_NextPart_001_01C92A29.78CA9E50 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, I found the following example (from CCL) to plot NBOs as obtained with = the NBO version implemented in Gaussian98 (I can also use Gaussian03) = and further Visualized with MOLEKEL, %chk=3DCH4.chk #p iop(6/7=3D3) gfinput pop=3Dnboread formcheck=3D(mo,basis) # MP2 6-31+G(d,p) # scf=3Dtight # guess=3Dread geom=3Dcheck # Density=3DMP2 CH4 MP2/6-31+G(d,p) 0 1 $NBO AO*=3DCS $END for this last line I also tried $NBO AONBO=3DCS $END I got the error message Error: Unrecognizable keyword >>CS << Program must halt. Error Error termination via Lnk1e in /usr/local/g98-A9/g98/l607.exe. Any idea than could help? Thanks in advance Pierre Vitorge http://www.lambe.univ-evry.fr/pvitorge http://www.vitorge.name ------_=_NextPart_001_01C92A29.78CA9E50-- From owner-chemistry@ccl.net Fri Oct 10 04:25:00 2008 From: "Mateusz Galuszka ccs[-]fqs.pl" To: CCL Subject: CCL: Dr. Stan van Gisbergen (SCM) at Fujitsu Seminar- Cambridge, 30.10.2008 Message-Id: <-37889-081010034904-30674-ZbkFe/8ZcJbPugo9kFNaLg[]server.ccl.net> X-Original-From: "Mateusz Galuszka" Date: Fri, 10 Oct 2008 03:49:00 -0400 Sent to CCL by: "Mateusz Galuszka" [ccs**fqs.pl] Dear CCL Subscribers, We are very happy to announce the change in our seminar schedule and the introduction of our next special guest speaker. Dr. Stan van Gisbergen from Scientific Computing & Modelling (http://www.scm.com) will give a presentation titled: "The ADF2008 release: new developments and applications in DFT" On our website (http://www.fqs.pl/seminars/2008-10-30) you will find an updated seminar schedule, as well as some informations regarding Dr. van Gisbergen, his company SCM and ADF software - the leading DFT package available on market. We hope that our new program will convince you to participate in our seminar. We look forward to receiving your registration and meeting you in Cambridge on 30th October. Best regards, Mateusz Galuszka -- ************************ Mateusz Galuszka FUJITSU ul. Starowislna 13-15 31-038 Krakow Poland Tel.: (+48) 12 429 43 45, Fax: (+48) 12 429 61 24 e-mail: ccs=-=fqs.pl URL: http://www.fqs.pl ************************ -------------------------------------------------------------------------- Dear CCL Subscribers, We are very proud to invite you to our 1st "Computational Chemistry and Molecular Modelling Solutions for Chemical and Materials Industry" Seminar in Cambridge, UK. The seminar will take place on 30th October, 2008 in The Trinity Centre - a conference centre of the Cambridge Science Park. The seminar will be devoted to general aspects of use of computational methods in chemical, materials and semiconductor industry. It will also be a great opportunity to present the latest computational solutions offered by FUJITSU company. Our invited speakers include Prof. Akira Takada from Asahi Glass Corporation, one of the largest glass and chemical companies in the World, and Dr. Chioko Kaneta, an expert in molecular simulations of semiconductor materials from Fujitsu Laboratories Japan. The participation in FUJITSU seminar is FREE OF CHARGE. In order to register to our seminar, please send us the filled registration form which can be downloaded, together with the information brochure, from our website: http://www.fqs.pl/seminars/2008-10-30 You can also simply send a message to ccs=-=fqs.pl. Please remember to register in advance as the order of registration will be important due to the limited number of seats. We hope that you find our proposition very interesting. If you would have any additional questions, please do not hesitate to contact us. We look forward to your reply. Best regards, Mateusz Galuszka -------------------------------------------------------------------------- From owner-chemistry@ccl.net Fri Oct 10 06:12:01 2008 From: "Ol Ga eurisco1#,#pochta.ru" To: CCL Subject: CCL:G: Re3: check the total number of molecular orbital Message-Id: <-37890-081010061015-8402-o5dLekg51a8hy2VhuJ3v4A+*+server.ccl.net> X-Original-From: "Ol Ga" Date: Fri, 10 Oct 2008 06:10:11 -0400 Sent to CCL by: "Ol Ga" [eurisco1(_)pochta.ru] Dear Veronique LEGRAND, I try to answer > I think we could consider my first problem solved. I understood the impossibility > to have all the informations I wanted. > For the second one, it's to say the number of orbitals, it's still confused. > So if you are agree, I would like just checking different parts. > -first, whatever the calculation .wfn writes only the non-zero occupation numbers. Right? Yes, Gaussian writes by Default (thanks by Prof. N. Sukumar for a comment about IOP) in .wfn only orbitals with the non-zero occupation numbers. > -You told me that the occupation numbers must be : 0,1 with UHF and > without density=current. Or 0,1 for UHF whatever the method? If density=current is in the route section Gaussian writes NOON (natural orbitals occupation numbers) of natural orbitals for UHF. And without density=current Gaussian writes occupation numbers of canonical orbitals for UHF (0 or 1 because it is a feature of the method) > And, in the other hand all non-zero numbers with density=current. Right? Yes. > But I'm in UMP2. I know that there is a big part claculated in HF > and after just the addition of the correction for the electronic > correlation. Does it change something to the value expected in occupation number? No, UHF density is used and Gaussian writes for UMP2 without density=current the same for UHF without density=current. > -I suppose I could read these occupation numbers on the output file > of Gaussian, but under which name? > I tried to find by myself, of course, and my hypothesis doesn't fit > with the caracteristics you give to me. It's to say: 0,1 ..... It is not necessary to look for 0 and 1 because it is a feature of canonical orbitals. > I asked myself whether there is an inversion somewhere. Becuse you > tell that with density=current the are all the MOs, but I observed > the contrary. I have more orbitals wihtout this keyword. I have already wrote you the explanation of the reason. But possible I was not concrete. By other words: Gaussian writes enumerated list of occupied _alpha_-orbitals after that Gaussian writes enumerated list of _beta_-occupied BUT the scheme of enumeration is unusual numbers of _beta_ begin from the next number of the last (and un-occupied) _alpha_orbital. Please, begin try to check this from more simple case, e.g. NH2. You will see that more clearly than in case of 300-400 orbitals. : -) > And an other point to finish. If I don't use density=current with > my MP2 method, is there something realised in MP2? I feel not, but in what I am in this case, HF? You are right. In this case Gaussian writes in .wfn only occupation numbers of canonical HForbitals. > Oh it's so complicated. Yes. Sometimes ... :-) My comment about IOP: IOP is the most powerful tool to do, to control, to supervise jobs in Gaussian. But, PLEASE, check and understand WHAT you DO. Sincerely, Ol Ga >> Sent to CCL by: "Ol Ga" [eurisco1-#-pochta.ru] >> Dear Veronique LEGRAND, >> >> I understood your _two_ problems after additional comments. >> About your first point: >> >> As it is noted on the native site of NBO programs in section FAQ >> >> http://www.chem.wisc.edu/~nbo5/faq.htm >> >> Q10. I tried to go to a higher-level MP2 or CASSCF treatment, but suddenly there were no NBO orbital energies and no table of 2nd-order perturbative energies? What's wrong? >> NBO evaluates "orbital energies" and 2nd-order stabilization energies only when there is a well-defined 1-electron effective Hamiltonian operator (e.g., Fock or Kohn-Sham operator). Such an operator is unavailable for correlated descriptions, except those of DFT type >> >> You can see it is methodological problem (not only a problem of NBO 3.1 and NBO 5). Obviously, if you want to use correlated methods with NBO you have only one choice it is DFT. >> >> About your second point: >> >> As it is noted on the native site of AIM (and .wfn) >> >> http://www.chemistry.mcmaster.ca/aimpac/notes/aimweb.txt >> >> Density=current is vital when running correlated jobs. Otherwise the SCF (HF) >> density is used for popultion analysis, and more importantly, in the wavefunction >> file. If all the orbital populations in your wavefunction file are 2.00 you can >> be sure you have a Hartree-Fock wfn. If all the orbitals have energy=0.0 you have >> a natural orbital description. For HF densities this is fine, but the individual >> MOs are meaningless - try again without density=current >> >> And additional comments from me : >> In the .wfnfile are printed orbitals which have non-zero occupation numbers. If you use the route section _without_ DENSITY=CURRENT >> >> #p UMP2(full)/6-31G** GFPrint GFinput Scf=VeryTight Output=WFN Punch=Archive iop(5/14=2) >> # Maxdisk=500000000 Pop=(Full,NBO) Test >> >> 0, 2 are occupation numbers of RHF orbitals and 0, 1 are occupation numbers of UHF orbitals. You will get a list _alpha_orbital_1, , _alpha_orbital_n (it is highest occupied _alpha_orbital) >> and list _beta_ orbital_(M+1) where M is number of atomic orbitals in your case in .wfnfile. >> Please, note an unusual sequence in the numbered list (n<(M+1)) . >> >> If you use the route section _with_ DENSITY=CURRENT >> >> #p MP2(full)/6-31G** GFPrint density=current GFinput Scf=VeryTight Output=WFN Punch=Archive iop(5/14=2) >> # Maxdisk=500000000 Pop=(Full,NBO) Test >> >> You will get a list of _all_ orbitals in .wfn because NBO analysis will be performed and _all_ orbitals have non-zero occupation numbers. >> >> So, you will get different numbers of orbitals in two cases. >> >> I wish you good luck. >> Sincerely, >> >> Ol Ga >> >> > Sent to CCL by: "Veronique LEGRAND" [vflegrand*_*free.fr] >> > First, I want thank you for your opinion on my problem, I feel less desesperate. >> > Maybe I omitted certain details in the last message. I know that >> > MP2 needs the density=current keywords, but when I used this syntax >> > to my NBO calculation, I hadn't the analysis of Perturbation Theory >> > part in the output. And I really need it to explain the electron >> > tranfer occuring in my molecule. So I was obliged to choose a less >> > optimum solution, it's to say omitted this keyword. If you have an other one, I take it. >> > About the other point: the number of orbitals. I checked it again. >> > And I realised thanks to you, that gaussian gives the same number of >> > Molecular orbitals in both case. The difference is in the file .wfn, >> > where in a case there are 127 and in the other 330. >> > It's unbelievable. So I just run these 2 files one more time, and I tried one another. >> > If I see something knew, or if it's like now I will tell you. >> > Sincerely yours. >> > Veronique From owner-chemistry@ccl.net Fri Oct 10 06:48:01 2008 From: "veronique LEGRAND vflegrand]![free.fr" To: CCL Subject: CCL:G: Re2:check the total number of molecular orbital Message-Id: <-37891-081010043613-6088-KSvuA2Sy/W+X/LkBREO++g-x-server.ccl.net> X-Original-From: "veronique LEGRAND" Date: Fri, 10 Oct 2008 04:36:08 -0400 Sent to CCL by: "veronique LEGRAND" [vflegrand=-=free.fr] Dear N.Sukumar, Thank you for this information, I didn't think at the IOp option. Sincerely Veronique > > To have g03 print ALL the orbitals to the .wfn file, include the option > IOp(99/18=-1) > > Thus: > # ... OUT=WFN IOp(99/18=-1) > > For details see http://www.gaussian.com/g_tech/overlay_9999.htm#99_18 > N. Sukumar > Associate Research Professor of Chemistry and Chemical Biology > Center for Biotechnology and Interdisciplinary Studies > Rensselaer Polytechnic Institute > http://reccr.chem.rpi.edu/ > > From owner-chemistry@ccl.net Fri Oct 10 07:45:00 2008 From: "Stan van Gisbergen vangisbergen,+,scm.com" To: CCL Subject: CCL: Amsterdam Density Functional (ADF) software, version ADF2008 released Message-Id: <-37892-081010065906-2796-Z5C0ryyueHrFojM1tx8Jrg[]server.ccl.net> X-Original-From: Stan van Gisbergen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 10 Oct 2008 12:22:12 +0200 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Stan van Gisbergen [vangisbergen|-|scm.com] Dear CCL subscribers, The Amsterdam Density Functional package (ADF) is a premium quality software package for quantum chemistry and materials science research using Density Functional Theory (DFT). ADF offers various spectroscopic properties and environment models for almost any molecule, and excels at transition metal and heavy element compounds. Scientific Computing & Modelling N.V. (SCM) proudly announces the release of version ADF2008, including the following enhancements: * Improved geometry optimization and transition state search, now default * Dispersion-corrected GGA XC functionals (Grimme) * For periodic structures in BAND: transition state search, numerical frequencies, ESR A-tensor and g-tensor, M06-L and TPSS forces, visualization of (partial) DOS * New COSMO-RS module: QM prediction of chemical engineering thermodynamics for fluids * DFTB module: fast density functional tight binding program * Ultrafast Bader AIM atomic properties * Magnetizability, polarizabilities at resonance * Check the release notes for various other enhancements: http:// www.scm.com/Doc/Doc2008.01/Background/Updates/page1.html ADF2008 is available on Windows, Linux, Mac, and UNIX. Download a free 30-day trial: http://www.scm.com/SCMForms/ TrialRequest.jsp or contact us for further information. Learn more about ADF2008 at the Fujitsu seminar (Cambridge, UK, 30 October): http://www.fqs.pl/seminars/2008-10-30 Best regards, Stan van Gisbergen, on behalf of the SCM team. http://www.scm.com E-mail: info(-)scm.com From owner-chemistry@ccl.net Fri Oct 10 12:45:01 2008 From: "Rick Venable venabler*nhlbi.nih.gov" To: CCL Subject: CCL: torsional/total energy MD negative? Message-Id: <-37893-081010123825-32366-JreSi3nAslcdyDEdyKto3A-*-server.ccl.net> X-Original-From: Rick Venable Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Fri, 10 Oct 2008 12:37:36 -0400 Mime-version: 1.0 Sent to CCL by: Rick Venable [venabler**nhlbi.nih.gov] MD force field energies are fairly relative, and in general energy differences are used; the absolute energy is somewhat arbitrary. -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov > Sent to CCL by: "javier sacr" [jsacristan ~ ictp.csic.es] > Hi guys, > I hope you can give me any idea about: > > After a long molecular dynamic simulation of a polymer under periodic boundary > conditions, dihedral and total energies are lower than zero, (negative). do > you know the physical meaning of that result? > total energy obtained at the end of the MD should be positive? > > thanks for reading and for your help > > js From owner-chemistry@ccl.net Fri Oct 10 15:40:00 2008 From: "Gustavo Seabra gustavo.seabra__gmail.com" To: CCL Subject: CCL:G: G03 on Barcelona's Message-Id: <-37894-081010153214-5716-vayRbmlatS9mjA8q/njIMQ(a)server.ccl.net> X-Original-From: "Gustavo Seabra" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 10 Oct 2008 15:32:01 -0400 MIME-Version: 1.0 Sent to CCL by: "Gustavo Seabra" [gustavo.seabra,+,gmail.com] On Thu, Oct 9, 2008 at 9:37 AM, zhendong zhao wrote: > I tested Phenom (9850) on AMD 780G chipset and NVIDIA nforce 750a SLI > chipset. Only X86_64bit g03 has weird problems on Phenom CPUs, > surprisingly, X86_32bit g03 is stable on Phenom CPUs! ( Binary G03 E.01 > shipped by Gassian Inc.) I'm curious... Have you tried compiling the code yourself? AFAIK, the Gaussian license /can/ include the source code, depending on where you are. My guess is that they just use some general compiler and make a general "x86_64" executable, but /maybe/ one could tweak the compiler options to avoid these problems, assuming you have access to source code. From owner-chemistry@ccl.net Fri Oct 10 19:22:00 2008 From: "zhendong zhao zzhao:-:olemiss.edu" To: CCL Subject: CCL:G: G03 on Barcelona's Message-Id: <-37895-081010174608-7010-763Fwc+5a3NIk5Ahf+FWzQ:server.ccl.net> X-Original-From: zhendong zhao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Fri, 10 Oct 2008 16:46:07 -0500 Mime-Version: 1.0 Sent to CCL by: zhendong zhao [zzhao=-=olemiss.edu] Hi, I did not try compiling G03 from source, because of compiling G03 requires PGI fortran, I do not have the new version. BTW, I should clarify that I use binary G03 optimized for AMD Opteron, not for Intel EMT64. ZZ On Fri, 10 Oct 2008 15:32:01 -0400 "Gustavo Seabra gustavo.seabra__gmail.com" wrote: > > Sent to CCL by: "Gustavo Seabra" [gustavo.seabra,+,gmail.com] > On Thu, Oct 9, 2008 at 9:37 AM, zhendong zhao wrote: > > I tested Phenom (9850) on AMD 780G chipset and NVIDIA nforce 750a > > SLI chipset. Only X86_64bit g03 has weird problems on Phenom CPUs, > > surprisingly, X86_32bit g03 is stable on Phenom CPUs! ( Binary G03 > > E.01 shipped by Gassian Inc.) > > I'm curious... Have you tried compiling the code yourself? AFAIK, the > Gaussian license /can/ include the source code, depending on where you > are. > > My guess is that they just use some general compiler and make a > general "x86_64" executable, but /maybe/ one could tweak the compiler > options to avoid these problems, assuming you have access to source > code. > > > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the {:} sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> >