From chemistry-request@www.ccl.net Tue Dec 22 05:54:17 1998 Received: from stark.udg.es (stark.udg.es [130.206.128.61]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id FAA18121 Tue, 22 Dec 1998 05:53:33 -0500 (EST) Received: from stark.udg.es (cactus.udg.es [130.206.128.70]) by stark.udg.es (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id LAA24008 for ; Tue, 22 Dec 1998 11:54:39 -0200 Message-ID: <367F7ABF.B65B08E6@stark.udg.es> Date: Tue, 22 Dec 1998 11:55:59 +0100 From: "Marta Forés i Bocsh" X-Mailer: Mozilla 4.04 [ca] (Win95; I) MIME-Version: 1.0 To: Lista de Quimica Subject: Re: Energy value for a specific initial orbital set Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all, I thank to all who replied my question about getting the energy value for an initial guess in Gaussian. The energy value for the last guess of a previous calculation can be obtained with the ‘guess=read’ and ‘scf(maxcyc=1)’ options, although being printed 'after two cycles' in the output file. The initial question and the Prof. S. Fau and D. Babic’s responses are summarized below. I am very grateful to them. Marta Initial question ---------------- We need to get the UB3LYP energy of a molecule with a specific guess obtained from a previous calculation. In GAUSSIAN, there is an option scf(maxcyc=N) that allows to specify the number of scf cycles (N) you want. If N=-1 the program does not do any scf cycle and gives you directly the nuclear energy, if N=0 the program does as many cycles as it is necessary to have the energy converged and if N=1 one gets the energy obtained after doing the second scf cycle (and with the #P option it does not give you the electronic energy difference between the two first cycles, which would permit you to know the fist energy value) Does anybody know if there is any way to obtain the energy value for a specific initial orbital set (obtained from a guess=read commend). Responses ------------- Prof. S. Fau It is a bit confusing. You are right with saying that the electronic energy of cycle 1 belongs to the SCF energy with the label "after 2 cycles", since the SCF energy is the sum of this electronic energy and the nuclear repulsion energy (computed in link 301). But I still think that this SCF energy "after 2 cycles" is the SCF energy that belongs to the guess. (I think the label "after 2 cycles" is wrong.) My arguments are as follows (using a single point calculation of H2 at rHH=1. as an example): To solve the SCF-equations, you take a guess for MOs which allows you to calculate the density matrix and the Fock-matrix. Then you diagonalize the Fock-matrix and finally you get the diagonal matrix of MO energies and a new set of MOs (and a new density matrix). Therefore the density matrix is changed, even if you perform only one SCF-cycle (GAUSSIAN uses differences between old and new density matrices as convergence criterion). With direct SCF GAUSSIAN's default procedure is to save the wavefunction (i.e. the MOs) after each cycle to allow a restart of the SCF. If the SCF is converged, the MOs are also available as a new guess. I repeated the calculations with the command lines 1: # rhf/6-31G(d,p) guess(SAVE,only) with rHH = 1. 2: # rhf/6-31G(d,p) scf(SAVE,maxcyc=1) geom=check guess=check 3: # rhf/6-31G(d,p) scf(restart,nosave,maxcyc=1) geom=check 4: # rhf/6-31G(d,p) scf(restart,SAVE,maxcyc=1) geom=check 5: # rhf/6-31G(d,p) scf(restart,nosave,maxcyc=1) geom=check 6: # rhf/6-31G(d,p) scf(restart,nosave,maxcyc=1) geom=check because H2 is to small to show energy changes if a converged WFN is used as a guess. I got the following energies: 1: no energy 2: -1.06975649801 <-- found better MOs and WROTE them to the checkpoint-file 3: -1.09870782510 <-- found better MOs 4: -1.09870782510 <-- found better MOs and WROTE them to the checkpoint-file 5: -1.09945738967 <-- found better MOs 6: -1.09945738967 <-- found better MOs ___________________________________ Dr. Stefan Fau Fachbereich Chemie, AK Frenking Philipps-Universität Marburg 35032 Marburg, Germany fau@chemie.uni-marburg.de ----------------------------------------------------------------------- Prof. D. Babic I DO NOT see anything strange or anything that would indicate that the energy reported in the first cycle does not correspond to initial orbi- tals. It might be that you don't know a few things that I also learned recently. There are two places in the checkpoint file where the orbitals are stored. The first one is where Guess(Save,Only) stores them and also where the final converged orbitals are saved. These orbitals are read into by Guess=Read command (for example) and you can also read them by performing formchk command. The orbitals obtained during the SCF calculation are stored in the different place in the checkpoint file and they are accessible ONLY by the Restart option. These orbitals are stored only if Save option is active in SCF (not Guess). These orbitals can not be read by formchk (unless one modifies it). The subroutine that controls SCF calculation is CycOpn in l502.F. First, the one- and two-electron parts of the Fock matrix are computed to- gether with one- and two-electron contributions to the energy. They are computed with the initial orbital set which can be from the first or the second orbital block in the checkpoint file, depending on whether Guess=Read is active or SCF(Restart). Then, Fock matrix is diagonalized and the new orbitals are obtained. If Save option is turned ON, they are stored in the second block in the chkpoint file. So the orbitals stored with MaxCyc=1 are not identical to the initial orbitals - they are intended for the next SCF- -cycle. If MaxCyc=1, the job ends, but the succeeding restart will start >from THESE orbitals, which were not yet used for calculation of energy. Darko Babic Institute "Rudjer Boskovic" HR-10001 Zagreb, P.O.B. 1016 Croatia From chemistry-request@www.ccl.net Tue Dec 22 08:46:00 1998 Received: from goodyear.goodyear.com (internet.goodyear.com [209.57.161.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA19069 Tue, 22 Dec 1998 08:46:00 -0500 (EST) Received: from imailhub.goodyear.com by goodyear.goodyear.com via smtpd (for www.ccl.net [192.148.249.5]) with SMTP; 22 Dec 1998 13:46:01 UT Received: from HQLMS001.GOODYEAR.COM (hqlms001.goodyear.com [163.243.51.60]) by goodyear.com (8.8.8/8.8.8) with SMTP id IAA25416 for ; Tue, 22 Dec 1998 08:42:29 -0500 (EST) Received: by HQLMS001.GOODYEAR.COM (Soft-Switch LMS 3.0) with snapi via NOTES id 0056650001255277; Tue, 22 Dec 1998 08:46:07 -0500 From: EILERT OFSTEAD To: Subject: Quantifying Agostic H--M Interactions? Message-ID: <0056650001255277000002L572*@MHS> Date: Tue, 22 Dec 1998 08:46:07 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id IAA19070 I would be interested in the comments of CCL'ers regarding preferred strategies for evaluating organometallic compounds which may have agostic interactions present. In particular, I want to compare the relative stabilities of isomers where only one has a probable agostic interaction. Both accuracy and efficiency are of value here, so some compromise might be expected. My interest includes both alkali metal and transition metal compounds. One would expect correlation effects to be important in these weak non-bonded interactions, so post-HF methods are probably indicated (pain! avoid if possible!), but since some of the DFT methods supposedly include correlation, I have explored them tentatively as well. Scatter!!! With Li complexes, the highest Li-H interaction **appears** to be indicated when using MP2/HF, but when I try the more efficient LMP2 method available in Jaguar, eg, a substantially higher stabilization seems indicated (+1 kcal. Real??). And DFT methods consistently give somewhat lower apparent stabilization energies, intermediate between MP2 and straight HF. What is a poor chemist to believe. Maybe that's life in the modeling world (at least in my short existence there). So, recommendations, references, etc would be much appreciated. thanks, and best wishes for the Holidays, Eilert eofstead@goodyear.com ------------------ From chemistry-request@www.ccl.net Tue Dec 22 10:27:20 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA20110 Tue, 22 Dec 1998 10:27:19 -0500 (EST) Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id KAA12648; Tue, 22 Dec 1998 10:27:18 -0500 (EST) Date: Tue, 22 Dec 1998 10:27:15 -0500 (EST) From: Jan Labanowski To: Ponec Robert EXCHANGE cc: CCL , Jan Labanowski Subject: Re: request for address In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The official page for GAMESS is: http://www.msg.ameslab.gov/GAMESS/GAMESS.html The instructions: "How to get a copy of GAMESS" are available at: http://www.msg.ameslab.gov/GAMESS/dist.menu.html and the information about PC GAMESS is available as link from the page above at http://classic.chem.msu.su/gran/gamess/index.html and the ftp site with PC Gamess is at: ftp://www.msg.ameslab.gov/FTP/PC-GAMESS/ or from the PC GAMESS www page at IOWA: http://www.msg.ameslab.gov/GAMESS/dist.pc.shtml Alex A. Granovsky web page is at http://classic.chem.msu.su/gran/index.html and his e-mail is: gran@classic.chem.msu.su (though he only knows if he read his mail). The archive of GAMESS users discussions is at: http://mineral.umd.edu/gamess-users/archive/date.html On Tue, 22 Dec 1998, Ponec Robert EXCHANGE wrote: > Dear CCL `ers > > I would like to ask for the e-mail address of Alex Granovsky who distributes > PC Gamess. I have been using some address since recentky but this does not > seem to work now and I am not sure whether the address was not changed. > > Many thanks beforehand. > > Robert Ponec > Institute of Chemical Process Fundamentals > Czech Academy of Sciences > Prague 6, Suchdol 2 > 165 02 Czech Republic > fax: 420 2 20920661 > tel:420 2 20390271 > email: rponec@icpf.cas.cz > > > Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | From chemistry-request@www.ccl.net Tue Dec 22 14:27:51 1998 Received: from cacr.ioc.ac.ru (cacr.ioc.ac.ru [193.233.3.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA25616 Tue, 22 Dec 1998 14:27:50 -0500 (EST) Received: from cacr.ioc.ac.ru (nmr-v [193.233.3.213]) by cacr.ioc.ac.ru (8.8.8/EM.SRV.10.8) with ESMTP id WAA15482 for ; Tue, 22 Dec 1998 22:27:54 +0300 (MSK) Message-ID: <36808EF1.42747B6C@cacr.ioc.ac.ru> Date: Tue, 22 Dec 1998 22:34:25 -0800 From: val Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.04 [en] (Win16; I) MIME-Version: 1.0 To: CCL_post Subject: Re: Linux vs Windows 95 vs Windows NT References: Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit > Easy accessibility from other hosts, for example. This makes your work > much more efficient if you can check the results and start a new job, say, > from home on Sunday. > > Regards, > * Przemek Czyryca, pczyryca@smurf.chem.usu.edu * i) Good! The above mentioned things are really true, since every linux machine is rather stable telnet, ftp, www and email server just after the installation without any additional work. ii) Moreover, one can use an automatic process control systems (like NQS, for example) to set up a number of jobs in sequential, parallel or mixed mode (i.e. during weekends, conference travels, vacations, or just on a multi-user quantum chemistry server) and the system will run all of them in intelligent manner taking into account the resources available. iii) Next, in some critical cases, when a task reaches the limit of the hardware, one can unload all the GUI applications and the XWindows itself. In this case the calculation process will use 99% CPU time and 99% of RAM available. The same hardly could be possible for any of w95/wnt machines (look how much memory and CPU time the GUI sometimes requires ;-) All the things pointed out in i) and ii) don't need GUI, so they will work perfectly correct, finely, GUI can be started again after the critical point completion (without having to restart the system). However, it's clear now that Linux-Windows problem does not have an universal solution. So, I would suggest to discuss more detailed questions, rather than L. vs W. in general. best regards, Valentin. ==================================================================== , , , , Valentin P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@www.ccl.net Thu Dec 24 17:44:48 1998 Received: from mcmail.cis.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.20.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA09249 Thu, 24 Dec 1998 17:44:48 -0500 (EST) Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA (8.8.8/8.8.8) with SMTP id RAA06031; Thu, 24 Dec 1998 17:44:36 -0500 (EST) Date: Thu, 24 Dec 1998 17:44:36 -0500 (EST) From: "C.F. Matta" To: EILERT OFSTEAD cc: chemistry@www.ccl.net Subject: Re: CCL:Quantifying Agostic H--M Interactions? In-Reply-To: <0056650001255277000002L572*@MHS> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Eilert, Here is an important paper: P. L. A. Popelier and G. Logothetis "Characterization of an Agostic Bond on the Basis of the Electron Density", J. Organometallic Chem. 555, 101-111 (1998). Cheers. Cherif Matta Chemistry Dept. McMaster University Hamilton, Ontario Canada L8S 4M1 On Tue, 22 Dec 1998, EILERT OFSTEAD wrote: > > > I would be interested in the comments of CCL'ers regarding preferred strategies > for evaluating organometallic compounds which may have agostic interactions > present. In particular, I want to compare the relative stabilities of isomers > where only one has a probable agostic interaction. Both accuracy and > efficiency are of value here, so some compromise might be expected. My > interest includes both alkali metal and transition metal compounds. > > One would expect correlation effects to be important in these weak non-bonded > interactions, so post-HF methods are probably indicated (pain! avoid if > possible!), but since some of the DFT methods supposedly include correlation, I > have explored them tentatively as well. Scatter!!! With Li complexes, the > highest Li-H interaction **appears** to be indicated when using MP2/HF, but > when I try the more efficient LMP2 method available in Jaguar, eg, a > substantially higher stabilization seems indicated (+1 kcal. Real??). And DFT > methods consistently give somewhat lower apparent stabilization energies, > intermediate between MP2 and straight HF. What is a poor chemist to believe. > > Maybe that's life in the modeling world (at least in my short existence > there). So, recommendations, references, etc would be much appreciated. > > thanks, and best wishes for the Holidays, > > Eilert > eofstead@goodyear.com > ------------------ > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > > From chemistry-request@www.ccl.net Wed Dec 23 03:13:29 1998 Received: from zzmkgtw.zzmk.unizh.ch (zzmkgtw.unizh.ch [130.60.67.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id DAA29172 Wed, 23 Dec 1998 03:13:28 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA05022; Wed, 23 Dec 1998 09:13:26 +0100 Message-Id: <3.0.3.32.19981223091823.006899c4@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Wed, 23 Dec 1998 09:18:23 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Winter recess question Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; Here is a question that someone might care to ponder during the "slowdown" between Christmas and New Year's Day. Consider an amphipathic molecule containing a linear alkyl moiety, e.g. an n-hexyl or n-octyl or n-decyl group. When the molecule passes between hydrophobic and hydrophilic milieux, it can be expected that the linear alkyl moiety will experience changes in conformation: in a hydrophobic environment the linear alkyl moiety may be stretched out, where as in a hydrophilic environment it will probaby curl up on itself. I should like to know if there have been any studies on the _rate_ at which such conformational transitions occur when paraffinic moieties such as those considered above move between organic <---> aqueous phases. Of course, relevent references are most welcome. Thanking in advance all responders, and wishing all readers a joyous holiday season and a happy, healthy, and successful New Year, I remain Yours sincerely, S. Shapiro toukie@zui.unizh.ch From chemistry-request@www.ccl.net Wed Dec 23 23:02:09 1998 Received: from pigeon.vu.edu.au (pigeon.vut.edu.AU [140.159.30.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA06443 Wed, 23 Dec 1998 23:02:06 -0500 (EST) Received: from students.vut.edu.au ([140.159.60.8]) by pigeon.vu.edu.au (8.9.1a/8.9.1) with ESMTP id PAA22353 for ; Thu, 24 Dec 1998 15:07:19 +1100 (EST) Received: from Adnan.vut.edu.au ([140.159.75.221]) by students.vut.edu.au (Netscape Messaging Server 3.5) with SMTP id AAA46DC for ; Thu, 24 Dec 1998 15:00:27 +1100 X-Sender: s9610264@students.vut.edu.au (Unverified) X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Thu, 24 Dec 1998 15:04:38 +1100 To: chemistry@www.ccl.net From: "Adnan Hazar" Subject: summary: pKa - organic amines Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Message-ID: <7718EDA41B.AAA46DC@students.vut.edu.au> Sometime ago I posted a question about the availability of pKa valuses for organic amines. Please see the original message and the responses below: --------------- Dear all, I've been looking for either experimental or theoretical/calculated pKa values for mono and bidentate amines at different temperatures. So far I've been unable to gather any substantial information. I'd be greatful for any pointers I'd also be interested in a free reliable s/w either for windows or unix-linux platform for determining pKa values. ===================== One source I've used for small-molecule pKas is the Smith and Martell database, which is available from NIST (NIST Standard Reference Database 46). If you can get access to Bielstein Crossfire, that is also excellent. It allows one to draw a molecule or fragment and search the chemical literature for articles about it. The listing of articles it gives includes information on which molecular properties are given in each article. I have found some very useful pKa data this way. Hope this helps, Mike ------------------------------------------------------------------------------ Michael K. Gilson, Ph.D., M.D. Phone: (301) 738-6217 Center for Advanced Research in Biotechnology Fax: (301) 738-6255 National Institute of Standards and Technology 9600 Gudelsky Drive http://www.carb.nist.gov/carb/gilson.html Rockville, MD 20850-3479 e-mail: gilson@carb.nist.gov ------------------------------------------------------------------------------ ===================== My favorite book is: 1)Perrin, D. D.; Dempsey, B.; Serjeant, E. P. pKa Predictions for Organic Acids and Bases; Chapman and Hall: London, 1981. It has more about Hammett constants, but certainly is a good book. This one discusses the experimental determination: 1)Albert, A.; Serjeant, E. P. The Determination of Ionization Constants. A Laboratory Manual; Chapman and Hall: London, 1971. There are also a couple of special publications of the Royal Society of London with big tabulations of pKa's dating from probably 20 years ago. Yvonne Martin Abbott Laboratories ===================== Although I'm only a licenciate student i may be able to be of some assistance: at the VUB, the university of brussels, there's a professor(P.Geerlings) who studies organic compounds via quantum mechanical procedures; i know he is currently collaborating with the agricultural engineering departement of my own university(catholic university of leuven) to calculate the acid-base properties of zeolites with dft, but a few months ago i read in a belgian chemical magazine(a very insignificant one that certainly does not leave belgium) that one of his (quantum-chemistry) students had recently finished her Ph.D dissertion, and guess what: it was about the acid-base properties of organic amines! Perhaps they might be able to help you further. The homepage of the vub is at: http://www.vub.ac.be and my own university is at: http://www.kuleuven.ac.be P.Geerlings' email-adress is: pgeerlin@algc1.vub.ac.be (try pgeerlin@vub.ac.be) but i do not know if check's his mail of course. Hope this helps. ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* ~*~*~*~**~*~*~**~*~*~**~*~*~*~**~*~*~*~ ~*~* Adnan Hazar ~*~* School of Life Sciences ~*~* VUT - Australia ~*~* ~*~* adnan.hazar@students.vut.edu.au ~*~* Adnan.Hazar@staff.vut.edu.au ~*~* ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* ~*~*~*~**~*~*~**~*~*~**~*~*~*~**~*~*~*~