From chemistry-request@server.ccl.net Wed Oct 17 08:13:22 2001 Received: from aleph.net.uniovi.es ([156.35.11.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9HCDMB31166 for ; Wed, 17 Oct 2001 08:13:22 -0400 Received: from CONVERSION-DAEMON.aleph.net.uniovi.es by aleph.net.uniovi.es (PMDF V6.0-24 #45227) id <01K9LZJUX2O000FGVV@aleph.net.uniovi.es> for chemistry@ccl.net; Wed, 17 Oct 2001 14:13:05 +0200 (MET) Received: from pinon.ccu.uniovi.es (pinon.ccu.uniovi.es [156.35.31.1]) by aleph.net.uniovi.es (PMDF V6.0-24 #45227) with ESMTP id <01K9LZJU7FNI00FIU5@aleph.net.uniovi.es>; Wed, 17 Oct 2001 14:12:59 +0200 (MET) Received: (from pueyo@localhost) by pinon.ccu.uniovi.es (8.9.2/8.9.2) id OAA29540; Wed, 17 Oct 2001 14:12:53 +0200 (METDST) Date: Wed, 17 Oct 2001 14:12:53 +0200 (METDST) From: Victor Lua~na Subject: Re: CCL:Orbital energies for 1st row transition metals. To: chemistry@ccl.net, owner-chemistry@server.ccl.net Message-id: <200110171212.OAA29540@pinon.ccu.uniovi.es> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT > Date: Tue, 16 Oct 2001 18:08:26 -0700 > From: Laurence Lavelle > Subject: CCL:Orbital energies for 1st row transition metals. > > The following question relates to a first year chemistry course that I teach. > > Cr ground state is [Ar]3d^5 4s^1 > > What would be the ground state for Cr^-1 ? > Explain the e- configuration and estimate the relative energy difference > between Cr and Cr^-1. Laurence, Most probably the ground state of Cr^{-1} will close the 4s shell and maintain the highest spin in the 3d half filled shell: K(2)L(8)3S(2)3P(6)4S(2)3D(5) 6S Non-relativistic restricted Hartree-Fock energy for this configuration is -1043.337094 hartree (*) compared to -1043.356371 hartree of the neutral Cr ground state. Cr^{-1} appears to be unstable according to these energies. Expect quite significant correlation effects though. May be you are interested in the orbital energies. In the neutral Cr atom e(4s) = -0.22205 hartree and e(3d) = -0.37360 hartree. In the Cr^{-1} ground state e(4s) = -0.01664 hartree and e(3d) = -0.21310 hartree. It can be noticed that Cr^{-1}-e(4s) predicts the wrong sign for the energy of the Cr^{-1} -> Cr and Cr-e(4s) is even worse. The orbital reorganization is so significant that the frozen orbital model assumed by the Koopman's rule is of no use in this case. I would say that this example has a low pedagogical value for a first year course except if you want to show the limitations of Koopman's theorem. (*) RHF calculations using a large STO basis set by Koga et al Phys. Rev. A. 47, 4510-4512 (1993) Check http://www.unb.ca/chem/ajit/ for the bases and other references. Regards, Victor Lua~na -- HomePage %%http://www3.uniovi.es/~quimica.fisica/qcg/vlc/luana.html%% Free codes %%http://www3.uniovi.es/~quimica.fisica/qcg/%% +----------------------------------------------+ +---^---/ / ! Victor Lua~na ! | ~ / Just in case ! Departamento de Quimica Fisica y Analitica ! | | you don't ! Universidad de Oviedo, 33006-Oviedo, Spain ! < / remember ! e-mail: %%victor@carbono.quimica.uniovi.es%% ! | / where Oviedo ! phone: +34-985-103491 fax: +34-985-103125 ! |____ ___/ is ;-) +----------------------------------------------+ \/ From chemistry-request@server.ccl.net Wed Oct 17 10:30:26 2001 Received: from hschipaa.hsc.usf.edu ([131.247.16.97]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9HEUPB03228 for ; Wed, 17 Oct 2001 10:30:25 -0400 Received: from hschipaa.hsc.usf.edu ([131.247.16.105]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with SMTP id KAA09610 for ; Wed, 17 Oct 2001 10:30:23 -0400 (EDT) Message-ID: <3BCD9603.318A2F70@mindless.com> Date: Wed, 17 Oct 2001 10:30:27 -0400 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: electrostatic isosurface with rasmol Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLer's, I've heard tell of people using rasmol to generate electrostatic isosurfaces. But there is no module in rasmol to do this. Is there an upgrade or an independent module you can put in rasoml to accomplish this? Thanks for all comments. David Smith From chemistry-request@server.ccl.net Wed Oct 17 09:37:09 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9HDb9B01757 for ; Wed, 17 Oct 2001 09:37:09 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id JAA00325; Wed, 17 Oct 2001 09:37:07 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3BCD829A.3825A5A5@cornell.edu> Date: Wed, 17 Oct 2001 09:07:38 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: CCL:Orbital energies for 1st row transition metals. References: <200110171212.OAA29540@pinon.ccu.uniovi.es> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Victor Lua~na wrote: > I would say that this example has a low > pedagogical value for a first year course except if you want to show the > limitations of Koopman's theorem. Hi all- I wasn't aware that first year chemistry students were being taught about Koopman's theorem. I have taught several first year chem classes and never seen it mentioned once. In fact, my own exposure to it didn't occur until I was a graduate student. Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Wed Oct 17 11:35:18 2001 Received: from sun1.udg.es ([130.206.45.89]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9HFZHB06000 for ; Wed, 17 Oct 2001 11:35:18 -0400 Received: from iqc.udg.es (phoenix.udg.es [130.206.128.117]) by sun1.udg.es (8.9.3/8.9.3/otb) with ESMTP id RAA23701 for ; Wed, 17 Oct 2001 17:34:56 +0100 (WET DST) Message-ID: <3BCDA5F4.A97DBFC6@iqc.udg.es> Date: Wed, 17 Oct 2001 17:38:28 +0200 From: Xavier Girones Torrent X-Mailer: Mozilla 4.72 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Help with reference title References: <3BCD9603.318A2F70@mindless.com> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLer's, I am turning mad finding the title of the following reference: Hirshfeld, FL Rzotkiewicz, S Molecular Physics, 1974, Vol. 27, page 1319. where the first definition of 'promolecule model' was done. Could someone please help me? Also, if the last page is available it would be quite useful in order to quote it in ACS reference style. I would also like to ask for a copy outside my university and I need the full reference. Thank you in advance for your help and time, Xavier Gironés Institute of Computational Chemistry University of Girona Girona, Spain David Smith wrote: > Dear CCLer's, > > I've heard tell of people using rasmol to generate electrostatic > isosurfaces. But there is no module in rasmol to do this. Is there an > upgrade or an independent module you can put in rasoml to accomplish > this? Thanks for all comments. > > David Smith > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Oct 17 04:16:56 2001 Received: from uscmail.usc.es ([193.144.75.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9H8GtB24959 for ; Wed, 17 Oct 2001 04:16:55 -0400 Received: from qfcronos (qfcronos.usc.es [193.144.74.154]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id KAA26820 for ; Wed, 17 Oct 2001 10:16:52 +0200 (MET DST) Message-ID: <001b01c156e4$abd9e280$9a4a90c1@usc.es> From: =?iso-8859-1?Q?Jes=FAs_Rodr=EDguez_Otero?= To: Subject: G98 linux with g77? Date: Wed, 17 Oct 2001 10:21:05 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0018_01C156F5.6E23C9E0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_0018_01C156F5.6E23C9E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Has anyone successfully tried to compile G98 with g77? Is necessary a lot of changes of the makefile? I have an Athlon with linux Mandrake 8.0 (kernel 2.4.3) Is the performance substantially worse than with the pgf77? thanks in advance ------=_NextPart_000_0018_01C156F5.6E23C9E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi
 
Has anyone successfully tried to = compile G98 with=20 g77?
Is necessary a lot of changes of = the=20 makefile?
 
I have an = Athlon with linux=20 Mandrake 8.0 (kernel 2.4.3)
 
Is the performance substantially worse = than with=20 the pgf77?
 
 
thanks in advance
 
 
------=_NextPart_000_0018_01C156F5.6E23C9E0-- From chemistry-request@server.ccl.net Wed Oct 17 12:33:57 2001 Received: from inrs-iaf-exchg.inrs-iaf.uquebec.ca ([198.168.44.212]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9HGXvB07835 for ; Wed, 17 Oct 2001 12:33:57 -0400 Received: by INRS-IAF-EXCHG with Internet Mail Service (5.5.2653.19) id ; Wed, 17 Oct 2001 12:34:46 -0400 Message-ID: <5F517746B331D411882400508BA24AD90F1161@INRS-IAF-EXCHG> From: "Wu, JianHui(IAF)(LAVAL)" To: "'chemistry@ccl.net'" Subject: SGI 750, benchmark? Date: Wed, 17 Oct 2001 12:34:44 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Dear All, I am considering to purchase a SGI750 (2x733 MHz or 2x800MHz Itanium, 2 MB cache, 1GB Memory, linux system). As it is a new system, I would like to hear from someone who is using it. Is it stable? how is the price/performance ratio? Any benchmark (e.g. Amber or some other MD code) for this system? Another option is O2 R12000 400 MHz (we already have a O2 R5000 300MHz). What I am looking for is the computational power. Any suggetion? Thanks a lot for your help, Jian Hui From chemistry-request@server.ccl.net Wed Oct 17 07:17:46 2001 Received: from orionl0.ccf.auth.gr ([155.207.199.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9HBHjB29986 for ; Wed, 17 Oct 2001 07:17:45 -0400 Received: from vanpc4 (vanpc4.chem.auth.gr [155.207.64.164]) by orionl0.ccf.auth.gr (8.11.6/8.11.4/8.11.4) with SMTP id f9HBHgk12896 for ; Wed, 17 Oct 2001 14:17:43 +0300 (EET DST) Organization: Message-ID: <002201c156fd$4be57c90$a440cf9b@chem.auth.gr> From: "Tasos V." To: Subject: SUMMARY: Solvent effect problem Date: Wed, 17 Oct 2001 14:17:22 +0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001F_01C15716.70677550" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 Disposition-Notification-To: "Tasos V." X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 This is a multi-part message in MIME format. ------=_NextPart_000_001F_01C15716.70677550 Content-Type: text/plain; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable Dear CCL'ers, A week ago I posted the following question: ----------------------QUESTION------------------------ I tried to run a calculation to estimate the HF energy value of a = Hydrogen aton in solution. The continuum models I used were: PCM, CPCM, IEFPCM and the Gaussian = version is 98W Revision A.7. The input file was as follows: # B3LYP/6-31+G(d) 5d SCRF(PCM,Solvent=3DWater) SCF=3DTight Test B3LYP/6-31+G(d) 5d SCRF=3DPCM H atom in water 0 2 H 0.000 0.000 0.000 78.39 G98w was unable to complete this calculation, the answer I got was: No nuclei in the second cavity Error termination via Lnk1e in G:\G98W\l502.exe. In an attempt to overcome this problem, I have also run a simple Onsager = model calculation, which, although afforded a HF energy value, = unfortunately, it yielded the same HF value for all different solvents = (n-Heptane, Acetonitrile, Water) I used. I would appreciate very much receiving your kind piece of advice. ------------------------SUMMARY OF REPLIES--------------------------- 1) Mary O'Connor=20 suggested me to try a different basis set (might have to go up to = 6-311++G(d,p) ) or try another software package (Jaquar will give the = value of a solvated proton).=20 2) Laurence Cuffe said that in the Onsager output the HF value in the archive entry is = not the right one, but I had to look in the body of the file. The = Onsager model responds to the dipole of the molecule and my atom has = none. 3) Dr. Cory Pye since the United-atom approximation that Gaussian uses, collapses all = hydrogens onto "heavy atom", he suggested that I would need to specify = RADII=3DXXX, where XXX is anything other than the = UAHF(UFF,BONDI,PAULING). -------------------------------------------------------------------------= --------------- Thanks to all of you for your replies, Indeed, the problem was the UAHF model that Gaussian uses by default. In = particular, it is unable to run a calculation for the Hydrogen atom, = although it runs calculations for all other atoms, like for instance, = Li, N, etc. This is allowed for the latter atoms due to their = hydridization, formal charge and molecular topology. Therefore, I tried to use different radius values for the hydrogen. = However, when I used the keyword RADII=3DXXX (where, XXX=3D1.2 or any = proper value, or XXX=3DUFF) the calculation used the default UAHF radii, = affording again an error termination. Hence, the only right keyword were = RADII=3DBONDI and/or RADII=3DPAULING, which afforded both a complete = calculation and normal results. =20 Anastasios Vafiadis PhD candidate Aristotle University of Thessaloniki School of Chemistry Lab of Applied Quantum Chemistry P.O. Box 135 54-006 Thessaloniki Greece e-mail: vafiad@chem.auth.gr ------=_NextPart_000_001F_01C15716.70677550 Content-Type: text/html; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable
Dear = CCL'ers,
A week ago I = posted the=20 following question:
----------------------QUESTION------------------------
I tried to run a calculation to estimate the HF = energy value=20 of a Hydrogen aton in solution.
The continuum models I used were: PCM, CPCM, IEFPCM = and the=20 Gaussian version is 98W Revision A.7.
The input file was as follows:
 
# B3LYP/6-31+G(d) 5d SCRF(PCM,Solvent=3DWater) = SCF=3DTight=20 Test
B3LYP/6-31+G(d) 5d SCRF=3DPCM H atom in water
0 2
H 0.000 0.000 0.000
78.39
 
G98w was unable to complete this calculation, the = answer I=20 got was:
 
No nuclei in the second cavity
Error termination via Lnk1e in = G:\G98W\l502.exe.
 
In an attempt to overcome this problem, I have also = run a=20 simple Onsager model calculation, which, although afforded a HF energy = value,=20 unfortunately, it yielded the same HF value for all different solvents=20 (n-Heptane, Acetonitrile, Water) I used.
I would appreciate very much receiving your kind = piece of=20 advice.
------------------------SUMMARY OF=20 REPLIES---------------------------
1) Mary O'Connor
 suggested me to try a different basis set = (might have=20 to go up to 6-311++G(d,p) ) or try another software package (Jaquar will = give=20 the value of a solvated proton).
 
2) Laurence Cuffe
 said that in the Onsager output the HF value = in the=20 archive entry is not the right one, but I had to look in the body of the = file.=20 The Onsager model responds to the dipole of the molecule and my atom has = none.
 
3) Dr. Cory Pye
since the United-atom approximation that = Gaussian uses,=20 collapses all hydrogens onto "heavy atom", he suggested that = I would need=20 to specify RADII=3DXXX, where XXX is anything other than the=20 UAHF(UFF,BONDI,PAULING).
------------------------------------------------------------= ----------------------------
Thanks to all of you for your replies,
 
Indeed, the problem was the UAHF model that = Gaussian uses by=20 default. In particular, it is unable to run a calculation for the = Hydrogen atom,=20 although it runs calculations for all other atoms, like for instance, = Li, N,=20 etc. This is allowed for the latter atoms due to their=20 hydridization, formal charge and molecular topology.
Therefore, I tried to use different radius = values for=20 the hydrogen. However, when I used the keyword RADII=3DXXX (where, = XXX=3D1.2 or any=20 proper value, or XXX=3DUFF) the calculation used the default = UAHF radii,=20 affording again an error termination. Hence, the only = right=20 keyword were RADII=3DBONDI and/or RADII=3DPAULING, which afforded both a = complete=20 calculation and normal results.
 
Anastasios Vafiadis
PhD candidate
Aristotle University of Thessaloniki
School of Chemistry
Lab of Applied Quantum Chemistry
P.O. Box 135
54-006 Thessaloniki
Greece
e-mail: vafiad@chem.auth.gr
<= /DIV> ------=_NextPart_000_001F_01C15716.70677550-- From chemistry-request@server.ccl.net Wed Oct 17 13:19:27 2001 Received: from mr3.cc.ic.ac.uk ([155.198.5.113]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9HHJRB08836 for ; Wed, 17 Oct 2001 13:19:27 -0400 Received: from origin.ch.ic.ac.uk ([155.198.224.252] helo=chcmga.ch.ic.ac.uk) by mr3.cc.ic.ac.uk with esmtp (Exim 3.31 #1) id 15tuLm-00074f-00 for chemistry@ccl.net; Wed, 17 Oct 2001 18:19:26 +0100 Received: from hbtower.ch.ic.ac.uk ([155.198.226.132] helo=argon.ch.ic.ac.uk) by chcmga.ch.ic.ac.uk with esmtp (Exim 2.02 #1) id 15tuLm-000eIj-00; Wed, 17 Oct 2001 18:19:26 +0100 Sender: krzys@ic.ac.uk Message-ID: <3BCDBD79.E3225F2B@argon.ch.ic.ac.uk> Date: Wed, 17 Oct 2001 18:18:49 +0100 From: Krzysztof Radacki Reply-To: k.radacki@ic.ac.uk Organization: Imperial College X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.4.2-2smp i686) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: isolobal vs. isoelectronic Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, just at this weekend I had nice discussion about isolobal particles. The starting point were small isoelectronic boron-clusters with different apical fragments. CH_2 is isoelectronic to BH_3. I've never thought about it before, but I've always presumed that it's mean also that they are isolobal. The argument from my opponent was the definition of isolobality: "the fragments are isolobal if they have equal number of orbitals with approximately the same symmetry, shape and energy". So he had argued that BH_3 has only one free orbital (not involved in B-H bond) and CH_2 two of them. So BH_3 is isolobal to CH_3(+) but only isoelectronic to CH_2. I've been really confused (as I've said never thought about it before), and asked him how to explain that already R. Hoffmann had shown in his Nobel-lecture that orbitals of d^6-ML_5 and CH_3(+) are isolobal and just on example of chemistry CH_2 <--o--> Cr(CO)_5 what leads to isolobal analogy between CH_2 <--o--> CH_3(+). (there was also comparison of CH_3(+), CH_2 and CH(-) as donor but I haven't used this argument) He hasn't explained but we've stopped our discussion in this point. Everything good but I can't get rid of it. Coming back to BH_3 and CH_2. Does really BH_3 give only one orbital to cluster. Or does CH_2 gives only two. My point of view is: CH_2 group has two hydrogen atoms - one in exo- and one in endo-position. The exo-one, as every exo-ligand, does not participate in cluster-Aufbau. Endo are parts of cluster so CH_2 gives 2 empty orbitals and one occupied with H-atom; BH_3 gives one empty, 2nd occupied with endo-H and 3rd occupied with mi-H. It means that both fragments are 3-orbitals donors. I know - this is first-year question - but better late than never :) Any comments are wellcomed. Krzys