From chemistry-request@server.ccl.net Thu Oct 4 17:15:05 2001 Received: from kweetal.tue.nl ([131.155.2.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f94LF4B02917 for ; Thu, 4 Oct 2001 17:15:04 -0400 Received: from stex1.chem.tue.nl (STEX1.chem.tue.nl [131.155.85.144]) by kweetal.tue.nl (8.11.6/8.11.6) with ESMTP id f94LF3P01764 for ; Thu, 4 Oct 2001 23:15:03 +0200 (MDT) Received: from eagle (t1502.chem.tue.nl [131.155.86.100]) by stex1.chem.tue.nl with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id TSVFPYNB; Thu, 4 Oct 2001 23:15:03 +0200 Message-ID: <001601c14d11$082e0120$64569b83@chem.tue.nl> From: "Tatyana E. Shubina" To: Subject: error message Date: Thu, 4 Oct 2001 23:13:27 +0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0013_01C14D2A.2CC29780" 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_0013_01C14D2A.2CC29780 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: quoted-printable Dear CCLers, During of optimisation of allyl cation I got error message and = calculation stopped: Cycle 1 Pass 0 IDiag 1: Petite list used in FoFDir. MinBra=3D 0 MaxBra=3D 1 Meth=3D 1. IRaf=3D 0 NMat=3D 1 IRICut=3D 1 DoRegI=3DT DoRafI=3DF = ISym2E=3D 1 JSym2E=3D1. nRTMD1 allocation error in MakMD1. Error termination via Lnk1e in /home/g98/l502.exe. Job cpu time: 0 days 0 hours 23 minutes 26.8 seconds. File lengths (MBytes): RWF=3D 14 Int=3D 0 D2E=3D 0 Chk=3D 3 = Scr=3D 1 The question is: what that error message mean and what is the solution? I have G98 A.7, SuSE 6.3 with 2.2.14 kernel. Thanks in advance for your help, Tatyana --=20 =20 file://` `\ Tatyana E. Shubina _,-"\% // /``\`\ Schuit Institute of Catalysis, >__ ^ |% // / } `\`\ Laboratory of Inorganic Chemistry and = Catalysis =20 / (%//.(((((((((((((\ Eindhoven University of Technology=20 | ' `-._ 5600 MB Eindhoven \ , ( \ _`-.__.-;%> The Netherlands=20 /_`\ \,"-=3D-'`\ \." `-..-'` TEL. +-31-40-2474916; FAX = +-31-40-2455054 TS/_/ /_/ email: T.E.Shubina@tue.nl = http://www.brainbench.com/transcript.jsp?pid=3D600030 ------=_NextPart_000_0013_01C14D2A.2CC29780 Content-Type: text/html; charset="koi8-r" Content-Transfer-Encoding: quoted-printable

Dear CCLers,

During of optimisation of allyl = cation I=20 got error message and calculation stopped:

Cycle   1 Pass = 0 IDiag=20 1:
Petite list used in FoFDir.
MinBra=3D 0 MaxBra=3D 1 = Meth=3D=20 1.
IRaf=3D       0 = NMat=3D   1=20 IRICut=3D       1 DoRegI=3DT DoRafI=3DF = ISym2E=3D 1=20 JSym2E=3D1.
nRTMD1 allocation error in MakMD1.
Error = termination=20 via Lnk1e in /home/g98/l502.exe.
Job cpu time: 0 = days 0=20 hours 23 minutes 26.8 seconds.
File lengths (MBytes): =20 RWF=3D   14 Int=3D    0 = D2E=3D    0=20 Chk=3D    3 Scr=3D    1

The question is: what that error = message mean=20 and what is the solution?

I have G98 A.7, SuSE 6.3 with 2.2.14 = kernel.

Thanks in advance for your = help,

Tatyana

--=20
           &nb= sp;   =20
           file://`=20 `\            = ; =20 Tatyana E. Shubina
_,-"\%   //=20 /``\`\            = Schuit=20 Institute of Catalysis,
>__ ^ |% // / }=20 `\`\          Laboratory of = Inorganic Chemistry and Catalysis      =
  =20 / (%//.(((((((((((((\      Eindhoven = University=20 of Technology
|   =20 '        =20 `-._          5600 MB=20 Eindhoven
\   ,     ( =20 \   _`-.__.-;%> The Netherlands
/_`\ \,"-=3D-'`\ = \."=20 `-..-'`    TEL. +-31-40-2474916; FAX=20 +-31-40-2455054
TS/_/      =20 /_/           &nbs= p; =20 email: T.E.Shubina@tue.nl
  =             &= nbsp;           =20 http://www= .brainbench.com/transcript.jsp?pid=3D600030

------=_NextPart_000_0013_01C14D2A.2CC29780-- From chemistry-request@server.ccl.net Fri Oct 5 07:16:48 2001 Received: from uscmail.usc.es ([193.144.75.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f95BGmB31184 for ; Fri, 5 Oct 2001 07:16:48 -0400 Received: from qfcronos (qfcronos.usc.es [193.144.74.154]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id NAA24027 for ; Fri, 5 Oct 2001 13:16:46 +0200 (MET DST) Message-ID: <008b01c14d8f$d98f6500$9a4a90c1@usc.es> From: =?iso-8859-1?Q?Jes=FAs_Rodr=EDguez_Otero?= To: Subject: NBO problem with LPs Date: Fri, 5 Oct 2001 13:21:15 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0088_01C14DA0.9C57F240" 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_0088_01C14DA0.9C57F240 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi I have a serious problem with NBO calculations with the two LPs of the = oxigen atoms. For instance, with the water molecule (HF, DFT or MP2) the two lone = pairs of the oxigen atoms adopt a very singular arrangement: one LP in the molecular plane (a hybrid aprox sp), an the other LP being = a pure p orbital, absolutely perpendicular to the plane. This is totally different to the expected: two LPs with sp3 character, = above and below the plane. Do NBO calculations work well??? Anybody has a similar problem?? Thanks in advance Jesus Rodriguez Otero qftjesus@usc.es ------=_NextPart_000_0088_01C14DA0.9C57F240 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

I have a serious problem with NBO = calculations with=20 the two LPs of the oxigen atoms.

For instance, with the water molecule = (HF, DFT or=20 MP2) the two lone pairs of the oxigen atoms adopt a very singular=20 arrangement:

one LP in the molecular plane (a hybrid = aprox sp),=20 an the other LP being a pure p orbital, absolutely perpendicular to = the=20 plane.

This is totally different to the = expected: two=20 LPs with sp3 character, above and below the plane.

Do NBO calculations work = well???

Anybody has a similar = problem??

Thanks in advance

Jesus Rodriguez Otero

qftjesus@usc.es

------=_NextPart_000_0088_01C14DA0.9C57F240-- From chemistry-request@server.ccl.net Fri Oct 5 03:20:45 2001 Received: from nenuphar.saclay.cea.fr ([132.166.192.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f957KZB21614 for ; Fri, 5 Oct 2001 03:20:40 -0400 Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.D20+Y2K) with ESMTP id JAA24414 for ; Fri, 5 Oct 2001 09:20:32 +0200 (MET DST) Received: from lycose.saclay.cea.fr (lycose.saclay.cea.fr [132.166.192.104]) by muguet.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.2.D20+Y2K) with ESMTP id JAA21956 for ; Fri, 5 Oct 2001 09:20:26 +0200 (MET DST) Received: from penelope.saclay.cea.fr (unverified) by lycose.saclay.cea.fr (Content Technologies SMTPRS 4.2.5) with ESMTP id ; Fri, 5 Oct 2001 09:14:15 +0200 Received: by penelope.saclay.cea.fr with Internet Mail Service (5.5.2653.19) id ; Fri, 5 Oct 2001 09:14:32 +0200 Message-ID: From: VITORGE Pierre 094605 To: "'John Bushnell'" , Ulrike Salzner Cc: ccl Subject: RE: size of s,p,d orbitals Date: Fri, 5 Oct 2001 08:59:17 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" IN pinciple it is not straightforward to compare the size of geometric entitis of different shapes. What can be "observed" is square the orbital (probability to find electrons); but the most conveninet for your question is certainly the density of probability, it can be "seen" with only the radial part of the orbital R, the corresponding density is (r R)^2 classically plotted. here you face the (mathematical) problem of eventually non symetrical distributions (eventually with several maxima) hence the maximum of the distribution is not necessarly very close to the mean distance. the order of the maxima are: 2p < 2s 3d < 3p < 3s Since 3s has 2 relative maxima at distances shorther than the maximum 3p has 1 relative maximum at distance shorther than the maximum hence the mean distances (for 3s, 3p and 3d) are closest than the maxima Pierre Vitorge CEA Saclay DEN/DPC/SCPA/LCRE Bat.450 pce 157D UMR 8587 (Universite d'Evry-CNRS-CEA) 91191 Gif sur Yvette cedex France pierre.vitorge@cea.fr phone +33 169-08-32-65, secretary: +33 169-08-32-50, fax: +33 169-08-32-42 http://perso.club-internet.fr/vitorgen/pierre/pierre.html pierre.vitorge@laposte.net -----Original Message----- From: John Bushnell [mailto:bushnell@chem.ucsb.edu] Sent: Friday, October 05, 2001 3:17 AM To: Ulrike Salzner Cc: ccl Subject: CCL:size of s,p,d orbitals Regarding the argument about "the lack of repulsion between the 2p orbital and a lower shell p-orbital", I would think that this would not be an issue. If there was such a thing as a "1p" orbital, it would be spherically symmetric when filled. Thus I wouldn't expect any inherently p-specific repulsion to such a filled subshell, if it existed. That is, the s orbital would also experience such a "lack of repulsion" :-) - John bushnell@chem.ucsb.edu On Thu, 4 Oct 2001, Ulrike Salzner wrote: > Dear Collegues, > until 1 hour ago, I firmly believed that p-orbitals are larger than s- > orbitals for atoms that are in the same row of the periodic table. Only > for the second row the sizes were about same. This conviction is mainly > due to a paper by Werner Kutzelnigg, Angew. Chem. 1984, 96, 262-286. I > further believed that s electrons are attracted stronger by the nuclei > because they have no node at the position of the nucleus and that the > similar size of s- and p-orbitals in the second row is due to the lack of > 1p orbitals and therefore cancellation of two effects: less attraction of > p electrons due to the node and lack of repulsion between 2p and a lower > shell p-orbital. This is also what I kept telling our first year students. > > Today a collegue approached me who teaches inorganic chemistry to our > third year students. She told me that she was surprized that the students > did not know that the order according to decreasing size is s > p > d > within the same row. After admitting that this was to be blamed on me, she > showed me the Inorganic Chemistry textbook by Huhee. There are plots of > radial distribution times r square, clearly indicating that the maximum > shifts to smaller values from s to p to d. Huhee quotes Herberg's "Atomic > Spectra and Atomic Structure" from 1944. In Kutzelniggs article the > average distance of electrons from the nucleus was used not radial > distribution times r square. > > The question now is: Do the two ways to determine the size of the orbitals > lead to different conclusions? Is there a mistake somewhere? Is there > newer information? Which orbitals are bigger? What is best method to > determine the size to explain bonding, hybridization, or lack thereof and > so on? > > Thanks in advance for suggestions, > Ulrike Salzner > =================================================================== > > Dr. Ulrike Salzner > Associate Professor > Department of Chemistry Tel.: (312) 290-2122 > Bilkent University Fax.: (312) 266-5097 > 06533 Bilkent, Ankara e-mail: salzner@fen.bilkent.edu.tr > Turkey > > ==================================================================== > > > > > > > -= 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 Fri Oct 5 09:35:24 2001 Received: from century.fen.bilkent.edu.tr ([139.179.97.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f95DZ2B03702 for ; Fri, 5 Oct 2001 09:35:06 -0400 Received: from fen.bilkent.edu.tr (fenII-121.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with ESMTP id QAA06731; Fri, 5 Oct 2001 16:32:32 +0300 (EET DST) Message-ID: <3BBDB71F.99539087@fen.bilkent.edu.tr> Date: Fri, 05 Oct 2001 16:35:28 +0300 From: Ulrike Salzner Organization: Bilkent University X-Mailer: Mozilla 4.77 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, chrirena@techunix.technion.ac.il, Pascal.Boulet@chiphy.unige.ch Subject: relative sizes of s-,p-,d-orbitals Content-Type: multipart/mixed; boundary="------------B3398ECFF5F8793FB19FA060" This is a multi-part message in MIME format. --------------B3398ECFF5F8793FB19FA060 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello everybody, thanks to everyone who replied to my question about relative sizes of s-,p-, and d-orbitals in one shell. To summarize: There are two cases and three approaches to distinguish. The first case deals with hydrogenic one-electron functions, the second deals with approximate orbitals for multi-electron systems. The dispute between my collegue and myself was actually due to this. I was thinking of many-electron atoms, she was teaching hydrogenic orbitals. But I learned something new, since I was not aware that this difference existed. The three approaches to define size are using 1) maxima in electron density, 2) average distance from the nucleus , 3) the size that is needed to include 90% or so of the electron density. The difficulty arises from the fact that wavefunctions approach zero at infinite distance from the nucleus but do not become identical zero and form the fact that position of maximum density and average density differ considerably. It seems clear that for hydrogenic orbitals all three approaches agree in that s > p > d. However, for many electron systems the situation appears to quite different and exactly like I always believed ( T H A N K S). The calculation done by Mikael Johansson on the Ar atom shows that 2s and 2p are almost of same size, p a little smaller, but 3s is significantly smaller than 3p. The method was large basis set DFT and the size is defined by the space that includes 90% and 95% of the electron density, respectively. The original replies are attached below. Sincerely, Ulrike Salzner This was an interesting question, succeeding in diverting me from things I should be doing :-) Without taking a stand on what method is the "best" I made a quick calculation on the argon-atom and compared the "sizes" of the 2s/2p and 3s/3p orbitals. Below is reported the radius of a spherical boundary around the atom which contains 90% resp. 95% of the electron density of the orbital in question: (the calculation was made on B3LYP/TZVP level, for no specific reason) 90% 95% 2s 0.65 0.74 a.u. 2p 0.63 0.72 3s 2.14 2.44 3p 2.64 3.06 So according to the above the 2s/2p-orbitals are about as big, whereas the 3s is smaller than the 3p. Other comments on the subject would be very welcome! Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson@helsinki.fi Phone: +358-9-191 50185 FAX : +358-9-191 50169 Subject: Re: CCL:size of s,p,d orbitals Date: Thu, 4 Oct 2001 15:16:44 +0200 From: Christoph van W�llen To: Ulrike Salzner References: 1 ...for hydrogenic orbitals, the exponential factor is the same, so I guess s orbitals are more compact (higher l-orbitals have an extra centrifugal barrier term in the potential). However in many-electron atoms the shielding of the nucleus by the "other" electrons may reverse the situation: within the same main quantum number, d orbitals see a more shielded nucleus than s orbitals. Looking at Hartree-Fock orbitals and their r, r^2, .... expectation values might give you the desired information. +---------------------------------+-------------------------------------+ | Prof. Christoph van W�llen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universit�t Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Stra�e des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+-------------------------------------+ Subject: Re: CCL:size of s,p,d orbitals Date: Thu, 04 Oct 2001 08:28:19 -0500 From: "Preston MacDougall" To: Ulrike Salzner Dear Dr. Salzner, As a theoretical chemist, making predictions comes naturally to me. I predict that you will be deluged with responses to your CCL posting, and some of them will simply astound you with their level of convolution. What I tell my students is that orbitals are just a scaffold. They are not strictly required, but they make computing wavefunctions, and explaining chemistry easier. Also, like scaffolds it is pointless to worry about the details of their appearance. Scaffolds and orbitals are simply not there when you examine a finished building, a real molecule, or an accurate wavefunction. If you are interested in some real properties of molecules that you can relate to chemical reactivity, please visit the online proceedings of the "ChemBond Workshop" at http://www.lctn.uhp-nancy.fr/ChemBond/TCA/ Here, you will find an international, theoretical discussion of the chemical bond. You can freely download all the papers in pdf format (it was also published by Theoretical Chemistry Accounts). My paper with Chris Henze may be of interest to you and your students, for at least a couple of reasons: it is not convoluted, it is based on observable functions, and it has some very attractive graphics (reviewed in "Nature", Aug. 9 issue, p588). Sincerely, Preston MacDougall P.S. Please do not post my response to CCL. -- Dr. Preston J. MacDougall Associate Professor Department of Chemistry, Box X101 Middle Tennessee State University Murfreesboro, TN 37132 Subject: Re: CCL:size of s,p,d orbitals Date: Thu, 4 Oct 2001 16:55:17 +0200 From: "Prof.Dr.Stefan Grimme" To: Ulrike Salzner References: 1 Dear Ulrike, I don't have Kutzelnigg's article at hand but all my QM textbooks tell me that (at least for H-atom functions) s is larger than p according to both criteria (max. of Psi^2*r^2 and or ). E.g. the value for hydrogen functions reads = const*(5/2 - L*(L+1)/2n^2). However, I don't think that this is important in practice because 1) what means "size"? 2) screening effects (as you mentioned) are important in many-electron systems so one has to look at the expectation values of e.g. HF-functions optimized for the atoms under consideration. Best wishes Stefan _________________________________________________________ Prof. Dr. Stefan Grimme Organisch-Chemisches Institut (Abt. Theoretische Chemie) Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) Email:grimmes@uni-muenster.de http://www.uni-muenster.de/Chemie/OC/research/grimme/ _________________________________________________________ Positions available for carrying out doctoral or postdoctoral studies in chemistry in M�nster: http://www.uni-muenster.de/Chemie/OC/positions/ _________________________________________________________ Subject: RE: size of s,p,d orbitals Date: Thu, 4 Oct 2001 19:36:34 +0200 From: Jordi Teixido To: "'Ulrike Salzner'" Hi Ulrike, (sorry for multiple mails this is the complete one) if you take average radius module for hydrogenlike atoms (1 single electron) we can analytically derive a mathematical formula depending on quantum numbers n and l only (I take it from Atkins' physical chemistry textbook) = (a/Z) (n^2) [1 + 1/2 (1 - { l(l+1) / n^2 })] a is Bohr radius so. i.e for n=4 l=0,1,2,3 we have 24 23 21 and 18 (a/Z) respectively (hope no mistake) anyway if the formula is correct for a given n the rightmost factor (1 - { l(l+1) / n*n }) gets lightly smaller for increasing l so does the average similar conclusions arise if you consider average < r^2 > for calculating or you need the full wavefunction (that spans from nuclei to infinity) not only the radial or harmonic parts (alone or squared ...). so perhaps this is the best 'sizing' method, of course you can do other sort of calculations, i.e. truncate the wavefunction to a given probability density (0.999 or 0.9 or, why not, 0.002) and from this truncated model repeat similar calculations to derive same or different conclusions. in hydrogenlike systems (1 electron) the energy of the wavefunction depends only on quantum number 'n' so orbitals with same 'n' but different 'l' (like those calculated above) form a degenerate set. So although the average is different for different Orbitals, the electronic energy remain the same This is again true for theoretical very large polyelectronic atoms with extremely large Z, but is false for real many-electron atoms, where the degeneracy is broken for different 'l' values, now lower 'l' values give 'lower' energy. Need to say, that now the orbital picture is not an analytical solution, is only a (very good) approximation. Of course the lower electron energy comes from a compromise Between more attraction with the nucleus (electrons closer to the nucleus) and less electronic repulsion (electrons more distant between them),and other factors (spin-orbit,.). The question is if this closeness to the nucleus in many-electron atom reverses or not the hydrogenlike result, not looking only to the energy distribution. Subject: Re: CCL:size of s,p,d orbitals Date: Thu, 4 Oct 2001 14:11:02 -0300 (ADT) From: Cory Pye To: Ulrike Salzner Hi Uli, For hydrogenic orbitals, _n,l= n^2 ( 1+ (1/2)(1 - l(l+1)/n^2))a_0/Z so the mean radius decreases as l increases Atkins, Physical Chemistry 6ed, p355. However for hydrogenic atoms, a 3s electron has the same energy as a 3p electron. So clearly, the mean radius cannot predict the energy levels. >From the same text, p364, the difference between s,p,d , etc in real atoms is due to penetration and shielding, i.e. the innermost maximum in a 3s orbital is further in than the innermost maximum of a 3p orbital, and hence the s orbitals penetrate to the nucleus more than the p orbitals do. As a result, the s electrons "see" more of the full nuclear charge, and are not shielded as much by other shells. ************* ! Dr. Cory C. Pye ***************** ! Assistant Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye@crux.stmarys.ca http://apwww.stmarys.ca/cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) Subject: Re: CCL:size of s,p,d orbitals Date: Thu, 4 Oct 2001 13:39:13 -0500 From: "Robert E. Harris" To: Ulrike Salzner , ccl The discussion given in Chs. 8 and 9 of Slater's Quantum Theory of Atomic Structure, v. I still seems to me one of the clearest on the subject. John C. Slater, Quantum Theory of Atomic Structure, v. I, McGraw Hill, New York, Toronto, London, 1960. REH Robert E. Harris Phone: 573-882-3274. Fax: 573-882-2754 Department of Chemistry, University of Missouri-Columbia Columbia, Missouri, USA 65211 Subject: Re: CCL:size of s,p,d orbitals Date: Thu, 4 Oct 2001 18:17:06 -0700 (PDT) From: John Bushnell To: Ulrike Salzner CC: ccl Regarding the argument about "the lack of repulsion between the 2p orbital and a lower shell p-orbital", I would think that this would not be an issue. If there was such a thing as a "1p" orbital, it would be spherically symmetric when filled. Thus I wouldn't expect any inherently p-specific repulsion to such a filled subshell, if it existed. That is, the s orbital would also experience such a "lack of repulsion" :-) - John bushnell@chem.ucsb.edu On Thu, 4 Oct 2001, Ulrike Salzner wrote: Subject: Re: CCL:size of s,p,d orbitals Date: Fri, 05 Oct 2001 01:32:49 -0400 From: "Samuel A. Abrash" To: salzner@fen.Bilkent.EDU.TR References: 1 Dear Dr. Salzner, I echo Robert Harris's recommendation of Slater's classic work, but also add the following. The plot of Psi^2(r) r2 dr vs r seek out the median (the r value for which the radial probability is maximized), which of course is the global maximum on the curve. (Note that I am including the radial portion of the function only). In this case for a given shell, rmaxd < rmaxp < rmaxs. An average is of course taken by the quantum mechanical formula = Integral Psi*(r) r Psi(r) r^2 dr. The reason that the latter is yields a different sequence of sizes than the former is the presence of core penetration. Remember that the probability function has n maxima for an s orbital, n-1, for a p orbital, n-2 maxima for a d orbital, and so on. Core penetration, which is larger when the L quantum number is smaller, refers to the fact that the smaller maxima for a given wavefunction, line up with the maxima for the inner shells. I.e. for a 3s orbital, the first maximum lines up approximately with the average position of the 1s electrons, the second with the 2s electrons. For the 3p orbital the first maximum lies between the position of the 1s and 2s electrons, and of course for 3d there is only one maximum, and no probability falling among the core electrons. This also explains the lower energy of 3s electrons relative to 3d electrons. The small fraction of time spend by the electrons in the region of core penetration result in substantial electrostatic stabilization. The effect is always higher for ns orbitals than np orbitals than nd orbitals. This should explain the difference in both the two size measures, and in the relative stability of the orbitals. Hybridization can be best thought of as a result of the following. When calculating the shapes of atomic orbitals, the potential is a coulomb potential between a point source nucleus and the electron cloud, and as a result has spherical symmetry. For this reason, the solutions (spherical harmonics) for the isolated atoms are solutions mapped onto a sphere. When calculating the shapes of atomic orbitals in molecules, the symmetry is based not on a potential of spherical symmetry, but of a symmetry based on the arrangement of the nuclei in the molecule, which has a lower symmetry than the isolated atomic problem. However, the atomic wavefunction in the molecule can still be expressed as a linear combination of the hydrogen-like atomic wavefunctions because the latter form a complete orthonormal set of functions. Hybridization is an approximate representation of the exact linear expansion of the true orbital in terms of these hydrogen-like orbitals. I hope this is of assistance. Please feel free to contact me at my e-mail address below if you have further questions. Best regards, Professor Samuel A. Abrash Samuel A. Abrash Associate Professor Department of Chemistry University of Richmond Richmond, VA 23173 Phone: (804) 289-8248 Fax: (804) 287-1897 E-mail: sabrash@richmond.edu http://www.richmond.edu/~sabrash "Research is to teaching as sin is to confession - if you don't participate in one you don't have anything to say at the other." Subject: RE: size of s,p,d orbitals Date: Fri, 5 Oct 2001 08:59:17 +0200 From: VITORGE Pierre 094605 To: "'John Bushnell'" , Ulrike Salzner CC: ccl IN pinciple it is not straightforward to compare the size of geometric entitis of different shapes. What can be "observed" is square the orbital (probability to find electrons); but the most conveninet for your question is certainly the density of probability, it can be "seen" with only the radial part of the orbital R, the corresponding density is (r R)^2 classically plotted. here you face the (mathematical) problem of eventually non symetrical distributions (eventually with several maxima) hence the maximum of the distribution is not necessarly very close to the mean distance. the order of the maxima are: 2p < 2s 3d < 3p < 3s Since 3s has 2 relative maxima at distances shorther than the maximum 3p has 1 relative maximum at distance shorther than the maximum hence the mean distances (for 3s, 3p and 3d) are closest than the maxima Pierre Vitorge CEA Saclay DEN/DPC/SCPA/LCRE Bat.450 pce 157D UMR 8587 (Universite d'Evry-CNRS-CEA) 91191 Gif sur Yvette cedex France pierre.vitorge@cea.fr phone +33 169-08-32-65, secretary: +33 169-08-32-50, fax: +33 169-08-32-42 http://perso.club-internet.fr/vitorgen/pierre/pierre.html pierre.vitorge@laposte.net -----Original Message----- From: John Bushnell [mailto:bushnell@chem.ucsb.edu] Sent: Friday, October 05, 2001 3:17 AM To: Ulrike Salzner Cc: ccl Subject: CCL:size of s,p,d orbitals Regarding the argument about "the lack of repulsion between the 2p orbital and a lower shell p-orbital", I would think that this would not be an issue. If there was such a thing as a "1p" orbital, it would be spherically symmetric when filled. Thus I wouldn't expect any inherently p-specific repulsion to such a filled subshell, if it existed. That is, the s orbital would also experience such a "lack of repulsion" :-) - John bushnell@chem.ucsb.edu On Thu, 4 Oct 2001, Ulrike Salzner wrote: --------------B3398ECFF5F8793FB19FA060 Content-Type: text/x-vcard; charset=us-ascii; name="salzner.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Ulrike Salzner Content-Disposition: attachment; filename="salzner.vcf" begin:vcard n:Salzner;Ulrike tel;fax:90-312-266-4579 tel;home:90-312-266-2781 tel;work:90-312-290-2122 x-mozilla-html:FALSE org:Bilkent University;Department of Chemistry adr:;;;Bilkent, Ankara;;06533 ;Turkey version:2.1 email;internet:salzner@fen.bilkent.edu.tr title:Associate Professor x-mozilla-cpt:;7072 fn:Ulrike Salzner end:vcard --------------B3398ECFF5F8793FB19FA060-- From chemistry-request@server.ccl.net Fri Oct 5 11:33:46 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f95FXiB07214 for ; Fri, 5 Oct 2001 11:33:45 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 15pWyq-0006f4-00; Fri, 05 Oct 2001 17:33:40 +0200 Received: from vejas.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id SAA29198 for ; Fri, 5 Oct 2001 18:06:11 +0200 (GMT) Date: Sat, 6 Oct 2001 05:32:23 +0200 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <1203677378.20011006053223@vaidila.vdu.lt> To: chemistry@ccl.net Subject: Re: CCL:linux cluster vs intranet In-reply-To: References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Have anybody any idea how to evaluate the solvatation influence to docking of ligands with strongly solvated functional groups ??? What king of software could solve that ? For example, AutoDock have solvatation of macro-molecule, but if I understand well, these solvatation parametres are mostly introduced for establishing hydrophobic/hydrophylic regions... Best regards Arturas Z. From chemistry-request@server.ccl.net Fri Oct 5 12:55:34 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f95GtXB09388 for ; Fri, 5 Oct 2001 12:55:33 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 15pYG2-0006jO-00; Fri, 05 Oct 2001 18:55:30 +0200 Received: from vejas.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id TAA29780 for ; Fri, 5 Oct 2001 19:28:02 +0200 (GMT) Date: Sat, 6 Oct 2001 06:54:14 +0200 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <798588973.20011006065414@vaidila.vdu.lt> To: ccl Subject: Re: CCL: docking ligand with solvatation effect ? In-reply-To: <1934467103.20011006054533@vaidila.vdu.lt> References: <1203677378.20011006053223@vaidila.vdu.lt> <1934467103.20011006054533@vaidila.vdu.lt> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Have anybody any idea how to evaluate the solvatation influence to docking of ligands with strongly solvated functional groups ??? What kind of software could solve that ? For example, AutoDock have solvatation of macro-molecule, but if I understand well, these solvatation parametres are mostly introduced for establishing hydrophobic/hydrophylic regions... Best regards Arturas Z. P.S. sorry for dublicated message From chemistry-request@server.ccl.net Fri Oct 5 14:07:13 2001 Received: from myth2.Stanford.EDU ([171.64.15.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f95I7DB11810 for ; Fri, 5 Oct 2001 14:07:13 -0400 Received: (from senos@localhost) by myth2.Stanford.EDU (8.11.6/8.11.6) id f95I77q17826; Fri, 5 Oct 2001 11:07:07 -0700 (PDT) Date: Fri, 5 Oct 2001 11:07:07 -0700 (PDT) From: Juan Pablo Senosiain To: Subject: CASPT2 using Gaussian98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear colleages, I performed CASSCF and CASPT2 calculations on O2 molecule using the cc-pvTZ basis set and 2 active spaces: 6elect, 4 orbitals (i.e. the degenerate pi system) and 8 electrons, 6 orbitals (sigma + sigma* + pi system). The two CASSCF calculations look reasonable, but the CASPT2 optimisations break the symmetry of the pi orbitals, resulting in HOMOs localized on a single atomic centre, and fail to converge. Does somebody have an insight on why this happens? many thanks. juan pablo _________________________________________________________ J u a n P a b l o S e n o s i a i n P e l a e z Materials Science and Engineering S t a n f o r d U n i v e r s i t y office: (650) 7230420 home: (415) 6416211 http://chemeng.stanford.edu/~senos _________________________________________________________ From chemistry-request@server.ccl.net Fri Oct 5 13:30:17 2001 Received: from phm.utoronto.ca ([128.100.70.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f95HUGB10811 for ; Fri, 5 Oct 2001 13:30:16 -0400 Received: from phm.utoronto.ca (lpk04.phm.utoronto.ca [128.100.70.180]) by phm.utoronto.ca (8.9.3+Sun/8.9.3) with ESMTP id NAA12913 for ; Fri, 5 Oct 2001 13:23:53 -0400 (EDT) Sender: william@phm.utoronto.ca Message-ID: <3BBDEDB0.65F7F59B@phm.utoronto.ca> Date: Fri, 05 Oct 2001 13:28:16 -0400 From: William Wei Reply-To: william@phm.utoronto.ca Organization: Faculty of Pharmacy, U of T X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Chemists CCLers Subject: SUMMARY:SSH on SGI IRIX6.5 Content-Type: multipart/alternative; boundary="------------2569F5F6419027A205D991E3" --------------2569F5F6419027A205D991E3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Dear CCLers: Two days ago, I ask help from here for the ssh problems. I have received a lot of replies and got a lot of useful informations. I just show my thanks to all of these friends. Here is a brief summary. for SSH and my resolution: From: Szilveszter Juhos: Hello, I did compiled ssh[d] for Irix though it was not an easy thing first time. I know its a nightmare, you can download it from the Cambridge Univ site: http://www-uxsup.csx.cam.ac.uk/CD/UCAM_SSH_CD_05/IRIX The problem is the sshd. If you need it, from the Irix freeware site you should to download automake, m4, autoconf and GNU make than compile the required libs (./configure; make install is the usual method). I spent a whole day, the current version I have is _very_ old. From: Aniko Simon We also use ssh, i.e.: OpenSSH_2.5.1p2 compiled successfully on (IRIX 6.5). That's what we are using... From: Simon BERNECHE There's a pre-compiled version of openssh on SGI web site: http://freeware.sgi.com/index-by-alpha.html From: Eugene Leitl Have you tried http://ssh.com/products/ssh/download.cfm What is the error message you get? Are you using GNU compilers? From: Jan Labanowski On the CCL Web site there are my notes on installation of Web servers and servlets/JSP stuff in http://www.ccl.net/cca/software/UNIX/apache/ Among them, there are my notes on installing Apache on IRIX. In the IRIX notes, there is a blurb on ssh installation on IRIX. You can have a look at these. Note that the notes are a few months old, i.e., obsolete. But the principles hopefully still apply. From: Rajarshi Guha How was the openssl installed? If it was from source did you do a make install? You would also need to update the library paths (I don't know the command on IRIX). You could also specifiy the library path of openssl in the configure command in the openssh directory. And from many others who gave the same informations. The following is my resolution: After I read the config.log. I found the openssl-0.9.6a is a 64bit lib. But openssh-2.9p2 is 32bit program. Maybe I do not know how to compile it with 64 bit. Anyone knows? So I downloaded the old version openssl-0.9.5a, for the openssh-2.9p2 does not work well with it, I compiled openssh-2.1.1p3. Now it works well. I hope this can help these who work with IRIX and want to use SSH! William. -- William Wei Tel: 1-416-946-7551 Faculty of Pharmacy Fax: 1-416-978-8511 19 Russell Street Email: william@phm.utoronto.ca Toronto, ON. M6G 3P7 Canada. --------------2569F5F6419027A205D991E3 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Dear CCLers:

Two days ago, I ask help from here for the ssh problems. I have received a lot of replies and got a lot of useful informations. I just show my thanks to all of these friends. Here is a brief summary. for SSH and my resolution:

From: Szilveszter Juhos:
Hello, I did compiled ssh[d] for Irix though it was not an easy thing
first time. I know its a nightmare, you can download it from the
Cambridge Univ
site: http://www-uxsup.csx.cam.ac.uk/CD/UCAM_SSH_CD_05/IRIX

The problem is the sshd. If you need it, from the Irix freeware site you
should to download automake, m4, autoconf and GNU make than compile the
required libs (./configure; make install is the usual method). I spent a
whole day, the current version I have is _very_ old.

From: Aniko Simon
We also use ssh, i.e.:
OpenSSH_2.5.1p2 compiled successfully on <our_machine> (IRIX 6.5).
That's what we are using...

From: Simon BERNECHE

There's a pre-compiled version of openssh on SGI web site:

http://freeware.sgi.com/index-by-alpha.html

From: Eugene Leitl
Have you tried http://ssh.com/products/ssh/download.cfm
What is the error message you get? Are you using GNU compilers?

From: Jan Labanowski
On the CCL Web site there are my notes on installation of Web servers
and servlets/JSP stuff in
http://www.ccl.net/cca/software/UNIX/apache/
Among them, there are my notes on installing Apache on IRIX.
In the IRIX notes, there is a blurb on ssh installation on IRIX.
You can have a look at these.
Note that the notes are a few months old, i.e., obsolete. But the principles
hopefully still apply.

From: Rajarshi Guha
How was the openssl installed? If it was from source did you do a make
install? You would also need to update the library paths (I don't know the
command on IRIX). You could also specifiy the library path of openssl in
the configure command in the openssh directory.

And from many others who gave the same informations. The following is my resolution:

After I read the config.log. I found the openssl-0.9.6a is a 64bit lib. But openssh-2.9p2 is 32bit program. Maybe I do not know how to compile it with 64 bit. Anyone knows? So I downloaded the old version openssl-0.9.5a, for the openssh-2.9p2 does not work well with it, I compiled openssh-2.1.1p3. Now it works well.

I hope this can help these who work with IRIX and want to use SSH!

William.

-- 
William Wei                    Tel: 1-416-946-7551
Faculty of Pharmacy            Fax: 1-416-978-8511
19 Russell Street              Email: william@phm.utoronto.ca
Toronto, ON. M6G 3P7
Canada.

--------------2569F5F6419027A205D991E3--