From chemistry-request@server.ccl.net Thu Oct 18 00:33:09 2001 Received: from sesosn01.astrazeneca.com ([212.209.42.131]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9I4X8B24595 for ; Thu, 18 Oct 2001 00:33:08 -0400 Received: from sesosn11.seso.astrazeneca.net (sesosn11.seso.astrazeneca.net [192.168.199.18]) by sesosn01.astrazeneca.com (8.9.3/8.9.3.DEF) with ESMTP id GAA22867 for ; Thu, 18 Oct 2001 06:33:07 +0200 (MET DST) From: parthiban.srinivasan@astrazeneca.com Received: from sesosn21.seso.astrazeneca.net (sesosn21.seso.astrazeneca.net [192.71.145.181]) by sesosn11.seso.astrazeneca.net (8.9.3/8.9.3) with ESMTP id GAA02115 for ; Thu, 18 Oct 2001 06:31:19 +0200 (MET DST) Received: from astra-cdc-x03.seso.astrazeneca.net (astra-cdc-x03.seso.astrazeneca.net [192.71.145.48]) by sesosn21.seso.astrazeneca.net (8.10.1/8.10.1) with ESMTP id f9I4VJQ15542 for ; Thu, 18 Oct 2001 06:31:19 +0200 (MET DST) Received: by astra-cdc-x03.seso.astrazeneca.net with Internet Mail Service (5.5.2650.21) id ; Thu, 18 Oct 2001 06:31:19 +0200 Message-ID: To: CHEMISTRY@ccl.net Subject: CCL: molecular diversity Date: Thu, 18 Oct 2001 06:44:00 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Dear CCLers: This is a very general question related to Lead Identification/molecular diversity. Could you share your experience/strategy/thoughts as to how to approach DIVERSITY for the selection of compounds from a large database. Every fundamental hints from you would be valuable to me. If there is much interest, I will be happy to summarise. Thanks in advance. S Parthiban From chemistry-request@server.ccl.net Thu Oct 18 07:32:33 2001 Received: from aleph.net.uniovi.es ([156.35.11.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9IBWWB11577 for ; Thu, 18 Oct 2001 07:32:32 -0400 Received: from CONVERSION-DAEMON.aleph.net.uniovi.es by aleph.net.uniovi.es (PMDF V6.0-24 #45227) id <01K9NCFN6NBK00HF98@aleph.net.uniovi.es> for chemistry@ccl.net; Thu, 18 Oct 2001 13:32:19 +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 <01K9NCFIDMU600H4LU@aleph.net.uniovi.es>; Thu, 18 Oct 2001 13:32:13 +0200 (MET) Received: (from pueyo@localhost) by pinon.ccu.uniovi.es (8.9.2/8.9.2) id NAA15244; Thu, 18 Oct 2001 13:32:04 +0200 (METDST) Date: Thu, 18 Oct 2001 13:32:04 +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: <200110181132.NAA15244@pinon.ccu.uniovi.es> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT > Date: Wed, 17 Oct 2001 09:07:38 -0400 > From: "Dr. Richard L. Wood" > Subject: CCL:Orbital energies for 1st row transition metals. > > 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. > To which Richard L. Wood wrote: > 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, You are giving to my words a meaning that I didn't wanted to imply but, in any case, the world is not limited to your 'alma mater' nor even to the USA and there are many different educational programs being taught. This includes programs where elementary quantum chemistry is introduced to first year students of chemistry. 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 Thu Oct 18 07:15:30 2001 Received: from web12901.mail.yahoo.com ([216.136.174.68]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9IBFUB11125 for ; Thu, 18 Oct 2001 07:15:30 -0400 Message-ID: <20011018111530.50484.qmail@web12901.mail.yahoo.com> Received: from [144.32.180.37] by web12901.mail.yahoo.com via HTTP; Thu, 18 Oct 2001 12:15:30 BST Date: Thu, 18 Oct 2001 12:15:30 +0100 (BST) From: =?iso-8859-1?q?Meike=20Reinhold?= Subject: Merz Kollman charges calculated with G98 To: ccl MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCler's I hope you don't mind me asking this question. I have calculated the MK charges ona trnaistion metal system and am looking for ways to visulise them and in th eend produce pretty pictures. The programs I have available in the moment are Molden, molekel and gOpenmol and only gOpenmol seems to be able to do so. However, I did not get the latter to work. If somebody out there has any good tips I would be most grateful to hear of them. Meike Reinhold P.S. My problem with gOpenmol which is only installed on my PC (Windows NT4.0) is that after I have inported the formated checkpoint file (created with Formcheck=all) and the imported the in the charges from the log file nothing seems to change. So maybe I am missing something here? ===== Meike Reinhold Chemistry Department University of York UK ____________________________________________________________ Nokia Game is on again. Go to http://uk.yahoo.com/nokiagame/ and join the new all media adventure before November 3rd. From chemistry-request@server.ccl.net Thu Oct 18 09:48:22 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9IDmMB15348 for ; Thu, 18 Oct 2001 09:48:22 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id JAA06173; Thu, 18 Oct 2001 09:48:21 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Thu, 18 Oct 2001 09:48:29 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GLE00CO0M482D@lvlmail.unitedcatalysts.com>; Thu, 18 Oct 2001 09:43:20 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id <4YZZ67QG>; Thu, 18 Oct 2001 09:48:00 -0400 Content-return: allowed Date: Thu, 18 Oct 2001 09:47:59 -0400 From: "Shobe, Dave" Subject: RE: isolobal vs. isoelectronic To: "'Krzysztof Radacki'" , CCL Message-id: <157A51F55AAAD3119CD70008C7B1629DDAB2E3@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 From: Krzysztof Radacki [mailto:k.radacki@ic.ac.uk] > 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 would have said that all three (BH3, CH3+, and CH2) were isoelectronic since this is just a matter of counting electrons (8 e- and 6 valence e- in each case). The # valence electrons has to be counted as well as the total, otherwise you reach conclusions such as Zn being "isoelectronic" to Ne3 and C5. However, CH2 would not be "isolobal" to BH3 or CH3+ because CH2 has a lone pair as well as an empty orbital. I forget the name for the relationship among for example {HCN, HSiP, HCAs, ...} where atoms are replaced by others in the same column of the periodic table. --David Shobe From chemistry-request@server.ccl.net Thu Oct 18 11:56:59 2001 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9IFuxB18632 for ; Thu, 18 Oct 2001 11:56:59 -0400 Received: from unix5.uvic.ca (unix5.uvic.ca [142.104.5.117]) by cascara.uvic.ca (8.11.6/8.11.6) with ESMTP id f9IFusQ59620; Thu, 18 Oct 2001 08:56:54 -0700 Date: Thu, 18 Oct 2001 08:56:54 -0700 (PDT) From: Roy Jensen To: "Shobe, Dave" cc: "'Krzysztof Radacki'" , CCL Subject: Re: CCL:isolobal vs. isoelectronic In-Reply-To: <157A51F55AAAD3119CD70008C7B1629DDAB2E3@lvlxch01.unitedcatalysts.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > I forget the name for the relationship among for example {HCN, HSiP, HCAs, > >...} where atoms are replaced by others in the same column of the periodic > table. isovalent, I believe. From chemistry-request@server.ccl.net Thu Oct 18 13:19:53 2001 Received: from physics.lsu.edu ([130.39.182.96]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9IHJrB30227 for ; Thu, 18 Oct 2001 13:19:53 -0400 Received: from localhost (vani@localhost) by physics.lsu.edu (8.9.2/8.9.2) with ESMTP id MAA23135 for ; Thu, 18 Oct 2001 12:17:13 -0500 (CDT) Date: Thu, 18 Oct 2001 12:17:13 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Subject: TIP$P water model (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Thanks for all the help regarding my previous query. I incorporated the TIP4P model. I have one question regarding the constraints in this model of water. To avoid the dynamics on the dummy particle ( as suggested in the GROMACS site, thanks to David Va der Spoel and Paul van Maaren), iam redistribuiting the forces on the dummy to the other three atoms. To do this every time step, i compute the positions of the dummy particle before passing all the coordinates to Ewald method. For the constraints part, i still have constraints only on OH, OH and HH bond. Do i need constraints between dummy particle(M) and other three atoms? If i don't want to use the rigid model, can i use a flexible model for TIP4P water? Can anyone give me some information about where i can get the parameters for the flexible model of TIP4P model of water(AMBER has parameters for TIP3P, i coudn't find parameters for TIP4P.) Thanks vani From chemistry-request@server.ccl.net Thu Oct 18 16:50:06 2001 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9IKo6B26807 for ; Thu, 18 Oct 2001 16:50:06 -0400 Received: from Laurence.mbi.ucla.edu (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id f9IKo6q03390 for ; Thu, 18 Oct 2001 13:50:06 -0700 (PDT) Message-Id: <5.1.0.14.2.20011018133345.039ad890@127.0.0.1> X-Sender: lavelle/mbi.ucla.edu@127.0.0.1 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 18 Oct 2001 13:53:16 -0700 To: CCL From: Laurence Lavelle Subject: Orbital energies for 1st row transition metals. Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed I'm still getting a number of responses (thanks), but before I get anymore reprimands for covering this topic in a first year course let me clarify. While discussing the ground state for Cr [Ar]3d^5 4s^1 and Cr^+1 [Ar]3d^5 there was general discussion about the relative filling of orbitals for ground state anions. In the past I have not discussed electronic configurations for negatively charged transition metals, hence my question below. So far I don't yet have a quantitative answer. My qualitative answer is that the orbital occupancy will depend on the relative energy difference between the degenerate 3d and the 4s orbitals and the spin pairing energy. Discussion welcome, Laurence Lavelle >Date: Tue, 16 Oct 2001 18:08:26 -0700 >To: CCL >From: Laurence Lavelle >Subject: 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. > >Discussion and comments welcome. > >Best, >Laurence Lavelle > > From chemistry-request@server.ccl.net Thu Oct 18 19:40:04 2001 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9INe2B01378 for ; Thu, 18 Oct 2001 19:40:04 -0400 Received: from samay (samay.ee.sc.edu [129.252.22.248]) by mailbox.engr.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id 481DR39P; Thu, 18 Oct 2001 19:34:35 -0400 Message-ID: <001e01c1582d$fecb6640$f816fc81@ee.sc.edu> From: "derosa" To: Subject: UFF Date: Thu, 18 Oct 2001 19:38:29 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear all: I have another question about Universal Force Field 1.02 as implemented in Cerius2. Do any of you know which unit are used for the electronegativity?, According to Cerius they are in Pauling which is obviously not correct since several of them are larger than 4. They seems to be in eV, for example UFF1.02 value for Li is 3.006 while according to one of my references (Density-Functional Theory of Atoms and Molecules, by Parr and Yang) this value is 3.01 which is given in eV. Other values agree fairly well, F(UFF1.02)=10.874 vs. F(Parr)=10.41 eV. But other values are awfully different like for example H(UFF1.02)=4.528, H(Parr)=7.18 eV, or Cu(UFF1.02)=3.729 while Cu(Parr)=4.48 eV. Is this different due to a parameterization obtain in different experiment or they are really given in a different unit. Thank you for your help Pedro From chemistry-request@server.ccl.net Thu Oct 18 20:59:58 2001 Received: from deakin.edu.au ([128.184.136.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9J0xuB04077 for ; Thu, 18 Oct 2001 20:59:57 -0400 Received: from [128.184.88.189] (128-184-88-189.bcs.deakin.edu.au [128.184.88.189]) by deakin.edu.au (8.11.4/8.11.4) with ESMTP id f9J0xH817210; Fri, 19 Oct 2001 10:59:18 +1000 (EST) Mime-Version: 1.0 X-Sender: lim@128.184.136.2 Message-Id: In-Reply-To: References: Date: Fri, 19 Oct 2001 10:32:21 +1000 To: Roy Jensen , "Shobe, Dave" From: "Kieran F Lim (Lim Pak Kwan)" Subject: Re: CCL:isolobal vs. isoelectronic Cc: "'Krzysztof Radacki'" , CCL Content-Type: text/plain; charset="us-ascii" ; format="flowed" At 9:47 AM -0400 18/10/01, Shobe, Dave wrote: >However, CH2 would not be "isolobal" to BH3 or CH3+ because CH2 has a lone >pair as well as an empty orbital. My text books state that isoelectronic means same number of electrons. USUALLY (not always) this implies same electronic configuration. by this definition, BH3, CH3+ and CH2 are isoelectronic. by extension, "isolobal" would mean same number/arrangement of lobes (ie near-same symmetry). CH4, NH3 (with lone pair) and H2O (with 2 lone pairs) are both isoelectronic and isolobal. note that this does not mean same symmetry since these molecules are Td, C3v and C2v. CH2 is a special case because it has two close electronic states singlet (lone pair and empty orbital) and doublet (diradical) BH3, CH3+ and singlet CH2 are both isoelectronic and isolobal. doublet CH2 has a very different electronic configuration. BH3, CH3+ and singlet CH2 are isoelectronic but not isolobal. At 9:47 AM -0400 18/10/01, Shobe, Dave wrote: >I forget the name for the relationship among for example {HCN, HSiP, HCAs, > >...} where atoms are replaced by others in the same column of the periodic >table. At 8:56 AM -0700 18/10/01, Roy Jensen wrote: >isovalent, I believe. Does "isovalent" refer to "valency"? Are NaCl and AgCl isovalent? I am not sure. I had heard (cannot remember where) and use "valence isoelectronic" but am very happy to be corrected if wrong. Kieran ------------------------------------------------------------ Dr Kieran F Lim Biol. and Chemical Sciences (Lim Pak Kwan) Deakin University ph: + [61] (3) 5227-2146 Geelong VIC 3217 fax: + [61] (3) 5227-1040 AUSTRALIA mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim ------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Oct 18 23:02:55 2001 Received: from front2.chartermi.net ([24.213.60.124]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9J32tB09531 for ; Thu, 18 Oct 2001 23:02:55 -0400 Received: from [24.247.80.10] (HELO Hppav) by front2.chartermi.net (CommuniGate Pro SMTP 3.5b2) with SMTP id 25253898; Thu, 18 Oct 2001 23:02:55 -0400 Message-ID: <000b01c1584a$8cb23d00$0201a8c0@Hppav> From: "Jim Kress" To: "derosa" , References: <000b01c156ac$eecc13c0$f816fc81@ee.sc.edu> Subject: Re: CCL:Universal Force Field (UFF) Date: Thu, 18 Oct 2001 23:02:54 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Would you please post the replies you get on the CCL list? The UFF papers and documentation are very vague and ill suited to people replicating the implementation of the UFF. Many people in the field would like to get clear, concise, useable answers to the questions you have posted. Thanks. Jim ----- Original Message ----- From: "derosa" To: Sent: Tuesday, October 16, 2001 9:42 PM Subject: CCL:Universal Force Field (UFF) > Dear all: > > I am trying to figure out how the Universal Force Field is > parameterized in Cerius2, particularly the torsion and the inversion > interactions. My source is the Paper of Rappe et al J. Am. Chem. Soc. 1992 > 114, 10024 and the set of parameter shown in the force field UFF 1.02. > > According to what I understood from that paper, the torsional energy > is given by > > E=1/2 V[1-cos(n*phi0)*cos(n*phi)] > > It is a little obscure for me how this parameters are defined > For sp2 centers connected to another sp2 center n=2 and phi0 is 180, which > is my case. so > > E=1/2 V [1-cos(2*phi)] > > My first question is how V is defined. In the mentioned paper there are two > different sum rules depending on whether the center is sp2 or sp3 however > only for sp3 centers V is defined as a function of a "torsional barrier > factor" of each atoms which is the only parameter (I could find) in the > force field. SO how is V defined (in cerius2) for sp2 centers, which is the > sum rule I should use?. > > With respect to the inversion, Rappe et al indicates that the inversion > energy is given by > > E=Kijkl( Co + C1 sin(Gamma)+ C2 cos(2Gamma)) > > However UFF, as implemented in cerius2 only offers two parameters, the > inversion barrier and the equilibrium inversion angle for each atoms. How > the other parameters are obtained?, is the previous formula the one that is > used in cerius2?. > > Any clarifying comment will be much appreciated. You can send the answers > directly to me at derosa@engr.sc.edu I will summarize if there is any > interest. > > Thank you very much for your help, > > Pedro > > > -= 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 Thu Oct 18 23:03:45 2001 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9J33jB09573 for ; Thu, 18 Oct 2001 23:03:45 -0400 Received: from Laurence.mbi.ucla.edu (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id f9J33iq16652 for ; Thu, 18 Oct 2001 20:03:44 -0700 (PDT) Message-Id: <5.1.0.14.2.20011018200127.039acd68@127.0.0.1> X-Sender: lavelle/mbi.ucla.edu@127.0.0.1 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 18 Oct 2001 20:06:54 -0700 To: CCL From: Laurence Lavelle Subject: Summary: Orbital energies for 1st row transition metals. Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed My original emails are first. Responses follow. Thanks to all. Laurence Lavelle >Date: Thu, 18 Oct 2001 13:53:16 -0700 >To: CCL >From: Laurence Lavelle >Subject: Orbital energies for 1st row transition metals. > >I'm still getting a number of responses (thanks), but before I get anymore >reprimands for covering this topic in a first year course let me clarify. >While discussing the ground state for Cr [Ar]3d^5 4s^1 and >Cr^+1 [Ar]3d^5 there was general discussion about the relative filling >of orbitals for ground state anions. In the past I have not discussed >electronic configurations for negatively charged transition metals, hence >my question below. > >So far I don't yet have a quantitative answer. My qualitative answer is >that the orbital occupancy will depend on the relative energy difference >between the degenerate 3d and the 4s orbitals and the spin pairing energy. > >Discussion welcome, >Laurence Lavelle > > >>Date: Tue, 16 Oct 2001 18:08:26 -0700 >>To: CCL >>From: Laurence Lavelle >>Subject: 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. >> >>Discussion and comments welcome. >> >>Best, >>Laurence Lavelle >> >> >To: Laurence Lavelle >Subject: Re: CCL:Orbital energies for 1st row transition metals. >X-mailer: FoxMail 3.0 beta 1 [cn] > >I think the ground state should be [Ar]3d^5 4s^2 for Cr^-1. As we know, >3d^5 is half-filled and the energy will be lower. >To: Laurence Lavelle >Subject: Re: CCL:Orbital energies for 1st row transition metals. > >This is an interesting question, but I would not give it to first year >students. Already the ground state of neutral Cr can not be explained >using the orbital approximation. A numerical treatment including electron >correlation is needed to account for it, since the total energy of the >atom is relevant not the sum of orbital energies. What kind of answer do >you expect from first year students? That the electron enters 4s because >of greater penetration of s- compared to d-electrons? I guess that >everything depends on electron correlation again. I don't think that >subtle details can be estimated easily and I would not ask first year >students to solve problems they can not possibly answer. >To: Laurence Lavelle >Subject: Re: CCL:Orbital energies for 1st row transition metals. > >Hello, > >For (french) first year students, the only answer is : >due to Hund's rule, I would propose that the electronic >configuration of Cr{-1} anion is [Ar]3d^5 4s^2. >First year students just know Slater rules to estimate >the electronic energy. >Thus: > >E(Cr)= E(Ar) + 5*E(3d) + E(4s Cr) >E(Cr-) = E(Ar) + 5*E(3d) + 2*E(4s Cr-) > >E(Cr-) - E(Cr) = 2*E(4s Cr-) - E(4s Cr) > >E(4s Cr) = -0.5*(2.95*2.95)/(3.8*3.8) u.a. >E(4s Cr-) = -0.5*(2.6*2.6)/(3.8*3.8) u.a > >where 3.8 is the value of n* for n=4 >2.95 is the value of Z* for the 4s electron of Cr >2.6 is the value of Z* for one 4s electron of Cr- > >Z*(4s Cr) = Z - 2*1 - 8*1 - 13*0.85 = 2.95 >Z*(4s Cr-) = Z - 2*1 - 8*1 - 13*0.85 -0.35 = 2.6 > >because the electrons are put together in "groups" >1rst grp : 1s >2nd grp : 2s2p >3rd grp : 3s3p >4th grp : 3d >5th grp : 4s4p >... > >I think that is not useful to develop further here. > >I was just wondering if Cr{-1} anion exists experimentaly? >I just demonstrate that Slater rules predict it to be more >stable than Cr atom, but I am not very confident with that >type of calculation for transition metal elements. > >Hope this helps. To: "chemistry@ccl.net" Subject: CCL:Orbital energies for 1st row transition metals. Sender: "Computational Chemistry List" > 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. From chemistry-request@server.ccl.net Thu Oct 18 23:22:12 2001 Received: from mercury.chem.nwu.edu (gwuxi@[129.105.116.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9J3MCB10369 for ; Thu, 18 Oct 2001 23:22:12 -0400 Received: from localhost (gwuxi@localhost) by mercury.chem.nwu.edu (8.11.3/8.11.3) with ESMTP id f9J3Loc16843; Thu, 18 Oct 2001 22:21:51 -0500 (CDT) Date: Thu, 18 Oct 2001 22:21:50 -0500 (CDT) From: Guosheng Wu X-X-Sender: To: "Kieran F Lim (Lim Pak Kwan)" cc: Roy Jensen , "Shobe, Dave" , "'Krzysztof Radacki'" , CCL Subject: Re: CCL:isolobal vs. isoelectronic In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 19 Oct 2001, Kieran F Lim (Lim Pak Kwan) wrote: > My text books state that isoelectronic means same number of electrons. > USUALLY (not always) this implies same electronic configuration. > > by this definition, BH3, CH3+ and CH2 are isoelectronic. If we check the textbooks for general chemistry with more sense of science, for every 3-4 pages, we may find at least one statement needs to be corrected. For "isoelectronic", it is just a very empirical word used to help undergraduate understand chemistry. If we are really interested in using it, maybe we need to be very careful to keep consistent with its "original"(when it was first coined) meaning :-) I spent a few minutes on the topic, and found much relevant info for the defination of "isoelectronic". Here just pick three of them: (1)Oxford online (2nd edition, using the NWU access) Isoelectronic: (Composed of atoms or molecules) having the same number of electrons. < this is the same as in many textbooks, and it is obvious too simple to be accurate.> (2)Webster's New World (4th edition, 1999) -----supposed to "define the English Language for the 21st century" Isoelectronic: designating or of any of two or more atoms which have the same number of electrons around the nucleus and similar spectral and physical properties. < By any means, this is much better, and it points out the "origination" of this word (my guess): similar properties from same number of electrons. Then CH4, BH3 and H2O can not be isoelectronics. Although they have same electronic configurations, the number of atoms in these molecules is not equal to each other, just like H2 and He should never be called "isoelectronic" if this word has more meaning than just "same number of electrons". (2)IUPAC 1994 http://www.chem.qmw.ac.uk/iupac/gtpoc/I.html#34 GLOSSARY OF TERMS USED IN PHYSICAL ORGANIC CHEMISTRY (IUPAC Recommendations 1994) Isoelectronic: Two or more molecular entities are described as isoelectronic if they have the same number of valence electrons and the same structure, i.e. number and connectivity of atoms, but differ in some of the elements involved. (a) CO, N2 and NO+ are isoelectronic (b) CH2=C=O and CH2=N=N are isoelectronic (c) CH3COCH3 and CH3N=NCH3 have the same number of electrons, but have different structures, hence they are not described as isoelectronic. Cheers. Guosheng Wu Department of Chemistry Northwestern University From chemistry-request@server.ccl.net Thu Oct 18 19:51:37 2001 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9INpZB01946 for ; Thu, 18 Oct 2001 19:51:35 -0400 Received: from samay (samay.ee.sc.edu [129.252.22.248]) by mailbox.engr.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id 481DRPBW; Thu, 18 Oct 2001 19:46:05 -0400 Message-ID: <004301c1582f$9a0c7760$f816fc81@ee.sc.edu> From: "derosa" To: Subject: Fw: CCL:Universal Force Field (UFF) Date: Thu, 18 Oct 2001 19:49:55 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 I got one request to summarize the answers to my request. I only received one answer but indeed was what I needed. Thank you so much Dr Senn for you prompt answer. Please see below the answer and well at the bottom the original question for your reference Thanks Pedro ----- Original Message ----- From: "Hans Martin Senn" To: "derosa" Sent: Wednesday, October 17, 2001 1:34 PM Subject: Re: CCL:Universal Force Field (UFF) Hi Pedro, I went through this a while ago when I was implementing the UFF into the ab initio MD code PAW. The Rappé paper is indeed not a prime example of clarity and conciseness; also there are errors in some of the formulas. I also referred to the implementation of UFF in Cerius2 to get some of the parameters. The "distillate" of my struggle with UFF is in my thesis (full text at http://e-collection.ethbib.ethz.ch/show?type=diss&nr=13972), Sect. 2.7.3. > According to what I understood from that paper, the torsional energy >is given by > >E=1/2 V[1-cos(n*phi0)*cos(n*phi)] > >It is a little obscure for me how this parameters are defined >For sp2 centers connected to another sp2 center n=2 and phi0 is 180, which >is my case. so > >E=1/2 V [1-cos(2*phi)] > >My first question is how V is defined. In the mentioned paper there are two >different sum rules depending on whether the center is sp2 or sp3 however >only for sp3 centers V is defined as a function of a "torsional barrier >factor" of each atoms which is the only parameter (I could find) in the >force field. SO how is V defined (in cerius2) for sp2 centers, which is the >sum rule I should use?. A general remark about paper vs. Cerius2: As far as I remember, not all parameters are acessible via the FF file in Cerius2; some (e.g., certain rules) must be hard-wired. Also, certain cases for which the paper gives a general rule are treated as "special cases" in Cerius2. This means, they are listed individually, rather than dealt with via the generator. For the torsions: See the corresponding table in my thesis. In the paper, your case (sp2-sp2 central bond) is covered by eq. 17. > >With respect to the inversion, Rappe et al indicates that the inversion >energy is given by > >E=Kijkl( Co + C1 sin(Gamma)+ C2 cos(2Gamma)) > >However UFF, as implemented in cerius2 only offers two parameters, the >inversion barrier and the equilibrium inversion angle for each atoms. How >the other parameters are obtained?, is the previous formula the one that is >used in cerius2?. The inversions are quite a mess, indeed... Cerius2: The exception list for the inversions tabulates K_ijkl and omega0_ijkl (with omega0_ijkl = 90° - gamma0_ijkl). It basically covers the cases of C_R or C_2 as central atoms bonded to O_2. In the generator, however, 2*K_ijkl is listed (note that E_barrier = 2*K_ijkl), together with omega0_ijkl. Paper (eq. 19): I assumed that the coefficients (if not given explicitly) are derived from the conditions mentioned. You can get expressions for C0, C1, C2 that depend only on gamma0_ijkl (or omega0_ijkl), considering that there is a minimum for E(omega0) = 0 and a maximum for E(omega=0) = E_barrier. See again my thesis. A final note: You might contact Rappé directly. I heard, he has actually a programme that implements the UFF (in an improved versions, UFF2). Maybe it's possible to obtain the code, which would make things quite a bit easier. Hope this helps... Cheers, Hans %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ORIGINAL QUESTION Dear all: I am trying to figure out how the Universal Force Field is parameterized in Cerius2, particularly the torsion and the inversion interactions. My source is the Paper of Rappe et al J. Am. Chem. Soc. 1992 114, 10024 and the set of parameter shown in the force field UFF 1.02. According to what I understood from that paper, the torsional energy is given by E=1/2 V[1-cos(n*phi0)*cos(n*phi)] It is a little obscure for me how this parameters are defined For sp2 centers connected to another sp2 center n=2 and phi0 is 180, which is my case. so E=1/2 V [1-cos(2*phi)] My first question is how V is defined. In the mentioned paper there are two different sum rules depending on whether the center is sp2 or sp3 however only for sp3 centers V is defined as a function of a "torsional barrier factor" of each atoms which is the only parameter (I could find) in the force field. SO how is V defined (in cerius2) for sp2 centers, which is the sum rule I should use?. With respect to the inversion, Rappe et al indicates that the inversion energy is given by E=Kijkl( Co + C1 sin(Gamma)+ C2 cos(2Gamma)) However UFF, as implemented in cerius2 only offers two parameters, the inversion barrier and the equilibrium inversion angle for each atoms. How the other parameters are obtained?, is the previous formula the one that is used in cerius2?. Any clarifying comment will be much appreciated. You can send the answers directly to me at derosa@engr.sc.edu I will summarize if there is any interest. Thank you very much for your help, Pedro