From owner-chemistry@ccl.net Wed Nov 8 01:36:01 2006 From: "James Robinson James.Robinson[a]prosonix.co.uk" To: CCL Subject: CCL: MD simulations using MMFF94x and MOE Message-Id: <-32959-061107202621-123456-0dm2CA95KKNCZ9XrXWvlkA(a)server.ccl.net> X-Original-From: "James Robinson" Date: Wed, 8 Nov 2006 00:54:44 -0000 Sent to CCL by: "James Robinson" [James.Robinson[a]prosonix.co.uk] Hi Sandeep, There has been debate before about the implimentation of dynamics in MOE. If memory serves Amber is often the preferred choice for MD of polypeptides. However, the analysis tools in MOE are very useful. Allow the calculation to run with some heating and try to use an end cooling step. Make sure MOE writes structures to a moe.MDB file during the simulation, it will get quite big, but MOE will handle it. That way you can check dihedral angles, trans amide bonds, volume, and other descriptors as you go. MOE may still lack some rigour in some implimentations like dyanmics, but as tool that can serves as qualitative/quantitative test for ideas in my opinion, it rocks! James Robinson, Oxford, UK. -----Original Message----- From: Sandeep Kumar kumarsan(_)jhu.edu [mailto:owner-chemistry**ccl.net] Sent: Tue 07/11/2006 18:55 To: James Robinson Subject: CCL: MD simulations using MMFF94x and MOE Sent to CCL by: "Sandeep Kumar" [kumarsan],[jhu.edu] Dear Members: I am trying to do MD calculations on a 28 residue peptide using MMFF94X forcefield as implemented in MOE to assess its conformational flexibility. I was wondering if somebody has experience of using MMFF94x forcefield for peptide simulations and how does it compare with other forcefields, say, AMBER or CHARMM? Another related question whether to do implicit solvation or explicit solvation simulations? I mean which is better and usually what should be the time scales for such simulations? Any advices shall be greatly appreciated. Yours sincerely, Sandeep Kumar ----------------------------------------------------------------------- Dr. Sandeep Kumar, Associate Research Scientist, Johns Hopkins University Department of Biology, 106 Mudd Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Phone: 410-516-8433, Email: kumarsan-.-jhu.edu. URL: https://jshare.johnshopkins.edu/skumar23/public_html/ Previous URL: http://www.lecb.ncifcrf.gov/~kumarsan From owner-chemistry@ccl.net Wed Nov 8 02:11:00 2006 From: "Gregory M Sandala sandala%%chem.usyd.edu.au" To: CCL Subject: CCL:G: SCRF errors with Gaussian Message-Id: <-32960-061108005108-15246-g8UyD0ac1XNQvI+gsyRclg . server.ccl.net> X-Original-From: "Gregory M Sandala" Date: Wed, 8 Nov 2006 00:51:07 -0500 Sent to CCL by: "Gregory M Sandala" [sandala ~~ chem.usyd.edu.au] Hello everyone. I'm trying to run some SCRF calculations with G03.D01 to generate charges for later use in Amber. However, it appears as though generating the solute cavity is creating various numerical instabilities. More specifically, I will get errors like: Warning! T(1549,1799)=0.81795801D+02 is big! T(1549,1549)=0.83983654D+02 T(1799,1799)=0.22200475D+02 Warning! T(****,****)=0.65648410D+38 is big! T(****,****)=-.65648410D+38 T(****,****)=0.65648410D+38 Inv2 failed in DMIVCS. Error termination via Lnk1e in /opt/g03d01/g03/l502.exe at Tue Oct 31 18:27:16 2006. OR ------------------------------------------------------------------------------ Polarizable Continuum Model (PCM) ================================= Model : PCM. Atomic radii : UA0 (Simple United Atom Topological Model). Polarization charges : Total charges. Charge compensation : None. Solution method : Matrix inversion. Cavity : GePol (RMin=0.200 OFac=0.890). Default sphere list used, NSphG= 92. Tesserae with average area of 0.200 Ang**2. Solvent : Diethylether, Eps = 4.335000 Eps(inf)= 0.000000 RSolv = 2.785000 Ang. ------------------------------------------------------------------------------ AdVTs1: ISph= 3199 is engulfed by JSph= 3202 but Ae( 3199) is not yet zero! Error termination via Lnk1e in /opt/g03d01/g03/l301.exe at Mon Oct 30 18:07:11 2006. The first error typically results when using radii=pauling and the second error occurs when using the default radii (UA0). For the past week I've played with various parameters (PCM method, OFAC, TSARE, etc.) but end up getting one of these errors. I'm becoming tired of 'playing' with these numerous and varied parameters (it's all like black magic!) and am curious to know whether others have come across such errors and, if so, how they managed to work around them. Thank you in advance. Best wishes, Greg -- Gregory M. Sandala School of Chemistry University of Sydney Sydney NSW 2006 Australia Ph: +61 2 9351 5361 sandala+*+chem.usyd.edu.au From owner-chemistry@ccl.net Wed Nov 8 03:46:00 2006 From: "Igor Avilov avilovi###averell.umh.ac.be" To: CCL Subject: CCL: Excited state electronic configurations Message-Id: <-32961-061108034226-25144-9u4y63jukxpa1sb35jZX1g^-^server.ccl.net> X-Original-From: "Igor Avilov" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 8 Nov 2006 09:42:07 +0100 MIME-Version: 1.0 Sent to CCL by: "Igor Avilov" [avilovi]^[averell.umh.ac.be] Dear Caroline, If you are interested in population analysis in the excited states, you must use a two-step jobs like the one below: %nproc=1 %mem=100MB %Chk=HCl_cis # CIS(Nstates=4)/STO-3G Test Input created by Zoa v2.0 HCl_cis 0 1 Cl -0.000030 -0.645000 -0.000250 H 0.000030 0.645000 0.000250 --Link1-- %nproc=1 %mem=100MB %Chk=HCl_cis %NoSave # CIS(Root=3,Read)/STO-3G Density=Current Pop=NPA Test Input created by Zoa v2.0 HCl_cis 0 1 Cl -0.000030 -0.645000 -0.000250 H 0.000030 0.645000 0.000250 In this way you will get the populations for third excited state. If you need populations for the first excited state, you can use a single-step job. Just include Density=Current keyword. As far as I know it is not possible to get the density for time-dependent calculations (TD keyword). I hope it help, although my answer may be incomplete. Best wishes, Igor Avilov. -----Original Message----- > From: owner-chemistry()ccl.net [mailto:owner-chemistry()ccl.net] Sent: mardi 7 novembre 2006 18:15 To: Igor Avilov Subject: CCL: Excited state electronic configurations Sent to CCL by: "Caroline Norris" [cn29::sussex.ac.uk] Dear All, I am in the process of calculating the potential energy curves of the lowest lying excited state of neutral vanadium oxide, and I was wondering if there's any way to determine the electronic configuration of the excited states. I've been using the pop=npa keyword, but this only details the ground state of the complex. Any help would be greatly appreciated. Thanks in advance, Caroline Norris cn29::sussex.ac.ukhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Nov 8 04:49:01 2006 From: "Didier ROGNAN didier.rognan . pharma.u-strasbg.fr" To: CCL Subject: CCL: atom renumbering Message-Id: <-32962-061108044715-24071-rBPBFXdK2UEHKeWiLLcBpw+/-server.ccl.net> X-Original-From: "Didier ROGNAN" Date: Wed, 8 Nov 2006 04:47:14 -0500 Sent to CCL by: "Didier ROGNAN" [didier.rognan ~~ pharma.u-strasbg.fr] Dear CCLers, Has anyone a solution to automatically renumber atoms for a compound library sharing the same core structure such that all core atoms have a unique atom number ? Many thanks for your anwser Dr. Didier ROGNAN Directeur de Recherche CNRS UMR 7175-LC1 Institut Gilbert-Laustriat 74, route du Rhin, B.P.24 F-67401 Illkirch direct line: +33 (0)3 90 24 42 35 secretary: +33(0)3 90 24 42 20 fax: +33 (0)3 90 24 43 10 email: didier.rognan]-[pharma.u-strasbg.fr www:http://bioinfo-pharma.u-strasbg.fr From owner-chemistry@ccl.net Wed Nov 8 07:21:00 2006 From: "Dr. Ponnadurai Ramasami ramchemi!A!intnet.mu" To: CCL Subject: CCL: electron affinity Message-Id: <-32963-061108062336-22918-Jk4LJqnQ/mUw6F1yBxONZw:server.ccl.net> X-Original-From: "Dr. Ponnadurai Ramasami" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0023_01C70348.29B78490" Date: Wed, 8 Nov 2006 15:11:27 +0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi-#-intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_0023_01C70348.29B78490 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear All I am calculating the electron affinity of carbon monoxide using = B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative). I am getting a negative value of -100.2 kJ/mol. The literature experimental value is 127.9 kJ/mol (I guess positive). Is this correct? Can electron affinity be negative? I will appreciate in case someone can help. Ramasami =20 ------=_NextPart_000_0023_01C70348.29B78490 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
Dear All
 
I am calculating the electron affinity = of carbon=20 monoxide using B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO,=20 negative).
I am getting a negative value of -100.2 = kJ/mol.
The literature experimental value is = 127.9 kJ/mol=20 (I guess positive).
 
Is this correct?
Can electron affinity be = negative?
 
I will appreciate in case someone can=20 help.
 
Ramasami
 
 
 
 
 ------=_NextPart_000_0023_01C70348.29B78490-- From owner-chemistry@ccl.net Wed Nov 8 08:02:00 2006 From: "Soren Eustis soren__jhu.edu" To: CCL Subject: CCL: electron affinity Message-Id: <-32964-061108075735-26466-a4e1RSOr9LFRD2BhHkgQbg-#-server.ccl.net> X-Original-From: "Soren Eustis" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 8 Nov 2006 07:57:36 -0500 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren/./jhu.edu] Your method and basis set seem more than adequate. Electron affinity can indeed be negative. However, in this case we know that is not true. I have had much success calculating EA's using both DFT and MP2 - with a few exceptions. A key thing to check is whether or not the multiplicity is input correctly. For this case, I might see if MP2 or even HF describes this system better. In fact, for this small of a molecule - one ought to be able to run a CCSD(T) calculation in a fairly short time. Regards, Soren Eustis -----Original Message----- > From: owner-chemistry=ccl.net [mailto:owner-chemistry=ccl.net] Sent: Wednesday, November 08, 2006 7:25 AM To: Eustis, Soren Subject: CCL: electron affinity Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi-#-intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_0023_01C70348.29B78490 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear All I am calculating the electron affinity of carbon monoxide using = B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative). I am getting a negative value of -100.2 kJ/mol. The literature experimental value is 127.9 kJ/mol (I guess positive). Is this correct? Can electron affinity be negative? I will appreciate in case someone can help. Ramasami =20 ------=_NextPart_000_0023_01C70348.29B78490 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
Dear All
 
I am calculating the electron affinity = of carbon=20 monoxide using B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO,=20 negative).
I am getting a negative value of -100.2 = kJ/mol.
The literature experimental value is = 127.9 kJ/mol=20 (I guess positive).
 
Is this correct?
Can electron affinity be = negative?
 
I will appreciate in case someone can=20 help.
 
Ramasami
 
 
 
 
 ------=_NextPart_000_0023_01C70348.29B78490--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Nov 8 08:36:00 2006 From: "Rafal A. Bachorz rafal.bachorz-*-chemie.uni-karlsruhe.de" To: CCL Subject: CCL: electron affinity Message-Id: <-32965-061108082518-14579-JtNA8j9XeB1A/V7pffb/hA:server.ccl.net> X-Original-From: "Rafal A. Bachorz" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 08 Nov 2006 14:26:26 +0100 MIME-Version: 1.0 Sent to CCL by: "Rafal A. Bachorz" [rafal.bachorz*_*chemie.uni-karlsruhe.de] Dear Dr. Ponnadurai Ramasami, > I am calculating the electron affinity of carbon monoxide using = > B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative). Do you use the same geometry for the neutral and anion? Normally there is some geometry relaxation upon electron attachment. When you use optimal geometries of neutral and anion, then you can calculate adiabatic electron affinity (AEA), which is defined AEA = E(N .. N) - E(A .. A), where the E(N .. N) and E(A .. A) are energies of the neutral and anion calculated at their optimal geometries corrected with the zero point vibration energies (ZPVE). It is important to take into account usually non-zero (and sometimes significant) contributions from ZPVE. > I am getting a negative value of -100.2 kJ/mol. > The literature experimental value is 127.9 kJ/mol (I guess positive). That is probably AEA, but I am not 100% sure. > Is this correct? I do not know, check the geometries. > Can electron affinity be negative? If the adiabatic electron affinity is negative, then it means that the E(A .. A) is higher than E(N .. N). That is of course possible. Best regards, Rafal Bachorz -- www.bachorz.eu From owner-chemistry@ccl.net Wed Nov 8 09:11:00 2006 From: "Dr. Ponnadurai Ramasami ramchemi,+,intnet.mu" To: CCL Subject: CCL: anharmonic constant Message-Id: <-32966-061108064117-2863-LZX5rjU6WeuiJitTQimYNQ%%server.ccl.net> X-Original-From: "Dr. Ponnadurai Ramasami" Content-Type: multipart/alternative; boundary="----=_NextPart_000_000D_01C7034A.BC8403A0" Date: Wed, 8 Nov 2006 15:29:52 +0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi#intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_000D_01C7034A.BC8403A0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear All I did a frequency calculation for carbon monoxide. #P b3lyp/6-311++G(2df,2pd) opt=3Dtight freq=3DVibRot maxdisk=3D2gb or #P b3lyp/6-311++G(2df,2pd) opt=3Dtight freq=3Danharm maxdisk=3D2gb However for this diatomic molecule, the anharmonic constant does not = appear in the output, although it appears for a triatomic molecule. Can anyone help? Thanks Ramasami =20 ------=_NextPart_000_000D_01C7034A.BC8403A0 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
Dear All
 
I did a frequency calculation for = carbon=20 monoxide.
 
#P b3lyp/6-311++G(2df,2pd) opt=3Dtight = freq=3DVibRot=20 maxdisk=3D2gb
or
#P b3lyp/6-311++G(2df,2pd) opt=3Dtight = freq=3Danharm=20 maxdisk=3D2gb
 
 
However for this diatomic molecule, the = anharmonic=20 constant does not appear in the output, although it appears for a = triatomic=20 molecule.
 
Can anyone help?
 
Thanks
 
Ramasami
 
 
 
 
 ------=_NextPart_000_000D_01C7034A.BC8403A0-- From owner-chemistry@ccl.net Wed Nov 8 09:47:00 2006 From: "Szabolcs Csepregi scsepregi~~chemaxon.com" To: CCL Subject: CCL: atom renumbering Message-Id: <-32967-061108091032-4606-5XbS3XDiYTqxKukhpZvAbw]-[server.ccl.net> X-Original-From: Szabolcs Csepregi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 08 Nov 2006 15:10:26 +0100 MIME-Version: 1.0 Sent to CCL by: Szabolcs Csepregi [scsepregi###chemaxon.com] Dear Didier, It is relatively easy to write a program for this with the use of JChem API. See example code at the end of this discussion on our forum: (atomrearranger.java) http://www.chemaxon.com/forum/ftopic519.html And you can create the atom ordering using substructure search: http://www.chemaxon.com/jchem/doc/guide/search/index.html#searchmem Best regards, Szabolcs Szabolcs Csepregi, PhD Director of Search Technologies, ChemAxon Ltd. http://www.chemaxon.com Skype: szabolcs.csepregi Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659 Didier ROGNAN didier.rognan . pharma.u-strasbg.fr wrote: > Sent to CCL by: "Didier ROGNAN" [didier.rognan ~~ pharma.u-strasbg.fr] > Dear CCLers, > > > Has anyone a solution to automatically renumber atoms for a compound library sharing the same core structure such that all core atoms have a unique atom number ? > > > Many thanks for your anwser > > Dr. Didier ROGNAN > Directeur de Recherche > CNRS UMR 7175-LC1 > Institut Gilbert-Laustriat > 74, route du Rhin, B.P.24 > F-67401 Illkirch > > direct line: +33 (0)3 90 24 42 35 > secretary: +33(0)3 90 24 42 20 > fax: +33 (0)3 90 24 43 10 > email: didier.rognan() pharma.u-strasbg.fr > www:http://bioinfo-pharma.u-strasbg.fr> > > > > From owner-chemistry@ccl.net Wed Nov 8 10:34:00 2006 From: "Mikael Johansson mikael.johansson+/-helsinki.fi" To: CCL Subject: CCL: electron affinity Message-Id: <-32968-061108102935-20408-xYRX9frJVm2UE4C0As6OmQ|,|server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 8 Nov 2006 17:29:28 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson]_[helsinki.fi] Hello Ramasami and All! On Wed, 8 Nov 2006, Dr. Ponnadurai Ramasami ramchemi!A!intnet.mu wrote: > I am calculating the electron affinity of carbon monoxide using = > B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative). > I am getting a negative value of -100.2 kJ/mol. > The literature experimental value is 127.9 kJ/mol (I guess positive). > > Is this correct? > Can electron affinity be negative? The sign should at least be correct; the CO anion is not stable. The following paper might be of interest: A. Dreuw, L. S. Cederbaum, "Long-lived high-spin states of small anions: 6PI state of CO-", Phys. Rev. A 59 (1999) 2702-2706. Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/ From owner-chemistry@ccl.net Wed Nov 8 11:09:00 2006 From: "Tanja van Mourik tanja.vanmourik:st-andrews.ac.uk" To: CCL Subject: CCL: electron affinity Message-Id: <-32969-061108104819-2819-K6tbzA+jmQQZK8dJikFcNg^-^server.ccl.net> X-Original-From: Tanja van Mourik Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 8 Nov 2006 15:47:15 +0000 MIME-Version: 1.0 Sent to CCL by: Tanja van Mourik [tanja.vanmourik*|*st-andrews.ac.uk] Hi Ramasami, You may be interested in the following book chapter: "Calculation of Electron Affinities. A Roadmap" T.H. Dunning, K.A. Peterson and T. van Mourik in The Dissociative Recombination of Molecules with Electrons, Ed. S. L. Guberman, (Kluwer Academic/Plenum Publishers, New York, 2002). Here we compared the accuracy of different methods (CISD, MPn, coupled cluster methods) and basis sets for the electron affinities of CN and O2. The electron affinities converge slowly with basis set, so large basis sets (with diffuse functions) are important. CCSD(T) gives electron affinities that are (almost) within chemical accuracy. Although DFT methods were not included in this investigation, based on the inconsistent results obtained with CCSD and MP2 (MP2 underestimates in one case and overestimates in the other), I would not expect B3LYP to give consistently reliable results for electron affinities. As also recommended by Soren, for a system of this size it would be best to use CCSD(T), or CCSDT if feasible, in combination with a basis set like aug-cc-pVQZ/5Z. Hope this helps, Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow School of Chemistry, University of St. Andrews North Haugh, St. Andrews Fife KY16 9ST, Scotland (UK) email: tanja.vanmourik:+:st-andrews.ac.uk web: http://chemistry.st-and.ac.uk/staffmember.php?id=tvm ================================================================= > Sent to CCL by: "Soren Eustis" [soren/./jhu.edu] > Your method and basis set seem more than adequate. Electron affinity can > indeed be negative. However, in this case we know that is not true. I have > had much success calculating EA's using both DFT and MP2 - with a few > exceptions. A key thing to check is whether or not the multiplicity is > input correctly. For this case, I might see if MP2 or even HF describes > this system better. In fact, for this small of a molecule - one ought to be > able to run a CCSD(T) calculation in a fairly short time. > > Regards, > > Soren Eustis > > > -----Original Message----- > > From: owner-chemistry:_:ccl.net [mailto:owner-chemistry:_:ccl.net] > Sent: Wednesday, November 08, 2006 7:25 AM > To: Eustis, Soren > Subject: CCL: electron affinity > > Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi-#-intnet.mu] > This is a multi-part message in MIME format. > > ------=_NextPart_000_0023_01C70348.29B78490 > Content-Type: text/plain; > charset="Windows-1252" > Content-Transfer-Encoding: quoted-printable > > Dear All > > I am calculating the electron affinity of carbon monoxide using = > B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative). > I am getting a negative value of -100.2 kJ/mol. > The literature experimental value is 127.9 kJ/mol (I guess positive). > > Is this correct? > Can electron affinity be negative? > > I will appreciate in case someone can help. > > Ramasami > > > > > =20 > > > ------=_NextPart_000_0023_01C70348.29B78490 > Content-Type: text/html; > charset="Windows-1252" > Content-Transfer-Encoding: quoted-printable > > > > charset=3Dwindows-1252"> > > > > >
Dear All
>
 
>
I am calculating the electron affinity = > of carbon=20 > monoxide using B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO,=20 > negative).
>
I am getting a negative value of -100.2 = > > kJ/mol.
>
The literature experimental value is = > 127.9 kJ/mol=20 > (I guess positive).
>
 
>
Is this correct?
>
Can electron affinity be = > negative?
>
 
>
I will appreciate in case someone can=20 > help.
>
 
>
Ramasami
>
 
>
 
>
 
>
 
>
> > cellPadding=3D0 width=3D320 border=3D0 x:str> > > 3949"=20 > width=3D108> > 3620"=20 > width=3D99> > 4132"=20 > width=3D113> > > >
style=3D"BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: = > #ece9d8; WIDTH: 240pt; BORDER-BOTTOM: #ece9d8; HEIGHT: 15.75pt; = > BACKGROUND-COLOR: transparent"=20 > width=3D320 colSpan=3D3 height=3D21> size=3D2>
 > > ------=_NextPart_000_0023_01C70348.29B78490--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > > > -- ================================================================= Tanja van Mourik Royal Society University Research Fellow School of Chemistry, University of St. Andrews North Haugh, St. Andrews Fife KY16 9ST, Scotland (UK) email: tanja.vanmourik:+:st-andrews.ac.uk web: http://chemistry.st-and.ac.uk/staffmember.php?id=tvm ================================================================= ------------------------------------------------------------------ University of St Andrews Webmail: https://webmail.st-andrews.ac.uk From owner-chemistry@ccl.net Wed Nov 8 11:44:01 2006 From: "Frank Jensen frj!^!ifk.sdu.dk" To: CCL Subject: CCL: SV: electron affinity Message-Id: <-32970-061108084817-30981-7pM2iJwIQ8u5BqyAUo/oFw.@.server.ccl.net> X-Original-From: "Frank Jensen" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 8 Nov 2006 14:46:59 +0100 MIME-Version: 1.0 Sent to CCL by: "Frank Jensen" [frj+/-ifk.sdu.dk] Beware that the EA calculated by DFT in most cases is _not_ a well-defined quantity. For most systems the extra electron in anions is not bound, _if_ a sufficiently flexible basis set is used. For (augmented) DZ and TZ type basis sets, this shows up as positive HOMO energies. If the HOMO is positive, the electron is not bound, and if you add enough diffuse basis functions, the extra electron detaches from the molecule. In other words, you can get essentially any result you want by choosing the basis set. There are a few exceptions, like CN- and perhaps also F-, where the EA is sufficiently large that the extra electron is bound, but CO- certainly does not belong to this class. With this being said, there is a large body of computational evidence showing that methods like B3LYP with a DZ or TZ type basis set augmented with diffuse functions (like aug-cc-pVDZ or 6-311+G**) does a fairly good job at reproducing the experimental EA results. The reason is that the limited basis set constrains the extra electron to be in roughly the right physical space, and the functional does a reasonable job at estimating the energy of this confined electron density. This gives you a reasonable estimate for the right physical reasons, but not for the right theoretical reasons. Check your HOMO energy for the anion. If it is positive, you are relying on 'good' results due to error cancellations and a lucky choice of functional and basis set, and sometimes your luck runs out..... Frank -----Oprindelig meddelelse----- Fra: owner-chemistry(a)ccl.net [mailto:owner-chemistry(a)ccl.net] Sendt: Wednesday, November 08, 2006 2:11 PM Emne: CCL: electron affinity Sent to CCL by: "Soren Eustis" [soren/./jhu.edu] Your method and basis set seem more than adequate. Electron affinity can indeed be negative. However, in this case we know that is not true. I have had much success calculating EA's using both DFT and MP2 - with a few exceptions. A key thing to check is whether or not the multiplicity is input correctly. For this case, I might see if MP2 or even HF describes this system better. In fact, for this small of a molecule - one ought to be able to run a CCSD(T) calculation in a fairly short time. Regards, Soren Eustis -----Original Message----- > From: owner-chemistry:_:ccl.net [mailto:owner-chemistry:_:ccl.net] Sent: Wednesday, November 08, 2006 7:25 AM To: Eustis, Soren Subject: CCL: electron affinity Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi-#-intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_0023_01C70348.29B78490 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear All I am calculating the electron affinity of carbon monoxide using = B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative). I am getting a negative value of -100.2 kJ/mol. The literature experimental value is 127.9 kJ/mol (I guess positive). Is this correct? Can electron affinity be negative? I will appreciate in case someone can help. Ramasami =20 ------=_NextPart_000_0023_01C70348.29B78490 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
Dear All
 
I am calculating the electron affinity = of carbon=20 monoxide using B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO,=20 negative).
I am getting a negative value of -100.2 = kJ/mol.
The literature experimental value is = 127.9 kJ/mol=20 (I guess positive).
 
Is this correct?
Can electron affinity be = negative?
 
I will appreciate in case someone can=20 help.
 
Ramasami
 
 
 
 
 ------=_NextPart_000_0023_01C70348.29B78490--http://www.ccl.net/cgi-bin/ ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://w ww.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Nov 8 12:19:00 2006 From: "Emi Psachoulia efthymia.psachoulia^-^merton.ox.ac.uk" To: CCL Subject: CCL:G: Gaussian calculation Message-Id: <-32971-061108085626-31805-FCAKmUIC8TfIw9ZVsjma7g _ server.ccl.net> X-Original-From: "Emi Psachoulia" Date: Wed, 8 Nov 2006 08:56:26 -0500 Sent to CCL by: "Emi Psachoulia" [efthymia.psachoulia!A!merton.ox.ac.uk] Hi, I tried to use Gaussian03 to do geometrical optimization of a phosphate anion and then to calculate its charges. I used for the geometry calculation HF/6-31G(d) Opt NoSymm and HF/6-31G(d,p) Opt NoSymm and then for the charge HF/6-31G* pop=mk iop(6/33=2) and HF/6-31G** pop=mk iop(6/33=2) respectively. I had an output for the geometry calculations, but not for the charges. I would like to ask you what the multiplicity is for system given that electrons delocalised. Also, what basis set shall I use? Thank you, Emi Psachoulia efthymia.psachoulia/a\merton.ox.ac.uk From owner-chemistry@ccl.net Wed Nov 8 12:54:00 2006 From: "polosan silviu spol68__yahoo.com" To: CCL Subject: CCL: Excited state electronic configurations Message-Id: <-32972-061107202621-23108-8Ox79JUWeX2Ohf0eAAAh/Q .. server.ccl.net> X-Original-From: polosan silviu Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1378242960-1162949174=:88350" Date: Tue, 7 Nov 2006 17:26:14 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: polosan silviu [spol68]=[yahoo.com] --0-1378242960-1162949174=:88350 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit What kind of command line you used? I mean method and basic set? Silviu "Caroline Norris cn29---sussex.ac.uk" wrote: Sent to CCL by: "Caroline Norris" [cn29::sussex.ac.uk] Dear All, I am in the process of calculating the potential energy curves of the lowest lying excited state of neutral vanadium oxide, and I was wondering if there's any way to determine the electronic configuration of the excited states. I've been using the pop=npa keyword, but this only details the ground state of the complex. Any help would be greatly appreciated. Thanks in advance, Caroline Norris cn29::sussex.ac.ukhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtDr. Silviu POLOSAN Faculty of Engineering, Kyoto Sangyo University, Kyoto 603-8555, Japan e-mails: polosan_._cc.kyoto-su.ac.jp; silv_._infim.ro --------------------------------- Sponsored Link Mortgage rates near historic lows: $150,000 loan as low as $579/mo. Intro-*Terms --0-1378242960-1162949174=:88350 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
What kind of command line you used? I mean method and basic set?
 
Silviu

"Caroline Norris cn29---sussex.ac.uk" <owner-chemistry_._ccl.net> wrote:
Sent to CCL by: "Caroline Norris" [cn29::sussex.ac.uk]
Dear All,
I am in the process of calculating the potential energy curves of the lowest lying excited state of neutral vanadium oxide, and I was wondering if there's any way to determine the electronic configuration of the excited states. I've been using the pop=npa keyword, but this only details the ground state of the complex. Any help would be greatly appreciated.
Thanks in advance,
Caroline Norris
cn29::sussex.ac.uk


http://www.ccl.net/cgi-bin/ccl/send_ccl_message
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Dr. Silviu POLOSAN
Faculty of Engineering, Kyoto Sangyo University, Kyoto 603-8555, Japan
e-mails: polosan_._cc.kyoto-su.ac.jp;
silv_._infim.ro

Sponsored Link

Mortgage rates near historic lows: $150,000 loan as low as $579/mo. Intro-*Terms --0-1378242960-1162949174=:88350-- From owner-chemistry@ccl.net Wed Nov 8 13:29:00 2006 From: "Gregory Sandala sandala._._.rsc.anu.edu.au" To: CCL Subject: CCL: electron affinity Message-Id: <-32973-061108083013-15796-PJ38Tf6+K1/W+rc2nK698w_._server.ccl.net> X-Original-From: Gregory Sandala Content-Type: multipart/alternative; boundary=Apple-Mail-2--430443 Date: Wed, 8 Nov 2006 13:52:43 +0100 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Gregory Sandala [sandala..rsc.anu.edu.au] --Apple-Mail-2--430443 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed You will find this resource helpful: http://webbook.nist.gov/chemistry/ion/#EA Best wishes, Greg On 08/11/2006, at 1:21 PM, Dr. Ponnadurai Ramasami ramchemi!A! intnet.mu wrote: > Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi-#-intnet.mu] > This is a multi-part message in MIME format. > > ------=_NextPart_000_0023_01C70348.29B78490 > Content-Type: text/plain; > charset="Windows-1252" > Content-Transfer-Encoding: quoted-printable > > Dear All > > I am calculating the electron affinity of carbon monoxide using = > B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative). > I am getting a negative value of -100.2 kJ/mol. > The literature experimental value is 127.9 kJ/mol (I guess positive). > > Is this correct? > Can electron affinity be negative? > > I will appreciate in case someone can help. > > Ramasami > > > > > =20 > > > ------=_NextPart_000_0023_01C70348.29B78490 > Content-Type: text/html; > charset="Windows-1252" > Content-Transfer-Encoding: quoted-printable > > > > charset=3Dwindows-1252"> > > > > >
Dear All
>
 
>
I am calculating the electron > affinity = > of carbon=20 > monoxide using B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E > (CO,=20 > negative).
>
I am getting a negative value of > -100.2 = > > kJ/mol.
>
The literature experimental value > is = > 127.9 kJ/mol=20 > (I guess positive).
>
 
>
Is this correct?
>
Can electron affinity be = > negative?
>
 
>
I will appreciate in case someone > can=20 > help.
>
 
>
Ramasami
>
 
>
 
>
 
>
 
>
> cellSpacing=3D0 = > > cellPadding=3D0 width=3D320 border=3D0 x:str> > > alt: = > 3949"=20 > width=3D108> > alt: = > 3620"=20 > width=3D99> > alt: = > 4132"=20 > width=3D113> > > >
style=3D"BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER- > LEFT: = > #ece9d8; WIDTH: 240pt; BORDER-BOTTOM: #ece9d8; HEIGHT: 15.75pt; = > BACKGROUND-COLOR: transparent"=20 > width=3D320 colSpan=3D3 height=3D21> size=3D2>
 HTML> > > ------=_NextPart_000_0023_01C70348.29B78490-- > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > --- Gregory M. Sandala School of Chemistry University of Sydney Sydney NSW 2006 Australia Ph: +61 2 9351 5361 sandala!A!chem.usyd.edu.au --Apple-Mail-2--430443 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 You will find this resource = helpful:


Best = wishes,
Greg

On 08/11/2006, at 1:21 = PM, Dr. Ponnadurai Ramasami ramchemi!A!intnet.mu wrote:

Sent to CCL by: "Dr. Ponnadurai Ramasami" = [ramchemi-#-intnet.mu]
This is a multi-part = message in MIME format.

Content-Type: text/plain;
charset=3D"Windows-1252"
Content-Transfer-Encoding: = quoted-printable

Dear All

I am calculating the electron = affinity of carbon monoxide using =3D
I am getting a negative value of = -100.2 kJ/mol.
The literature experimental = value is 127.9 kJ/mol (I guess positive).

Is this = correct?
Can electron affinity be = negative?

I will appreciate in case someone can = help.

Ramasami




=A0 =A0 =3D20


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of = carbon=3D20
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127.9 = kJ/mol=3D20
(I guess = positive).</FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2>Is = this correct?</FONT></DIV>
<DIV><FONT face=3D3DArial size=3D3D2>I = will appreciate in case someone can=3D20
<DIV><FONT face=3D3DArial = size=3D3D2>Ramasami</FONT></DIV>
<DIV><FONT face=3D3DArial = size=3D3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3D3DArial = size=3D3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3D3DArial = size=3D3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3D3DArial = size=3D3D2>&nbsp;</DIV>
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---
Gregory M. = Sandala
School of Chemistry
University of Sydney
Sydney = NSW 2006
Australia
Ph:=A0=A0+61 2 9351 5361

= --Apple-Mail-2--430443-- From owner-chemistry@ccl.net Wed Nov 8 14:03:00 2006 From: "Karl Irikura karl.irikura- -nist.gov" To: CCL Subject: CCL:G: electron affinity Message-Id: <-32974-061108102338-19952-ad+1GNE3jQhWx4rW1xOZcQ_-_server.ccl.net> X-Original-From: Karl Irikura Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Wed, 08 Nov 2006 08:54:05 -0500 Mime-Version: 1.0 Sent to CCL by: Karl Irikura [karl.irikura-x-nist.gov] Hi. In the chemistry WebBook (http://webbook.nist.gov/chemistry/) the EA is listed as 1.3261 eV (or 127.95 kJ/mol) but there is an annotation by John Bartmess (Univ. Tennessee) that G3(MP2) calculations predict the anion to be unbound by > 1.5 eV (> 140 kJ/mol). Your calculation also predicts the anion to be unbound. There is a paper by EPF Lee et al. [CPL 336(5-6) 479 (2001)] concluding that the anion is unstable. So your result appears qualitatively correct. The actual value you get will depend strongly upon the basis set. Try it! Add (in Gaussian, keyword is "extrabasis") a diffuse s-function with exponent of 0.0001 to the basis set on one of the atoms. The calculated EA should get close to zero; the diffuse function mimics a continuum function, allowing the added electron to avoid the molecule. Electron affinity, as a thermodynamic quantity, must be non-negative (unless, arguably, a metastable anion is long-lived; see Lee's paper, or papers by L-S Wang about multiply charged anions). But sometimes resonances in electron scattering are loosely described as states of negative electron affinity. Regards, Karl At 07:39 AM 11/8/2006, you wrote: >Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi-#-intnet.mu] >This is a multi-part message in MIME format. > >------=_NextPart_000_0023_01C70348.29B78490 >Content-Type: text/plain; > charset="Windows-1252" >Content-Transfer-Encoding: quoted-printable > >Dear All > >I am calculating the electron affinity of carbon monoxide using = >B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative). >I am getting a negative value of -100.2 kJ/mol. >The literature experimental value is 127.9 kJ/mol (I guess positive). > >Is this correct? >Can electron affinity be negative? > >I will appreciate in case someone can help. > >Ramasami > > >-----=_NextPart_000_0023_01C70348.29B78490------------------------------------------------ Dr. Karl K. Irikura National Institute of Standards and Technology 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301-975-2510 fax: 301-869-4020 e-mail: karl.irikura#%#nist.gov http://www.nist.gov/compchem/ ---------------------------------------------- From owner-chemistry@ccl.net Wed Nov 8 14:39:00 2006 From: "Hugo O Villar hugo:+:altoris.com" To: CCL Subject: CCL: SARvision- New Release Message-Id: <-32975-061108115940-8976-XZRDMublr/wV0SdRz5ONvw^_^server.ccl.net> X-Original-From: "Hugo O Villar" Date: Wed, 8 Nov 2006 11:59:39 -0500 Sent to CCL by: "Hugo O Villar" [hugo*_*altoris.com] CCLers, In the past some people from this list have expressed an interest in SARvision, our chemoinformatics software. Some of you are already users. We have just had a new release, version 2.4. If you are interested, you can get a demo of the product by visiting our website www.chemapps.com and clicking on the Products tab. There is an active link to download the demo. The demo is fully functional for 2 weeks. There you can also find a link that outlines what is new in this version. SARvision is a desktop software application that identifies chemical motifs present in chemical datasets and organizes available biological and biochemical data, such as those that may result from high throughput screening, according to the scaffolds it identifies. The program facilitates R-table generation and facilitates data reporting as well. The user can quickly navigate chemical information and create tables with the data available that can be exported into applications such as Microsoft Word and Excel. Among the new features, we have comparison of the scaffold content of different libraries, added graphical capabilities to plot properties by scaffolds A Linux version (without GUI)for scaffold identification is also available if you let meknow you are interested. SARvision is used by chemoinformaticians, medicinal chemists, high throughput screeners and even patent agents. Thanks! Hugo =========================== Hugo O. Villar, Ph.D. Chemapps, An Altoris Project. 11575 Sorrento Valley Road 214 San Diego, CA 92121 858.259.8161 Phone 858.259.8162 Fax www.altoris.com www.chemapps.com