From owner-chemistry@ccl.net Sat Feb 25 11:48:00 2006 From: "luis simon luissimonrubio=-=hotmail.com" To: CCL Subject: CCL:G: Transition state for recombination of dibromomercury Message-Id: <-31001-060224164905-9270-d13bc3mUg8HuskBwXZnnXQ]|[server.ccl.net> X-Original-From: "luis simon" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 24 Feb 2006 22:02:02 +0100 MIME-Version: 1.0 Sent to CCL by: "luis simon" [luissimonrubio|a|hotmail.com] Which is the multiplicity in your input file? I suggest that you try multiplicity 3 instead of 1 for the dirradical TS structure (if you did not do it before). I do not know why, but it worked for me in a very different reaction. Regards: Luis ----- Original Message ----- > From: "Ian Hovell HOVELL]|[cetem.gov.br" To: "SimÃ³n, Luis Manuel " Sent: Friday, February 24, 2006 9:12 PM Subject: CCL:G: Transition state for recombination of dibromomercury > Sent to CCL by: Ian Hovell [HOVELL/./cetem.gov.br] > This message is in MIME format. Since your mail reader does not understand > this format, some or all of this message may not be legible. > > ------_=_NextPart_001_01C6393D.C86E54E0 > Content-Type: text/plain; > charset="iso-8859-1" > > Dear CCLers, > I am assuming a linear transition state for the recombination of a bromine > radical with the bromomercury radical forming the dibromo molecule. > According to Nikolai (J Phys. Chem. A 2005, 109, 8765-8773) the two bond > lengths are 2.539 and 4.567 angstroms produced a transition state calculated > using CI methods. > I am trying to produce, without much success, a transition state for this > recombination reaction at the mpw1pw91 DFT level. In either full or partial > (where only one bond is relaxed) optimisations, the radicals either join > forming the dibromo molecule, and hence no imaginary frequency, or separate > completly according to the starting bond lengths. > > I am using the built in SDD basis set and G03w. The output produces a > warning that the bromine might be hypervalent but has no d functions - could > this be the problem or this this level of calculation just not up to finding > the transition state for this system? > All ideas would be welcome and a summary will be posted if this post > generates interest. > TIA > Ian > > > Ian Hovell - Ph.D. > NUCLEO DE MODELAGEM MOLECULAR-NMM > Centro de Tecnologia Mineral - CETEM > Ministerio da Cincia e da Tecnologia- MCT > Avenida Ip, No 900 - Cidade Universitaria > Ilha do Fundo Rio de Janeiro RJ Brasil > CEP 21941-590 > tel 00 55 (xx) 3865 7344 ou 3865 - 7216 > Fax 00 55 (xx) 22602837 ou 2290-4286 > e-mail hovell###cetem.gov.br > > > > ------_=_NextPart_001_01C6393D.C86E54E0 > Content-Type: text/html; > charset="iso-8859-1" > > > > > > > > >

Dear > CCLers,

I am assuming a > linear transition state for the recombination of a bromine radical with the > bromomercury radical forming the dibromo molecule.

According to Nikolai > (J Phys. Chem. A 2005, 109, 8765-8773) the two bond lengths are 2.539 and 4.567 > angstroms produced a transition state calculated using CI > methods.

I am trying to > produce, without much success, a transition state for this recombination > reaction at the mpw1pw91 DFT level. In either full or partial (where only one > bond is relaxed) optimisations, the radicals either join forming the dibromo > molecule, and hence no imaginary frequency, or separate completly according to > the starting bond lengths.

class=718415311-24022006>

I am using the built > in SDD basis set and G03w. The output produces a warning that the bromine might > be hypervalent but has no d functions - could this be the problem or this this > level of calculation just not up to finding the transition state for this > system?

All ideas would be > welcome and a summary will be posted if this post generates > interest.

class=718415311-24022006>TIA

class=718415311-24022006>Ian

class=718415311-24022006>

Ian Hovell - Ph.D.
NUCLEO DE MODELAGEM > MOLECULAR-NMM
Centro de Tecnologia Mineral - CETEM
Ministerio da Cincia > e da Tecnologia- MCT
Avenida Ip, No 900 - Cidade Universitaria
Ilha do > Fundo Rio de Janeiro RJ Brasil
CEP 21941-590
tel 00 55 (xx) 3865 7344 ou > 3865 - 7216
Fax 00 55 (xx) 22602837 ou 2290-4286
e-mail href="mailto:hovell###cetem.gov.br">hovell###cetem.gov.br

> > ------_=_NextPart_001_01C6393D.C86E54E0--> > > > From owner-chemistry@ccl.net Sat Feb 25 12:50:00 2006 From: "Mariusz Radon mariusz.radon%a%gmail.com" To: CCL Subject: CCL:G: problem with PCM in g03 Message-Id: <-31002-060225124341-16466-W0q2WdzHLyJvxnhzMYTRRA(~)server.ccl.net> X-Original-From: "Mariusz Radon" Content-Type: multipart/alternative; boundary="----=_Part_12633_28785460.1140889404731" Date: Sat, 25 Feb 2006 18:43:24 +0100 MIME-Version: 1.0 Sent to CCL by: "Mariusz Radon" [mariusz.radon]_[gmail.com] ------=_Part_12633_28785460.1140889404731 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear CCLers, I'm trying to use PCM model in g03. My input is as follows #P B3LYP/Gen UHF SCF=3D(Fermi,Sleazy) SCRF(PCM,Solvent=3DH2O) Guess=3DRead Integral(Grid=3DSG1) #P GFINPUT IOP(6/7=3D3) Symmetry(PG=3DCs,Follow) Opt(loose) (this is rough optimisation in water). Although 2 times SCF(SCRF) has converged and 2 steps of geometry optimisation has been done I got the following error in the 3rd step: Polarizable Continuum Model (PCM) =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D Model : PCM. Atomic radii : UA0 (Simple United Atom Topological Model). Polarization charges : Total charges. Charge compensation : None. Solution method : Matrix inversion. Cavity : GePol (RMin=3D0.200 OFac=3D0.890). Default sphere list used, NSphG=3D 27. Tesserae with average area of 0.200 Ang**2. 1st derivatives : Analytical V*U(x)*V algorithm (CHGder, D1EAlg=3D0). Cavity 1st derivative terms included. Solvent : Water, Eps=3D 78.390000. --------------------------------------------------------------------------= ---- Using symmetry in molecular cavity generation. AdVTs1: ISph=3D 281 is engulfed by JSph=3D 284 but Ae( 281) is not yet = zero! Error termination via Lnk1e in /usr/local/g03/l301.exe at Thu Feb 23 23:54:12 2006. Job cpu time: 0 days 7 hours 6 minutes 27.8 seconds. File lengths (MBytes): RWF=3D 674 Int=3D 0 D2E=3D 0 Chk=3D = 23 Scr=3D 1 The same story is with other solvents I've tried (THF, Chlorobenzene), but the error occurs earlier (in 2nd and 1st step respectively). What may be th= e reason? I've no idea what is wrong, particularly that the last geometry doesn't seem to be spoiled in any way, moreover SCF(SCRF) can be done at this geometry without any error. Thanks in advance. Best wishes, Mariusz -- Mariusz Rado\'n e-mail: mradon/at/chemia.uj.edu.pl e-mail & im: mariusz.radon/at/gmail.com ------=_Part_12633_28785460.1140889404731 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear CCLers,

I'm trying to use PCM model in g03. My input is as follows

#P B3LYP/Gen UHF SCF=3D(Fermi,Sleazy) SCRF(PCM,Solvent=3DH2O) Guess=3DRead = Integral(Grid=3DSG1)
#P GFINPUT IOP(6/7=3D3) Symmetry(PG=3DCs,Follow) Opt(loose)

(this is rough optimisation in water). Although 2 times SCF(SCRF) has converged and 2 steps of geometry optimisation has been done I got the following error in the 3rd step:

Polarizable Continuum Model (PCM)
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Model          &nbs= p;     : PCM.
Atomic radii         : UA0 (S= imple United Atom Topological Model).
Polarization charges : Total charges.
Charge compensation : None.
Solution method      : Matrix inversion.
Cavity          &nb= sp;    : GePol (RMin=3D0.200 OFac=3D0.890).
            &nb= sp;           Default sphere list used, NSphG=3D   27.
            &nb= sp;           Tesserae with average area of 0.200 Ang**2.
1st derivatives      : Analytical V*U(x)*V a= lgorithm (CHGder, D1EAlg=3D0).
            &nb= sp;           Cavity 1st derivative terms included.
Solvent          &n= bsp;   : Water, Eps=3D 78.390000.
---------------------------------------------------------------------= ---------
Using symmetry in molecular cavity generation.
AdVTs1: ISph=3D 281 is engulfed by JSph=3D 284 but Ae(&nb= sp; 281) is not yet zero!
Error termination via Lnk1e in /usr/local/g03/l301.exe at Thu Feb 23 = 23:54:12 2006.
Job cpu time: 0 days 7 hours 6 minutes 27.8 seconds= .
File lengths (MBytes): RWF=3D    674 Int=3D      0 D2E=3D      0 Chk=3D     23 Scr=3D      1<= br clear=3D"all">
The same story is with other solvents I've tried (THF, Chlorobenzene), but the error occurs earlier (in 2nd and 1st step respectively). What may be the reason? I've no idea what is wrong, particularly that the last geometry doesn't seem to be spoiled in any way, moreover SCF(SCRF) can be done at this geometry without any error.

Thanks in advance.

Best wishes,
Mariusz

--
Mariusz Rado\'n
e-mail: mradon/at/chemia.uj.edu.pl
e-mail = & im: mariusz.radon/at/gmail.com
------=_Part_12633_28785460.1140889404731-- From owner-chemistry@ccl.net Sat Feb 25 13:46:00 2006 From: "luis simon luissimonrubio(!)hotmail.com" To: CCL Subject: CCL:G: Transition state for recombination of dibromomercury Message-Id: <-31003-060225132644-4834-mhmGvCWKb97lUG8JeArnAA:+:server.ccl.net> X-Original-From: "luis simon" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Sat, 25 Feb 2006 19:26:52 +0100 MIME-Version: 1.0 Sent to CCL by: "luis simon" [luissimonrubio:_:hotmail.com] After reading the message from David Shobe I am not pretty sure if I did right changing the multiplicity to 3 in a diradical reaction. My first attempts were to set multiplicity to 1 in the transition state search, but as this did not produce any result, I considered to change it to 3 (although it lacks logic for me) and I obtained a converged transition state with one imaginary frequency corresponding to the bond that was forming in the reaction. The level of theory that I was using was certainly poor: UHF/3-21G, but I considered that the neccesity for multiplicity 3 was some artifact of the unrestristed HF. Although I am convinced by David arguments about the unnecesity of a TS, I keep still a doubt: how can QM method it distinguish between the homolitic (i.e. diradical) and the heterolytic (anion/cation) reaction. Does it rely exclusivelly on the unrestristed/restristed HF method? I am really sorry for posting the "trick" that I found now that I consider that probably I was wrong, and I specially apologize to Ian Hovell if I was terribly wrong. But could anyone please answer my former question? Thanks: Luis ----- Original Message ----- > From: "Shobe, David dshobe(-)sud-chemieinc.com" To: "SimÃ³n, Luis Manuel " Sent: Saturday, February 25, 2006 2:54 AM Subject: CCL:G: Transition state for recombination of dibromomercury > Sent to CCL by: "Shobe, David" [dshobe,sud-chemieinc.com] > Ian, > > Radical recombination reactions often don't have a TS, and it's not unusual to have a TS at one level of theory and no TS at another. > > My advice is to run a PES (potential energy scan) varying the Hg-Br distance. If the energy is a monotonic function of the bond length, then there is no transition state (according to whichever level of theory you are using). > > --David Shobe, Ph.D., M.L.S. > Süd-Chemie, Inc. > phone (502) 634-7409 > fax (502) 634-7724 > > Don't bother flaming me: I'm behind a firewall. > > > > -----Original Message----- > > From: owner-chemistry|ccl.net [mailto:owner-chemistry|ccl.net] > Sent: Friday, February 24, 2006 2:44 PM > To: Shobe, David > Subject: CCL:G: Transition state for recombination of dibromomercury > > Sent to CCL by: Ian Hovell [HOVELL/./cetem.gov.br] This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. > > ------_=_NextPart_001_01C6393D.C86E54E0 > Content-Type: text/plain; > charset="iso-8859-1" > > Dear CCLers, > I am assuming a linear transition state for the recombination of a bromine radical with the bromomercury radical forming the dibromo molecule. > According to Nikolai (J Phys. Chem. A 2005, 109, 8765-8773) the two bond lengths are 2.539 and 4.567 angstroms produced a transition state calculated using CI methods. > I am trying to produce, without much success, a transition state for this recombination reaction at the mpw1pw91 DFT level. In either full or partial (where only one bond is relaxed) optimisations, the radicals either join forming the dibromo molecule, and hence no imaginary frequency, or separate completly according to the starting bond lengths. > > I am using the built in SDD basis set and G03w. The output produces a warning that the bromine might be hypervalent but has no d functions - could this be the problem or this this level of calculation just not up to finding the transition state for this system? > All ideas would be welcome and a summary will be posted if this post generates interest. > TIA > Ian > > > Ian Hovell - Ph.D. > NUCLEO DE MODELAGEM MOLECULAR-NMM > Centro de Tecnologia Mineral - CETEM > Ministerio da Cincia e da Tecnologia- MCT Avenida Ip, No 900 - Cidade Universitaria Ilha do Fundo Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 7344 ou 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell###cetem.gov.br > > > > ------_=_NextPart_001_01C6393D.C86E54E0 > Content-Type: text/html; > charset="iso-8859-1" > > > > >

Dear CCLers,

I am assuming a linear transition state for the recombination of a bromine radical with the bromomercury radical forming the dibromo molecule.

According to Nikolai (J Phys. Chem. A 2005, 109, 8765-8773) the two bond lengths are 2.539 and 4.567 angstroms produced a transition state calculated using CI methods.

I am trying to produce, without much success, a transition state for this recombination reaction at the mpw1pw91 DFT level. In either full or partial (where only one bond is relaxed) optimisations, the radicals either join forming the dibromo molecule, and hence no imaginary frequency, or separat! > e completly according to the starting bond lengths.

I am using the built in SDD basis set and G03w. The output produces a warning that the bromine might be hypervalent but has no d functions - could this be the problem or this this level of calculation just not up to finding the transition state for this system?

All ideas would be welcome and a summary will be posted if this post generates interest.

TIA

class=718415311-24022006>Ian

class=718415311-24022006>

Ian Hovell - Ph.D.
NUCLEO DE MODELAGEM MOLECULAR-NMM
Centro de Tecnologia Mineral - CETEM
Ministerio da Cincia e da Tecnologia- MCT
Avenida Ip, No 900 - Cidade Universitaria
Ilha do Fundo Rio de Janeiro RJ Brasil
CEP 21941-590
tel 00 55 (xx) 3865 7344 ou > 3865 - 7216
Fax 00 55 (xx) 22602837 ou 2290-4286
e-mail hovell###cetem.gov.br

> > ------_=_NextPart_001_01C6393D.C86E54E0--> > > >