From owner-chemistry@ccl.net Tue Mar 3 03:16:00 2009 From: "Marcel Swart marcel.swart#icrea.es" To: CCL Subject: CCL: Transition states vrs reactants Message-Id: <-38731-090303030046-26301-jlxpyt9Y/CgpJL3xeq66Pw:_:server.ccl.net> X-Original-From: Marcel Swart Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Tue, 3 Mar 2009 07:54:10 +0100 MIME-Version: 1.0 Sent to CCL by: Marcel Swart [marcel.swart,,icrea.es] A very typical example is the bimolecular nucleophilic substitution reaction= , X(-) + CH3Y =3D> CH3X + Y(-) where the energy of the TS is many times lower than that of reactants. (depending on the nature of X,Y, or the central particle, or the substituents on it) But it does have a central barrier w.r.t. a reactant-complex. See for instance Figure 1 in J.Comput.Chem. 2007, 28, 1551. Quoting "Richard Tia richtiagh a gmail.com" : > > Sent to CCL by: "Richard Tia" [richtiagh~~gmail.com] > Hi everybody, > > To those who have some experience in computing reaction pathways, =20 > how would you rationalize a situation where the 'transition state' =20 > is lower in energy than the reactants? Is this a common occurrence? =20 > Could it be that the located TS is for a side reaction? Could the =20 > 'TS' just be an artifact? > > I would be very grateful if someone could offer some suggestions as =20 > to the chemistry involved here. Thanks in advance. =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=3D=3D dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart,icrea.es marcel.swart,udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =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=3D=3D From owner-chemistry@ccl.net Tue Mar 3 03:50:00 2009 From: "mahmoud khedr mkkhedr]*[hotmail.com" To: CCL Subject: CCL: Transition states vrs reactants Message-Id: <-38732-090303023339-24295-wRZUBQJskNNhBPM9RKHbjg---server.ccl.net> X-Original-From: mahmoud khedr Content-Type: multipart/alternative; boundary="_b8019bc6-ba65-41dd-892e-762655d06610_" Date: Tue, 3 Mar 2009 07:00:43 +0000 MIME-Version: 1.0 Sent to CCL by: mahmoud khedr [mkkhedr.]![.hotmail.com] --_b8019bc6-ba65-41dd-892e-762655d06610_ Content-Type: text/plain; charset="windows-1256" Content-Transfer-Encoding: 8bit Dear Sir, I think the reactant you started with is not the right minimum. So you have to find the optimum structure for the reactant. If your molecule is planer for instance, try to make some group out of plane to decrease the steric hindrance of that group. Also it is a good idea to follow the reaction path through the IRC method starting with the transition state structure you have to see which the reactants and products. I hope these help. Best regards, Mahmoud > From: owner-chemistry]![ccl.net > To: mkkhedr]![hotmail.com > Subject: CCL: Transition states vrs reactants > Date: Mon, 2 Mar 2009 15:05:03 -0500 > > > Sent to CCL by: "Richard Tia" [richtiagh~~gmail.com] > Hi everybody, > > To those who have some experience in computing reaction pathways, how would you rationalize a situation where the 'transition state' is lower in energy than the reactants? Is this a common occurrence? Could it be that the located TS is for a side reaction? Could the 'TS' just be an artifact? > > I would be very grateful if someone could offer some suggestions as to the chemistry involved here. Thanks in advance. > > Richard Tia > KNUST > Kumasi > Ghana> > _________________________________________________________________ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us --_b8019bc6-ba65-41dd-892e-762655d06610_ Content-Type: text/html; charset="windows-1256" Content-Transfer-Encoding: 8bit Dear Sir,

I think the reactant you started with is not the right minimum. So you have to find the optimum structure for the reactant. If your molecule is planer for instance, try to make some group out of plane to decrease the steric  hindrance of that group.

Also it is a good idea to follow the reaction path through the IRC method starting with the transition state structure you have to see which the reactants and products.

I hope these help.

Best regards,
Mahmoud

> From: owner-chemistry]![ccl.net
> To: mkkhedr]![hotmail.com
> Subject: CCL: Transition states vrs reactants
> Date: Mon, 2 Mar 2009 15:05:03 -0500
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> Sent to CCL by: "Richard Tia" [richtiagh~~gmail.com]
> Hi everybody,
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> To those who have some experience in computing reaction pathways, how would you rationalize a situation where the 'transition state' is lower in energy than the reactants? Is this a common occurrence? Could it be that the located TS is for a side reaction? Could the 'TS' just be an artifact?
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> I would be very grateful if someone could offer some suggestions as to the chemistry involved here. Thanks in advance.
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> Richard Tia
> KNUST
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Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! Try it! --_b8019bc6-ba65-41dd-892e-762655d06610_-- From owner-chemistry@ccl.net Tue Mar 3 06:36:00 2009 From: "V ronique LEGRAND vflegrand,,free.fr" To: CCL Subject: CCL:G: How to check orbital permutation ? Message-Id: <-38733-090303063322-10260-D7u3/xqXYxPsDvoyf8UYrQ[#]server.ccl.net> X-Original-From: "V ronique LEGRAND" Date: Tue, 3 Mar 2009 06:33:18 -0500 Sent to CCL by: "V ronique LEGRAND" [vflegrand**free.fr] Hello everybody, I'm working on a radical. To work on the good form I have to permute orbital. So do choose the orbitals I performed an NBO calculation. After I used the option "permute" of Gausssian: #P UB3LYP/6-311+G(d,p) SP guess=(permute) GFPrint GFinput Scf=Tight iop(5/14=2) Maxdisk=50000000 Pop=(Full,NBO)Test I observed something strange : -In the NBO output, there are not the same numbers of orbitals in "Orbital energies and kinetic energies"(891) and in alpha-orbital description(895). It's a problem, because I have to write the index of orbitals to permute. So when I list the new order of orbitals, the last number is 895, but Gaussian stopped and said there are only 891 orbitals. So which list I have to choose? And why this difference? -secondly: I liked to check if the permutation has been well done, even if I see the novel order written in the output of the permutation work. So I performed an NBO: #P UB3LYP/6-311+G(d,p) SP guess=(permute) GFPrint GFinput Scf=Tight iop(5/14=2) Maxdisk=50000000 Pop=(Full,NBO)Test But when I read the orbitals occupancy is like nothing appened. I have the same values like in the beginning. I don't understand. I someone have an idea, I will receive it with pleasure. Thank you very much Vronique From owner-chemistry@ccl.net Tue Mar 3 10:48:01 2009 From: "Kalju Kahn kalju]=[chem.ucsb.edu" To: CCL Subject: CCL: Transition states vrs reactants Message-Id: <-38734-090303044001-14541-QbKvKjnjDuqGouNayjWc8g]-[server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 3 Mar 2009 01:00:16 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju!A!chem.ucsb.edu] Richard, Please note that the SN2 example by Marcel is for the gas phase reaction. Then, the anion is unsolvated, and the charge-dipole interaction between X(-) and CH3Y is strong. There is a normal significant barrier w.r.t. isolated reactants for such reactions in water. Thus, you may want to see if your TS is still lower in the presence of the solvent before worrying about other things. Hope this helps, Kalju > > Sent to CCL by: Marcel Swart [marcel.swart,,icrea.es] > > A very typical example is the bimolecular nucleophilic substitution > reaction, > X(-) + CH3Y => CH3X + Y(-) > where the energy of the TS is many times lower than that of reactants. > (depending on the nature of X,Y, or the central particle, or the > substituents on it) > > But it does have a central barrier w.r.t. a reactant-complex. > See for instance Figure 1 in J.Comput.Chem. 2007, 28, 1551. > > Quoting "Richard Tia richtiagh a gmail.com" : > >> >> Sent to CCL by: "Richard Tia" [richtiagh~~gmail.com] >> Hi everybody, >> >> To those who have some experience in computing reaction pathways, >> how would you rationalize a situation where the 'transition state' >> is lower in energy than the reactants? Is this a common occurrence? >> Could it be that the located TS is for a side reaction? Could the >> 'TS' just be an artifact? >> >> I would be very grateful if someone could offer some suggestions as >> to the chemistry involved here. Thanks in advance. > > =================================== > dr. Marcel Swart > > ICREA researcher at > Institut de Química Computacional > Universitat de Girona > > Parc Científic i Tecnològic > Edifici Jaume Casademont (despatx A-27) > Pic de Peguera 15 > 17003 Girona > Catalunya (Spain) > > tel > +34-972-183240 > fax > +34-972-183241 > e-mail > marcel.swart(a)icrea.es > marcel.swart(a)udg.edu > web > http://www.icrea.cat/Web/ScientificForm.aspx?key=372 > http://iqc.udg.edu/~marcel > ===================================> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Tue Mar 3 11:22:01 2009 From: "Aniko Simon aniko()simbiosys.ca" To: CCL Subject: CCL: eHiTS Lightning 2009 is released: Fast, Accurate and Green Message-Id: <-38735-090303105123-20506-zKKvkgJAo8gPJUTglczaSw-$-server.ccl.net> X-Original-From: "Aniko Simon" Date: Tue, 3 Mar 2009 10:51:19 -0500 Sent to CCL by: "Aniko Simon" [aniko##simbiosys.ca] Dear CCLers, SimBioSys Inc. announced the release of eHiTS 2009 - a new version of its molecular docking and virtual screening software. The new release builds on eHiTS' strengths of its fine, systematic and exhaustive search algorithm, its automatic protonation state handling, and its unique knowledge-based scoring function. It delivers the following new features: * An average 10x hardware-based speedup on IBM's Cell/B.E. platforms. * An improved scoring function up-to-date with the latest experimental data. * Scoring function pre-tuned for 500 new protein classes. * Dramatically improved correlation between score and binding affinity. "This is a low-cost and green hardware solution that saves on operational costs like cooling, electricity and space," says Zsolt Zsoldos SimBioSys' chief scientist, "it delivers the same high quality results as traditional platforms, and opens up the virtual screening paradigm to small companies who could not afford the IT infrastructure required for the process" The PlayStation solution directly delivers on two key issues in today's dire market conditions: significant cost reduction with no compromise to quality, and lower environmental footprint due to lower power consumption. To see the full press release click on: http://www.simbiosys.ca/whatsnew/news/index.html or see it on our blog: http://www.simbiosys.ca/blog/2009/02/26/simbiosys-inc-releases-a-new-version-of-ehits/ If you are interested in evaluating the latest version, please fill in a demo request at: http://www.simbiosys.ca/products/demo_request.html and we will reply shortly. Thank you, Best regards, Aniko -- Aniko Simon, Ph.D. | SimBioSys Inc. | Tel: 1-416-741-4263 http://www.simbiosys.ca/ | blog: http://www.simbiosys.ca/blog/ From owner-chemistry@ccl.net Tue Mar 3 11:57:00 2009 From: "Kavitha Velappan kavitha.velappan(a)gmail.com" To: CCL Subject: CCL: IRC calculation Message-Id: <-38736-090303094857-10008-JU47sYTc63iuPXMcFSVQEw(0)server.ccl.net> X-Original-From: "Kavitha Velappan" Date: Tue, 3 Mar 2009 09:48:53 -0500 Sent to CCL by: "Kavitha Velappan" [kavitha.velappan_-_gmail.com] Hi all, I tried to do IRC calculation to follow the reaction path for conformer interconversion (Dimethoxymethane G+G- to G-G- conformer - rotation around OCH3 bond). The route section looks like this: #N RB3LYP/6-31++G** IRC=(CalcFC,maxpoints=12) The initial geometry was that of the TS connecting the two conformers computed using QST2 option. Part of the IRC output is given below: ENERGY RX.COORD R1 R2 R3 1 -560.37953 -1.01084 1.41943 1.66379 1.66680 2 -560.37949 -0.91206 1.41938 1.66370 1.66681 3 -560.37945 -0.81579 1.41937 1.66360 1.66682 4 -560.37942 -0.72229 1.41938 1.66352 1.66684 5 -560.37940 -0.65263 1.41934 1.66346 1.66685 6 -560.37938 -0.58346 1.41939 1.66342 1.66686 7 -560.37936 -0.51894 1.41933 1.66337 1.66686 8 -560.37935 -0.45252 1.41942 1.66338 1.66688 9 -560.37933 -0.36983 1.41937 1.66324 1.66689 10 -560.37931 -0.28133 1.41950 1.66336 1.66692 11 -560.37929 -0.19147 1.41936 1.66305 1.66689 12 -560.37929 -0.16685 1.42001 1.66297 1.66710 13 -560.37928 -0.09663 1.41961 1.66332 1.66695 14 -560.37927 -0.09652 1.42003 1.66321 1.66712 15 -560.37925 0.00000 1.41991 1.66347 1.66706 16 -560.37927 0.09652 1.42003 1.66321 1.66712 17 -560.37929 0.16685 1.42001 1.66297 1.66710 In one direction 14 points are computed while in another direction only 2 points are computed. Also the last point (point 1) does not correspond to a minima (G+G-/G-G- conformer). When I viewed the output the geometries did not vary much. Also I used the default option and run the IRC calculation in the forward and reverse directions separately. But that doesn't seem to solve the problem because irrespective of the keyword (forward/reverse option) the reaction always proceeds in the same direction. Now my question is 1) Should I make a guess for the TS and run a TS calculation using QST3 option? or 2) Should I change the keywords for the IRC calculation? I would be grateful if anyone could help me solve this IRC problem. Thank you very much for your help in advance! Kavitha Email: kavitha.velappan^gmail.com From owner-chemistry@ccl.net Tue Mar 3 14:01:00 2009 From: "akef afaneh akef_afnh[a]yahoo.com" To: CCL Subject: CCL: Transition states vrs reactants Message-Id: <-38737-090303125224-9663-Qa54S7izL7b++O9Dfdcriw=server.ccl.net> X-Original-From: akef afaneh Content-Type: text/plain; charset=us-ascii Date: Tue, 3 Mar 2009 08:52:08 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: akef afaneh [akef_afnh~!~yahoo.com] Hi Richard, It depends on the starting materials. If one of the starting materials is charged, then you need to stabilize this charge species, by using the solvation model with the write solvent. If you did not do this then the TS will be more stable than the starting materials, because the charge will be distributed on more than one center. More delocalization of the charge, more stable species. Good Luck Akef T. Afaneh Chemistry Department University of Manitoba Winnipeg, Manitoba, Canada. --- On Mon, 3/2/09, Richard Tia richtiagh a gmail.com wrote: > From: Richard Tia richtiagh a gmail.com > Subject: CCL: Transition states vrs reactants > To: "Afaneh, Akef Taha " > Date: Monday, March 2, 2009, 3:05 PM > Sent to CCL by: "Richard Tia" > [richtiagh~~gmail.com] > Hi everybody, > > To those who have some experience in computing reaction > pathways, how would you rationalize a situation where the > 'transition state' is lower in energy than the > reactants? Is this a common occurrence? Could it be that the > located TS is for a side reaction? Could the 'TS' > just be an artifact? > > I would be very grateful if someone could offer some > suggestions as to the chemistry involved here. Thanks in > advance. > > Richard Tia > KNUST > Kumasi > Ghana > > > > -= This is automatically added to each message by the > mailing script =- > To recover the email address of the author of the message, > please change > the strange characters on the top line to the !=! sign. You > can also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: > http://www.ccl.net/chemistry/searchccl/index.shtml From owner-chemistry@ccl.net Tue Mar 3 23:23:01 2009 From: "Syed Tarique Moin tarisyed|,|yahoo.com" To: CCL Subject: CCL: Van der Waal parameter for iron Message-Id: <-38738-090303051808-22206-Ii1/JNW9XCKJtAQwiGP20A|-|server.ccl.net> X-Original-From: "Syed Tarique Moin" Date: Tue, 3 Mar 2009 05:18:02 -0500 Sent to CCL by: "Syed Tarique Moin" [tarisyed,+,yahoo.com] Dear CCL subscribers, I m working on force field development of complex iron. I want to know the non-bonded Van der Waal parameter of iron for amber forcefield. Regards