From owner-chemistry@ccl.net Wed May 2 04:25:00 2007 From: "Gert von Helden helden-,-fhi-berlin.mpg.de" To: CCL Subject: CCL: computing cross sectional area of a molecule Message-Id: <-34172-070502035455-2443-z5416we8AKZrGd2PVZhJXA]-[server.ccl.net> X-Original-From: Gert von Helden Content-Type: multipart/alternative; boundary=Apple-Mail-1-67479660 Date: Wed, 2 May 2007 09:24:18 +0200 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Gert von Helden [helden,+,fhi-berlin.mpg.de] --Apple-Mail-1-67479660 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear Senthil, have a look at: http://bowers.chem.ucsb.edu/theory_analysis/cross-sections/index.shtml Best regards, Gert von Helden On May 1, 2007, at 9:31 PM, Senthil Natesan sen.natesan]=[yahoo.com wrote: > > Sent to CCL by: "Senthil Natesan" [sen.natesan|-|yahoo.com] > > Dear Colleagues, > > Can anyone suggest me a program or method to compute cross > sectional area of a given molecule?.. > > Thanks in advance.. > > Senthil Natesan > > > > -= 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)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > ------------------------------------- Gert von Helden Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin tel.: +49-30-8413 5615 fax: +49-30-8413 5603 --Apple-Mail-1-67479660 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Dear Senthil,
have a look = at:

http://bowers.chem.ucsb.edu/theory_analysis/cross-sections/index.sht= ml

Best = regards,

Gert = von Helden



On May 1, = 2007, at 9:31 PM, Senthil Natesan sen.natesan]=3D[yahoo.com = wrote:


Sent to CCL by: "Senthil=A0 Natesan" = [sen.natesan|-|yahoo.com]

Dear Colleagues,

Can = anyone suggest me a program or method to compute cross sectional area of = a given molecule?..
Thanks in advance..

Senthil = Natesan



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=



-------------------------------------

Gert von Helden

=

Fritz-Haber-Institut der = Max-Planck-Gesellschaft

Faradayweg 4-6

14195 Berlin

tel.: +49-30-8413 5615

fax: +49-30-8413 5603

=

= --Apple-Mail-1-67479660-- From owner-chemistry@ccl.net Wed May 2 05:40:01 2007 From: "Michel Petitjean ptitjean-.-itodys.jussieu.fr" To: CCL Subject: CCL: computing cross sectional area of a molecule Message-Id: <-34173-070502042016-4886-1UOF7US3qInhXFe6IbApcg:+:server.ccl.net> X-Original-From: Michel Petitjean Date: Wed, 2 May 2007 10:19:38 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean:-:itodys.jussieu.fr] To: chemistry*|*ccl.net Subject: CCL: Re: computing cross sectional area of a molecule Which one ? The smallest one ? The largest one ? Or relative to a specified projection ? Also, do you take in account the van der Waals spheres shadow or not ? Michel Petitjean, Email: petitjean*|*itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean*|*ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.spheres.html Sent to CCL by: "Senthil Natesan" [sen.natesan|-|yahoo.com] > Dear Colleagues, > Can anyone suggest me a program or method to compute cross sectional area of a given molecule?.. > Thanks in advance.. > Senthil Natesan From owner-chemistry@ccl.net Wed May 2 13:37:00 2007 From: "Per Jr. Greisen pgreisen,+,gmail.com" To: CCL Subject: CCL: Polyrate on model of enzyme Message-Id: <-34174-070502133012-12355-ZpeyRKOH5aCGNWmIKGZCDg:-:server.ccl.net> X-Original-From: "Per Jr. Greisen" Content-Type: multipart/alternative; boundary="----=_Part_8082_27458915.1178125259734" Date: Wed, 2 May 2007 19:00:59 +0200 MIME-Version: 1.0 Sent to CCL by: "Per Jr. Greisen" [pgreisen-,-gmail.com] ------=_Part_8082_27458915.1178125259734 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all, I am trying to estimate the k_cat value and other attributes from a reaction. I have the geometry for the transition state and performed an IRC. I would like to use the program POLYRATE in order to estimate the TST/VTST. My problem is that from the examples in polyrate - you have to specify etc. the reactant 1/2, transition state, and product 1/2. Can I just specify my whole model as one reactant,TS, and product? Any help or advice appreciated. Thanks in advance Best regards, ------=_Part_8082_27458915.1178125259734 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all,

I am trying to estimate the k_cat value and other attributes from a reaction. I have the geometry for the transition state and performed an IRC. I would like to use the program POLYRATE in order to estimate the TST/VTST. My problem is that from the examples in polyrate - you have to specify etc. the reactant 1/2, transition state, and product 1/2.

Can I just specify my whole model as one reactant,TS, and product?

Any help or advice appreciated. Thanks in advance

Best regards,

------=_Part_8082_27458915.1178125259734-- From owner-chemistry@ccl.net Wed May 2 14:11:00 2007 From: "Panida Surawatanawong paninid*gmail.com" To: CCL Subject: CCL: A problem with restart in ORCA Message-Id: <-34175-070502130120-8875-fSfG2QvFy/lvDJnqLzkWdA^server.ccl.net> X-Original-From: "Panida Surawatanawong" Content-Type: multipart/alternative; boundary="----=_Part_39096_27368587.1178121671107" Date: Wed, 2 May 2007 11:01:11 -0500 MIME-Version: 1.0 Sent to CCL by: "Panida Surawatanawong" [paninid]![gmail.com] ------=_Part_39096_27368587.1178121671107 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all, I tried to calculate EPR parameters for iron complexes with ORCA. The scf calculation doesn't converge within 125 cycles which is the default. However, it seems almost converge, so I restarted the calculation by using the same gbw file. According to the ORCA manual, I added the input lines like this. ... # %scf Guess MORead MOInp "FeO42m.gbw" end # ... But I got the error message in the output file. --------------------- INITIAL GUESS: MOREAD --------------------- Cannot open GBW file: FeO42m.gbw An error has occured in the SCF module CALLING COMMAND: orca_scf /data/panidasu/orcaTest/FeO42m/ORCA/bs7/PBE/FeO42m.gbw b RETURN CODE : 512 ABORTING THE RUN I do have the gbw file from previous calculation, so I don't know why it cannot open the gbw file. I would appreciate any suggestion. Thank you, Panida Surawatanawong ------=_Part_39096_27368587.1178121671107 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all,
I tried to calculate EPR parameters for iron complexes with ORCA. The scf calculation doesn't converge within 125 cycles which is the default. However, it seems almost converge, so I restarted the calculation by using the same gbw file. According to the ORCA manual, I added the input lines like this.
...
#
%scf
Guess MORead
MOInp "FeO42m.gbw"
end
#
...

But I got the error message in the output file.

---------------------
INITIAL GUESS: MOREAD
---------------------
Cannot open GBW file: FeO42m.gbw

An error has occured in the SCF module
CALLING COMMAND: orca_scf /data/panidasu/orcaTest/FeO42m/ORCA/bs7/PBE/FeO42m.gbw b
RETURN CODE    : 512
ABORTING THE RUN

I do have the gbw file from previous calculation, so I don't know why it cannot open the gbw file. I would appreciate any suggestion.

Thank you,
Panida Surawatanawong
------=_Part_39096_27368587.1178121671107-- From owner-chemistry@ccl.net Wed May 2 14:46:00 2007 From: "Fedor t.goumans{:}ucl.ac.uk" To: CCL Subject: CCL:G: Summary: large imaginary frequency in coronene when diffuse functions are used Message-Id: <-34176-070502120750-2259-h+Qq0spj//HnsoJ5P2AkOQ|*|server.ccl.net> X-Original-From: Fedor Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Wed, 02 May 2007 17:07:32 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor [t.goumans-.-ucl.ac.uk] Dear CCL-ers, A summary of what I found out thusfar about the imaginary frequency in coronene for certain approaches. Cory Pye and Marcel Swart helped to find the stable structures corresponding to the saddle point. The stable structure is of D3D-symmetry, which is found by manually displacing the structure along (bits of) the B2G-imaginary mode. Gaussian's IRC apparently has sufficient numerical noise to misjudge the symmetry after stepping along the imaginary mode (C2H). The symmetry-determining algorithms are of course very sensitive to slight numerical differences in cartesian coordinates. The resulting optimised stable structure is 'ruffled' with alternative upward and downward displacement out of the plane by ~0.003A for the central carbon atoms and less for the other atoms. It is very comparable in energy to the flat structure (~0.3 kJ/mol). Thanks to Errol Lewars, Stefan Grimme, Steven Bachrach and Paul Schleyer for pointing out the paper J. Am. Chem. Soc., 2006, 128(9), 9342 where imaginary frequencies are observed for different methodologies/basis sets in benzene. These imaginary frequencies are also reported for large Pople basis sets by Steve Williams. This basis-set dependent effect is very likely related to that in coronene and, as Petar Todorov pointed out, in other PAHs as well. In this paper, this basis set effect is attributed to a an intramolecular basis set incompleteness error. To illustrate how sensitive the basis set effect might be: with MPWB1K the ruffled structure is preferred if a 6-31+G* basis is used as well as when a split 6-31+G*(central)/6-31G*(peripheral) basis is used. However, as Grzegorz Mazur pointed out, at the HF/6-31+G* level the flat D6H structure is preferred, while for the split basis it is unstable and the ruffled D3D structure is preferred instead. In both my and previous (JACS-paper cited) calculations the aromatics are planar when Dunning's basis (aug-cc-pVnZ) are used, but not always when Pople basis sets with diffuse function are used. I have not fully pinned down yet what the underlying reason for the basis set dependent nonplanarity is, although I do feel that Isaac Bersuker's suggestion of a basis-set dependent pseudo Jahn-Teller effect is very plausible. A question that comes to mind is if this tendency for puckering may be "real", especially for the larger PAHs in view of the structure of graphene recently determined to be corrugated (Nature, 2007, 446, 60)? Thanks for all your help, Kind regards, Fedor From owner-chemistry@ccl.net Wed May 2 16:21:00 2007 From: "Yousef Sharifi ysharifi ~ gmail.com" To: CCL Subject: CCL: Dmol3 questions Message-Id: <-34177-070502161837-31707-5GFurxzs5vQRM84ZKtpeZA!A!server.ccl.net> X-Original-From: "Yousef Sharifi" Date: Wed, 2 May 2007 16:18:34 -0400 Sent to CCL by: "Yousef Sharifi" [ysharifi-*-gmail.com] I have a question about Dmol3. Consider finding the transition state for this reaction: C2H5Cl+OH- ->C2H5OH+Cl-, when you optimize the reactants, the OH- sticks to C2H2Cl and creates the final product. This happens no matter how far you put the molecules but you need them as two separate molecules in the reactants side. I have tried their TSSearch for some other reactions and it has some trouble with medium and fine quality calculations. For example for CH4+H->CH3+H2 Dmol only finds the TS if you use coarse quality calculation, increasing the quality to medium or fine will not lead to transition state. Is there any bug in Dmol?