=0A

Yes. Curved bond path is a signif= icance of both stong bond and weak interaction. The Laplacian of bond criti= cal points (BCPs) gives further information about the bonding nature.<= /DIV>=0A

=0A

= Senthilnathan

=0A

= =0A

=0A

=0AFrom: may abdelghani m= ay01dz%yahoo.fr <owner-chemistry##ccl.net>
To: "Senthilnathan, Dhurairaj " <zenthil= 03##yahoo.co.in>
Sent:= Wed, 20 April, 2011 3:22:18 PM
Sub= ject: CCL: Curved bond paths

=0A=0A=0A=0A

Dear CCLers,
If you "Curved bond paths" ( AIM analysis), do= es this mean that You have a weak bond?
Thanks a lot
=

--0-202234711-1303312886=:36544-- From owner-chemistry@ccl.net Wed Apr 20 11:57:00 2011 From: "errol lewars elewars---trentu.ca" To: CCL Subject: CCL: Any relation between Imaginary frequency and barrier height? Message-Id: <-44435-110420112940-16781-TTv3DcpCgZwBb8M8qdVVzQ:-:server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 20 Apr 2011 11:29:39 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars!A!trentu.ca] 2011 April 20 Recall that the magnitude of the imaginary frequency is a measure of the curvature (second derivative of energy with respect to geometry) of the transition state region along the reaction coordinate. Intuitively, for a series of related reactions, a small (considering the real part of the imaginary number) imaginary frequency should correspond to a low barrier and a large imaginary frequency to a high barrier (sketch the reaction profiles). In other words, for a low barier the transition region may be relatively flat. Intuitively. Here are some activation energies and TS freqs I quickly did using AM1 (not very good for energies). The reaction is the Diels-Alder addition of the dienophile H2C=CH-X with s-cis-1,3-butadiene. All energies in kJ mol-1. X activ E TS freq (i units) NH3+ 73 801 NO 89 838 NO2 90 844 CHO 95 857 OH 96 937 H 97 921 CN 98 884 F 104 938 NH2 107 885 Cl 109 936 Br 112 927 E. Lewars == upendra Adhikari upendra.adhikari./a\.aggiemail.usu.edu wrote: > Sent to CCL by: "upendra Adhikari" [upendra.adhikari|a|aggiemail.usu.edu] > Dear all, > While calculating for the transition state I got different magnitude of imaginary frequencies for different methods, in some cases I got like -100 cm-1 and for some cases -300 cm-1, so I was wondering that is there any relationship between the magnitude of imaginary frequency with barrier height or geometry or something like that? > > Thank you!! > > Upendra> > > From owner-chemistry@ccl.net Wed Apr 20 12:33:00 2011 From: "Arne Dieckmann adieckma,googlemail.com" To: CCL Subject: CCL:G: Vibrational analysis with implicit solvation Message-Id: <-44436-110420120147-14003-VDZzTojmaUSjWlO/7lle6A[*]server.ccl.net> X-Original-From: "Arne Dieckmann" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: 20 Apr 2011 18:01:33 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: "Arne Dieckmann" [adieckma#,#googlemail.com] Hi Andreas, thanks for your answer. I can understand the points you are making in that J Phys Chem A paper. However, I still don't know which contributions are included in the free energy Gaussian calls "Sum of electronic and thermal Free Energies". It has a different values when performing the frequency calculation in the gas phase or in solution, so I guess some implicit solvent contribution must be factored in, right? Cheers, Arne On Apr 20, 2011, at 3:22 PM, Andreas Klamt klamt||cosmologic.de wrote: > > Sent to CCL by: Andreas Klamt [klamt(_)cosmologic.de] > Dear Arne, > > this issue is quite confusing. I have already commented a few times on this issue in the CCL. I do not want to repeat that here. > An analysis is also given in > J Phys Chem A. 2010 Dec 30;114(51):13442-4. Epub 2010 Dec 6. > Comment on the correct use of continuum solvent models. > > Hope this helps. > > Andreas > > Am 20.04.2011 13:43, schrieb Arne Dieckmann adieckma++googlemail.com: >> Sent to CCL by: "Arne Dieckmann" [adieckma_-_googlemail.com] >> Dear all, >> >> I am performing a vibrational analysis in Gaussian03 using the M05-2X functional and implicit solvation. The way I see the results is that the effect of solvation is already included in in the free energy ("Sum of electronic and thermal Free Energies="). Is that correct or do I need to apply the correction for free energy to the "total free energy in solution" (that's what it's called in the Gaussian output) estimated by the variational PCM calculation? >> >> >> Cheers, >> Arne> >> >> > > > -- > PD. Dr. Andreas Klamt > CEO / Geschäftsführer > COSMOlogic GmbH& Co. KG > Burscheider Strasse 515 > D-51381 Leverkusen, Germany > > phone +49-2171-731681 > fax +49-2171-731689 > e-mail klamt\a/cosmologic.de > web www.cosmologic.de > > HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamthttp://www.ccl.net/chemistry/sub_unsub.shtml> > From owner-chemistry@ccl.net Wed Apr 20 13:31:00 2011 From: "Tijesunimi John Odebode tijesunimi\a/yahoo.com" To: CCL Subject: CCL:G: Error in gaussian Message-Id: <-44437-110420132908-4974-9lH8Vxz7UkPdIV5BTNGMvg.:.server.ccl.net> X-Original-From: "Tijesunimi John Odebode" Date: Wed, 20 Apr 2011 13:29:06 -0400 Sent to CCL by: "Tijesunimi John Odebode" [tijesunimi*yahoo.com] I am getting an error in gaussian that says 'operation on none existent file.' Can someone tell me what that means, and how I can rectify this error? Thanks From owner-chemistry@ccl.net Wed Apr 20 16:39:00 2011 From: "Thomas Manz thomasamanz(-)gmail.com" To: CCL Subject: CCL:G: problem with geometry optimization in g09 Message-Id: <-44438-110420163531-8566-UEV7XlG0nNEERBhDeWTEiQ++server.ccl.net> X-Original-From: Thomas Manz Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 20 Apr 2011 16:35:22 -0400 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz!A!gmail.com] Hi Walter, An sto-3g or 3-21G basis set is extremely small, so unless your system contains more than a few hundred atoms it's probably not an appropriate choice. The 6-311++G** or another triple zeta basis set with polarization and diffuse functions would be a better choice if your system contains fewer than about 200 atoms. Generally speaking, you would be better off using a correlated electron method like density functional theory (e.g., B3LYP) than a semi-empirical or hartree-fock calculation. If your system contains hundreds of atoms, consider using a pure DFT functional like PW91PW91 with a density fitting basis set (e.g., PW91PW91/6-311++G**/auto). Unless there is a compelling reason to keep the Fe atoms fixed, why not relax the whole structure? Route line of the following type might be suitable: # opt B3LYP/6-311++G** scf=(fermi,maxcycle=400) You can find further instructions for how to perform a calculation of this type in the Gaussian manual at www.gaussian.com. Sincerely, Tom On Wed, Apr 20, 2011 at 10:32 AM, Walter Ca on wcanon[]ciq.uchile.cl wrote: > > Sent to CCL by: "Walter Ca on" [wcanon ~ ciq.uchile.cl] > Hi, my name is Walter and we have the following problem. > we are trying to perform a partial geometry optimization of some hydrogens atoms using g09, in a system with 3 Fe(III) atoms, in wich those 3 Fe(III) atoms are fixed. the system have charge +3. I have try from semi-empirical methods to UHF with some simple basis set like sto-3g or 3-21G, because i only want to optimized hydrogens atoms. > Can anyone help me to try to fix this problem. > Thanks > Walter> http://www.ccl.net/cgi-bin/ccl/send_ccl_message> http://www.ccl.net/cgi-bin/ccl/send_ccl_message> http://www.ccl.net/chemistry/sub_unsub.shtml> http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Wed Apr 20 17:13:00 2011 From: "Cory Pye cpye=ap.smu.ca" To: CCL Subject: CCL:G: Gaussian error? Message-Id: <-44439-110420113320-20182-EZn9EpMDfqqLiNqB3RMMJA _ server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 20 Apr 2011 12:38:45 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye _ ap.smu.ca] Hello, Based on my experience with numerical analysis, my guess would be that this is an error in calculating the generalized inverse of a rectangular matrix. One way to do this is through a singular value decomposition (SVD). As to what the matrix is, it might be related to a coordinate conversion (say from Cartesians to redundant internals) or it could be a mapping from one basis set to another (say, during a guess=read). I don't know for sure. If the coordinate system didn't span the full Cartesian space you might get this type of error, in which case the solution would be to explicitly add some coordinates. -Cory On Tue, 19 Apr 2011, Maura Mooney mmooney05]![qub.ac.uk wrote: > > Sent to CCL by: "Maura Mooney" [mmooney05|a|qub.ac.uk] > Hi all, > > I've seen this error posted previously but have not seen any solutions, as yet. > I am running a gaussian rhf GeoOpt, but it fails to complete. > > SDV returned info= 518 to GenInv. > SVD failed for GenInv. > > Error termination via Lnkle in ... > > Can anyone help with the source of this error? > > Thanx> > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye:-:crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Wed Apr 20 18:02:00 2011 From: "errol lewars elewars^trentu.ca" To: CCL Subject: CCL: Any relation between Imaginary frequency and barrier height? Message-Id: <-44440-110420175443-17894-WA20riSxXTvA9mMA+VdWsw ~ server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 20 Apr 2011 17:54:47 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars:+:trentu.ca] Unfortunately, the Table of freqs and energies got scrambled. E. Lewars === errol lewars elewars---trentu.ca wrote: > > Sent to CCL by: errol lewars [elewars!A!trentu.ca] > 2011 April 20 > > Recall that the magnitude of the imaginary frequency is a measure of > the curvature (second derivative of energy with respect to geometry) > of the transition state region along the reaction coordinate. > Intuitively, for a series of related reactions, a small (considering > the real part of the imaginary number) imaginary frequency should > correspond to a low barrier and a large imaginary frequency to a high > barrier (sketch the reaction profiles). In other words, for a low > barier the transition region may be relatively flat. Intuitively. > > Here are some activation energies and TS freqs I quickly did using AM1 > (not very good for energies). The reaction is the Diels-Alder addition > of the dienophile H2C=CH-X with s-cis-1,3-butadiene. All energies in > kJ mol-1. > X activ E TS freq (i units) NH3+ 73 > 801 NO 89 838 NO2 > 90 844 CHO 95 857 OH > 96 937 H 97 921 CN > 98 884 F 104 938 NH2 > 107 885 Cl 109 936 Br > 112 927 > > > E. Lewars > == > > > upendra Adhikari upendra.adhikari.~!~.aggiemail.usu.edu wrote: >> Sent to CCL by: "upendra Adhikari" >> [upendra.adhikari|a|aggiemail.usu.edu] >> Dear all, >> While calculating for the transition state I got different magnitude >> of imaginary frequencies for different methods, in some cases I got >> like -100 cm-1 and for some cases -300 cm-1, so I was wondering that >> is there any relationship between the magnitude of imaginary >> frequency with barrier height or geometry or something like that? >> >> Thank you!! >> >> Upendrahttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> >