From owner-chemistry@ccl.net Sat Aug 21 07:58:00 2010 From: "Emran Heshmati heshmaty*o*yahoo.com" To: CCL Subject: CCL:G: Linux Message-Id: <-42576-100821075144-8262-7+/FsjijJ+2kxAHZs6YdbA:_:server.ccl.net> X-Original-From: Emran Heshmati Content-Type: multipart/alternative; boundary="0-2112713401-1282391499=:63336" Date: Sat, 21 Aug 2010 04:51:39 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Emran Heshmati [heshmaty,,yahoo.com] --0-2112713401-1282391499=:63336 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Daer friends=20 I want to work with GAUSSIAN 03 under Linux. which version of Linux is more= suitable? Best Regards Emran Heshmati P Save a tree... please don't print this e-mail unless you really need to =0A=0A --0-2112713401-1282391499=:63336 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Daer friends
I want to work with GAUSSIAN 03 under Linux. which version of = Linux is more suitable?

Best Regards
Emran = Heshmati
P Save a tree... please don't print this e-mail unless y= ou really need to


--0-2112713401-1282391499=:63336-- From owner-chemistry@ccl.net Sat Aug 21 08:33:00 2010 From: "Laxman Pandey lpandey**gmail.com" To: CCL Subject: CCL: Confirmation search utility Message-Id: <-42577-100820195621-25671-sSf71vWAguoQUUQXXAHEzw^-^server.ccl.net> X-Original-From: Laxman Pandey Content-Type: multipart/alternative; boundary=0016364ec7ae4e9b96048e4a0b8c Date: Fri, 20 Aug 2010 19:56:15 -0400 MIME-Version: 1.0 Sent to CCL by: Laxman Pandey [lpandey|,|gmail.com] --0016364ec7ae4e9b96048e4a0b8c Content-Type: text/plain; charset=ISO-8859-1 Hello, I am extremely sorry if this has already been mentioned in the forums (I googled it a few times but it did not lead me in the right direction). I am trying to find different confirmations for a floppy molecule and was wondering if there is a utility available that gives a number of confirmations using simple Molecular Mechanics or Semi-empirical methods. Regards, Laxman Pandey --0016364ec7ae4e9b96048e4a0b8c Content-Type: text/html; charset=ISO-8859-1 Hello,

I am extremely sorry if this has already been mentioned in the forums (I
googled it a few times but it did not lead me in the right direction). I am
trying to find different confirmations for a floppy molecule and was
wondering if there is a utility available that gives a number of
confirmations using simple Molecular Mechanics or Semi-empirical methods.

Regards,
Laxman Pandey --0016364ec7ae4e9b96048e4a0b8c-- From owner-chemistry@ccl.net Sat Aug 21 09:08:01 2010 From: "Fuming Ying fmying(_)gmail.com" To: CCL Subject: CCL: MD and MC computations in GAMESS-US Message-Id: <-42578-100821032126-22397-ADPZSnZBydNLOQx1ls+izg===server.ccl.net> X-Original-From: "Fuming Ying" Content-Type: multipart/alternative; boundary="====003__MESSAGE__ID__54yg6f6h6y456345====" Date: Sat, 21 Aug 2010 00:21:19 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Fuming Ying" [fmying- -gmail.com] --====003__MESSAGE__ID__54yg6f6h6y456345==== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 SGVqLA0KSSB3YW50IHRvIGRvIE1EIGFuZCBNb250ZSBDYXJsbyhNQykgY2FsY3VsYXRpb25zIHdp dGggR0FNRVNTLVVTIHBhY2thZ2UgZm9yIHNtYWxsIG1vbGVjdWxlcywgaS5lLiBMaUYgaW4gd2F0 ZXIgY2x1c3RlcnMuIFdhdGVyIG1vbGVjdWxlcyBhcmUgdHJlYXRlZCBhcyBFRlAgYW5kIExpRiBp cyB0aGUgUU0gcGFydC4gVGhlcmUgYXJlIHNvbWUgcXVlc3Rpb25zIHRoYXQgSSdtIG5vdCBzdXJl 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[elsayed.elmes^^^yahoo.com] Dear CCL community, With regard the cluster solvated transition metal ion like Cu(II) or Zn (II) or other TM ion in the first row of TM series, I suggest that the maximum number of H2O molecules which may form the first solvation shell is equal to the largest coordination number of these metal ions, and any further water molecules will form a secondary solvation shell. It is known in aqueous solution metal ion of late first row TM form octahedral structures especially with water molecules [M(H2O)6]2+, so it is expected that the first solvation shell is the first coordination sphere. Your comments about this suggestion would be helpful and appreciated. Thanks for help Sayed ------------------------------ Sent to CCL by: "Sayed Mesa" [elsayed.elmes*yahoo.com] Dear Andreas, John and all I am very thankful for wise answer from Andreas. Also, I would like to thank John. I have still question about how can I know 4 waters molecules are enough to form metal-water cluster? I looked for literature and I found a related paper: "Ab Initio Study of M+:18-Crown-6 Microsolvation" J. Phys. Chem. A 1997, 101, 2723-2731. Unfortunately, studied metals in this paper do not include transition metal. For transition metal like Zn (II) or Ni (II) how can I define number of solvated water molecules? Thanks in advance Sayed ------------------------------------ >Sent to CCL by: John McKelvey [jmmckel,+,gmail.com] I certainly am no expert on this, but first, when investigating reaction energies geometries should be optimized and zero-point point vibrational energies should be computed. As to COSMO-RS, special software from Andreas Klamt at Klamt(-)Cosmologic.de is needed. (I forwarded your original message to him but he is traveling and will likely get back to you later.) However, COSMO solvation energies can be computed in several programs; the program(s) available to you is not stated. Best regards, John McKelvey. ---------------------------------------- >Sent to CCL by: Andreas Klamt [klamt|-|cosmologic.de] Dear Sayed, since I was in holidays, I am answering delayed: Let me first say that your are not using COSMO-RS in Gaussian, but just used the keyword COSMO-RS!!!. Gaussian never had a COSMO-RS module. It just had a COSMO-RS, which did the settings of C-PCM in a way, that it finally was writing COSMO files, which could be post-processed by our COSMO-RS program COSMOtherm. COSMO-RS itself is a thermodynamic postprocessing of COSMO calculations for solutes and solvents, which yields the chemical potential of the almost arbitrary solvutes X in pure and mixed solvents as a function of concentration and temperature. For more information about COSMO-RS see our homepage www.cosmologic.de, or my book "COSMO-RS: > From quantum chemistry to fluid phase thermodynamics and drug design", Elsevier, 2005. Regarding your questions: 1) Yes, the scenario seems to be right, if the the metal in the metal-ligand is no longer solvent exposed, and if your metal-water cluster is sufficiently large to prevent solvent exposition of the metal. I am not sure whether 4 waters are enough. 2) You need to do geometry optimization in solution separately! At the end you should follow the scheme for reaction calculations, which I proposed several times here in CCL, i.e. - calculate the gasphase reaction at high level, incl. vibr. corrections. - add dG of solvation (from COSMO-RS or from another solvation model) for educts and products - for dH do the same, i.e. first calculate it in the gasphase and then take dH of solvation from COSMO-RS and add it on both sides. Please note that only COSMO-RS gives both, dG and dH od solvation separately. Other solvation models just give dG of solvation. Please also note, that by calculating vibrational corrections explicitly in solution does not work, as pointed out a few times in CCL. Regards Andreas From owner-chemistry@ccl.net Sat Aug 21 11:02:00 2010 From: "errol lewars elewars+*+trentu.ca" To: CCL Subject: CCL: Confirmation search utility Message-Id: <-42580-100821103053-19776-HVHmSqU/0XKcEjNkXQkdcw##server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 21 Aug 2010 10:30:46 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars%%trentu.ca] 2010 August 21 I think several of the well-known program suites can perform systematic (stepwise rotation about C-C bonds) and Monte Carlo conformation searches; check their prospectuses online. PCModel (Serena Software) can (still?) do a stochastic MM search for the global minimum of a small molecule. E. Lewars == Laxman Pandey lpandey**gmail.com wrote: > Hello, > > I am extremely sorry if this has already been mentioned in the forums (I > googled it a few times but it did not lead me in the right direction). > I am > trying to find different confirmations for a floppy molecule and was > wondering if there is a utility available that gives a number of > confirmations using simple Molecular Mechanics or Semi-empirical methods. > > Regards, > Laxman Pandey