From owner-chemistry@ccl.net Tue Jun 12 09:19:01 2007 From: "Sergio Emanuel Galembeck segalemb~!~usp.br" To: CCL Subject: CCL:G: Gaussian/NBO/zero and first order perturbational energies Message-Id: <-34464-070612064720-9588-fwbd616JxCCIVBSj8pwLhQ-$-server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Tue, 12 Jun 2007 07:47:11 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb=-=usp.br] Dear David, If you have access to NBO 5.0 you can use the Natural Steric Analysis for the quantification of steric interactions in atoms and molecules. Best regards, Sergio Citando "David Santos Carballal spectrum_dav ~~ operamail.com" : > > Sent to CCL by: "David Santos Carballal" [spectrum_dav-x-operamail.com] > Dear CCL'rs: > The Gaussian output of the NBO's (3.1) just gives the second order > perturbational energies. These energies can be used to quantify > conjugative effects of the molecular systems. > I want to estimate steric repulsions on molecular systems using zero > and first order perturbational energies. > Is this idea correct? > Any suggest to obtain the zero and first order contributions to the > energy in Gaussian are welcome. > David Santos > > -- > _______________________________________________ > Surf the Web in a faster, safer and easier way: > Download Opera 9 at http://www.opera.com > > Powered by Outblaze> > > > From owner-chemistry@ccl.net Tue Jun 12 09:53:00 2007 From: "barry.hardy{=}tiscali.ch" To: CCL Subject: CCL: Screening, ADMET workshops Message-Id: <-34465-070612092448-26430-Hp6hDAVydeF86+p5+KCpxw__server.ccl.net> X-Original-From: Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 12 Jun 2007 15:24:06 +0200 MIME-Version: 1.0 Sent to CCL by: [barry.hardy]*[tiscali.ch] Alongside the eCheminfo Community of Practice meeting at Bryn Mawr College, Philadelphia this year (see link at bottom) we are holding the following two workshops discussing latest methods, applications, best practices for comparative studies and validation, and areas of opportunity for collaboration and cross-sector and international cooperation: Virtual Screening & Docking - Comparative Methodology & Best Practice Forum, Conference Session and Workshop 15-16 October 2007 http://www.echeminfo.com/COMTY_screeningforumbm07 http://barryhardy.blogs.com/cheminfostream/virtual_screening/index.html ADME & Predictive Toxicology Methodology & Best Practice Forum, Conference Session and Workshop 17-19 October 2007 http://www.echeminfo.com/COMTY_admeforumbm07 http://barryhardy.blogs.com/theferryman/toxicology/index.html Both workshops will be supported pre- and post-event by wiki-based material preparation and group communications. best regards Barry Hardy Barry Hardy, PhD Community of Practice Manager Douglas Connect Switzerland Tel: +41 61 851 0170 Latest Advances in Drug Discovery & Development 15-19 October 2007 Bryn Mawr College, Philadelphia, USA Discovery Program and Schedule on Website: http://echeminfo.colayer.net/COMTY_conferencesprog07 Registration: Contact Nicki Douglas, +41 61 851 0461, nicki.douglas (-at-) douglasconnect.com. Academic, early registration (through 30 June) and group discounts are available. From owner-chemistry@ccl.net Tue Jun 12 20:35:01 2007 From: "Chad Risko risko=-=northwestern.edu" To: CCL Subject: CCL: ORCA and ECP basis sets Message-Id: <-34466-070612200237-27063-ey6VUXEDFuv++f3z4s6diQ,+,server.ccl.net> X-Original-From: "Chad Risko" Date: Tue, 12 Jun 2007 20:02:34 -0400 Sent to CCL by: "Chad Risko" [risko^northwestern.edu] As a new user of ORCA, I would like to perform calculations on a small gold-containing system with the LANL2DZ ECP basis set. I noticed in the manual for version 2.6 that ECP basis sets were not included. Is it possible, however, to input manually the basis set (using the %basis section) as obtained from EMSL? Also, what format from EMSL should one choose since ORCA is not currently an option? Thanks! Chad A note to the ORCA website administrators (if they are viewing): I tried submitting a similar question via the ORCA homepage and had the following returned to my email account: Failed to deliver to '' Sender not allowed to use SMTP-Relay Is this a problem on my end? Thanks. From owner-chemistry@ccl.net Tue Jun 12 21:59:01 2007 From: "Gary W Breton gbreton|,|berry.edu" To: CCL Subject: CCL: Limitations of DFT Message-Id: <-34467-070612211534-15218-Mzko45kY7zYPeskfe0v3vw#,#server.ccl.net> X-Original-From: "Gary W Breton" Date: Tue, 12 Jun 2007 21:15:29 -0400 Sent to CCL by: "Gary W Breton" [gbreton a berry.edu] I recently submitted a manuscript for publication revolving around the decomposition of a strained class of heterocyclic compounds. Three potential decomposition mechanisms were proposed. The first mechanism can be ruled out for reasons not important here. The second mechanism (B) is a quasi-concerted elimination (this *could* be symmetrical or asymmetrical...no telling as of yet). The final mechanism (C) occurs via cleavage of one of the strained bonds to form a transient diradical (of unknown lifetime) followed by further bond cleavage to ultimately lead to the same products as would be observed by mechanism A. The experimental results were not conclusive in differentiating beteen the mechanisms, so I proposed in the manuscript that a purely computationally-based follow-up paper on the intermediates, transition states (with IRC calculations), etc. at the DFT B3LYP/6-311+G(d,p) level of theory(a paper I am currently working on) would help to distiguish between the mechanisms. I had used DFT calculations at the same level of theory on a similar class of compounds before (a JOC paper that has been published) and had no problems with reviewers. However, one of the reviewers on *this* manuscript objected to the use of the DFT calculations with the following: "With regards to using DFT calculations to distinguish between mechanisms B and C, I would put no confidence in such a result. It is well known that DFT calculations greatly overemphasize the stabilization provided by delocalization, so they have a built-in bias towards concerted reactions, which is useful if the reaction actually is concerted, but a disaster if it is not." Is this a true statement? And, if so, where can I find more about this limitation of DFT theory? I have searched but come up empty so far. Plus, I'm not sure exactly what the reviewer means, since the diradical intermediate of mechanism C would also be subject to delocalization effects...possibly even greater than those expected by a "concerted" reaction! Also (and I hate the thought of this because I have put so much time into these calculations already) if DFT calculations are NOT sufficient, what should I be looking at? Thanks again for any advice, Gary Breton Berry College (btw...I went 2 years without submitting a question to CCL and now I find myself submitting 2 questions in a week's time!)