From owner-chemistry@ccl.net Fri Dec 12 02:57:01 2008 From: "Andreas Klamt klamt/./cosmologic.de" To: CCL Subject: CCL: translational entropy in solution Message-Id: <-38289-081212024612-18496-AmWkR+T1F+H5JrNJXTJ9GA[-]server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 12 Dec 2008 08:45:54 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt%a%cosmologic.de] > > Let us for a moment assume that A = B i.e. consider > >> A +A --> AA >> >> and the interactions and surface of AA are just twice the interactions >> of A. We may consider the case of 2 cyclohexane molecules getting bound >> together by a virtual stiff bond which is long enough so that there are >> no relevant interactions between the 2 parts. In the gasphase this leads >> to a large loss of free energy due to the loss of the translational and >> rotational free energy (not just entropy) of one of the particles >> > > Actually if there is a loss in the entropy of the system its free energy increases: > > dG = dH - TdS > dS < 0 , dG increases. > Sorry for being a little unprecise here regardig the sign, but I think it is clear what I am talking about. > Also, there is an increase in the enthalpy of the system(considering that no kind of interaction is going on between A and A,what is quite contradictory anyway) after the reaction. The new vibrational modes in AA are going to have a zero point energy that is bigger than the rotational and translational energies of the reagents, increasing the enthalpy of the system, which is another reason for an increase in G and for this reaction to be non-spontaneous > > >> I believe that the physics is correct here. The solvent definitely >> reduces the motional (kinetic) phase space. The molecules cannot move >> and rotate as freely as they can in the gasphase, and hence the part of >> the free energy arising from the integration over momentum and >> rotational momentum must be reduced in solution. Obviously, and here I >> agree with the other people in the discussion, the solute can take all >> positions and orientations, as in the gasphase, and hence the free >> energy arsing from these integrals are the same as in the gasphase. >> > > Actually, although the solute can take all positions and orientations, in solution some of these are going to be very disfavored energetically, while others are going to be more favored, and that is introduced by the term U (potential energy) in the integral used to calculate the molecular partition function. So the molecular partition function is not going to be the same as in the gas phase. > Indeed, I mentioned this in the next partof my last CCL entry (see below) . My argument is that these contributions are unlikely to cancel. Indeed, I have no estimate which contribution is stronger. We have no chance to sest that, because my virtual case of a dimerization with a virtual long connection between the two parts will never be realized in nature. Association here alway goes along with interactions and hence with large changes in the interaction integrals. Usually the overall external polarity of the dimer will be strongly reduced in association. Hence we will never be able to proof my arguments in reality. > > >> Obviously, in reality, if we generate real close contact associates or >> even product molecules, the loss of the external degrees of freedom will >> be partly compensated by additional internal vibrational modes. But it >> is unlikely that this exactly matches the loss of external degrees of >> freedom. Please note, that usually the change in the vibrational free >> energies upon solvation is parameterized int the surface proportinal >> part of solvation models, i.e. the non-electrostatic parts. >> > > Non-electrostactic contributions in most of the solvent models also(actually they should, but in most cases don't) account for the change in all of the other components of free energy. What about COSMO-RS? I don't have access to your book and I'm going to read a paper on COSMO-RS soon, but I'm very curious on the physical foundations of the 2 extra terms (the one proportional to lnV and the one that depends on the temperature) you've mentioned. Where does these terms come from? What is parametrized in the model? > There are typically 3 contributions to the non-electrostatic terms: 1) the "cavitation energy" often expressed as a kind of solvent specific surface tension. This part is not required in COSMO-RS but it automatically aises from the statistical thermodynamics for the slute and solvent surface interactions. The free energy required to break the solvent-solvent contacts in order to enable solute-solvent contacts automatically and termodynamically consistently follows rom that. Hence COSMO-RS does not need such a thing as a solvent surface tension: This automatically follows from the sigma-profile (COSMO charges) of the solvent. 2) the non-electrostatic interactions: The hydrogen bond interations in COSMO-RS are part of the surface interations taken into account in the statistical thermodynamics, quantified approximately based on the surface polarities (COSMO polarization charge densities) of donor and acceptor. The vdW-interactions are the weekest part of COSMO-RS: They are just taken into account as surface proportial with element specific vdW-surface tensions (one of the 2 element specific parameters of COSMO-RS, the other being the element specific radius). We assume that the the vdW-interactions have a generic temperature dependence (hence a split into enthalpic and entropic contributions). Other solvation models need to parameterize all this into empirical corrections or solvent specific radii scaling, ... > >> This >> allows for the treatment of phase diagrams, vapor pressures, .... the >> entire fluid phase equilibrium thermodynamics. And in difference to >> dielectric solavtion models COSMO-RS yields entropic and enthalpic >> contributions of the solvation energy (because it does a statistical >> thermodynamics!!!) For example, it correctly describes the solvation of >> alkanes n water as a mainly entropic effect, in best agreement with the >> experiment. >> > > Do you mean that COSMO-RS yields each component(translational/rotational/vibrational/electronic) of entropy and enthalpy or that it only separates the free energy of solvation in enthalpy and entropy contributions? No, COSMO-RS does not yield all the contributions separately. What we can separate are the electrostatic, hydrogen bonding and vdWs contribution to the interaction enthalpy. The other components are essentially parameterized into the few adjusted pareters of COSMO-RS. Since there is no fundamental theory of the translations, rotations and vibrations in solution, there is no chance to do this rigorously. And fitting to exp. free energies of solvation does not allow us to split the contributions with respect to the physical origin. But we can quite clearly say that we find a significant (~3 kcal/mol at 298 K) contribution to the free energy of solvation which is directly connected to the molecule and not indirectly via its interactions and surface. Best regards Andreas -- -------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt.:.cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------- Please note our COSMO-RS Symposium in 2009 (For details see: http://www.cosmologic.de/Symposium/symposium.html) From owner-chemistry@ccl.net Fri Dec 12 14:56:00 2008 From: "John McKelvey jmmckel/./gmail.com" To: CCL Subject: CCL: Hard drives and linux Message-Id: <-38290-081212141607-29268-wVy+niNOuqFBnw2vsON/jQ a server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_5839_21937730.1229109354705" Date: Fri, 12 Dec 2008 14:15:54 -0500 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel]![gmail.com] ------=_Part_5839_21937730.1229109354705 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline CClers, Hopefully this is not too far out of CCL's area, but then again, many of have to be [seudo sys mgr at the same time. I am starting to run MP2 geometry optimizations, and there ia a lot of disk use, and I want to either stripe disks or use a 10KRPM scratch drive. The Western Digital "green" 10KRPM drives have been recommended, and fewer drives are advantageous... HOWEVER, WD says that they do not support Linux [their drives SATA II 300GBS _can_ be used if the drive is jumpered, which knocks it down to a 150GBS capability. Thoughts/experience anyone? Many thanks, John McKelvey ------=_Part_5839_21937730.1229109354705 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline CClers,

Hopefully this is not too far out of CCL's area, but then again, many of have to be [seudo sys mgr at the same time.  I am starting to run MP2 geometry optimizations, and there ia a lot of disk use, and I want to either stripe disks or use a 10KRPM scratch drive.  The Western Digital "green" 10KRPM drives have been recommended, and fewer drives are advantageous... HOWEVER, WD says that they do not support Linux [their drives SATA II 300GBS _can_ be used if the drive is jumpered, which knocks it down to a 150GBS capability.

Thoughts/experience anyone?

Many thanks,

John McKelvey



------=_Part_5839_21937730.1229109354705-- From owner-chemistry@ccl.net Fri Dec 12 15:42:01 2008 From: "Marek Freindorf mfrein.:.ccr.buffalo.edu" To: CCL Subject: CCL: Workshop on electronic structure calculations Message-Id: <-38291-081212153253-11784-tIejHE0Rmi7+0SQBFBOLtA||server.ccl.net> X-Original-From: Marek Freindorf Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 12 Dec 2008 15:32:33 -0500 MIME-Version: 1.0 Sent to CCL by: Marek Freindorf [mfrein%ccr.buffalo.edu] Dear colleague, Q-Chem Inc. would like to invite you to a workshop entitled "Quantum leap into the future: advances in methods and applications of electronic structure calculations". At the workshop, leaders in academia and industry will present new and improved computational methods for a wide range of chemical and biological applications. In addition, a hands-on training session, a poster session, and dinner will provide ample opportunities to meet these experts and learn the basic and advanced features of the state-of-the-art computational tools in soon-to-be-released Q-Chem 3.2. Q-Chem is a leading ab initio electronic structure program, with capabilities ranging from the highest performance density functional theory/Hartree-Fock (DFT/HF) calculations to high level post-HF correlation methods to combined quantum mechanical/classical mechanical (QM/MM) calculations. The two-day workshop will take place on the 19th and 20th of March, 2009, in the Pittsburgh Supercomputer Center, Pittsburgh, PA. Register by January 19th and receive a free one year group license for new customers, or a free upgrade for existing customers. Please visit the workshop home page for details (http://www.q-chem.com/ws_hh.html). Invited speakers (in alphabetical order): * Dr. Shawn Brown (Pittsburgh Supercomputer Center): Quantum simulations on supercomputers * Dr. Dan Cheney (Bristol-Myers Squibb): Comparison of correlated methods in the context of computer-aided drug design * Prof. Peter Gill (Australian National University): EDF1, EDF2 functionals, maximum overlap method for converging SCF calculations, fast HF for large basis sets * Prof. Martin Head-Gordon (UC Berkeley): New development in DFT functionals, and post-HF correlations including various MP2, active space and local methods * Prof. John Herbert (Ohio State University): Ab initio dynamics and excited states calculation * Dr. Jing Kong (Q-Chem Inc.): DFT with dispersion and fast DFT algorithms * Prof. Anna Krylov (University of Southern California): New development in coupled-cluster theory * Dr. Joerg Kussman (Pennsylvania State University): NMR for large structures * Dr. Lee Woodcock (NIH): QM/MM with CHARMM * Prof. Yingkai Zhang (New York University): QM/MM with Tinker I apologize if you have received multiple copies of this email. We look forward to seeing you at the workshop. Sincerely, Jing Kong, Ph.D. CEO & Chief Scientist From owner-chemistry@ccl.net Fri Dec 12 16:17:00 2008 From: "anjan roy aroy25_+_gmail.com" To: CCL Subject: CCL:G: Gaussian on the fly increase processors Message-Id: <-38292-081212132646-11389-wIt+MJArtDZOy/rZCx+OLA(_)server.ccl.net> X-Original-From: "anjan roy" Date: Fri, 12 Dec 2008 13:26:42 -0500 Sent to CCL by: "anjan roy" [aroy25() gmail.com] Hi, I am doing a TD-DFT gaussian calculation and would like to increase the number of processors (from 4 to 8) while the job is running( or pause it, modify it and run it). Is this possible? how? Thank you in advance Anjan