From owner-chemistry@ccl.net Mon Dec 22 20:54:00 2008 From: "Tiejun Cheng need47\a/gmail.com" To: CCL Subject: CCL: SYBYL with dual monitors Message-Id: <-38355-081222205216-32230-h+Qq0spj//HnsoJ5P2AkOQ\a/server.ccl.net> X-Original-From: "Tiejun Cheng" Date: Mon, 22 Dec 2008 20:52:10 -0500 Sent to CCL by: "Tiejun Cheng" [need47^gmail.com] Hi, CCLers Recently I equipped my Dell precision p470 workstation with dual monitors, but I found SYBYL software does not work well. Every time at its starting up, the graphic interface will span over two screens (normally should be only one), I need to manually resize the window. Any suggestions to make it easier? Thanks in advance. Jay From owner-chemistry@ccl.net Mon Dec 22 23:58:00 2008 From: "Richard Henchman henchman-*-manchester.ac.uk" To: CCL Subject: CCL: translational entropy and solvation Message-Id: <-38356-081222234637-5818-QC0C/v7tn3S2AwXa3ct9Jw/./server.ccl.net> X-Original-From: "Richard Henchman" Date: Mon, 22 Dec 2008 23:46:33 -0500 Sent to CCL by: "Richard Henchman" [henchman-#-manchester.ac.uk] I am referring to solvation at constant pressure, the conditions under which experiments are usually carried out. The excluded volume in this case would correspond roughly to the shell between the solute's surface (inaccessible to the solvent) and its solvent-accessible surface i.e. the excluded volume is roughly proportional to surface area. This contrasts to the case at constant volume for which the excluded volume would be the entire solvent-accessible volume of the solute (I don't want to get caught up in definitions of exactly where these surfaces lie). As for the 3/2 k versus 5/2 k issue, I agree that the literature seems rather split. To clarify my understanding, the extra entropy, k, often called the communal entropy, would be present in the entropy of a solute in an ideal solution in the thermodynamic limit of large N i.e. one has 5/2 k. It comes from Stirling's approximation of N^N/N!. However, when one considers the partial molar entropy of an ideal solution (dS/dN)_p,T which is the entropic component of the chemical potential, then an extra -k arises and cancels to leave 3/2 k. One usually considers the chemical potential for solvation since the standard Gibbs free energy of solvation equals the difference in chemical potentials of solution and gas phases. This is the case I was referring to in my earlier email. As for cyclohexane, I haven't tried it just yet, but I wouldn't expect it to be too far off. Best wishes, Richard Henchman > "Andreas Klamt klamt%a%cosmologic.de" wrote: > > Sent to CCL by: Andreas Klamt [klamt\a/cosmologic.de] > Just a short reply: > - I personly am not that happy that the cell method always is applied to > aqueous systems. Here we have strong contributions to enthalpy and > entropy for the formation of hydrogen bonds, ... Would your method also > apply for a cylohexane? If yes, what are the results? > - I am confused by your statement that the solute reduces the entropy of > the solvent by the excluded volume: As far as I can see solvation is > usually considered at constant pressure, not at constant volume. It is > assumed that the solvent can get the missing volume elsewhere. > - And I am not happy that you agree with my regarding the 3/2 vs. 5/2 RT > for the translational entropy of a molecule in the gasphase: Meanwhile > Frank Jensen told me that his erratum was wrong and that is should be > 5/2, and he sent me a plausible derivation of that. The Atkins book also > says 5/2. When you look to the internet you find 3/2 and 5/2 about > equally often, and you find nice derivations for both. I am completely > confused now and have to clarify this for myself over Christmas. Is > there a difference in the ensembles considered? I do not find that in > the premisses of the literature derivations. > - I admit that I did not take into account that in a classical ensemble > the reduction of the kinetic energy would correspond to a temperature > decrease. I myself am not sure about the degree of quantum effects here. > Anyway, in a quantum system we cannot do the integrals for position and > momentum separately and the discussion becomes useless. > > I am afraid that at the end of the discussion we will have to admit that > there is no way to define or to measure the translational entropy of a > solute in solution. I only can say that empirically we find the > described significant free energy change of ~3 kcal/mol in the > previously described A + A --> AA reaction, where all surface > proportional, electrostatic, and hydrogen bonding interactions of AA are > just twice those of A. > > Best regards > > Andreas >