From owner-chemistry@ccl.net Sat Mar 10 16:35:01 2007 From: "ebright HMS amber.hms|gmail.com" To: CCL Subject: CCL: ionization state of polyamine compounds Message-Id: <-33774-070308173831-6269-1lsoqi9sL8smx4ng+mCCTw]_[server.ccl.net> X-Original-From: "ebright HMS" Content-Type: multipart/alternative; boundary="----=_Part_248632_8230973.1173389123271" Date: Thu, 8 Mar 2007 16:25:23 -0500 MIME-Version: 1.0 Sent to CCL by: "ebright HMS" [amber.hms%a%gmail.com] ------=_Part_248632_8230973.1173389123271 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCL users: I am simulating a polyamine compound and just wondering how to set the ionization states for polyamine compounds with two amine groups. Should the compound bears a charge of +2 or neutral in a pH 7.4 water solvent. I hope to run docking and dynamic simulations for it binding with DNA. Thanks for any input ! best Yong ------=_Part_248632_8230973.1173389123271 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCL users:

I am simulating a polyamine compound and just wondering how to set the ionization
states for polyamine compounds with two amine groups. Should the compound bears a
charge of +2 or neutral in a pH 7.4 water solvent. I hope to run docking and dynamic
simulations for it binding with DNA. Thanks for any input !

best

Yong



------=_Part_248632_8230973.1173389123271-- From owner-chemistry@ccl.net Sat Mar 10 17:10:00 2007 From: "Qiang Chang qichang#aecom.yu.edu" To: CCL Subject: CCL:G: calculating transition dipole derivative with fchk file form G03 Message-Id: <-33775-070309122842-21686-6EzMuIDat9IbTSE1t7eSYg+*+server.ccl.net> X-Original-From: "Qiang Chang" Date: Fri, 9 Mar 2007 12:28:38 -0500 Sent to CCL by: "Qiang Chang" [qichang||aecom.yu.edu] I am extracting transition dipole derivative from the fchk filr generated by G03. Here are my questions about the fchk file. 1. There is a dipole derivative section in the .fchk file. As I understood, they are the derivatives of the dipole with respect to the Cartesian coordinates of each atom in the molecule. Are the atomic coordinates mass weighted or not? Besides, are the atoms listed in the same order as in the .log file? 2. How are these numbers organized? If there are N atoms in the molecule, then there are 9*N numbers. My understanding is the following. The fisrt 3*N correspond to the derivatives of the x component of the dipole with respect to the 3*N Cartesian coordinates of the N atoms, the next 3*N numbers correspond to the y component, and so on. Among the fist 3*N numbers, the first 3 numbers are the dipole derivatives with respect to the first atom's coordinates, the next 3 numbers are to the second atoms' coordinates, and so on. 3. Are the force constants in .fchk file derivatives with respect to mass-weighted coordinates or not? How are they organized? Is it given as the upper or lower triangular matrix? Is it ordered as the first column, then the 2nd column, and so on? In the .log file, the same force constants matrix is given as a lower triangular matrix. However, I cannot figure out how to match it with the same matrix given in the .fchk file. Thank you very much for the help in advance. Qiang From owner-chemistry@ccl.net Sat Mar 10 17:45:00 2007 From: "Carsten A. Ullrich ullrichc(a)missouri.edu" To: CCL Subject: CCL: Gordon Research Conference on TDDFT, July 15-20, 2007 Message-Id: <-33776-070309130019-5271-Xepe/52SZEji7/uTnHkX+A^^server.ccl.net> X-Original-From: "Carsten A. Ullrich" Date: Fri, 9 Mar 2007 13:00:16 -0500 Sent to CCL by: "Carsten A. Ullrich" [ullrichc(~)missouri.edu] Dear Colleagues: we would like to invite you to participate in a new Gordon Research Conference on Time-Dependent Density-Functional Theory. http://www.grc.uri.edu/programs/2007/timeden.htm July 15-20, 2007 Colby College, Waterville, Maine Chairs: Carsten A. Ullrich and Kieron Burke Co-Chair: Angel Rubio Time-dependent density-functional theory (TDDFT) provides an efficient, elegant, and formally exact way of describing the dynamics of interacting many-body quantum systems, circumventing the need for solving the full time-dependent Schrdinger equation. In the 20 years since it was first rigorously established in 1984, the field of TDDFT has made rapid and significant advances both formally as well as in terms of successful applications in chemistry, physics and materials science. Today, TDDFT has become the method of choice for calculating excitation energies of complex molecules, and is becoming increasingly popular for describing optical and spectroscopic properties of a variety of materials such as bulk solids, clusters and nanostructures. Other growing areas of applications of TDDFT are nonlinear dynamics of strongly excited electronic systems and molecular electronics. The purpose and scope of this Gordon Research Conference is to provide a platform for discussing the current state of the art of the rapidly progressing, highly interdisciplinary field of TDDFT, to identify and debate open questions, and to point out new promising research directions. The conference will bring together experts with a diverse background in chemistry, physics, and materials science. Invited speakers and discussion leaders: Roi Baer Evert J. Baerends Stefano Baroni Andre Bandrauk Harold Baranger Thomas Brabec Mark Casida Roberto Car James Chelikowsky Giulia Galli Fillipp Furche Andreas Goerling E.K.U. Gross Stefan Kurth David Langreth Manfred Lein Neepa Maitra Miguel Marques Nicola Marzari Oleg Prezhdo Lucia Reining Angel Rubio Tamar Seideman Annabella Selloni Tchavdar Todorov Sergei Tretiak Meta van Faassen Troy Van Voorhis Giovanni Vignale Sincerely, ******************************************** Carsten A. Ullrich Assistant Professor Department of Physics & Astronomy University of Missouri Columbia, MO 65211 Phone: (573) 882-2467, Fax: (573) 882-4195 e-mail: ullrichc],[missouri.edu http://web.missouri.edu/~ullrichc Office: 424 Physics ******************************************** From owner-chemistry@ccl.net Sat Mar 10 18:19:00 2007 From: "VITORGE Pierre 094605 Pierre.VITORGE a cea.fr" To: CCL Subject: CCL: free_energy_of_hydration_from_free_energy_of_solvation Message-Id: <-33777-070309224551-12345-LDiCxc5tLExStP5g7nfXCQ*o*server.ccl.net> X-Original-From: "VITORGE Pierre 094605" Date: Fri, 9 Mar 2007 22:19:17 +0100 Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE-.-cea.fr] Solvation (hydration) can be considered as a reaction, namely hydration of A corresponds to Reraction A(g) -> A(sol) Reaction.1 where Notation (g) is for gas phase, while (sol) is for in solution (=solvated), when the solvent is water, a usual notation is (aq). It is not clear what you mean when you wrote "[ delG(hyd) ]" Using Notation delta_solG for Gibs energy of hydration, delta_hydG(A) = G(A(sol) - G(A(g)) Note that delta_hydG(A) = delta_rG(1), which is the Gibbs energy of Reaction.1 For your reactions A+B ---> TS Rreaction.2 TS ---> C Reaction 3 A+B ---> C Reaction 4 you can calculate delta_rG_i(gaz) and delta_rG_i(aq) typically delta_rG_4(gaz) = G(C(g)) - G(A(g))- G(B(g)) delta_rG_4(aq) = G(C(aq)) - G(A(aq))- G(B(aq)) >from linear combinations (= thermodynamic cycles) you can deduce many other equations (and corresponding reactions), typically including delta_rG_4(aq) - delta_rG_4(gaz) = delta_hydG(C) - delta_hydG(A) - delta_hydG(B) Pierre Vitorge l.01.69.08.32.65 http://www.vitorge.name ________________________________ De: nihcho[*]barc.gov.in [mailto:owner-chemistry(a)ccl.net] Date: jeu. 08/03/2007 05:57 =C0: VITORGE Pierre 094605 Objet : CCL: free energy of hydration from free energy of solvation Sent to CCL by: nihcho-*-barc.gov.in Free energy of hydration is nothing but a special case of free energy of solvation, where solvent is water. Free energy of solvation (hydration) generally defined as the change in free energy when a particular species is transfered from vacuum to the splvent (water). This has nothing to do with a reaction. If however you want to calculate change in solvation (or hydration) free energy between the reactant and product, then simply subtract. In case of a reaction, a more important quantity is the potential of mean force (PMF), which is nothing but free energy change as a function of a suitable reaction coordinate or order parameter (which describe the reaction). Hope this will help. Niharendu Choudhury ----------------------------------------- Dr. N. Choudhury Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre Mumbai 400 085 INDIA email: niharc2002%%yahoo.com, niharc2007%%gmail.com, nihcho%%barc.gov.in Quoting "CCL CCL computationalchemist .. gmail.com" : > Dear Friends, > > this may be a naive question, but i'm very new to the field. so, forgive me > if i'm wrong. > > I was struggling with a problem, since morning. Could be fine if any one > helps me to come out. > > I, have a system say,, A+B ---> TS ---> C > > I computed the free energy of solvation [ delG(solv) ] for all these species > ( chemsol - online programe) and they are ( solvent being water), > > A = -19.9 > B = -9.6 > TS = -36.3 > C = -50.9 > My question is how to calculate free energy of hydration, [ delG(hyd) ] > from these value. > > Any pointers or suggestions will be greatly apprciated. > > > > > > -- > Regards, > Dr. Sanjay >