From owner-chemistry@ccl.net Tue Jul 14 04:39:00 2009 From: "Kalju Kahn kalju*|*chem.ucsb.edu" To: CCL Subject: CCL: Dipolar interactions in polar medium Message-Id: <-39774-090713135145-4282-WAblihHHRp0J61iRYD+s6w*_*server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 13 Jul 2009 10:51:33 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju\a/chem.ucsb.edu] Mark, The way I usually think about solvent effects is in terms on net dipole moments, not in terms of "bad dipolar interactions". In your case, antiperiplanar conformation has zero dipole moment due to symmetry; synclinal conformer has a dipole moment. Thus, polar solvent stabilizes the synclinal conformation more than it stabilizes the antiperiplanar one, and the energy difference betweeen the two is lowered in polar solvents. A classic example, studied by too many to be named here, is 1,2-dichloroethane (anti and gauche minima, syn rotational saddle point). Best regards, Kalju > For simplicity, assume the compound XCH2CH2Y has two conformers. The > first > conformer has X and Y arranged antiperiplanar. The second conformer has X > and Y synclinal. The relative population of the two conformers in the gas > phase would depend on the dipolar interaction of X and Y. Now assume that > X > and Y were both electronegative and the compound was dissolved in a polar > medium. Would the polar medium stabilize the bad dipolar interaction and > lessen the energy difference between conformers? Or would the polar > medium > exacerbate the situation and increase the energy difference between > conformers? I tend to think the former is true. Is this correct? > > Thanks, > > > Mark > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Tue Jul 14 10:00:01 2009 From: "modeling09 modeling09++chemie.uni-erlangen.de" To: CCL Subject: CCL: Molecular Modeling Workshop and Model(l)ing'09 in Erlangen, Germany Message-Id: <-39775-090714085611-29260-862VEDOYFbUERS9ntaaudQ-#-server.ccl.net> X-Original-From: modeling09 Content-Disposition: inline Content-Type: text/plain; charset="US-ASCII"; format="flowed" Date: Tue, 14 Jul 2009 13:59:50 +0200 MIME-Version: 1.0 Sent to CCL by: modeling09 [modeling09[A]chemie.uni-erlangen.de] Dear list subscribers, this year, the Molecular Modeling Workshop in Erlangen (formerly known as "Darmstadt workshop") takes place Sunday 6th - Monday 7th September 2009 as a satellite meeting to Model(l)ing'09, an international conference on occasion to Tim Clark's 60th birthday. As every year, an interesting and successful workshop depends on your contributions. Therefore let me invite you to submit talks and/or poster titles for the workshop via the registration form http://www.chemie.uni-erlangen.de/modeling09/modeling09_register.php I also want to encourage you to attend Model(l)ing'09 - A Molecular Graphics and Modeling Society (MGMS) International Meeting focussing on all aspects of Computational Chemistry and Drug Design. Abstracts for contributed posters are most welcome! Plenary Speakers at Model(l)ing'09 are: Richard Catlow (London) Andreas Hirsch (Erlangen) Pavel Jungwirth (Prague) Frank Neese (Bonn) Leo Radom (Sydney) Arieh Warshel (Los Angeles) ** The registration for both events is open! ** Please take into account that the deadline for all abstract submissions is Friday 31 July 2009. I am happy to announce that a limited number of bursaries for students is available upon request. Please apply for travel support to modeling09[]chemie.uni-erlangen.de For details about both meetings, especially the **completed list of invited speakers** please visit http://www.modeling09.com I am looking forward to seeing you in Erlangen! -Harald Lanig -- ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 harald DOT lanig AT chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.chemie.uni-erlangen.de/lanig Visit Erlangen - join us at Model(l)ing 2009 http://www.modeling09.com ------------------------------------------------------------------------ From owner-chemistry@ccl.net Tue Jul 14 10:34:01 2009 From: "Giulia Caron giulia.caron%x%unito.it" To: CCL Subject: CCL: OpenCDLig application Message-Id: <-39776-090714102136-13085-+WuMetM5vo1ev41fxcB33A||server.ccl.net> X-Original-From: "Giulia Caron" Date: Tue, 14 Jul 2009 10:21:33 -0400 Sent to CCL by: "Giulia Caron" [giulia.caron]![unito.it] Dear all, I would like to suggest you to have a look at OpenCDLig, a community maintained source of experimental resources (K, the association constant of a CD/L complex and 3D structures) related to cyclodextrin complexes. The application is freely available at https://kdd.di.unito.it/casmedchem More details at the following address http://www.casmedchem.unito.it/how_to_use_.html and in the published paper (Esposito, R.; Ermondi, G. and Caron, G. OpenCDLig: A free web application for sharing resources about cyclodextrin/ligand complexes, Journal of Computer-Aided Molecular Design, 2009 in press) downloadable from http://www.springerlink.com/content/n790525j28227183/ Best regards Giulia Caron From owner-chemistry@ccl.net Tue Jul 14 11:09:00 2009 From: "John McKelvey jmmckel{:}gmail.com" To: CCL Subject: CCL: TD-DFT and what it means... Message-Id: <-39777-090714104512-29307-XaFf6Z8WQoRk3hqJkLYt4w=-=server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=001636e1fd01464e0a046eab6276 Date: Tue, 14 Jul 2009 10:37:54 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel__gmail.com] --001636e1fd01464e0a046eab6276 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Folks, Happy to have input on this.. Would I be wrong in thinking that the use of TDDFT is a little unclear in its current usage? It seems to me that the *default/common* usage means RPA, and means Tamm-Dankoff when specifically described. Cheers, John McKelvey. --001636e1fd01464e0a046eab6276 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Folks,

Happy to have input on this..=A0

Would I be wrong in = thinking that the use of TDDFT is a little unclear in its current usage?=A0= It seems to me that the default/common usage means RPA, and=A0 mean= s Tamm-Dankoff when specifically described.

Cheers,

John McKelvey.
--001636e1fd01464e0a046eab6276-- From owner-chemistry@ccl.net Tue Jul 14 11:44:01 2009 From: "Rebecca C Wade rebecca.wade~!~eml-r.villa-bosch.de" To: CCL Subject: CCL: SDA (Simulation of Diffusional Association) version 5 release Message-Id: <-39778-090714111203-17772-vDRx32rTofxfz+xZIS8+lQ]_[server.ccl.net> X-Original-From: "Rebecca C Wade" Date: Tue, 14 Jul 2009 11:11:59 -0400 Sent to CCL by: "Rebecca C Wade" [rebecca.wade#eml-r.villa-bosch.de] Release of a major new version of the SDA software for the Simulation of Diffusional Association ------------------------------------------------------------------------ We are pleased to announce the release of version 5 of SDA at: http://projects.eml.org/mcm/software/SDA. SDA can be used to simulate the diffusional association of two proteins or other molecules given the atomic structure of the bound complex of the two molecules. SDA can be used to calculate bimolecular association rates, record Brownian dynamics trajectories or encounter complexes and calculate bimolecular electron transfer rate constants. New features in SDA5 include the addition of non-polar desolvation forces to the existent electrostatic forces, and options to compute electron transfer rate constants. These are described in a recent application to study protein-protein electron transfer, see: Gabdoulline RR and Wade RC. On the contributions of diffusion and thermal activation to electron transfer between Phormidium laminosum plastocyanin and cytochrome f : Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events. J. Am. Chem. Soc. (2009) 131 9230-9238. doi:10.1006/jmbi.1999.2919. A number of new analysis tools have been added and the software has been modified for improved flexibility and efficiency. SDA is freely available for academic and non-commercial use and can be downloaded from http://projects.eml.org/mcm/software/SDA. Commercial users may acquire a license. This version of SDA has been developed in the Molecular and Cellular Modeling Group (MCM) at EML Research with the support of the Klaus Tschira Foundation and the Center for Modelling and Simulation in the Biosciences (BIOMS) in Heidelberg. The authors can be contacted through the MCM software manager at: mcmsoft.:.eml-r.villa-bosch.de Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Telephone: +49 (0)6221 - 533 - 279 Fax: +49 (0)6221 - 533 - 298 Rebecca Wade --------------------------------------------------------------- Rebecca Wade Group Leader Molecular and Cellular Modeling EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Germany Tel: +49-6221-533 247 Fax: +49-6221-533 298 Email: rebecca.wade.:.eml-r.villa-bosch.de http://www.eml-r.org/english/homes/wade/ --------------------------------------------------------------- From owner-chemistry@ccl.net Tue Jul 14 14:34:00 2009 From: "VITORGE Pierre 094605 Pierre.VITORGE[-]cea.fr" To: CCL Subject: CCL: pKa calculation of strong acid Message-Id: <-39779-090714142825-30645-iaXKucAK0t9kmO3ETlg+sQ%a%server.ccl.net> X-Original-From: "VITORGE Pierre 094605" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 14 Jul 2009 20:28:08 +0200 MIME-Version: 1.0 Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE[a]cea.fr] Yes using umbrella sampling is certainly a method, but I do not know = whether it will work. HCl/H2O(l) is such a common system that estimation = of its pKa might exist in the literature: in old times people have tried = to make general pKa scales in different solvents -not only water- the = pKa value you are looking might have been estimated this way. When you = wrote below "the pKa in aqueous solution is around -6", where does this = -6 value come from? Isn't it enough for your estimation? Note that 1 = log10 uncertainty on pKa (which is a big uncertainty for solution = chemistry) corresponds to only less that 6 kJ.mol-1, which might be less = than the accuracy of deltaG calculations by molecular modelling in = liquid water. Pierre Vitorge -----Message d'origine----- De=A0: owner-chemistry+pierre.vitorge=3D=3Dcea.fr * ccl.net = [mailto:owner-chemistry+pierre.vitorge=3D=3Dcea.fr * ccl.net] De la part = de Kefa Lu kefa.lu!A!gmail.com Envoy=E9=A0: jeudi 9 juillet 2009 23:53 =C0=A0: VITORGE Pierre 094605 Objet=A0: CCL: pKa calculation of strong acid Sent to CCL by: Kefa Lu [kefa.lu!^!gmail.com] Hi, all, Really appreciate for all the replys. What I actually need to know is the difference of dissociation energy H+ = or binding energy of H+ to Cl- in water and in a protein I'm studying=20 right now. A problem is, HCl usually completely dissociates into H+ and=20 Cl-. So how can I find a way to estimate the free energy of binding a H+ = to Cl-? Just calculate the potential of mean force using umbrella=20 sampling method? Or is there any better idea to do this? Thanks. Kefa VITORGE Pierre 094605 Pierre.VITORGE%a%cea.fr wrote: > Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE*cea.fr] > Dave, > > pKa =3D -6 in aqueous solution, means it cannot be measured. We are = both right: the value cannot be measured, but it might very well be the = good value, which I am explaining below. > > pKa =3D -lgKa is a definition of pKa, where=20 > Ka =3D [H+] [Cl-] / [HCl] > [X] is the concentration of species X, here X is an aqueous specie = (H+, Cl- or HCl). For simplicity I am using concentrations meaning the = (small) activity corrections are included in Ka. > > A first (chemical) meaning of pKa is (pH) half point reaction, namely = for 50% dissociation [Cl-]_1/2 =3D [HCl]_1/2, where subscript _1/2 is to = stress concentrations are for special (chemical) conditions. = Consequently > Ka =3D [H+]_1/2 equivalently > pKa =3D -lg[H+]_1/2 and > pKa=B0 =3D pH_1/2 a well known formula in solution chemistry, where = superscript=B0 is for standard conditions (infinite dilution where = -lg[H+] -> pH) > > In this respect pKa of strong acid has no finite value, since strong = acid means completely dissociated in any chemical conditions, namely = [HCl]=3D0; which is indeed not possible for finite values of Ka. > However, Ka can directly be measured only when the dissociated form = can be detected, typically if the detection limit is 1% only pKa > -2 = can be directly measured, and "no finite value" actually means "> -2". > > (Partial) conclusion: do not write pKa of strong acid; it is chocking = for those who currently measure or use pKas knowing the meanings of the = concept. > > Another meaning of pKa is form thermodynamics: delta_rG =3D -RTlnK = here applied to K =3D Ka. You can very well calculate > delta_rGa =3D G(H+) + G(Cl-) - G(HCl) > (again note they are aqueous species, especially not HCl(g)), where = G(X) can be taken from thermochemical data bases (as G(X) =3D = delta_fG(X)) or calculated by molecular modelling.=20 > Now imagine delta_rGa have been estimated in this way giving pKa=3D-6. = This means that in the most favourable conditions to form HCl, typically = 10 mol.L-1 total HCl concentration, the concentrations of the actual = species in solution would be > [H+] # 10 mol.L-1 > [Cl-] # 10 mol.L-1 > [HCl] =3D 10^-6 mol.L-1, which can probably not be detected, but might = very well exist. The reasoning still stand even for concentrations less = than Avogadro Number per litre, and the result is meaningful: the (Ka) = reaction can be used in thermodynamic cycles, typically with another = acid-base reaction to decide in which way the proton will be = transferred. > > Conclusion: what is your actual problem? Do you really need the pKa of = HCl in liquid water? Or is it only part of your calculations? In this = later case can it be cancelled out by using other calculation = strategies?=20 > This was actually the origin of my remark. > > Pierre Vitorge > > -----Message d'origine----- > De : owner-chemistry+pierre.vitorge=3D=3Dcea.fr*|*ccl.net = [mailto:owner-chemistry+pierre.vitorge=3D=3Dcea.fr*|*ccl.net] De la part = de case case~!~biomaps.rutgers.edu > Envoy=E9 : mercredi 8 juillet 2009 16:44 > =C0 : VITORGE Pierre 094605 > Objet : CCL: pKa calculation of strong acid > > > Sent to CCL by: case [case##biomaps.rutgers.edu] > > On Tue, Jul 07, 2009, VITORGE Pierre 094605 Pierre.VITORGE^^cea.fr = wrote: > =20 >> The pKa of a strong acid have no finite value, namely it does not = exist. >> =20 > > These values certainly exist. For the HCl example that was in the > original post, the pKa in aqueous solution is around -6, although this > seems to have a big uncertainty. You would have to spend some time to > find the original determination -- a secondary reference to start from > would be Albert and Serjeant, "The Determination of Ionization = Constants", > Chapman & Hall, 1984. > > ....dave = casehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spa= mmers.txt > > > -=3Dhis is automatically added to each message by the mailing script = =3D-> > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Jul 14 20:15:01 2009 From: "lyzhao lyzhao++zjnu.cn" To: CCL Subject: CCL: TD-DFT and what it means... Message-Id: <-39780-090714201405-3829-r3AiRm4MFdn8CpDTvPF7/Q-*-server.ccl.net> X-Original-From: "lyzhao" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 15 Jul 2009 08:13:47 +0800 Mime-Version: 1.0 Sent to CCL by: "lyzhao" [lyzhao(~)zjnu.cn] Dear John McKelvey jmmckel{:}gmail.com, Please refer to Chem. Rev. 2005, 105, 4009-4037. Best regards!! ======================================================== -------------------------------------------------------- Youzhao Lan Date:2009-07-15 ======================================================== > From:John McKelvey jmmckel{:}gmail.com Date:2009-07-15 00:20:43 To:Lan, Youzhao Cc: Subject:CCL: TD-DFT and what it means... Folks, Happy to have input on this.. Would I be wrong in thinking that the use of TDDFT is a little unclear in its current usage? It seems to me that the *default/common* usage means RPA, and means Tamm-Dankoff when specifically described. Cheers, John McKelvey.