From owner-chemistry@ccl.net Sun Jun 7 01:41:01 2009 From: "Yutao Yue yutao.yue(~)gmail.com" To: CCL Subject: CCL: PH-dependent ab-initio calculations Message-Id: <-39459-090607010757-11983-+pru4QUvyy939xBuOOOiAQ!^!server.ccl.net> X-Original-From: Yutao Yue Content-Type: multipart/alternative; boundary=0016e6464ee282a154046bba19a0 Date: Sat, 6 Jun 2009 23:55:42 -0400 MIME-Version: 1.0 Sent to CCL by: Yutao Yue [yutao.yue_._gmail.com] --0016e6464ee282a154046bba19a0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thank you both very much dear Andreas and Walter, the information is very helpful and after some readings (COSMOtherm theory intro and Karlsberg website are awsome!) now I have a much more clear idea about what and how one can do about the problem. Is it true that for those molecules without any chance of grabbing and releasing H+ (protonation state) or OH- (not sure how to name that), the pH of solvent has no influence on the properties of the molecule? Or maybe som= e but limited influence? If otherwise what kind of influence would it be? (I assume that solvent are always neutral while separate charges H3O+ and OH- have very low concentration comparing to the solvent itself) On the other hand, for molecules like individual amino acids or proteins, other than adding/subtracting H+/OH- to the chemical structure of the molecules (and the subsequent changes in structures and other properties), are there any other significant influence of pH on the molecules? Sorry for bringing up more questions and I really appreciate your time and help. Regards, Yutao Yue On Fri, Jun 5, 2009 at 2:19 AM, Andreas Klamt klamt++cosmologic.de < owner-chemistry*o*ccl.net> wrote: > > Sent to CCL by: Andreas Klamt [klamt(a)cosmologic.de] > Dear Yutao, > > pH-dependent ab-initio calculations in general are impossible. The pH of > the solvent does change the equilibrium between protonated and > deprotonated species, but you will always have to decide which species > you want to consider in your ab-initio calculation. (in the following I > assume that you mean generally QM methods, including DFT, when you say > ab-initio). Beyond the H3O+ and OH- concentrations, which anyway are > very small, the pH does not change the solvent properties significantly. > I.e. what you need to do is to calculate the protonated and deprotonated > species in your solvent (usually water) using a good solvation model, > calculate the pKa from the free energy difference of both solvated > species, and then calculate the population of the species at a given pH. > > Our COSMOtherm program in combination with a QM propgram being able to > write the required DFT/COSMO files, e.g. TURBOMOLE, does provide the > infrastructure to do so, not only in water but in any solvent. > > Andreas > > Yutao Yue Yutao.Yue*_*gmail.com schrieb: > >> Sent to CCL by: "Yutao Yue" [Yutao.Yue^_^gmail.com] >> Hello dear friends, does anybody know how to do an ab-initio calculation >> of a molecular system under a certain PH value? Has there been much >> development on PH-dependent ab-initio methods? Maybe some PH-dependent >> empirical methods? Thanks for any information. >> >> Regards, >> Yutao Yue >> >> > > -- > PD. Dr. Andreas Klamt > CEO / Geschaeftsf=FChrer > COSMOlogic GmbH & Co. KG > Burscheider Strasse 515 > D-51381 Leverkusen, Germany > > phone +49-2171-731681 > fax +49-2171-731689 > e-mail klamt|*|cosmologic.de > web www.cosmologic.de > > HRA 20653 Landgericht Koeln, GF: Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Landgericht Koeln, GF: Dr. Andreas Klamt > > > > > - This is automatically added to each message by the mailing script -http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --0016e6464ee282a154046bba19a0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thank you both very much dear Andreas and Walter, the information is very h= elpful and after some readings (COSMOtherm theory intro and Karlsberg websi= te are awsome!) now I have a much more clear idea about what and how one ca= n do about the problem.

Is it true that for those molecules without any chance of grabbing and = releasing H+ (protonation state) or OH- (not sure how to name that), the pH= of solvent has no influence on the properties of the molecule? Or maybe so= me but limited influence? If otherwise what kind of influence would it be? = (I assume that solvent are always neutral while separate charges H3O+ and O= H- have very low concentration comparing to the solvent itself)

On the other hand, for molecules like individual amino acids or protein= s, other than adding/subtracting H+/OH- to the chemical structure of the mo= lecules (and the subsequent changes in structures and other properties), ar= e there any other significant influence of pH on the molecules?

Sorry for bringing up more questions and I really appreciate your time = and help.

Regards,
Yutao Yue

On= Fri, Jun 5, 2009 at 2:19 AM, Andreas Klamt klamt++cosmologic.de <owner-chemistry*o*ccl.net> wrote:

Sent to CCL by: Andreas Klamt [klamt(a)cosmologic.de]
Dear Yutao,

pH-dependent ab-initio calculations in general are impossible. The pH of the solvent does change the equilibrium between protonated and
deprotonated species, but you will always have to decide which species
you want to consider in your ab-initio calculation. (in the following I
assume that you mean generally QM methods, including DFT, when you say
ab-initio). Beyond the H3O+ and OH- concentrations, which anyway are
very small, the pH does not change the solvent properties significantly. I.e. what you need to do is to calculate the protonated and deprotonated species in your solvent (usually water) using a good solvation model,
calculate the pKa from the free energy difference of both solvated
species, and then calculate the population of the species at a given pH.
Our COSMOtherm program in combination with a QM propgram being able to
write the required DFT/COSMO files, e.g. TURBOMOLE, does provide the
infrastructure to do so, not only in water but in any solvent.

Andreas

Yutao Yue Yutao.Yue*_*gmail.= com schrieb:

Sent to CCL by: "Yutao =A0Yue" [Yutao.Yue^_^gmail.com]
Hello dear friends, does anybody know how to do an ab-initio calculation of= a molecular system under a certain PH value? Has there been much developme= nt on PH-dependent ab-initio methods? Maybe some PH-dependent empirical met= hods? Thanks for any information.

Regards,
Yutao Yue



--
PD. Dr. Andreas Klamt
CEO / Geschaeftsf=FChrer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone =A0 +49-2171-731681
fax =A0 =A0 +49-2171-731689
e-mail =A0klamt|*|cosmol= ogic.de
web =A0 =A0 www.cosm= ologic.de

HRA 20653 Landgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Landgericht Koeln, GF: Dr. Andreas Klamt




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--0016e6464ee282a154046bba19a0-- From owner-chemistry@ccl.net Sun Jun 7 03:00:01 2009 From: "Kalju Kahn kalju!^!chem.ucsb.edu" To: CCL Subject: CCL: unit conversion of force constant Message-Id: <-39460-090607025020-12633-lbfEz6gawauIZ6g78jPxAA^server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 6 Jun 2009 23:50:11 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju**chem.ucsb.edu] Aneesh, This is how I calculate wave numbers from force constants: Ang_per_Meter = 1e+10 amu = 1.660538782e-27 lightspeed = 29979245800 # [cm /s ] omega = sqrt(fc_J_ang2 * Ang_per_Meter * Ang_per_Meter / amu ) waven = omega / ( 2 * pi * lightspeed ) You need to solve this for fc_J_ang2 in terms of waven, I suppose. Kalju > > Sent to CCL by: "anessh cna" [aneeshcna%%gmail.com] > Dear CCL users, > I am doing vibrational analysis for calculating the bond and angle > force constant for developing force field parameters for an > organic molecule. Can anyone help me in converting the force > constant in N/m to kJ/mol/A**2 or kJ/mol/rad**2 ?. Here I am tring > to calculate force constant from frequencies. > > Thanks in advance > > Aneesh > aneeshcna^^gmail.com> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Sun Jun 7 12:51:00 2009 From: "Soaring Bear soaringbear*yahoo.com" To: CCL Subject: CCL: Database of Natural substrates Message-Id: <-39461-090605170151-29209-AA+PzJeLLvMgYVhXJU78SQ,,server.ccl.net> X-Original-From: Soaring Bear Content-Type: text/plain; charset=us-ascii Date: Fri, 5 Jun 2009 13:01:21 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Soaring Bear [soaringbear ~~ yahoo.com] > Sent to CCL by: Iain Wallace [iain.m.wallace-,-gmail.com] > I was wondering if anybody knows of a database where I > could get a list/structures of natural substrates (not > products), like ATP or ethanol. > I am trying to separate a list of compounds into natural > substrates or not from the STITCH database. > The closest I could find is the BRENDA database, but that > is proving to be quite hard to parse, and the ZINC database > doesn't have anything like this. sounds like you're looking for PDB-Ligand http://pmid.us/15608186 Soaring Bear Ph.D. Pharmacology soaringbear at yahoo.com http://soaringbear.com/nature/WeedsforNeeds.html http://www.nlm.nih.gov/mesh/presentations/bear_2005_aug/index.htm author of http://HerbMed.org From owner-chemistry@ccl.net Sun Jun 7 14:50:01 2009 From: "li_qiang_000739::wuxiapptec.com li_qiang_000739::wuxiapptec.com" To: CCL Subject: CCL: Do you have the experience about Stereo LCD monitor for molecular modeling? Message-Id: <-39462-090607042546-29114-eGV+40BO/Usxv32d4ASUvw%server.ccl.net> X-Original-From: "li_qiang_000739 .. wuxiapptec.com" Content-Language: zh-CN Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Sun, 7 Jun 2009 15:53:14 +0800 MIME-Version: 1.0 Sent to CCL by: "li_qiang_000739-x-wuxiapptec.com" [li_qiang_000739-x-wuxiapptec.com] Dear all, Do you have the experience about Stereo LCD monitor for molecular modeling? We have a Samsung(r) SyncMaster 2233RZ 120 Hz LCD display, its resolution i= s 1680x1050. The signal input is DVI-DL. I try the LCD on one HP Xw6600 workstation with Quadro FX3700 graphics card= . The operation system is CentOS 5.3, so I update the latest nVidia driver = and set the xorg.conf with " Option "stereo" "3"". But I can get the hardware stereo in our modeling software. Who can tell me how to do it? Thank you for advance. Best regards, Li Qiang CADD Laboratory WUXI AppTec Co., Ltd. E-mail: li_qiang_000739/a\wuxiapptec.com Address: No.1 Building, 288 Fute Zhong Road, WaiGaoQiao Free Trade Zone, Shanghai, P.R.China PostCode: 200131 Tel: 86-21-50463316 Fax: 86-21-50461000 Web Site: www.wuxiapptec.com Save paper. Protect the environment. Print only when necessary. This e-mail transmission may contain confidential or legally privileged inf= ormation belongs to WuXi AppTec Co., Ltd. The content of this transmission = is intended only for the individual or entity named in the e-mail address. = If you are not the intended recipient, you are hereby notified that any dis= closure, copying, distribution, or reliance upon the content of this e-mail= is strictly prohibited. If you have received this e-mail transmission in error, please reply to sen= der so that we can arrange correct delivery. Then please delete this messag= e from your inbox. From owner-chemistry@ccl.net Sun Jun 7 15:25:02 2009 From: "Jesus Planesas planesaj~~hotmail.com" To: CCL Subject: CCL: Docking-scoring functions Message-Id: <-39463-090607065714-25506-RwfKvVQGXEpiuB5zSlYXlw]=[server.ccl.net> X-Original-From: "Jesus Planesas" Date: Sun, 7 Jun 2009 06:57:11 -0400 Sent to CCL by: "Jesus Planesas" [planesaj*hotmail.com] Dear all Before starting to dock a chemical library of potential ligands with MOE (chemcorp.com) I'm trying to evaluate the best docking/scoring MOE function using a set of ligands with known experimental IC_50. Anybody knows and article or a detailed job where I can see step by step an exemple of one evaluation like this? And if it's done with MOE it'll be fantastic Thanks Jesus