From owner-chemistry@ccl.net Wed Jun 22 03:31:01 2011 From: "Bonoit Bonoit bonoit_10%%yahoo.fr" To: CCL Subject: CCL: Entropy Message-Id: <-44946-110622032815-30506-dI/TWcPS7EK556KuJCIj9w+*+server.ccl.net> X-Original-From: "Bonoit Bonoit" Date: Wed, 22 Jun 2011 03:28:13 -0400 Sent to CCL by: "Bonoit Bonoit" [bonoit_10[]yahoo.fr] Hello everyone, I'm writing to enquire about the negative values of the thermodynamic data of entropy (S) for some species especially in aqueous systems. My question is as follow; Why we have this negative sign? i mean what is the origin of this? What is the significance of such value of S? It can be just equal or greater than zero? Thank you. Bonoit From owner-chemistry@ccl.net Wed Jun 22 04:54:00 2011 From: "Andreas Klamt klamt[*]cosmologic.de" To: CCL Subject: CCL: Entropy Message-Id: <-44947-110622043532-14133-MFxjwMaRh9khpMkFV4usLw(a)server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 22 Jun 2011 10:35:23 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt[a]cosmologic.de] Dear Benoit, I guess you talk about alkane-like compounds in water. The free energy of transfer of alkane from its neat liquid to water is known to be a large negative value (corresponding with the low solubility of alkane in water) and it is known to be entirely entropic. The later is obvious > from the fact that the solubility of alkanes in water has a minimum at about room temperature, which means that dH is zero and dG is entirely -TdS. Within the COSMO-RS model this entropy loss of alkane in water is just (predictively!) explained by the fact that the non-polar surface segments of alkane can only slect the very few non-polar surface segments of water as partners, and selection of a small number out of a large means strong loss of entropy. (See e.g. A. Klamt, Fluid Phase Equilibria 206 (2003) 223–235 Prediction of the mutual solubilities of hydrocarbons and water with COSMO-RS ) In the molecular dynamics and MC simulation world the same fac is explained in more nebulous words as the change of the water structure close to the surface of non-polar molecules. Anyway, i am sure that this is the reason for the negative entropy of alkanes in water, obviously depending on the reference state for defining the S=0. Andreas Am 22.06.2011 09:28, schrieb Bonoit Bonoit bonoit_10%%yahoo.fr: > Sent to CCL by: "Bonoit Bonoit" [bonoit_10[]yahoo.fr] > Hello everyone, > I'm writing to enquire about the negative values of the thermodynamic data of entropy (S) for some species especially in aqueous systems. > My question is as follow; > Why we have this negative sign? i mean what is the origin of this? > What is the significance of such value of S? > It can be just equal or greater than zero? > Thank you. > Bonoit> > > -- PD. Dr. Andreas Klamt CEO / Geschäftsführer 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 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Wed Jun 22 05:55:01 2011 From: "Emmanuel Aubert emmanuel.aubert---crm2.uhp-nancy.fr" To: CCL Subject: CCL: Freq on optimized exicted state Message-Id: <-44948-110622052847-10041-7lXsYbiiytIt9iVxJYPwiQ(~)server.ccl.net> X-Original-From: Emmanuel Aubert Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 22 Jun 2011 11:28:38 +0200 MIME-Version: 1.0 Sent to CCL by: Emmanuel Aubert [emmanuel.aubert-$-crm2.uhp-nancy.fr] Dear Subscribers, after optimizing the ground state of a molecule I calculated the vertical UV-vis transitions by TD-DFT (Gausian09), and I optimized the excited state of interest. However I have some trouble on performing frequency calculations on this optimized excited state : is it possible (and how ?) to restart such a calculation from chk/rwf if the allocated time is not enough ? Best regards, Emmanuel. From owner-chemistry@ccl.net Wed Jun 22 06:51:01 2011 From: "Andreas Klamt klamt(a)cosmologic.de" To: CCL Subject: CCL: Entropy (corrected) Message-Id: <-44949-110622064652-32595-7D14hD3z1TQAu+/jwig91g!A!server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 22 Jun 2011 12:46:45 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt(_)cosmologic.de] Sorry, in my previous message I had a mistake ("large negative" value should be "large positive") Dear Benoit, I guess you talk about alkane-like compounds in water. The free energy of transfer of alkane from its neat liquid to water is known to be a large positive value (corresponding with the low solubility of alkane in water) and it is known to be entirely entropic. The later is obvious > from the fact that the solubility of alkanes in water has a minimum at about room temperature, which means that dH is zero and dG is entirely -TdS, which means dS is negative. Within the COSMO-RS model this entropy loss of alkane in water is just (predictively!) explained by the fact that the non-polar surface segments of alkane can only slect the very few non-polar surface segments of water as partners, and selection of a small number out of a large means strong loss of entropy. (See e.g. A. Klamt, Fluid Phase Equilibria 206 (2003) 223–235 Prediction of the mutual solubilities of hydrocarbons and water with COSMO-RS ) In the molecular dynamics and MC simulation world the same fac is explained in more nebulous words as the change of the water structure close to the surface of non-polar molecules. Anyway, I am sure that this is the reason for the negative entropy of alkanes in water, obviously depending on the reference state for defining the S=0. Andreas Am 22.06.2011 09:28, schrieb Bonoit Bonoit bonoit_10%%yahoo.fr: > Sent to CCL by: "Bonoit Bonoit" [bonoit_10[]yahoo.fr] > Hello everyone, > I'm writing to enquire about the negative values of the thermodynamic data of entropy (S) for some species especially in aqueous systems. > My question is as follow; > Why we have this negative sign? i mean what is the origin of this? > What is the significance of such value of S? > It can be just equal or greater than zero? > Thank you. > Bonoit> > > -- PD. Dr. Andreas Klamt CEO / Geschäftsführer 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 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Wed Jun 22 08:08:00 2011 From: "Eldar Mamin yeldar443[a]mail.ru" To: CCL Subject: CCL: calculation of frequences Message-Id: <-44950-110622055951-15486-7PsYfBPBEsHUvUKgHqKZRw(-)server.ccl.net> X-Original-From: "Eldar Mamin" Date: Wed, 22 Jun 2011 05:59:49 -0400 Sent to CCL by: "Eldar Mamin" [yeldar443[#]mail.ru] Dear CCL Subscribers, I want to estimate rate constant of some reaction (ozone + double bond) in MRMP2(14,11)/aug-cc-pvdz level of theory. There are two TS to compare the rate constants through each of them. In my ability only one approch is avaliable now- to calculate IRC curve in CASSCF(14,11) and then run MRMP2 job for points of the curve - because of abcence of mrmp2 gradient thechnique. A have found an activation barrier, but how should i find a frequenses to calculate thermodynamic functions H, S , which are need to estimate rate constant with theory of transition state? When i run any job( for frequenses) with other method for TS-point in MRMP2 i really make a job not in stationary point of PES of this other method and result will not be sensitive. What can you advise me in the case? Eldar Mamin, yeldar443^^^mail.ru From owner-chemistry@ccl.net Wed Jun 22 09:47:00 2011 From: "Paolo Tosco paolo.tosco,,unito.it" To: CCL Subject: CCL: Open3DALIGN 2.0 GPLv3 release Message-Id: <-44951-110622094441-15117-peijPlaOKHMmUHtwjNbSiw a server.ccl.net> X-Original-From: "Paolo Tosco" Date: Wed, 22 Jun 2011 09:44:38 -0400 Sent to CCL by: "Paolo Tosco" [paolo.tosco|unito.it] Dear CCLers, Open3DALIGN 2.0 has been released under the terms of GPLv3: http://open3dalign.org Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN can carry out conformational searches and unsupervised rigid-body alignment on three-dimensional molecule datasets. Different algorithms have been implemented to perform single and multi-conformation superimpositions on one or more templates. Alignments can be accomplished by matching pharmacophores, heavy atoms or a combination of the two. All methods have been successfully validated on eight comprehensive datasets previously gathered by Sutherland and co-workers; the full validation suite is available for download from the website. High computational performance has been attained through efficient parallelization of the code. Open3DALIGN constitutes an ideal complement to Open3DQSAR, our recently released open-source tool focused on MIF computation and 3D-QSAR model building, since it shares with the former the same file formats and user interface. The unsupervised nature of the alignment algorithms, together with its scriptable interface, make Open3DALIGN an ideal component of high-throughput, automated cheminformatics workflows. Open3DALIGN runs on all mainstream operating systems (Windows 32/64-bit, Linux 32/64-bit, Solaris x86 32/64-bit, Intel Mac OS X 32/64-bit). Open3DALIGN is available free of charge under the terms of GPLv3; for further information, visit http://open3dalign.org Kind regards, Paolo Tosco Department of Drug Science and Technology Faculty of Pharmacy, University of Turin Via Pietro Giuria 9, 10125 Torino, Italy Thomas Balle Department of Medicinal Chemistry The Faculty of Pharmaceutical Sciences, University of Copenhagen, 2 Universitetsparken, 2100 Copenhagen, Denmark From owner-chemistry@ccl.net Wed Jun 22 15:11:00 2011 From: "Sergio Mares aveazulms-.-yahoo.com" To: CCL Subject: CCL: Energy minimisation dilemma Message-Id: <-44952-110622134147-27917-WCEfqx7TYwjIc6ieQoo9kg[#]server.ccl.net> X-Original-From: "Sergio Mares" Date: Wed, 22 Jun 2011 13:41:41 -0400 Sent to CCL by: "Sergio Mares" [aveazulms-*-yahoo.com] Dear CCL list subscribers, My protein homology model has been minimised using different packages: GROMACS (Gromos96 forcefield) Chimera (Amber forcefield) Yasara (Yasara forecefield) The best minimising software was Yasara as judged by the MolProbity server (e.g reduced ramachandran outliers, reduced number of bad atom contacts, etc). However, minimisation moved the model away from the template structure (RMSD about 1 A). Although Gromacs did not do as well as Yasara in terms of the parameters measured by MolProbity, it was capable of maintaining the model close to the template structure as demonstrated by a relatively low RMSD of about 0.4 A. Which structure would be more reliable to use for further studies e.g. molecular docking? Thank you very much in advance, Sergio From owner-chemistry@ccl.net Wed Jun 22 19:08:01 2011 From: "Simmie, John john.simmie]-[nuigalway.ie" To: CCL Subject: CCL: calculation of frequences Message-Id: <-44953-110622144342-15538-iISZevllvk+yX9Trnayj4w-,-server.ccl.net> X-Original-From: "Simmie, John" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CC310C.38E9F1DC" Date: Wed, 22 Jun 2011 19:43:05 +0100 MIME-Version: 1.0 Sent to CCL by: "Simmie, John" [john.simmie a nuigalway.ie] This is a multi-part message in MIME format. ------_=_NextPart_001_01CC310C.38E9F1DC Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Technically, only frequencies at the same level of theory are meaningful = for transition states or species in general. However if this is not possible then use simpler levels for which the TS = exists (this is a must) and do a frequency calculation at this level. Effectively you can "divorce" the energy calculation (activation = barrier) from the frequency calculation which gives you the entropy, = rotational constants, etc needed to compute the A-factor and hence the = rate constant.=20 Prof. John M. Simmie:: Combustion Chemistry Centre National University of Ireland, Galway =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Sent to CCL by: "Eldar Mamin" [yeldar443[#]mail.ru] Dear CCL Subscribers, I want to estimate rate constant of some reaction (ozone + double bond) in MRMP2(14,11)/aug-cc-pvdz level of theory. There are two TS to compare = the rate constants through each of them.=20 In my ability only one approch is avaliable now-=20 to calculate IRC curve in CASSCF(14,11) and then run MRMP2 job for = points of the curve - because of abcence of mrmp2 gradient thechnique. A = have found an activation barrier, but how should i find a frequenses to = calculate thermodynamic functions H, S , which are need to estimate rate = constant with theory of transition state? When i run any job( for = frequenses) with other method for TS-point in MRMP2 i really make a job not in = stationary point of PES of this other method and result will not be = sensitive. What can you advise me in the case?=20 Eldar Mamin, yeldar443]^[mail.ru ------_=_NextPart_001_01CC310C.38E9F1DC-- From owner-chemistry@ccl.net Wed Jun 22 19:43:01 2011 From: "Babak Khalili khalili.babak_._gmail.com" To: CCL Subject: CCL: ctDNA Message-Id: <-44954-110622152906-11390-uEYk47gkxDFfRNRFQiuIJQ-*-server.ccl.net> X-Original-From: Babak Khalili Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 22 Jun 2011 23:58:42 +0430 MIME-Version: 1.0 Sent to CCL by: Babak Khalili [khalili.babak~!~gmail.com] Dear Jeva Follow this link to make the closest model based on FASTA sequence of ctDNA. You can find the best FASTA from ncbi. http://swissmodel.expasy.org/workspace/ Regards, Babak Khalili Hadad, Asst. Prof. of Computational Biochemistry On 06/21/2011, Jevahcel Strong jevahcel,hotmail.com wrote: > > Sent to CCL by: "Jevahcel Strong" [jevahcel:hotmail.com] > Hi Folks, > > I am trying to work on the Calf Thymus DNA, but I cannot find its crystal > structure. Could anybody please kindly offer me some information regarding > this, like pdb entries. > Any of your kind help will be very appreciated > > Sincerely > Jevah> > > From owner-chemistry@ccl.net Wed Jun 22 20:18:01 2011 From: "Babak Khalili khalili.babak(~)gmail.com" To: CCL Subject: CCL: ctDNA Message-Id: <-44955-110622152533-7567-xT08Ewhc0dMlR6bX3QmSIw(a)server.ccl.net> X-Original-From: Babak Khalili Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 22 Jun 2011 23:55:00 +0430 MIME-Version: 1.0 Sent to CCL by: Babak Khalili [khalili.babak\a/gmail.com] Dear Jeva Follow this link to make the closest model based on FASTA sequence of ctDNA. You can find the best FASTA from ncbi. http://swissmodel.expasy.org/workspace/ Regards, Babak Khalili Hadad, Asst. Prof. of Computational Biochemistry On 06/21/2011, Close, David M. CLOSED[A]mail.etsu.edu wrote: > > Sent to CCL by: "Close, David M." [CLOSED%a%mail.etsu.edu] > Jevah: > > I am not sure there is a crystal structure of DNA. There are lots of > crystal structures of oligomers with good resolution. I think however you > will have to look at your hydration levels and decide if you have A or > B-DNA, and then find a suitable oligomer structure that has a similar base > run that you are interested in. > > Regards, Dave Close. > > -----Original Message----- >> From: owner-chemistry+closed==etsu.edu(~)ccl.net >> [mailto:owner-chemistry+closed==etsu.edu(~)ccl.net] On Behalf Of Jevahcel >> Strong jevahcel,hotmail.com > Sent: Tuesday, June 21, 2011 10:40 AM > To: Close, David M. > Subject: CCL: ctDNA > > > Sent to CCL by: "Jevahcel Strong" [jevahcel:hotmail.com] > Hi Folks, > > I am trying to work on the Calf Thymus DNA, but I cannot find its crystal > structure. Could anybody please kindly offer me some information regarding > this, like pdb entries. > Any of your kind help will be very appreciated > > Sincerely > Jevahhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Wed Jun 22 20:52:01 2011 From: "Bradley Rose brose,live.com" To: CCL Subject: CCL:G: Multiple Step Minimization and Energy Job in Gaussian 09 Message-Id: <-44956-110622192818-26899-RhiWx0h4gQrQVRTQF06gcw*server.ccl.net> X-Original-From: "Bradley Rose" Date: Wed, 22 Jun 2011 19:28:16 -0400 Sent to CCL by: "Bradley Rose" [brose#live.com] Hello I was wanting to create an input file for Gaussian 09 to run a minimization and then run a single point energy calculation on the resulting geometry with one input file since I am calculating energies for a number of derivatives. I would like to use two different check files if possible. My attempts have not been successful in all the variations that I have tried, an example (incorrect) input I have been testing for H2 is shown below %mem=1GB %chk=H2PM3 # opt=calcfc freq pm3 geom=connectivity PM3 minimization + frequency 0 1 H -2.49523788 -0.29761904 0.00000000 H -3.09523788 -0.29761904 0.00000000 1 2 1.0 2 --Link1-- %mem=1GB %chk=H2HF # HF/6-31G(d) geom=read SP energy calc Thanks in advance. Brad Rose brose * live.com