From owner-chemistry@ccl.net Fri Jun 5 02:23:00 2009 From: "Andreas Klamt klamt++cosmologic.de" To: CCL Subject: CCL: PH-dependent ab-initio calculations Message-Id: <-39439-090605021937-2107-WA20riSxXTvA9mMA+VdWsw++server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 05 Jun 2009 08:19:05 +0200 MIME-Version: 1.0 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 calculatio= n of a molecular system under a certain PH value? Has there been much dev= elopment on PH-dependent ab-initio methods? Maybe some PH-dependent empir= ical methods? Thanks for any information. > > Regards, > Yutao Yue > --=20 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 From owner-chemistry@ccl.net Fri Jun 5 05:38:02 2009 From: "andras.borosy^givaudan.com" To: CCL Subject: CCL: semi-empirical vs force field Message-Id: <-39440-090605052721-7222-vVbHBel6tzNtxpHD/CYtqA,+,server.ccl.net> X-Original-From: andras.borosy|a|givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 002FE923C12575CC_=" Date: Fri, 5 Jun 2009 10:43:18 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy-.-givaudan.com This is a multipart message in MIME format. --=_alternative 002FE923C12575CC_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, When can semi-empirical methods (like PM6-DH [1]) replace force fields in=20 modelling of macromolecules? Best regards, Dr. Andr=E1s P=E9ter Borosy 1) http://pubs.acs.org/doi/abs/10.1021/ct9000922 --=_alternative 002FE923C12575CC_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,

When can semi-empirical methods (like PM6-DH [1]) replace force fields in modelling of macromolecules?

Best regards,

Dr. Andr=E1s P=E9ter Borosy
1) http://pubs.acs.org/doi/abs/10.10= 21/ct9000922

--=_alternative 002FE923C12575CC_=-- From owner-chemistry@ccl.net Fri Jun 5 08:03:00 2009 From: "Berger Raphael berger^-^chem.helsinki.fi" To: CCL Subject: CCL:G: detect permutation of atoms in xyz files Message-Id: <-39441-090605075153-30875-dM9ws74t6jBB00yOO4sZrQ/a\server.ccl.net> X-Original-From: Berger Raphael Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 5 Jun 2009 13:51:20 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Berger Raphael [berger*o*chem.helsinki.fi] Dear Readers, consider the following problem: You have got two .xyz files containing the same molecular structures but differ in a) the sequence of atoms and b) in trans-rotational positioning What is the sequence of atoms in file2 expressed in terms of the sequence of atoms in file1? More concrete: I need some command line script solving that task. Is anyone aware of such a tool? My idea would be to first find a standard orientation for both structures (maybe like Gaussian does; is there a separae tool for that?) and label the atom names uniquly (Si -> Si1, C -> C3, ...) and sort both of them lexicographically according to the size of the cartesian coordiantes, In this way one gets one Permutation functions for each file, which can be combined (and inverted) to get the permutation. Any help is greatfully acknowledged! Best regards RB "Dann miass-ma fesd boarisch ren, das uns da Globalisierungswind ned o~konn!" S. H. Papst Benedikt XVI, 2006 From owner-chemistry@ccl.net Fri Jun 5 08:44:01 2009 From: "Harish Hiranaik harish:+:apsarain.com" To: CCL Subject: CCL: please help me. Message-Id: <-39442-090605010240-26736-iOp7WLDunAWG1bU8y4Dvig]=[server.ccl.net> X-Original-From: "Harish Hiranaik" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Fri, 5 Jun 2009 09:49:20 +0530 MIME-Version: 1.0 Sent to CCL by: "Harish Hiranaik" [harish!=!apsarain.com] Dear Try the same thing with Turbomole - Quantum Chemistry Package by Ahlrich With Regards, Harish Hiranaik Sr Marketing Executive, Apsara Innovations Pvt Ltd No. 217, 8th 'C' Main, 1st Block, Kalyan Nagar Bangalore - 560043 Land Line: +91 80 25459285 & 25459652 Fax : +91 80 25459285 Cell : +91 9844613815 Email : harish!^!apsarain.com., Web : www.apsarain.com ----- Original Message ----- > From: "Minho Kim astro33=ajou.ac.kr" To: "Hiranaik, Harish Tatyarao " Sent: Wednesday, June 03, 2009 7:05 AM Subject: CCL: please help me. > > Sent to CCL by: "Minho Kim" [astro33-#-ajou.ac.kr] > > Hello! > > I calculated ground state of phenol using HF & MP2 method. > > HF method calculated well, but MP2 has a big problem. > > Freq. Calc. result has an imagenary number, so vibration frequency has > minus value. > > I calculated several geometry of phenol, but they converged same result. > > why did't MP2 method calculate well? How can I do? > > Sorry, my English is very poor. Thank you for read. > > ----------------------------------------------- > > You can get LOG file. > > http://astrostars.v3webhard.com/chemical/phenol_opt7.log> -------------------------------------------------------------------------------- No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.5.339 / Virus Database: 270.12.53/2155 - Release Date: 06/04/09 17:55:00 From owner-chemistry@ccl.net Fri Jun 5 10:03:01 2009 From: "Gustavo Seabra gustavo.seabra(-)gmail.com" To: CCL Subject: CCL: semi-empirical vs force field Message-Id: <-39443-090605095908-26701-d/3SCY4FZw7ewJJJDPi/3A]=[server.ccl.net> X-Original-From: Gustavo Seabra Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 5 Jun 2009 09:52:36 -0400 MIME-Version: 1.0 Sent to CCL by: Gustavo Seabra [gustavo.seabra[-]gmail.com] On Fri, Jun 5, 2009 at 4:43 AM, andras.borosy^givaudan.com wrote: > > Dear Colleagues, > > When can semi-empirical methods (like PM6-DH [1]) replace force fields in > modelling of macromolecules? That will happen precisely at 5:35PM (EST) on Feb 30th, 2011. (Sorry, I just couldn't help it :-) OK, seriously now. At this point, we don't really have an answer. In fact, the answer will also depend on what calculation are you talking about: Do you want to do simple minimizations? Then it's already possible to do it with purely semi-empirical methods. Do you want molecular dynamics or Monte Carlo simulations? Then, it unlikely that it will happen anytime soon, since even with those methods it would take way too long to get any significant statistics. Finally, one needs to be careful here as to why would you want that. Depending on what you are looking for, semi-empirical methods may offer no advantage over well-designed and well-parametrized classical force fields, like the latest generations of force fields. And may even hurt you: being mostly parametrized with small organic molecules in gas phase, the semi-empirical parameters are not necessarily always transferable to the condensed phase calculations of large biological molecules. Gustavo. From owner-chemistry@ccl.net Fri Jun 5 10:38:01 2009 From: "Michel Petitjean petitjean.chiral---gmail.com" To: CCL Subject: CCL:G: detect permutation of atoms in xyz files Message-Id: <-39444-090605101514-1035-mhmGvCWKb97lUG8JeArnAA]=[server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 5 Jun 2009 15:02:11 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral-,-gmail.com] Hi Raphael, Use CSR, downloadable for free at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR It should output the rotation + translation + pairwise correspondence you are looking for. However, you must provide an input format such as ml2 (sybyl mol2), hin (hyperchem), etc. Best wishes, Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean[a]cea.fr, petitjean.chiral[a]gmail.com http://petitjeanmichel.free.fr/itoweb.petitjean.html ---------- Forwarded message ---------- > From: Berger Raphael berger^-^chem.helsinki.fi Date: 2009/6/5 Subject: CCL:G: detect permutation of atoms in xyz files To: "Petitjean, Michel " Sent to CCL by: Berger Raphael [berger*o*chem.helsinki.fi] Dear Readers, consider the following problem: You have got two .xyz files containing the same molecular structures but differ in a) the sequence of atoms and b) in trans-rotational positioning What is the sequence of atoms in file2 expressed in terms of the sequence of atoms in file1? More concrete: I need some command line script solving that task. Is anyone aware of such a tool? My idea would be to first find a standard orientation for both structures (maybe like Gaussian does; is there a separae tool for that?) and label the atom names uniquly (Si -> Si1, C -> C3, ...) and sort both of them lexicographically according to the size of the cartesian coordiantes, In this way one gets one Permutation functions for each file, which can be combined (and inverted) to get the permutation. Any help is greatfully acknowledged! Best regards RB "Dann miass-ma fesd boarisch ren, das uns da Globalisierungswind ned o~konn!" S. H. Papst Benedikt XVI, 2006 From owner-chemistry@ccl.net Fri Jun 5 11:12:01 2009 From: "S. Bill S_Bill36]=[yahoo.co.uk" To: CCL Subject: CCL: Prevent hydrogen bond Message-Id: <-39445-090605111122-3546-xhZUSBzW49HRM9djqi/3lg#server.ccl.net> X-Original-From: "S. Bill" Date: Fri, 5 Jun 2009 11:11:18 -0400 Sent to CCL by: "S. Bill" [S_Bill36{=}yahoo.co.uk] Dear CCl Users I have water molecule in my system, and during optimization, this water molecule forming hydrogen bond with one carboxyle group. I am trying to do optimization without forming hydrogen bond, I know I should let it to form hydroghen bond, but I am testing one phenomena. So, how can I prevent water molecule from forming hydrogen bond? Any ideas please Thanks in Advance S. bill From owner-chemistry@ccl.net Fri Jun 5 11:47:01 2009 From: "Tom Stockfisch t.stockfisch(-)cox.net" To: CCL Subject: CCL:G: detect permutation of atoms in xyz files Message-Id: <-39446-090605111455-6668-uUTIwfHHz+mWAaeW8BGycg ~ server.ccl.net> X-Original-From: Tom Stockfisch Content-Type: multipart/alternative; boundary=Apple-Mail-1--380285812 Date: Fri, 5 Jun 2009 08:14:46 -0700 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Tom Stockfisch [t.stockfisch.__.cox.net] --Apple-Mail-1--380285812 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi RB - This is actually a significant problem to solve if you want to do it correctly. A strategy that works is: convert both structures to unique smiles for each set of topologically equivalent atoms: try a permutation compute the rms error of the two structures If you want the method not to be ridiculously slow on highly symmetric molecules you need to be clever in which permutations you try. There are commercial software packages that do this. Tom Tom Stockfisch t.stockfisch__cox.net http://www.tstockfisch.com On Jun 5, 2009, at 3:51 AM, Berger Raphael berger^-^chem.helsinki.fi wrote: > > Sent to CCL by: Berger Raphael [berger*o*chem.helsinki.fi] > Dear Readers, > > consider the following problem: > > You have got two .xyz files containing the same molecular > structures but differ in > a) the sequence of atoms and > b) in trans-rotational positioning > What is the sequence of atoms in file2 expressed in terms of the > sequence of atoms in file1? > > > More concrete: I need some command line script solving that task. > Is anyone aware of such a tool? > > My idea would be to first find a standard orientation for both > structures > (maybe like Gaussian does; is there a separae tool for that?) and > label the atom names uniquly (Si -> Si1, C -> C3, ...) and sort > both of them > lexicographically according to the size of the cartesian coordiantes, > In this way one gets one Permutation functions for each file, which > can be combined (and inverted) to get the permutation. > > Any help is greatfully acknowledged! > Best regards > RB > > "Dann miass-ma fesd boarisch ren, das uns da Globalisierungswind > ned o~konn!" > S. H. Papst Benedikt XVI, 2006 > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changehttp://www.ccl.net/chemistry/ > sub_unsub.shtmlConferences: http://server.ccl.net/ > chemistry/announcements/conferences/> > --Apple-Mail-1--380285812 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Hi RB -

This is actually a significant problem to = solve if you want to do it correctly.
A strategy that works = is:
= convert both structures to unique smiles
for each = set of topologically equivalent atoms:
= try a permutation
compute the rms error of = the two structures
If you want the method not to be = ridiculously slow on highly symmetric molecules
you need to be = clever in which permutations you try.

There are = commercial software packages that do = this.

Tom

Tom = Stockfisch
http://www.tstockfisch.com

On Jun 5, 2009, at = 3:51 AM, Berger Raphael berger^-^chem.helsinki.fi wrote:


Sent to = CCL by: Berger Raphael [berger*o*chem.helsinki.fi]
Dear Readers,

consider the following = problem:

You have got two .xyz files containing the same = molecular structures but differ in
a) the = sequence of atoms and
b) in trans-rotational = positioning
What is the sequence of atoms in = file2 expressed in terms of the sequence of atoms in file1?


More = concrete: I need some command line script solving that task. Is anyone = aware of such a tool?
My idea would be to first find a = standard orientation for both structures
(maybe = like Gaussian does; is there a separae tool for that?) and label the = atom names uniquly (Si -> Si1, C -> C3, ...) and sort both of = them
lexicographically according to = the size of the cartesian coordiantes,
In this = way one gets one Permutation functions for each file, which can be = combined (and inverted) to get the permutation.

Any help = is greatfully acknowledged!
Best = regards
RB

"Dann = miass-ma fesd boarisch ren, das uns da Globalisierungswind ned = o~konn!"
S. H. Papst Benedikt XVI, = 2006



-=3D This is = automatically added to each message by the mailing script =3D-
To recover the email address of the author of the = message, please change
the strange characters on = the top line to the __ sign. You can also
look up = the X-Original-From: line in the mail header.

E-mail = to subscribers: CHEMISTRY__ccl.net= or use:

E-mail to administrators: CHEMISTRY-REQUEST__ccl.net = or use

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= --Apple-Mail-1--380285812-- From owner-chemistry@ccl.net Fri Jun 5 12:25:01 2009 From: "James Robinson james.robinson*_*prosonix.co.uk" To: CCL Subject: CCL: semi-empirical vs force field Message-Id: <-39447-090605121843-24811-DX3AaX60eHsf+zB3Ps0h8A^server.ccl.net> X-Original-From: "James Robinson" Date: Fri, 5 Jun 2009 12:18:39 -0400 Sent to CCL by: "James Robinson" [james.robinson^-^prosonix.co.uk] Try it, and remember to apply MMOK (13 kcal mol) correction for cis-trans amide bonds. Any one can model, its is your examination afterwards that provides the critique. So think like a chemist when examining the results. By all means try it..you just never know. Dr James J Robinson BSc(HONS) PhD MRSC Senior Scientist Prosonix Ltd The Magdalen Centre Robert Robinson Avenue The Oxford Science Park Oxford, OX4 4GA, UK T: +44 (0) 1865 784243 F: +44 (0) 1865 754251 http://www.prosonix.co.uk P Please consider the environment - do you really need to print this email? For more information about Prosonix please visit our website at www.prosonix.co.uk Prosonix Limited registered office is One London Wall, London, EC2Y 5AB, United Kingdom. Registered in England and Wales, number 5679156. ******************************************************************************************** Any opinions expressed in this email are those of the individual and not necessarily the Company. This email and any files transmitted with it, including replies and forwarded copies (which may contain alterations) subsequently transmitted from the Company, are confidential and solely for the use of the intended recipient. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is strictly prohibited. ******************************************************************************************** -------------------------------------------------------------------------------- > From: owner-chemistry+james.robinson==prosonix.co.uk- -ccl.net [mailto:owner-chemistry+james.robinson==prosonix.co.uk- -ccl.net] On Behalf Of andras.borosy^givaudan.com Sent: 05 June 2009 09:43 To: James Robinson Subject: CCL: semi-empirical vs force field Dear Colleagues, When can semi-empirical methods (like PM6-DH [1]) replace force fields in modelling of macromolecules? Best regards, Dr. Andrs Pter Borosy 1) http://pubs.acs.org/doi/abs/10.1021/ct9000922 From owner-chemistry@ccl.net Fri Jun 5 12:59:01 2009 From: "Esteban Gabriel Vega Hissi egvega|gmail.com" To: CCL Subject: CCL: Prevent hydrogen bond Message-Id: <-39448-090605125112-17623-lSavQdbgNqz9rAZl5pJVWQ ~~ server.ccl.net> X-Original-From: Esteban Gabriel Vega Hissi Content-Type: multipart/alternative; boundary=0016365ee96ee16fd2046b9cb109 Date: Fri, 5 Jun 2009 13:50:50 -0300 MIME-Version: 1.0 Sent to CCL by: Esteban Gabriel Vega Hissi [egvega|a|gmail.com] --0016365ee96ee16fd2046b9cb109 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi S.Bill, I have an idea I've never tested before. You can use NBO Analysis to identify the orbitals (or the interaction LP --> BD*) involved in the hydrogen bond(s) you want to delete. After that, you can run a calculation employing "NBO Del" methodology deleting what you identified before. You can make single point and optimization calculations with the orbitals deleted. Hope this is valid and help you Esteban 2009/6/5 S. Bill S_Bill36]=[yahoo.co.uk > > Sent to CCL by: "S. Bill" [S_Bill36{=}yahoo.co.uk] > Dear CCl Users > I have water molecule in my system, and during optimization, this water > molecule forming hydrogen bond with one carboxyle group. I am trying to do > optimization without forming hydrogen bond, I know I should let it to form > hydroghen bond, but I am testing one phenomena. > So, how can I prevent water molecule from forming hydrogen bond? > Any ideas please > Thanks in Advance > S. bill> > > --0016365ee96ee16fd2046b9cb109 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi S.Bill,

I have an idea I've never tested before. You can use = NBO Analysis to identify the orbitals (or the interaction LP -->=A0 BD*)= involved in the hydrogen bond(s) you want to delete. After that, you can r= un a calculation employing "NBO Del" methodology deleting what yo= u identified before. You can make single point and optimization calculation= s with the orbitals deleted.

Hope this is valid and help you

Esteban

2009/6/5 S. Bill S_Bill36]=3D[yah= oo.co.uk <owner-chemistry---ccl.net>

Sent to CCL by: "S. =A0Bill" [S_Bill36{=3D}yahoo.co.uk]
Dear CCl Users
I have water molecule in my system, and during optimization, this water mol= ecule forming hydrogen bond with one carboxyle group. I am trying to do opt= imization without forming hydrogen bond, I know I should let it to form hyd= roghen bond, but I am testing one phenomena.
So, how can I prevent water molecule from forming hydrogen bond?
Any ideas please
Thanks in Advance
S. bill



-=3D This is automatically added to each message by the mailing script =3D-=
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--0016365ee96ee16fd2046b9cb109-- From owner-chemistry@ccl.net Fri Jun 5 13:57:00 2009 From: "Rashid, Ali ARashid/a\ppg.com" To: CCL Subject: CCL: Prevent hydrogen bond Message-Id: <-39449-090605124242-12179-bJK43DAxQVgwk+Yv/FSDDw]_[server.ccl.net> X-Original-From: "Rashid, Ali" Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Fri, 5 Jun 2009 12:12:26 -0400 MIME-Version: 1.0 Sent to CCL by: "Rashid, Ali" [ARashid|*|ppg.com] What phenomena are you trying to test? -----Original Message----- > From: owner-chemistry+arashid=3D=3Dppg.com[A]ccl.net [mailto:owner-chemistry+= arashid=3D=3Dppg.com[A]ccl.net] On Behalf Of S. Bill S_Bill36]=3D[yahoo.co.uk Sent: Friday, June 05, 2009 11:11 AM To: Rashid, Ali Subject: CCL: Prevent hydrogen bond Sent to CCL by: "S. Bill" [S_Bill36{=3D}yahoo.co.uk] Dear CCl Users I have water molecule in my system, and during optimization, this water mol= ecule forming hydrogen bond with one carboxyle group. I am trying to do opt= imization without forming hydrogen bond, I know I should let it to form hyd= roghen bond, but I am testing one phenomena. So, how can I prevent water molecule from forming hydrogen bond? Any ideas please Thanks in Advance S. bill -=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 Fri Jun 5 14:32:00 2009 From: "Ernst-Walter Knapp knapp:+:chemie.fu-berlin.de" To: CCL Subject: CCL: PH-dependent ab-initio calculations Message-Id: <-39450-090605115933-11606-7s2glx0U4MVwqZfrWI7/Aw||server.ccl.net> X-Original-From: Ernst-Walter Knapp Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Fri, 05 Jun 2009 17:17:14 +0200 MIME-Version: 1.0 Sent to CCL by: Ernst-Walter Knapp [knapp|a|chemie.fu-berlin.de] Dear Yutao Yue, if you want to titrate a protein have a lock at the webpage http://agknapp.chemie.fu-berlin.de/karlsberg/ If you want to calculate pKa of organic molecules have a look at: ChemPhysChem *5* (2004) 1513–1522 Sincerely, Walter Knapp -- |---------------------------------------------------------------------| | Dr. Ernst-Walter Knapp email: knapp/a\chemie.fu-berlin.de | | Free University of Berlin Tel.: +49 30 838 54387 | | Department of Biology, Chemistry, Pharmacy Fax.: +49 30 838 56921 | | Institute of Chemistry & Biochemistry | | Macromolecular Modeling and Simulation of Biomolecular Systems | | Fabeckstrasse 36A | | D-14195 Berlin | | Germany www: http://agknapp.chemie.fu-berlin.de | |---------------------------------------------------------------------| 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> > From owner-chemistry@ccl.net Fri Jun 5 15:07:00 2009 From: "William F. Coleman wcoleman%wellesley.edu" To: CCL Subject: CCL:G: hexagonal periodic systems in GaussView 4 Message-Id: <-39451-090605094523-23687-hK4wKlAncmPkAV803M7JKA~!~server.ccl.net> X-Original-From: "William F. Coleman" Content-Type: multipart/alternative; boundary="--=_--1d9d83ce.1d9d81a0.c64eca01" Date: Fri, 05 Jun 2009 09:11:29 -0400 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman^wellesley.edu] This is a multi-part message in MIME format. ----=_--1d9d83ce.1d9d81a0.c64eca01 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit I am putting together some experiments in solid state chemistry for inorganic and physical chemistry courses using Gaussian 03. Part of this will deal with building solid structures using the GaussView PCB module. My question has to do with what appears to be a number of missing space groups. Am I completely blind, or is it a senior moment (always highly likely) or are there no hexagonal space groups available. I could do my portion in Crystal Maker, but before buying it for the laboratories I would like to find out if I am just missing something in GaussView. Thanks in advance for any information you can provide, Flick Coleman _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html Editor, JCE WebWare and JCE Featured Molecules http://www.jce.divched.org/JCEDLib/WebWare/ http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html ----=_--1d9d83ce.1d9d81a0.c64eca01 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <=21DOCTYPE HTML PUBLIC =22-//W3C//DTD HTML 4.0 Transitional//EN=22>
I am putting together some experiment= s in solid state chemistry for inorganic and physical chemistry courses usi= ng Gaussian 03.  Part of this will deal with building solid structures= using the GaussView PCB module.  My question has to do with what appe= ars to be a number of missing space groups.  Am I completely blind, or= is it a senior moment (always highly likely) or are there no hexagonal space groups available.

I could do my portion in Crystal Make= r, but before buying it for the laboratories I would like to find out if I = am just missing something in GaussView.

Thanks in advance for any information= you can provide,

Flick Coleman

_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481


Editor, JCE WebWare and JCE Featured = Molecules

----=_--1d9d83ce.1d9d81a0.c64eca01-- From owner-chemistry@ccl.net Fri Jun 5 15:49:00 2009 From: "David Gallagher gallagher.da[*]gmail.com" To: CCL Subject: CCL: Prevent hydrogen bond Message-Id: <-39452-090605154540-10569-3ho9D5iKCXmuaJSqzFxVXg:-:server.ccl.net> X-Original-From: David Gallagher Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Fri, 05 Jun 2009 12:45:01 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da]|[gmail.com] One approach that often works (depending on the program you are using and what you are trying to achieve) is simply to move the water molecule 20 Angstroms away from the other molecule (or however far it takes), to prevent it from finding the other moiety during the optimization. Alternatively, move the water molecule away and lock one atom on it and also one atom on the substrate, to allow the optimizations to proceed while keeping the molecules separated. I have used these approaches in MOPAC and other QM and MM methods with success. A distance constraint (if available) could achieve the same effect. David Gallagher CACheResearch.com At 08:11 AM 6/5/2009, S. Bill S_Bill36]=[yahoo.co.uk wrote: >Sent to CCL by: "S. Bill" [S_Bill36{=}yahoo.co.uk] >Dear CCl Users >I have water molecule in my system, and during optimization, this >water molecule forming hydrogen bond with one carboxyle group. I am >trying to do optimization without forming hydrogen bond, I know I >should let it to form hydroghen bond, but I am testing one phenomena. >So, how can I prevent water molecule from forming hydrogen bond? >Any ideas please >Thanks in Advance >S. bill From owner-chemistry@ccl.net Fri Jun 5 16:35:00 2009 From: "Jerome Kieffer jerome.Kieffer*_*terre-adelie.org" To: CCL Subject: CCL:G: detect permutation of atoms in xyz files Message-Id: <-39453-090605125506-19795-H4GfxyatwKBbp35/necG+g\a/server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Fri, 5 Jun 2009 18:54:26 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer/a\terre-adelie.org] On Fri, 5 Jun 2009 13:51:20 +0300 (EEST) "Berger Raphael berger^-^chem.helsinki.fi" wrote: > My idea would be to first find a standard orientation for both structures > (maybe like Gaussian does; is there a separae tool for that?) and label=20 > the atom names uniquly (Si -> Si1, C -> C3, ...) and sort both of them > lexicographically according to the size of the cartesian coordiantes, > In this way one gets one Permutation functions for each file, which can b= e=20 > combined (and inverted) to get the permutation. I tried the same except that I sorted vs the distance to the center of the molecule, atom type by atom type, then I did a Kabsch-optimised rotation. It works pretty well. Hope this helps, I can even provide the piece of code doing it (but integrated in a bigger software). --=20 J=E9r=F4me KIEFFER =20 http://www.terre-adelie.org From owner-chemistry@ccl.net Fri Jun 5 20:45:01 2009 From: "Dr. Daniel Glossman-Mitnik dglossman|gmail.com" To: CCL Subject: CCL: software for IR spectrum analysis Message-Id: <-39454-090605203932-28602-wVy+niNOuqFBnw2vsON/jQ|,|server.ccl.net> X-Original-From: "Dr. Daniel Glossman-Mitnik" Content-Language: es-mx Content-Type: multipart/alternative; boundary="----=_NextPart_000_0033_01C9E602.9782E1F0" Date: Fri, 5 Jun 2009 17:25:12 -0600 MIME-Version: 1.0 Sent to CCL by: "Dr. Daniel Glossman-Mitnik" [dglossman]^[gmail.com] This is a multi-part message in MIME format. ------=_NextPart_000_0033_01C9E602.9782E1F0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear netters: I am looking for software that, given a calculated IR spectrum, can do the automatical assignment of vibrational modes. Usually, one do this by using software that can animate each vibrational mode, and then assign it by inspection. What I am looking is for some software that can do this automatically. The same thing for UV-Vis spectra, assigning the electronic transitions, would be nice too. Thanks in advance. Best regards, Daniel Red MONEAR - CIMAV, SC E-mail: daniel.glossman+*+cimav.edu.mx dglossman+*+gmail.com ------=_NextPart_000_0033_01C9E602.9782E1F0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear = netters:

 

I am looking for software that, = given a calculated IR spectrum, can do the

automatical assignment of = vibrational modes. Usually, one do this by using

software that can animate each = vibrational mode, and then assign it by

inspection.  What I am = looking is for some software that can do this

automatically. =

The same thing for UV-Vis = spectra, assigning the electronic transitions,

would be nice = too.

 

Thanks in advance. Best = regards,

 

Daniel

 

 

Red MONEAR – CIMAV, = SC

E-mail:  daniel.glossman+*+cimav.edu.mx=

          =     dglossman+*+gmail.com

 

 

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