From owner-chemistry@ccl.net Tue Aug 17 06:16:00 2010 From: "Ol Ga eurisco1=pochta.ru" To: CCL Subject: CCL:G: GEN doesn't work Message-Id: <-42536-100817053621-14590-SvKBXgkL+JJVX8o0YDeVGg() server.ccl.net> X-Original-From: "Ol Ga" Date: Tue, 17 Aug 2010 05:36:18 -0400 Sent to CCL by: "Ol Ga" [eurisco1:-:pochta.ru] Dear Jane, 6-311+G* is all-electronic basis set. Hence, you don't need PSEUDO=READ. The correct input is # B3LYP/GEN OPT molecule specification N C H O 0 6-31G(d) **** Fe 0 6-311+G* **** Sincerely, Ol Ga ========================= > From: janeyin600]=[gmail.com Sent: Tuesday, August 17, 2010 6:49 AM To: Ga, Ol Subject: CCL:G: GEN doesn't work Hi there, I had a GEN error in my Gaussian output. This is my input: # B3LYP/GEN OPT PSEUDO=READ molecule specification N C H O 0 6-31G(d) **** Fe 0 6-311+G* **** Fe 0 6-311+G* And this is the end of my output: Unrecognized potential number 6 in GetPot. Error termination via Lnk1e in /usr/local/g03/l301.exe at Sat Aug 14 21:08:16 2010. Does anyone know what the "unrecognized potential number" means in here? Thank you very much! Jane From owner-chemistry@ccl.net Tue Aug 17 08:36:00 2010 From: "VITORGE Pierre 094605 Pierre.VITORGE[-]cea.fr" To: CCL Subject: CCL:G: Problem with Geometry Optimisation using PCM Message-Id: <-42537-100817041718-16123-TL7fmqAOlz/iGNJ0A+nVDw++server.ccl.net> X-Original-From: "VITORGE Pierre 094605" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 17 Aug 2010 10:17:04 +0200 MIME-Version: 1.0 Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE(-)cea.fr] Dear Honman, I often had similar problems: Gaussian98 and Gaussian03 probably have problems in optimising geometries with PCM. It seems that you finally succeeded. Now you have imaginary frequencies, why don't you try to change the initial geometry as usual in such cases? -- Pierre -----Message d'origine----- De : owner-chemistry+pierre.vitorge==cea.fr-$-ccl.net [mailto:owner-chemistry+pierre.vitorge==cea.fr-$-ccl.net] De la part de Honman Yau honman.yau*student.unsw.edu.au Envoyé : lundi 16 août 2010 12:32 À : VITORGE Pierre 094605 Objet : CCL: Problem with Geometry Optimisation using PCM Sent to CCL by: "Honman Yau" [honman.yau#student.unsw.edu.au] Dear all, I have been trying to run a geometry optimisation on a pair of para- substituted aryl diazonium salt, one of which a dication (p-trimethylamino) and the other a zwitterion (p-sulfonate), without much success. The ultimate goal is to look at the change in charge distribution (and perhaps the LUMOs) with and without the interaction between the pair. After searching for possible solutions on forums, blogs and mailing lists including everything I could find on CCL...) for a couple of weeks (and tried different things in between) I have now reached the point where I think that I must be doing something silly and it would be lovely if someone could point out a mistake (or two, or more... such as using other solvation models?), provide suggestions on tackling the problem, or suggest alternatives (or all of the above!). As an aside, after looking for similar studies in the literature, it appears that some people just simply take their gas phase optimsied structures and, without further geometry optimisation in a PCM, do subsequent calculations with them in PCM - is this generally acceptable? I personally find that quite strange and cannot justify it (apart from the fact that it may cause sleep deprivation). The following is, in chronological order, what I have attempted so far: N.B. For all of the calculations below I specified the charge of the system as +2 and multiplicity as 1. Geometry optimisation of the pair in the gas phase completed without hassles, resulting in an end-on interaction of the sulfonate group with a slightly bent dication. Frequency calculation was then performed on the optimised structure; no imaginary frequencies were found in a frequency calculation. Using this structure, geometry optimisation with the following route card was performed with: #P B3LYP/6-31G* OPT SCRF=(PCM,Solvent=Acetonitrile) The job often just abnormally terminated without any error messages and never converged even after a few OPT=Restart. Frequency calculations using the route card: #P B3LYP/6-31G* FREQ SCRF=(PCM,Solvent=Acetonitrile) returned a few imaginary frequencies, mostly rotation of the aromatic ring bearing the sulfonate functionality and bending-like movements of the species - all about the center of interaction. > From there I tried modifying the starting structure slightly a couple of times, but to no avail. Smaller or larger basis sets and OPT=gdiis did not help either. I thought perhaps it could be a problem with PCM and after digging around the web for a bit I tried again with: #P B3LYP/6-31+G* OPT=(maxcycle=512) SCRF=(Read,PCM,Solvent=Acetonitrile) Geom=Allcheckpoint . OFac=0.8 RMin=0.5 The job ran a bit better (did not stop without warning) but the energies kept cycling and failed to converge. So I tried again with: #P B3LYP/6-31+G* OPT=(maxcycle=512) SCRF=(Read,PCM,Solvent=Acetonitrile) NOSYMM . OFac=0.8 RMin=0.5 NOSYMMCAV When it failed to converge for the first time, I did a frequency calculation then optimised again with ReadFC: #P B3LYP/6-31+G* OPT=(ReadFC,maxcycle=512) SCRF=(Read,PCM,Solvent=Acetonitrile) NOSYMM . OFac=0.8 RMin=0.5 NOSYMMCAV Then the job eventually converged with (finally!) a normal termination. Unfortunately when I did a frequency calculation: #P B3LYP/6-31+G* FREQ SCRF=(Read,PCM,Solvent=Acetonitrile) NOSYMM . OFac=0.8 RMin=0.5 NOSYMMCAV I got five imaginary frequencies... :( That pretty much sums up what I have done so far. Thank you very much in advance for any suggestions! Kind regards, Honman School of Chemistry University of New South Wales Sydney NSW 2052 Australia Contact e-mail: honman.yau{}student.unsw.edu.auhttp://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 Tue Aug 17 09:11:07 2010 From: "jaleel uc jaleel.uc[]gmail.com" To: CCL Subject: CCL: computer aided organic synthesis Message-Id: <-42538-100817071848-32006-ozbKPj+hPPU8JvLVWHrDrQ..server.ccl.net> X-Original-From: jaleel uc Content-Type: multipart/alternative; boundary=00504501477a7479a3048e031cf4 Date: Tue, 17 Aug 2010 16:48:40 +0530 MIME-Version: 1.0 Sent to CCL by: jaleel uc [jaleel.uc|*|gmail.com] --00504501477a7479a3048e031cf4 Content-Type: text/plain; charset=ISO-8859-1 Dear all can you sugget me a software for computer aided organic synthesis Thanks -- Dr U.C.A.Jaleel. Asst Professor in cheminformatics Cheminformatics Division( UGC) Malabar Christian College Calicut University --00504501477a7479a3048e031cf4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear all
=A0
=A0
can you sugget me a software for computer aided organic synthesis
=A0
Thanks

--
Dr U.C.A.Jaleel.
Asst Professor = in cheminformatics
Cheminformatics Division( UGC)
Malabar Christian = College
Calicut University
--00504501477a7479a3048e031cf4-- From owner-chemistry@ccl.net Tue Aug 17 10:54:00 2010 From: "Gabriel Urquiza urquizagabes###gmail.com" To: CCL Subject: CCL: PDB file construction Message-Id: <-42539-100817105304-24884-BK/6d/vZG75mo0xZbh5P/g|-|server.ccl.net> X-Original-From: Gabriel Urquiza Content-Type: multipart/alternative; boundary=0016e64c1bbccac860048e061a79 Date: Tue, 17 Aug 2010 11:52:57 -0300 MIME-Version: 1.0 Sent to CCL by: Gabriel Urquiza [urquizagabes===gmail.com] --0016e64c1bbccac860048e061a79 Content-Type: text/plain; charset=ISO-8859-1 Greetings CCL subscribers Does anyone have information about a good application for writing PDB files > from dihedral angles (phi,psi,omega and possibly tau angles)? I was using the CRANKITE suite *lipa* program, but it seems it doesn't write side chain atoms, which makes it a bit useless to my purposes. I would really appreciate if someone could give me some light in this problem. It is very important for me. regards Gabriel Urquiza --0016e64c1bbccac860048e061a79 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Greetings CCL subscribers

Does anyone have information a= bout a good application for writing PDB files from dihedral angles (phi,psi= ,omega and possibly tau angles)? I was using the CRANKITE suite lipa= =A0program, but it seems it doesn't write side chain atoms, which makes= it a bit useless to my purposes. I would really appreciate if someone coul= d give me some light in this problem. It is very important for me.

regards

Gabriel Urquiza
--0016e64c1bbccac860048e061a79-- From owner-chemistry@ccl.net Tue Aug 17 11:37:01 2010 From: "=?GB2312?B?0vO9oQ==?= janeyin600---gmail.com" To: CCL Subject: CCL:G: GEN doesn't work Message-Id: <-42540-100817113558-1106-ZQnDd+6ZlDLfJJdV3qgZrg a server.ccl.net> X-Original-From: =?GB2312?B?0vO9oQ==?= Content-Type: multipart/alternative; boundary=000e0cd2dd48eaf82a048e06b32f Date: Tue, 17 Aug 2010 10:35:45 -0500 MIME-Version: 1.0 Sent to CCL by: =?GB2312?B?0vO9oQ==?= [janeyin600*gmail.com] --000e0cd2dd48eaf82a048e06b32f Content-Type: text/plain; charset=ISO-8859-1 Thank you very much, Ol Ga! I will try it again. Jane 2010/8/17 Ol Ga eurisco1=pochta.ru > > Sent to CCL by: "Ol Ga" [eurisco1:-:pochta.ru] > Dear Jane, > > 6-311+G* is all-electronic basis set. Hence, you don't need PSEUDO=READ. > The correct input is > > > # B3LYP/GEN OPT > > molecule specification > N C H O 0 > 6-31G(d) > **** > Fe 0 > 6-311+G* > **** > > Sincerely, > Ol Ga > > > ========================= > > From: janeyin600]=[gmail.com > Sent: Tuesday, August 17, 2010 6:49 AM > To: Ga, Ol > Subject: CCL:G: GEN doesn't work > > > Hi there, > > I had a GEN error in my Gaussian output. > > This is my input: > # B3LYP/GEN OPT PSEUDO=READ > > molecule specification > N C H O 0 > 6-31G(d) > **** > Fe 0 > 6-311+G* > **** > > Fe 0 > 6-311+G* > > > And this is the end of my output: > Unrecognized potential number 6 in GetPot. > Error termination via Lnk1e in /usr/local/g03/l301.exe at Sat Aug 14 > 21:08:16 2010. > Does anyone know what the "unrecognized potential number" means in here? > Thank you very much! > > Jane> > > --000e0cd2dd48eaf82a048e06b32f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Thank you very much, Ol Ga! I will try it again.
=A0
Jane=A0

2010/8/17 Ol Ga eurisco1=3Dpochta.ru <owner-chemistry/a\ccl.net>

Sent to CCL by: "Ol =A0= Ga" [eurisco1:-:pochta= .ru]
Dear Jane,

6-311+G* is all-electronic basis set. Hence, you don'= t need PSEUDO=3DREAD. The correct input is


# B3LYP/GEN OPT

molecule specification
N C H O 0
6-31G(d)
**= **
Fe 0
6-311+G*
****

Sincerely,
Ol Ga


= =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=
> From: =A0janeyin600]=3D[gmail.com
Sent: Tuesday, August 17, 2010 6:49 AM
To: Ga, Ol
Subject: CCL:G: GEN= doesn't work


Hi there,

I had a GEN error in my Gaussian= output.

This is my input:
=A0# B3LYP/GEN OPT PSEUDO=3DREAD
molecule specification
N C H O 0
6-31G(d)
****
Fe 0
6-311+= G*
****

Fe 0
6-311+G*


And this is the end of my output:Unrecognized potential number 6 in GetPot.
Error termination via Lnk1e= in /usr/local/g03/l301.exe at Sat Aug 14 21:08:16 2010.
Does anyone kno= w what the "unrecognized potential number" means in here?
Thank you very much!

Jane



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--000e0cd2dd48eaf82a048e06b32f-- From owner-chemistry@ccl.net Tue Aug 17 15:32:08 2010 From: "Ba Tai Truong Truong.BaTai**chem.kuleuven.be" To: CCL Subject: CCL: adiabatic ionization potential and adiabatic ionization energy Message-Id: <-42541-100817145137-29605-qb1yJAWj7Rhgb94hGf3L3w ~~ server.ccl.net> X-Original-From: Ba Tai Truong Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 17 Aug 2010 20:48:52 +0200 MIME-Version: 1.0 Sent to CCL by: Ba Tai Truong [Truong.BaTai###chem.kuleuven.be] Dear CCL members Could you tell exactly what is difference between the adiabatic ionization potential and adiabatic ionization energy? Thank you very much Best regards From owner-chemistry@ccl.net Tue Aug 17 16:07:01 2010 From: "vadiraj kurdekar vadirajgcppc(-)yahoo.co.in" To: CCL Subject: CCL: computer aided organic synthesis Message-Id: <-42542-100817114218-13185-GsyM0a05gkrt1AbOzjm9Zw(~)server.ccl.net> X-Original-From: vadiraj kurdekar Content-Type: multipart/alternative; boundary="0-415155871-1282059726=:3036" Date: Tue, 17 Aug 2010 21:12:06 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: vadiraj kurdekar [vadirajgcppc:+:yahoo.co.in] --0-415155871-1282059726=:3036 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable hello Dr U.C.A.Jaleel =A0 chemaxon`s reactor module can be used to generate virtual library of possia= ble compounds for given reaction and reactants but reaction mechanisum and = other parameters (selectivity) should be defined properly.=20 its free for academic user =A0 With Regards, =A0 Vadiraj Kurdekar, Pharmacy group, Birla Institute of Technology and Science-Pilani, Rajasthan, India. Mobile: + 91 9460763664 --- On Tue, 17/8/10, jaleel uc jaleel.uc[]gmail.com wrote: > From: jaleel uc jaleel.uc[]gmail.com Subject: CCL: computer aided organic synthesis To: "Kurdekar, Vadiraj " Date: Tuesday, 17 August, 2010, 4:48 PM Dear all=20 =A0 =A0 can you sugget me a software for computer aided organic synthesis=20 =A0 Thanks --=20 Dr U.C.A.Jaleel. Asst Professor in cheminformatics=20 Cheminformatics Division( UGC) Malabar Christian College=20 Calicut University =0A=0A --0-415155871-1282059726=:3036 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
hello Dr U.C.A.Jaleel
 
chema= xon`s reactor module can be used to generate virtual library of possiable c= ompounds for given reaction and reactants but reaction mechanisum and other= parameters (selectivity) should be defined properly.
its free for academic user
 
With Regards,
 
Vadiraj Kurdekar,
Pharmacy group,
Bir= la Institute of Technology and Science-Pilani,
Rajasthan,
India.
M= obile: + 91 9460763664


--- On Tue, 17/8/10, jaleel uc jaleel.= uc[]gmail.com <owner-chemistry%%ccl.net> wrote:

From: jaleel uc jaleel.uc[]gmail.com <owner-ch= emistry%%ccl.net>
Subject: CCL: computer aided organic synthesis
To= : "Kurdekar, Vadiraj " <vadirajgcppc%%yahoo.co.in>
Date: Tu= esday, 17 August, 2010, 4:48 PM

Dear all
 
 
can you sugget me a software for computer aided organic synthesis
 
Thanks

--
Dr U.C.A.Jaleel.
Asst Professor in= cheminformatics
Cheminformatics Division( UGC)
Malabar Christian Co= llege
Calicut University
=
--0-415155871-1282059726=:3036-- From owner-chemistry@ccl.net Tue Aug 17 16:42:01 2010 From: "Wolf-D. Ihlenfeldt wdi^^^xemistry.com" To: CCL Subject: CCL: AW: computer aided organic synthesis Message-Id: <-42543-100817103054-9929-UK+IxeeK4I6oLJ1mTW0pgA^^^server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: de Content-Type: multipart/alternative; boundary="----=_NextPart_000_0051_01CB3E29.92234F80" Date: Tue, 17 Aug 2010 16:30:56 +0200 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi*xemistry.com] This is a multi-part message in MIME format. ------=_NextPart_000_0051_01CB3E29.92234F80 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Theresa: http://www.molecular-networks.com/products/theresa Von: owner-chemistry+wdi==xemistry.com~~ccl.net [mailto:owner-chemistry+wdi==xemistry.com~~ccl.net] Im Auftrag von jaleel uc jaleel.uc[]gmail.com Gesendet: Dienstag, 17. August 2010 13:19 An: Ihlenfeldt, Wolf D Betreff: CCL: computer aided organic synthesis Dear all can you sugget me a software for computer aided organic synthesis Thanks -- Dr U.C.A.Jaleel. Asst Professor in cheminformatics Cheminformatics Division( UGC) Malabar Christian College Calicut University ------=_NextPart_000_0051_01CB3E29.92234F80 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Theresa:

 

http://www.mo= lecular-networks.com/products/theresa

 

 

 

Von:<= /b> owner-chemistry+wdi=3D=3Dxemistry.com~~ccl.net [mailto:owner-chemistry+wdi=3D=3Dxemistry.com~~ccl.net] Im Auftrag von = jaleel uc jaleel.uc[]gmail.com
Gesendet: Dienstag, 17. August 2010 13:19
An: Ihlenfeldt, Wolf D
Betreff: CCL: computer aided organic = synthesis

 

Dear all

 

 

can you sugget me a software for computer aided = organic synthesis

 

Thanks

--
Dr U.C.A.Jaleel.
Asst Professor in cheminformatics
Cheminformatics Division( UGC)
Malabar Christian College
Calicut University

------=_NextPart_000_0051_01CB3E29.92234F80-- From owner-chemistry@ccl.net Tue Aug 17 19:23:00 2010 From: "neranjan perera neranjan007!A!gmail.com" To: CCL Subject: CCL: bader chargers Message-Id: <-42544-100817190617-23581-zNYixfYX+kSpa3irxhVIAQ-,-server.ccl.net> X-Original-From: neranjan perera Content-Type: multipart/alternative; boundary=00032555a42e7d998c048e0cfe0e Date: Tue, 17 Aug 2010 19:06:07 -0400 MIME-Version: 1.0 Sent to CCL by: neranjan perera [neranjan007],[gmail.com] --00032555a42e7d998c048e0cfe0e Content-Type: text/plain; charset=ISO-8859-1 Hi, how can i convert "bader chargers" to "atomic partial chargers"? Thanks. Neranjan Perera. neranjan007 *-* gmail.com -- Graduate Student Department of Chemistry University of Connecticut --00032555a42e7d998c048e0cfe0e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,
=A0=A0 how can i convert "bader chargers" to "atomic = partial chargers"?

Thanks.


Neranjan Perera.
nera= njan007 *-* gmail.com
--
Graduate Student
Department of Chemistry
University of Connecticut

--00032555a42e7d998c048e0cfe0e-- From owner-chemistry@ccl.net Tue Aug 17 20:44:02 2010 From: "Sayed Mesa elsayed.elmes[*]yahoo.com" To: CCL Subject: CCL: COSMO-RS, enthalpy and free energy of complexation Message-Id: <-42545-100817184333-1873-QTSK6M3f/1F8NgNs+FMNPg%a%server.ccl.net> X-Original-From: "Sayed Mesa" Date: Tue, 17 Aug 2010 18:43:24 -0400 Sent to CCL by: "Sayed Mesa" [elsayed.elmes**yahoo.com] Dear All, A couple of days ago, I sent to inquire about COSMO-RS, please see below: Could anybody kindly answer this inquiry? --------------------------------------------------------------------- I am calculating the enthalpy and free energy for complexation reaction between transition metal with chelate ligand (has four N-atoms for coordination) in both gas phase and solvent (COSMO-RS). In both cases I used tetrasolvated cluster of water molecules around the transition metal (i.e. bare metal is not used). So the reaction will be: L + [M(H2O)4]2+ ---- [ML]2+ + 4H2O (either in gas or in solvent). I have two questions; the first: is this scenario is right? If yes please confirm me by a reference if possible. The second question, is I need to do geometry optimization for reactants and products again in solvent or single point calculations is enough for calculating the enthalpy and free energy for complexation? Thanks in advance Sayed From owner-chemistry@ccl.net Tue Aug 17 21:19:01 2010 From: "Egon Willighagen egon.willighagen{}gmail.com" To: CCL Subject: CCL: CINF session on Chemical Data with Semantic Web technologies Message-Id: <-42546-100817153117-17508-zd3Hy6CArN2wqPC2ypki+Q/./server.ccl.net> X-Original-From: Egon Willighagen Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 17 Aug 2010 21:30:48 +0200 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [egon.willighagen:-:gmail.com] Dear ACS-Boston 2010 participants, with this email I would like to ask your attention to the three Semantic Web sessions on Sunday morning, and Monday morning and afternoon. During these sessions 15 presentations will be given on how the Resource Description Framework is changing cheminformatics; in three sessions links to computational chemistry, knowledge management, and general applications are demonstrated, with wide variety of chemical disciplines as context, including toxicology, chemometrics, eScience, databases, wet lab experimentation, lipidomics, text mining, drug discovery and health care, gene-disease-pathway modeling, and chemical patents. You are all kindly invited to attend these exiting sessions of which the full program is available at: http://egonw.github.com/acsrdf2010/ with kind regards, Egon Willighagen -- Dr E.L. Willighagen Post-doc ]![ Uppsala University (only until 2010-09-30) Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers From owner-chemistry@ccl.net Tue Aug 17 21:53:01 2010 From: "Radoslaw Kaminski rkaminski.rk[#]gmail.com" To: CCL Subject: CCL: bader chargers Message-Id: <-42547-100817212129-10844-nR6ysY7kKZ8RBh7hudaVzw,,server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=0015174c45f4fec9e7048e0ee155 Date: Tue, 17 Aug 2010 21:21:19 -0400 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk]^[gmail.com] --0015174c45f4fec9e7048e0ee155 Content-Type: text/plain; charset=ISO-8859-1 What do you understand by these 'atomic partial charges'? Radek 2010/8/17 neranjan perera neranjan007!A!gmail.com > Hi, > how can i convert "bader chargers" to "atomic partial chargers"? > > Thanks. > > > Neranjan Perera. > neranjan007 *-* gmail.com > > -- > Graduate Student > Department of Chemistry > University of Connecticut > > > -- Radoslaw Kaminski, M.Sc. Eng. Ph.D. Student Crystallochemistry Laboratory Department of Chemistry University of Warsaw Pasteura 1, 02-093 Warszawa, Poland http://acid.ch.pw.edu.pl/~rkaminski/ --0015174c45f4fec9e7048e0ee155 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable What do you understand by these 'atomic partial charges'?

Ra= dek


2010/8/17 neranjan perera neranja= n007!A!gmail.com <owner-chemistry^_^ccl.net>
Hi,
=A0=A0 how= can i convert "bader chargers" to "atomic partial chargers&= quot;?

Thanks.


Neranjan Perera.
neranjan007 *-* gmail.com

--
Graduate Student
Department of Chemistry
University of Connecticut




--
Radoslaw Kaminsk= i, M.Sc. Eng.
Ph.D. Student
Crystallochemistry Laboratory
Departme= nt of Chemistry
University of Warsaw
Pasteura 1, 02-093 Warszawa, Pol= and
http://acid.ch.pw.edu.pl/~= rkaminski/
--0015174c45f4fec9e7048e0ee155-- From owner-chemistry@ccl.net Tue Aug 17 23:34:00 2010 From: "neranjan perera neranjan007]*[gmail.com" To: CCL Subject: CCL: bader chargers Message-Id: <-42548-100817233233-30264-48W9KCwLwo8ihTM1VWrEAQ%%server.ccl.net> X-Original-From: neranjan perera Content-Type: multipart/alternative; boundary=0016e6d7e045ef6fb2048e10b6e1 Date: Tue, 17 Aug 2010 23:32:26 -0400 MIME-Version: 1.0 Sent to CCL by: neranjan perera [neranjan007]-[gmail.com] --0016e6d7e045ef6fb2048e10b6e1 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hi, In the paper " G. Henkelman et al. / Computational Materials Science 36 (2006) 354=96360" , they have got bader chargers for water (H2O) as, For Hydrogen 0.4238 e Oxygen 9.1566 e and then converted these Bader chargers into atomic partial charges; Hydrogen +0.58 Oxygen -1.16 So I want to know how to do the above conversion ? Thanks Neranjan Perera. On Tue, Aug 17, 2010 at 9:21 PM, Radoslaw Kaminski rkaminski.rk[#]gmail.com wrote: > What do you understand by these 'atomic partial charges'? > > Radek > > > 2010/8/17 neranjan perera neranjan007!A!gmail.com < > owner-chemistry|,|ccl.net > > > Hi, >> how can i convert "bader chargers" to "atomic partial chargers"? >> >> Thanks. >> >> >> Neranjan Perera. >> neranjan007 *-* gmail.com >> >> -- >> Graduate Student >> Department of Chemistry >> University of Connecticut >> >> >> > > > -- > Radoslaw Kaminski, M.Sc. Eng. > Ph.D. Student > Crystallochemistry Laboratory > Department of Chemistry > University of Warsaw > Pasteura 1, 02-093 Warszawa, Poland > http://acid.ch.pw.edu.pl/~rkaminski/ > -- --0016e6d7e045ef6fb2048e10b6e1 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hi,
=A0In the paper " G. Henkelman et al. / Computational Materials= Science 36 (2006) 354=96360" , they have got bader chargers for water= (H2O) as,
For=A0=A0 Hydrogen=A0=A0 0.4238 e
=A0=A0=A0=A0=A0=A0=A0 = Oxygen=A0=A0=A0=A0 9.1566 e
=A0
and then converted these Bader chargers into atomic partial charges;=
=A0=A0=A0=A0=A0=A0 Hydrogen=A0=A0 +0.58
=A0=A0=A0=A0=A0=A0 Oxygen= =A0=A0=A0=A0=A0 -1.16

So I want to know how to do the above convers= ion ?


Thanks
Neranjan Perera.

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0
<= br>
On Tue, Aug 17, 2010 at 9:21 PM, Radoslaw Kam= inski rkaminski.rk[#]gmail.c= om <owner-chemistry---ccl.net> wrote:
What do you under= stand by these 'atomic partial charges'?

Radek


2010/8/17 neranjan perera neranjan007!A!gmail.com <owner-chemistry|,|ccl.net>

Hi,
=A0=A0 how= can i convert "bader chargers" to "atomic partial chargers&= quot;?

Thanks.


Neranjan Perera.
neranjan007 *-* gmail.com

--
Graduate Student
Department of Chemistry
University of Connecticut




--
Radoslaw Kaminski, M.Sc. Eng.
Ph.D. Student
Cryst= allochemistry Laboratory
Department of Chemistry
University of Warsaw=
Pasteura 1, 02-093 Warszawa, Poland
http:/= /acid.ch.pw.edu.pl/~rkaminski/



--

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