Dear Dr. Hachmann and Dr. Kumar,

Many thanks for your very helpful replies and for the excellent ref= erences.

>=A0 Did you set up your delta-SCF as restricted open s= hell or unrestricted?

I used the default settings in Gaussian09 which is unrestricted for t= he cation, but I would appreciate any advise here. I notice that the delta = SCF values only differ by 0.07 eV but the orbital energies are significantl= y different (cation gas phase alpha HOMO and LUMO values of -6.48 eV and -6= .36 eV as compared with the unrestricted beta gas phase HOMO and LUMO value= s of -10.65 eV and -8.76 eV).

I had two follow up questions here.

1. Using R= OB3LYP results in degenerate alpha and beta orbitals?

2. Is it advised to do cation optimization with UB3LYP instead of B3LYP?=

Thanks again and very best wishes,

Sco= tt

On 15 May 2013 04:30, Ramesh Kumar rameshch= itumalla^gmail.com <<= a href=3D"mailto:owner-chemistry]-[ccl.net" target=3D"_blank">owner-chemistry= ]-[ccl.net> wrote:

Sent to CCL by: Ramesh Kumar [rameshchitumalla(a)gmail.com]
Dear Scott,

The reply from Dr. Johannes Hachmann is really very useful.
The orbital energy of a cation is much lower than that of its
corresponding neutral molecule and again it comes =A0very near to the
case similar to neutral molecule in the presence of a polar solvent.
For some numbers you can see CPL 396 (2004) 43-48.

--
With Best Regards:

CH. Ramesh Kumar
Senior Research Fellow,
Computational Chemistry Lab,
Indian Institute of Chemical Technology(IICT),
Tarnaka,
Hyderabad.

-=3D This is automatically added to each message by the mailing script =3D-=
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--047d7bacb3d460d66804dcd429df-- From owner-chemistry@ccl.net Thu May 16 08:07:00 2013 From: "darren.rhodes darren.rhodes,,gmail.com" To: CCL Subject: CCL: in silico biotargets fishing - reverse screening Message-Id: <-48699-130516035544-13789-xGmpTdEeG+B0NvTg9kF44g],[server.ccl.net> X-Original-From: "darren.rhodes" Content-Type: multipart/alternative; boundary=485b3970ceba55e9a204dcd12f1b Date: Thu, 16 May 2013 08:55:07 +0100 MIME-Version: 1.0 Sent to CCL by: "darren.rhodes" [darren.rhodes|a|gmail.com] --485b3970ceba55e9a204dcd12f1b Content-Type: text/plain; charset=ISO-8859-1 This package on CRAN may be of interest http://cran.r-project.org/web/packages/rcdk/vignettes/rcdk.pdf On 15 May 2013 10:15, zhoujinming zhou_jim!=!hotmail.com < owner-chemistry]|[ccl.net> wrote: > Dear CCLer > > Does some have the free script for compound similarity comparison using > SMILES format, the one with Java should be better. Please give some advice. > > Many Thanks. > > JinMING > > > > > -- "I have no doubt that if a party creates and sends an electronically created document then he will be treated as having signed it to the same extent that he would in law be treated as having signed a hard copy of the same document. The fact that the document is created electronically as opposed to as a hard copy can make no difference." Pelling J in Mehta v J Pereira Fernandes SA [2006] EWHC 813 (Ch) Key ID:- 0xB76FE0B9 http://pgpkeys.mit.edu:11371/ --485b3970ceba55e9a204dcd12f1b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

This package on CRAN may be of interest http://cran.r-proj= ect.org/web/packages/rcdk/vignettes/rcdk.pdf

On 15 May 2013 10:15, zhoujinming zhou_j= im!=3D!hotmail.com <= ;owner-chemist= ry]|[ccl.net> wrote:

Dear CCLer
=A0
Does some have the free script f= or compound similarity comparison using SMILES format, the one with Java sh= ould be better.=A0 Please give some advice.
=A0
Many Thanks.
=A0JinMING
=A0

--
"I have no doubt t= hat if a party creates and sends an electronically created document then he= will be treated as having signed it to the same extent that he would in la= w be treated as having signed a hard copy of the same document. The fact th= at the document is created electronically as opposed to as a hard copy can = make no difference." =A0Pelling J in Mehta v J Pereira Fernandes SA [2= 006] EWHC 813 (Ch)

Key ID:- 0xB76FE0B9 http://pgpkeys.mit.edu:11371/

--485b3970ceba55e9a204dcd12f1b-- From owner-chemistry@ccl.net Thu May 16 08:42:00 2013 From: "Harald Lanig harald.lanig=-=fau.de" To: CCL Subject: CCL: MGMS-DS: Symposium on Theoretical Chemistry 2013 in Erlangen, Germany Message-Id: <-48700-130516071110-32183-yAZ15DO9HVRTaDJO3ylpfg]![server.ccl.net> X-Original-From: Harald Lanig Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 16 May 2013 13:10:34 +0200 MIME-Version: 1.0 Sent to CCL by: Harald Lanig [harald.lanig ~ fau.de] Dear mailing list members, we would like to let you know that the *49th Symposium on Theoretical Chemistry 2013* will take place in Erlangen from September 22nd - 26th this year. The subject areas of the Symposium have been extended this year to cover not only classical Theoretical Chemistry, but also Modeling and Simulation! Details of the Symposium are available under http://www.chemie.uni-erlangen.de/stc2013/index.php Best wishes Tim Clark, Andreas G�rling, Bernd Meyer and Dirk Zahn. -- ------------------------------------------------------------------------ PD 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 ------------------------------------------------------------------------ From owner-chemistry@ccl.net Thu May 16 09:16:00 2013 From: "Mariusz Radon mariusz.radon{=}gmail.com" To: CCL Subject: CCL:G: b3lyp* Message-Id: <-48701-130515153511-6936-MlhDo5MgI87aOVuibu+VxA,,server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 15 May 2013 21:34:40 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon[a]gmail.com] On 13.05.2013 11:55, mala alhaji sainna alhajisainna _ yahoo.co.uk wrote: > Sent to CCL by: "mala alhaji sainna" [alhajisainna*|*yahoo.co.uk] > Hi Everyone, > > I will highly appreciate it if some one can guide me on how to use the b3lyp* functional; I tried getting > an iop for it on the gaussian website but it doesnt seems to be there and i am not sure how it is used. > > Many thanks, > Mala > The University of Manchester > Hi, You can obtain B3LYP* functional as User-Defined Model based on BLYP functional. Consult the Gaussian 09 docs about "User-Defined Model": http://www.gaussian.com/g_tech/g_ur/k_dft.htm The values of the coefficients in the model are probably given in the Marcus Reiher's original paper (DOI: 10.1007/s00214-001-0300-3) where this functional has been first defined. Anyway, they are the same as in the original B3LYP, except the factor weighting the HF exchange (which is 0.15, instead of 0.20). Regards, Mariusz> > -- Dr Mariusz Radon, Ph.D. Coordination Chemistry Group Faculty of Chemistry Jagiellonian University ul. Ingardena 3, 30-060 Krakow, Poland http://www.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Thu May 16 09:51:00 2013 From: "Johannes Hachmann jh=chemistry.harvard.edu" To: CCL Subject: CCL:G: Orbital energies for neutral and cation species in vacuum and solution Message-Id: <-48702-130516090641-23733-pGDiVp1ighV498Yf1rQN7w]=[server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Thu, 16 May 2013 09:06:27 -0400 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh^-^chemistry.harvard.edu] Hi Scott, The decision between U and RO is tricky and in my opinion there is no golden bullet - both approaches have their problems :). The U results may not give you a good quantum state, in particular if you have excessive spin contamination, while RO is not very flexible and does not allow for DODS, i.e., the R part cannot adequately account for the interactions with the unpaired electron. In my experience, U results tend to be better, but one has to be more careful how to interpret them. If you have very large spin polarization this indicates that your electronic structure is too complicated for a single-reference approach and you may want to try something more sophisticated than DFT. All bets are off then for the DFT results: you know that RO will be bad, while U results *may* still be ok (but somewhat artificially so). If you use U for the cation, you should try using U for the neutral molecule as well (don't forget to break spin symmetry in your guess!). If the molecule is complicated and the neutral one already shows spin polarization, you *may* get some error cancellation, since both species are treated on the same footing. I would then also use U for the respective geometry optimizations. Hope this helps Best Johannes ----------------------------------------------- Dr. Johannes Hachmann Research Associate Harvard University Department of Chemistry and Chemical Biology 12 Oxford St, Rm M104A Cambridge, MA 02138 ----------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh==chemistry.harvard.edu++ccl.net [mailto:owner- > chemistry+jh==chemistry.harvard.edu++ccl.net] On Behalf Of Scott McKechnie > jsm78]![cam.ac.uk > Sent: Thursday, 16 May, 2013 07:28 > To: Hachmann, Johannes > Subject: CCL:G: Orbital energies for neutral and cation species in vacuum and > solution > > Dear Dr. Hachmann and Dr. Kumar, > > > Many thanks for your very helpful replies and for the excellent references. > > > Did you set up your delta-SCF as restricted open shell or unrestricted? > > I used the default settings in Gaussian09 which is unrestricted for the cation, > but I would appreciate any advise here. I notice that the delta SCF values only > differ by 0.07 eV but the orbital energies are significantly different (cation gas > phase alpha HOMO and LUMO values of -6.48 eV and -6.36 eV as compared > with the unrestricted beta gas phase HOMO and LUMO values of -10.65 eV and > -8.76 eV). > > > I had two follow up questions here. > > > 1. Using ROB3LYP results in degenerate alpha and beta orbitals? > > > 2. Is it advised to do cation optimization with UB3LYP instead of B3LYP? > > > Thanks again and very best wishes, > > Scott > > > > > On 15 May 2013 04:30, Ramesh Kumar rameshchitumalla^gmail.com chemistry,+,ccl.net> wrote: > > > > Sent to CCL by: Ramesh Kumar [rameshchitumalla(a)gmail.com] > Dear Scott, > > The reply from Dr. Johannes Hachmann is really very useful. > The orbital energy of a cation is much lower than that of its > corresponding neutral molecule and again it comes very near to the > case similar to neutral molecule in the presence of a polar solvent. > For some numbers you can see CPL 396 (2004) 43-48. > > > > -- > With Best Regards: > > CH. Ramesh Kumar > Senior Research Fellow, > Computational Chemistry Lab, > Indian Institute of Chemical Technology(IICT), > Tarnaka, > Hyderabad.> > > > E-mail to subscribers: CHEMISTRY,+,ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST,+,ccl.net or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > > From owner-chemistry@ccl.net Thu May 16 10:27:00 2013 From: "Cina Foroutan-Nejad canyslopus(-)yahoo.co.uk" To: CCL Subject: CCL: Charged systems in electric field Message-Id: <-48703-130516100158-29347-9ByEhgSJzx+m+je1QgFFbQ#,#server.ccl.net> X-Original-From: "Cina Foroutan-Nejad" Date: Thu, 16 May 2013 10:01:56 -0400 Sent to CCL by: "Cina Foroutan-Nejad" [canyslopus~!~yahoo.co.uk] Dear CCLers, I am looking for a practical solution for measuring the binding energy of a charged complex in uniform electric field. As far as I know this is not a trivial task! For neutral systems without electric field one can employ the following equation for a charged complex: E(binding)[AB+]= E[AB+] - {EA + E[B+]} However, for charged systems in external field the total energy is a gauge dependent property. Does anyone know an example in literature that someone measured the binding energy of charged species in electric filed? Any help will be highly appreciated. With my sincere regards, Cina Foroutan-Nejad ------------------------------------------------------------------------ From owner-chemistry@ccl.net Thu May 16 12:09:01 2013 From: "Scott McKechnie jsm78/./cam.ac.uk" To: CCL Subject: CCL:G: Orbital energies for neutral and cation species in vacuum and solution Message-Id: <-48704-130516120540-21745-Cdc6lyqnvY5oFsiz1Xy4Wg*server.ccl.net> X-Original-From: Scott McKechnie Content-Type: multipart/alternative; boundary=001a11c2ce1607d0ff04dcd809f1 Date: Thu, 16 May 2013 17:05:29 +0100 MIME-Version: 1.0 Sent to CCL by: Scott McKechnie [jsm78 ~~ cam.ac.uk] --001a11c2ce1607d0ff04dcd809f1 Content-Type: text/plain; charset=ISO-8859-1 Hi Johannes, Many thanks for your reply and sorry to drag this discussion on but would the above comments change for quite simple systems? For instance, my main concern is about the calculations of delta SCF (vertical and adiabatic) values for organic dye molecules. I'm guessing a benchmark study would be advisable to investigate the sensitivity? Best wishes, Scott On 16 May 2013 14:06, Johannes Hachmann jh=chemistry.harvard.edu < owner-chemistry * ccl.net> wrote: > > Sent to CCL by: "Johannes Hachmann" [jh^-^chemistry.harvard.edu] > Hi Scott, > > The decision between U and RO is tricky and in my opinion there is no > golden > bullet - both approaches have their problems :). The U results may not give > you a good quantum state, in particular if you have excessive spin > contamination, while RO is not very flexible and does not allow for DODS, > i.e., the R part cannot adequately account for the interactions with the > unpaired electron. In my experience, U results tend to be better, but one > has to be more careful how to interpret them. If you have very large spin > polarization this indicates that your electronic structure is too > complicated for a single-reference approach and you may want to try > something more sophisticated than DFT. All bets are off then for the DFT > results: you know that RO will be bad, while U results *may* still be ok > (but somewhat artificially so). > > If you use U for the cation, you should try using U for the neutral > molecule > as well (don't forget to break spin symmetry in your guess!). If the > molecule is complicated and the neutral one already shows spin > polarization, > you *may* get some error cancellation, since both species are treated on > the > same footing. I would then also use U for the respective geometry > optimizations. > > Hope this helps > > Best > > Johannes > > ----------------------------------------------- > Dr. Johannes Hachmann > Research Associate > Harvard University > Department of Chemistry and Chemical Biology > 12 Oxford St, Rm M104A > Cambridge, MA 02138 > ----------------------------------------------- > > > > -----Original Message----- > > From: owner-chemistry+jh==chemistry.harvard.edu..ccl.net [mailto:owner- > > chemistry+jh==chemistry.harvard.edu..ccl.net] On Behalf Of Scott > McKechnie > > jsm78]![cam.ac.uk > > Sent: Thursday, 16 May, 2013 07:28 > > To: Hachmann, Johannes > > Subject: CCL:G: Orbital energies for neutral and cation species in vacuum > and > > solution > > > > Dear Dr. Hachmann and Dr. Kumar, > > > > > > Many thanks for your very helpful replies and for the excellent > references. > > > > > Did you set up your delta-SCF as restricted open shell or > unrestricted? > > > > I used the default settings in Gaussian09 which is unrestricted for the > cation, > > but I would appreciate any advise here. I notice that the delta SCF > values > only > > differ by 0.07 eV but the orbital energies are significantly different > (cation gas > > phase alpha HOMO and LUMO values of -6.48 eV and -6.36 eV as compared > > with the unrestricted beta gas phase HOMO and LUMO values of -10.65 eV > and > > -8.76 eV). > > > > > > I had two follow up questions here. > > > > > > 1. Using ROB3LYP results in degenerate alpha and beta orbitals? > > > > > > 2. Is it advised to do cation optimization with UB3LYP instead of B3LYP? > > > > > > Thanks again and very best wishes, > > > > Scott > > > > > > > > > > On 15 May 2013 04:30, Ramesh Kumar rameshchitumalla^gmail.com > chemistry,+,ccl.net> wrote: > > > > > > > > Sent to CCL by: Ramesh Kumar [rameshchitumalla(a)gmail.com] > > Dear Scott, > > > > The reply from Dr. Johannes Hachmann is really very useful. > > The orbital energy of a cation is much lower than that of its > > corresponding neutral molecule and again it comes very near to the > > case similar to neutral molecule in the presence of a polar > solvent. > > For some numbers you can see CPL 396 (2004) 43-48. > > > > > > > > -- > > With Best Regards: > > > > CH. Ramesh Kumar > > Senior Research Fellow, > > Computational Chemistry Lab, > > Indian Institute of Chemical Technology(IICT), > > Tarnaka, > > Hyderabad.> > > > > > > E-mail to subscribers: CHEMISTRY,+,ccl.net or use:> > > E-mail to administrators: CHEMISTRY-REQUEST,+,ccl.net or use> > Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/> > > > --001a11c2ce1607d0ff04dcd809f1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hi Johannes,

Many thanks for your r= eply and sorry to drag this discussion on but would the above comments chan= ge for quite simple systems? For instance, my main concern is about the cal= culations of delta SCF (vertical and adiabatic) values for organic dye mole= cules. I'm guessing a benchmark study would be advisable to investigate= the sensitivity?

Best wishes,

Scott

=A0 =A0

On 16 May 2013 14:06= , Johannes Hachmann jh=3Dchemistry= .harvard.edu <owner-chemistry * ccl.net> wrote:

Sent to CCL by: "Johannes Hachmann" [jh^-^chemistry.harvard.edu]
Hi Scott,

The decision between U and RO is tricky and in my opinion there is no golde= n
bullet - both approaches have their problems :). The U results may not give=
you a good quantum state, in particular if you have excessive spin
contamination, while RO is not very flexible and does not allow for DODS, i.e., the R part cannot adequately account for the interactions with the unpaired electron. In my experience, U results tend to be better, but one has to be more careful how to interpret them. If you have very large spin polarization this indicates that your electronic structure is too
complicated for a single-reference approach and you may want to try
something more sophisticated than DFT. All bets are off then for the DFT results: you know that RO will be bad, while U results *may* still be ok (but somewhat artificially so).

If you use U for the cation, you should try using U for the neutral molecul= e
as well (don't forget to break spin symmetry in your guess!). If the molecule is complicated and the neutral one already shows spin polarization= ,
you *may* get some error cancellation, since both species are treated on th= e
same footing. I would then also use U for the respective geometry
optimizations.

Hope this helps

Best

Johannes

-----------------------------------------------
Dr. Johannes Hachmann
Research Associate
Harvard University
Department of Chemistry and Chemical Biology
12 Oxford St, Rm M104A
Cambridge, MA 02138
-----------------------------------------------

> -----Original Message-----
> From: owner-chemistry+jh=3D=3Dchemistry.harvard.edu..cc= l.net [mailto:owner-
> chemistry+jh=3D=3Dchemistry.h= arvard.edu..ccl.net] O= n Behalf Of Scott McKechnie
> jsm78]![cam.ac.uk > Sent: Thursday, 16 May, 2013 07:28
> To: Hachmann, Johannes
> Subject: CCL:G: Orbital energies for neutral and cation species in vac= uum
and
> solution
>
> Dear Dr. Hachmann and Dr. Kumar,
>
>
> Many thanks for your very helpful replies and for the excellent
references.
>
> > =A0Did you set up your delta-SCF as restricted open shell or unre= stricted?
>
> I used the default settings in Gaussian09 which is unrestricted for th= e
cation,
> but I would appreciate any advise here. I notice that the delta SCF va= lues
only
> differ by 0.07 eV but the orbital energies are significantly different=
(cation gas
> phase alpha HOMO and LUMO values of -6.48 eV and -6.36 eV as compared<= br> > with the unrestricted beta gas phase HOMO and LUMO values of -10.65 eV= and
> -8.76 eV).
>
>
> I had two follow up questions here.
>
>
> 1. Using ROB3LYP results in degenerate alpha and beta orbitals?
>
>
> 2. Is it advised to do cation optimization with UB3LYP instead of B3LY= P?
>
>
> Thanks again and very best wishes,
>
> Scott
>
>
>
>
> On 15 May 2013 04:30, Ramesh Kumar rameshchitumalla^gmail.com <owner-
> chemistry,+,ccl.net&g= t; wrote:
>
>
>
> =A0 =A0 =A0 Sent to CCL by: Ramesh Kumar [rameshchitumalla(a)gmail.com]
> =A0 =A0 =A0 Dear Scott,
>
> =A0 =A0 =A0 The reply from Dr. Johannes Hachmann is really very useful= .
> =A0 =A0 =A0 The orbital energy of a cation is much lower than that of = its
> =A0 =A0 =A0 corresponding neutral molecule and again it comes =A0very = near to the
> =A0 =A0 =A0 case similar to neutral molecule in the presence of a pola= r solvent.
> =A0 =A0 =A0 For some numbers you can see CPL 396 (2004) 43-48.
>
>
>
> =A0 =A0 =A0 --
> =A0 =A0 =A0 With Best Regards:
>
> =A0 =A0 =A0 CH. Ramesh Kumar
> =A0 =A0 =A0 Senior Research Fellow,
> =A0 =A0 =A0 Computational Chemistry Lab,
> =A0 =A0 =A0 Indian Institute of Chemical Technology(IICT),
> =A0 =A0 =A0 Tarnaka,
> =A0 =A0 =A0 Hyderabad.>
>
>

> =A0 =A0 =A0 E-mail to subscribers: CHEMI= STRY,+,ccl.net or use:>=

> =A0 =A0 =A0 E-mail to administrators: CHEMISTRY-REQUEST,+,ccl.net or use> =A0 Conferenc= es:
> http://server.ccl.net/chemistry/announcements/conference= s/>

>
>
>
>

-=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 cha= nge
E-mail to subscribers: CHEMISTRY * ccl.n= et or use:
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--001a11c2ce1607d0ff04dcd809f1-- From owner-chemistry@ccl.net Thu May 16 12:53:00 2013 From: "Cina Foroutan-Nejad canyslopus_+_yahoo.co.uk" To: CCL Subject: CCL: Charged systems in electric field Message-Id: <-48705-130516124910-21566-U49d8D+91G0BKszqQcBcmA++server.ccl.net> X-Original-From: Cina Foroutan-Nejad Content-Type: multipart/alternative; boundary="-1712059246-1229839048-1368722942=:66651" Date: Thu, 16 May 2013 17:49:02 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Cina Foroutan-Nejad [canyslopus]*[yahoo.co.uk] ---1712059246-1229839048-1368722942=:66651 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCLers,=0A=0AI am sorry for resending me request! I was so distracted = that did not read my message!=0AI think no one will understand my message!= =0AHere is the correct question:=0A=0AI am looking for a practical solution= for measuring the binding energy of a=A0=0Acharged complex in uniform elec= tric field. As far as I know this is not a=A0=0Atrivial task!=0AFor neutral= or charged systems without electric field one can employ the following=A0= =0Aequation for measuring the binding nergy:=0A=0AE(binding)[AB+]=3D E[AB+]= - {EA + E[B+]}=0A=0AHowever, for charged systems in external field the tot= al energy is a gauge=A0=0Adependent property. Does anyone know an example i= n literature that someone=A0=0Ameasured the binding energy of charged speci= es in electric filed?=A0=0AAny help will be highly appreciated.=A0=0A=0AWit= h my sincere regards,=0ACina Foroutan-Nejad=0A=0A=0A_______________________= _________=0A From: Cina Foroutan-Nejad canyslopus(-)yahoo.co.uk =0ATo: "Foroutan-Nejad, Cina " =0ASent: Thursday, 16 May 2013, 16:01=0ASubject: CCL: Charged systems in= electric field=0A =0A=0A=0ASent to CCL by: "Cina=A0 Foroutan-Nejad" [canys= lopus~!~yahoo.co.uk]=0ADear CCLers,=0A=0AI am looking for a practical solut= ion for measuring the binding energy of a =0Acharged complex in uniform ele= ctric field. As far as I know this is not a =0Atrivial task!=0AFor neutral = systems without electric field one can employ the following =0Aequation for= a charged complex:=0A=0AE(binding)[AB+]=3D E[AB+] - {EA + E[B+]}=0A=0AHowe= ver, for charged systems in external field the total energy is a gauge =0Ad= ependent property. Does anyone know an example in literature that someone = =0Ameasured the binding energy of charged species in electric filed? =0AAny= help will be highly appreciated. =0A=0AWith my sincere regards,=0ACina For= outan-Nejad=0A-------------------------------------------------------------= -----------=0A=0A=0A=0A-=3D This is automatically added to each message by = the mailing script =3D-=0ATo recover the email address of the author of the= message, please change=0Athe strange characters on the top line to the =-= s= ign. You can also=0A= =0A=0A=0A=A0 =A0 =A0 http:/= /www.ccl.net/cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: CH= EMISTRY-REQUEST=-=ccl.net or use=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl= /send_ccl_message=0A=0A=0A=A0 =A0 =A0 http://www.ccl= .net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at: htt= p://www.ccl.net=0A=0A=0AConferences: http://se= rver.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messages: htt= p://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounces f= rom CCL with 5.7.1 error, check:=0A=A0 =A0 =A0 http://www.ccl.net/spammers.= txt=0A=0A---1712059246-1229839048-1368722942=:66651 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear CCL= ers,

I am so= rry for resending me request! I was so distracted that did not read my mess= age!

I think no one will understand my message!

Here is the correct question:

<= span style=3D"font-family: 'times new roman', 'new york', times, serif;">I = am looking for a practical solution for measuring the binding energy of a&n= bsp;
charged complex in uniform electric field. As far as I know this is = not a
trivial task!
For neutral or charged systems without electr= ic field one can employ the following
equation for measuring the binding ne= rgy:

E(binding)[AB+]=3D E[AB+] - {EA + E[B+]}

However, for charged systems in= external field the total energy is a gauge
dependent property. Doe= s anyone know an example in literature that someone
measured the binding energy = of charged species in electric filed?
Any help will be highly appre= ciated.

With my sincere regards,
Cina Foroutan-Nejad

From: Cin= a Foroutan-Nejad canyslopus(-)yahoo.co.uk <owner-chemistry=-=ccl.net> To: "Foroutan-Nejad, Ci= na " <canyslopus=-=yahoo.co.uk>
Sent: Thursday, 16 May 2013, 16:01
Subject: CCL: Charged systems in electr= ic field

Sent to = CCL by: "Cina Foroutan-Nejad" [canyslopus~!~yahoo.co.uk]
Dear CCLe= rs,

I am looking for a practical solution for measuring the binding = energy of a
charged complex in uniform electric field. As far as I know= this is not a
trivial task!
For neutral systems without electric fi= eld one can employ the following
equation for a charged complex:

E(binding)= [AB+]=3D E[AB+] - {EA + E[B+]}

However, for charged systems in exter= nal field the total energy is a gauge
dependent property. Does anyone k= now an example in literature that someone
measured the binding energy o= f charged species in electric filed?
Any help will be highly appreciate= d.

With my sincere regards,
Cina Foroutan-Nejad
-------------= -----------------------------------------------------------

= -=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 chang= e=

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---1712059246-1229839048-1368722942=:66651-- From owner-chemistry@ccl.net Thu May 16 13:27:00 2013 From: "Suman Layek slayek],[universaldisplay.com" To: CCL Subject: CCL:G: [Junk released by User action] RE: CCL:G: Only for professionaal in using Cores ! Message-Id: <-48706-130516072159-4955-rhXaKTe4N1/tpXOmN6VPyQ~!~server.ccl.net> X-Original-From: Suman Layek Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 16 May 2013 02:58:50 +0000 MIME-Version: 1.0 Sent to CCL by: Suman Layek [slayek++universaldisplay.com] Try %nprocshared=8 ________________________________ > From: owner-chemistry+slayek==universaldisplay.com(~)ccl.net [owner-chemistry+slayek==universaldisplay.com(~)ccl.net] on behalf of RAMY EHAB romio.1001:yahoo.com [owner-chemistry(~)ccl.net] Sent: Wednesday, May 15, 2013 4:41 PM To: Suman Layek Subject: CCL:G: Only for professionaal in using Cores ! I have a Dell Workstation computer with 2 processors quad core 2 * 12 Mb cache .. how can i use the 8 cores in using gaussian09w as it is limited to 4 cores ,and when i wrote #nproc=8 it gave me error ,, any solution to use the 8 cores ? From owner-chemistry@ccl.net Thu May 16 14:02:01 2013 From: "Nicolas Cheron ncheron ~~ fas.harvard.edu" To: CCL Subject: CCL: compound similarity comparison Message-Id: <-48707-130516095321-20595-uzlduPO5zokyq9rb93Gyew.@.server.ccl.net> X-Original-From: Nicolas Cheron Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 16 May 2013 09:52:30 -0400 MIME-Version: 1.0 Sent to CCL by: Nicolas Cheron [ncheron.-$-.fas.harvard.edu] Hi, You can also use jcsearch http://www.chemaxon.com/jchem/doc/user/Jcsearch.html. If you want to look for similarities between InputFile.smi and Database.smi with a treshold of 0.1 (threshold is a value between 0 and 1, the closer to 0 the more similar the structures) you can use this kind of script: Smiles_Array=(` awk '{ print $1 ; }' InputFile.smi `) Smiles_Size=` wc -l InputFile.smi | awk '{ print $1 ; }' ` x=0 while [ $x -lt ${Smiles_Size} ]; do echo "#### ${Smiles_Array[$x]} ####" >> Results.smi jcsearch -q "${Smiles_Array[$x]}" Database.smi -t:i:0.1 >> Results.smi echo " " >> Results.smi x=`expr $x + 1` done Nicolas 2013/5/16 Johannes Hachmann jh#%#chemistry.harvard.edu : > > Sent to CCL by: "Johannes Hachmann" [jh+/-chemistry.harvard.edu] > Hi Jinming, > > You are looking for fingerprinting and you can use openbabel for that: > http://openbabel.org/wiki/Tutorial:Fingerprints > > Best wishes > > Johannes > > ----------------------------------------------- > Dr. Johannes Hachmann > Research Associate > Harvard University > Department of Chemistry and Chemical Biology > 12 Oxford St, Rm M104A > Cambridge, MA 02138 > ----------------------------------------------- > > > >> -----Original Message----- >> From: owner-chemistry+jh==chemistry.harvard.edu[A]ccl.net [mailto:owner- >> chemistry+jh==chemistry.harvard.edu[A]ccl.net] On Behalf Of zhoujinming >> zhou_jim#hotmail.com >> Sent: Wednesday, 15 May, 2013 21:36 >> To: Hachmann, Johannes >> Subject: CCL: compound similarity comparison >> >> Dear CCLer >> >> Does some have the free script for compound similarity comparison using >> SMILES format, the one using Java language should be better. Please give > some >> advice. >> >> Many Thanks. >> >> JinMING> > From owner-chemistry@ccl.net Thu May 16 14:37:00 2013 From: "kalyan onekalyan,yahoo.com" To: CCL Subject: CCL:G: b3lyp* Message-Id: <-48708-130516114459-18927-U/Mob69gdrvbolzzLoZ3vQ(0)server.ccl.net> X-Original-From: kalyan Content-Type: multipart/alternative; boundary="1679980782-161845208-1368719089=:85182" Date: Thu, 16 May 2013 08:44:49 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: kalyan [onekalyan|a|yahoo.com] --1679980782-161845208-1368719089=:85182 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi =0A=0A=0Ahttp://www.gaussian.com/g_tech/g_ur/k_dft.htm=0AThis is quite g= ood guidline =0A=0Aalso you can follow this Linki below =0A=0Ahttp://www.th= ch.uni-bonn.de/tc/index.php?section=3Ddownloads&subsection=3DDFT-D3&lang=3D= english=0ADownload the code, compile it and run the calculation with the st= ructures =0Aoptimized with B3LYP. It will give you the the dispersion corre= ction =0Awithin 0.1 second. For most cases, I think a single point calculat= ion is enough. =0AOf course, if anybody knows how to run a DFT-D3 calculati= on on G09 with IOP, I also would like to know, thanks!=0A=0A=0Akalyan =0A= =0A=0A=0A=0A=0A>________________________________=0A> From: Mariusz Radon ma= riusz. radon{=3D}gmail. com =0A>To: "Dhar, Kalyan = kumar " =0A>Sent: Wednesday, May 15, 2= 013 9:34 PM=0A>Subject: CCL:G: b3lyp*=0A> =0A>=0A>=0A>Sent to CCL by: Mariu= sz Radon [mariusz.radon[a]gmail.com]=0A>On 13.05.2013 11:55, mala alhaji sa= inna alhajisainna _ yahoo.co.uk wrote:=0A>> Sent to CCL by: "mala alhaji=A0= sainna" [alhajisainna*|*yahoo.co.uk]=0A>> Hi Everyone,=0A>> =0A>> I will h= ighly appreciate it if some one can guide me on how to use the b3lyp* funct= ional; I tried getting =0A>> an iop for it on the gaussian website but it d= oesnt seems to be there and i am not sure how it is used.=0A>> =0A>> Many t= hanks,=0A>> Mala =0A>> The University of Manchester=0A>> =0A>=0A>Hi,=0A>=0A= >You can obtain B3LYP* functional as User-Defined Model based on BLYP=0A>fu= nctional. Consult the Gaussian 09 docs about "User-Defined Model":=0A>http:= //www.gaussian.com/g_tech/g_ur/k_dft.htm=0A>=0A>The values of the coefficie= nts in the model are probably given in the=0A>Marcus Reiher's original pape= r (DOI: 10.1007/s00214-001-0300-3)=0A>where this functional has been first = defined. Anyway, they are the same=0A>as in the original B3LYP, except the = factor weighting the HF=0A>exchange (which is 0.15, instead of 0.20).=0A>= =0A>Regards,=0A>Mariusz> =0A>> =0A>=0A>=0A>-- =0A>Dr Mariusz Radon, Ph.D.= =0A>Coordination Chemistry Group=0A>Faculty of Chemistry=0A>Jagiellonian Un= iversity=0A>ul. Ingardena 3, 30-060 Krakow, Poland=0A>http://www.chemia.uj.= edu.pl/~mradon=0A>=0A>=0A>=0A>-=3D This is automatically added to each mess= age by the mailing script =3D-=0A>To recover the email address of the autho= r of the message, please change=0A>the strange characters on the top line t= o the #%# sign. You can also=0A>look up the X-Original-From: line in the mail= header.=0A>=0A=0A>=A0 =A0= =A0=0A>=0A>E-mail to admin= istrators: CHEMISTRY-REQUEST#%#ccl.net or use=0A>=A0 =A0 =A0 http://www.ccl.n= et/cgi-bin/ccl/send_ccl_message=0A>=0A=0A>=A0 =A0 = =A0=0A>=0A>Before posting, che= ck wait time at: http://www.ccl.net=0A>=0A=0A==0A= >=0A=0A= >=0A=0A>=A0 =A0 =A0 ==0A>=0A>RTFI: http://www.ccl.net/chemistry/a= boutccl/instructions/=0A>=0A>=0A>=0A>=0A>=0A>=0A> --1679980782-161845208-1368719089=:85182 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Hi =

= http://www.gaussian.com/g_tech/g_ur/k_dft.htm

This is quite = good guidline

also you can follow this Linki below

http://www.thch.uni-bonn.de/tc/index.php?section=3D= downloads&subsection=3DDFT-D3&lang=3Denglish

Download=0A the code, compile= it and run the calculation with the structures =0Aoptimized with B3LYP. It= will give you the the dispersion correction =0Awithin 0.1 second. For most= cases, I think a single point calculation is=0A enough.
Of course, if = anybody knows how to run a DFT-D3 calculation on G09 with IOP, I also would= like to know, thanks!

= kalyan

From: Mariusz Radon mariusz. radon{=3D}gmail. com <owner-chemistry#%#ccl.net&g= t;
To: "Dhar, Kalyan k= umar " <kalyan.dhar#%#mail.polimi.it>
Sent: Wednesday, May 15, 2013 9:34 PM
<= span style=3D"font-weight: bold;">Subject: CCL:G: b3lyp*

Sent to CCL by: Mariusz = Radon [mariusz.radon[a]gmail.com]
On 13.05.2013 11:55, mala alhaji sainn= a alhajisainna _ yahoo.co.uk wrote:
> Sent to CCL by: "mala alhaji&nb= sp; sainna" [alhajisainna*|*yahoo.co.uk]
> Hi Everyone,
>
> I will = highly appreciate it if some one can guide me on how to use the b3lyp* func= tional; I tried getting
> an iop for it on the gaussian website but = it doesnt seems to be there and i am not sure how it is used.
>
&= gt; Many thanks,
> Mala
> The University of Manchester
>=

Hi,

You can obtain B3LYP* functional as User-Defined Model = based on BLYP
functional. Consult the Gaussian 09 docs about "User-Defin= ed Model":
http://www.gaussian.com/g_tech/g_ur/k_dft.htm

The= values of the coefficients in the model are probably given in the
Marcu= s Reiher's original paper (DOI: 10.1007/s00214-001-0300-3)
where this fu= nctional has been first defined. Anyway, they are the same
as in the ori= ginal B3LYP, except the factor weighting the HF
exchange (which is 0.15, instead of 0.20).

Regards,
Mariusz>
>

--
Dr Mariusz Radon, Ph.D.
Coordination Chemistry Group
Faculty= of Chemistry
Jagiellonian University
ul. Ingardena 3, 30-060 Krakow,= Poland
http://www.chemia.uj.edu.pl/~mradon

-=3D This is aut= omatically added to each message by the mailing script =3D-
To recover t= he email address of the author of the message, please change
the strange= characters on the top line to the #%# sign. You can also
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Before posting, check wait time at: http://www.ccl.net

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Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml &nbs= p; htt= p://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/che= mistry/aboutccl/instructions/

--1679980782-161845208-1368719089=:85182-- From owner-chemistry@ccl.net Thu May 16 23:49:00 2013 From: "Klemens Noga klemens.noga(a)gmail.com" To: CCL Subject: CCL:G: b3lyp* Message-Id: <-48709-130516181529-5734-esAULNRVyQdt+/YZBEzV1Q]=[server.ccl.net> X-Original-From: Klemens Noga Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Fri, 17 May 2013 00:15:03 +0200 Mime-Version: 1.0 (Mac OS X Mail 6.3 $1503$) Sent to CCL by: Klemens Noga [klemens.noga!A!gmail.com] On 16 May 2013, at 17:44, "kalyan onekalyan,yahoo.com" wrote: > Hi > > http://www.gaussian.com/g_tech/g_ur/k_dft.htm > This is quite good guidline > also you can follow this Linki below > http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english > Download the code, compile it and run the calculation with the structures optimized with B3LYP. It will give you the the dispersion correction within 0.1 second. For most cases, I think a single point calculation is enough. Hi, I do not agree that in the most cases SP is enough. You could check papers by Grimme and others in which is clearly stated that, DFT without dispersion correction gives totally wrong geometries for certain systems. Personally I've studied several weak adducts bonded with weak hydrogen bonds, in which without addition of dispersion correction on geometry optimization level, you cannot get geometries that are stable enough to reproduce data from experiments. Of course this correction (on geometry optimization level) was not so important in similar adducts bonded with stronger H-bonds. It those cases addition dispersion correction on final geometry was enough to get relatively good energetics and thermodynamics. > Of course, if anybody knows how to run a DFT-D3 calculation on G09 with IOP, I also would like to know, thanks! > In newest revision of Gaussian (D.01) which has just arrived (released on 10 May 2013) there is new keyword implemented for dispersion correction which include two DFT-D3 correction variants. It is called EmpiricalDispersion=PFD, GD3 or GD3BJ and quote from release notes "explicitly request Petersson-Frisch dispersion [Austin12] or Grimme�s D3 dispersion [Grimme10] or D3BJ dispersion [Grimme11].". Best regards, Klemens > > kalyan >