From owner-chemistry@ccl.net Fri Aug 31 06:17:00 2012 From: "Hans De Winter hans!A!silicos-it.com" To: CCL Subject: CCL: Align-it 1.0.3 Message-Id: <-47511-120831061630-8708-1ohQo01JTmYhSHkHdbE9Zw[-]server.ccl.net> X-Original-From: "Hans De Winter" Date: Fri, 31 Aug 2012 06:16:29 -0400 Sent to CCL by: "Hans De Winter" [hans,,silicos-it.com] Hi all, Align-it 1.0.3 has been released as of today. Align-it is using the Open Babel C++ as its core API. Align-it is an open source tool for the alignment of database molecules to a reference compound using pharmacophore matches. You can download the new release from the website of Silicos-it (www.silicos-it.com). New features include improved format specification possibilities for the reference file, database file and output file. Happy aligning! Hans From owner-chemistry@ccl.net Fri Aug 31 14:49:01 2012 From: "Gustavo L.C. Moura gustavo.moura*ufpe.br" To: CCL Subject: CCL: Polarization Basis Functions Message-Id: <-47512-120831144732-24473-+/EbPwLwHMxpl7ZvwtHawg:+:server.ccl.net> X-Original-From: "Gustavo L.C. Moura" Date: Fri, 31 Aug 2012 14:47:31 -0400 Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura~!~ufpe.br] Dear CCL Readers, How are the exponents of the polarization functions determined in a basis set? Taking carbon as an example, I know that we may determine the exponents of the s and p basis functions through the minimization of the electronic energy of an atomic calculation. But, how to determine the exponents of the d, or even f, basis functions if they do not contribute to the energy of the isolated atom? I apologize if this question sounds too basic, but I failed to find an answer to this question in the internet or in my books. Thank you very much in advance for helping me with this question. Sincerely yours, Gustavo L.C. Moura From owner-chemistry@ccl.net Fri Aug 31 15:58:00 2012 From: "Van Dam, Hubertus J HubertusJJ.vanDam-x-pnnl.gov" To: CCL Subject: CCL: Polarization Basis Functions Message-Id: <-47513-120831155646-24372-0Etum3y5MAX41u1rXSmW1A..server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 31 Aug 2012 12:56:37 -0700 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam|*|pnnl.gov] Hi Gustavo, I think the simple answer is that you are right if you want to optimize the exponents with an effective 1-electron model. However, when you introduce electron correlation (i.e. some kind of CI treatment) then the "unoccupied" d and f's do contribute. I think you might find some information that is useful on this point in the papers that discuss the creation of ANO (Atomic Natural Orbital) basis sets. I hope this helps, Huub -----Original Message----- > From: owner-chemistry+hubertus.vandam==pnnl.gov===ccl.net [mailto:owner-chemistry+hubertus.vandam==pnnl.gov===ccl.net] On Behalf Of Gustavo L.C. Moura gustavo.moura*ufpe.br Sent: Friday, August 31, 2012 11:48 AM To: Van Dam, Hubertus J Subject: CCL: Polarization Basis Functions Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura~!~ufpe.br] Dear CCL Readers, How are the exponents of the polarization functions determined in a basis set? Taking carbon as an example, I know that we may determine the exponents of the s and p basis functions through the minimization of the electronic energy of an atomic calculation. But, how to determine the exponents of the d, or even f, basis functions if they do not contribute to the energy of the isolated atom? I apologize if this question sounds too basic, but I failed to find an answer to this question in the internet or in my books. Thank you very much in advance for helping me with this question. Sincerely yours, Gustavo L.C. Mourahttp://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 Fri Aug 31 16:33:01 2012 From: "Jussi Lehtola jussi.lehtola(!)helsinki.fi" To: CCL Subject: CCL: Polarization Basis Functions Message-Id: <-47514-120831161137-32133-wywgWr7cXmzCIU5cbILraA%server.ccl.net> X-Original-From: Jussi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 31 Aug 2012 23:11:17 +0300 Mime-Version: 1.0 Sent to CCL by: Jussi Lehtola [jussi.lehtola:+:helsinki.fi] On Fri, 31 Aug 2012 14:47:31 -0400 "Gustavo L.C. Moura gustavo.moura*ufpe.br" wrote: > Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura~!~ufpe.br] > Dear CCL Readers, > How are the exponents of the polarization functions > determined in a basis set? Taking carbon as an example, I know that > we may determine the exponents of the s and p basis functions through > the minimization of the electronic energy of an atomic calculation. > But, how to determine the exponents of the d, or even f, basis > functions if they do not contribute to the energy of the isolated > atom? I apologize if this question sounds too basic, but I failed to > find an answer to this question in the internet or in my books. Thank > you very much in advance for helping me with this question. Sincerely > yours, Gustavo L.C. Moura To determine polarization functions you need to use some other model system than the atom in order to perform the energy optimization. Optimal polarization functions depend somewhat on the chemical environment, so many different molecules are often studied and then the exponents averaged somehow to form the production basis set. See e.g. Jensen's papers [JCP 115, 9113 (2001)]. On the other hand, correlation functions (which are often also called polarization functions) can be determined from atomic calculations, e.g. Dunning's work [JCP 90, 1007 (1989)]. It's also possible to forget all about energy optimization and tune basis sets directly for particular properties using completeness-optimization [JCC 27, 434 (2006)]. In fact, I have a paper coming out soon on automatical basis set formation [JCP 137, ??? (2012), doi: 10.1063/1.4749272]. -- -------------------------------------------------------- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.lehtola^^^helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland -------------------------------------------------------- Jussi Lehtola, FM Tohtorikoulutettava jussi.lehtola^^^helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -------------------------------------------------------- From owner-chemistry@ccl.net Fri Aug 31 17:19:00 2012 From: "Amy Austin amy_jean_austin~~yahoo.com" To: CCL Subject: CCL:G: Polarization Basis Functions - APNO Message-Id: <-47515-120831171811-12049-1TX1ljP7QbCSnUe4f9MR0w%a%server.ccl.net> X-Original-From: Amy Austin Content-Type: multipart/alternative; boundary="1073417382-1060922733-1346447883=:31984" Date: Fri, 31 Aug 2012 14:18:03 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Amy Austin [amy_jean_austin*yahoo.com] --1073417382-1060922733-1346447883=:31984 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Gustavo,=0A=0AThere are various algorithms. As Huub points out, I think = this is a good one to follow:=0A=0A=E2=80=9COn the Optimization of Gaussian= Basis sets,=E2=80=9D G. A. Petersson, S. Zhong, J. A. Montgomery, Jr., and= M. J. Frisch, J. Chem. Phys.118, 1101 (2003).=0A=0AAll my best,=0A=0AAmy= =0A=0A=0A=0A________________________________=0A From: "Van Dam, Hubertus J = HubertusJJ.vanDam-x-pnnl.gov" =0ATo: "Austin, Amy = J " =0ASent: Friday, August 31, 2012 3:= 56 PM=0ASubject: CCL: Polarization Basis Functions=0A =0A=0ASent to CCL by:= "Van Dam, Hubertus J" [HubertusJJ.vanDam|*|pnnl.gov]=0AHi Gustavo,=0A=0AI = think the simple answer is that you are right if you want to optimize the e= xponents with an effective 1-electron model. However, when you introduce el= ectron correlation (i.e. some kind of CI treatment) then the "unoccupied" d= and f's do contribute. I think you might find some information that is use= ful on this point in the papers that discuss the creation of ANO (Atomic Na= tural Orbital) basis sets.=0A=0AI hope this helps,=0A=0A=C2=A0 =C2=A0 Huub= =0A=0A-----Original Message-----=0A> From: owner-chemistry+hubertus.vandam= =3D=3Dpnnl.gov_-_ccl.net [mailto:owner-chemistry+hubertus.vandam=3D=3Dpnnl.= gov_-_ccl.net] On Behalf Of Gustavo L.C. Moura gustavo.moura*ufpe.br=0ASent= : Friday, August 31, 2012 11:48 AM=0ATo: Van Dam, Hubertus J=0ASubject: CCL= : Polarization Basis Functions=0A=0A=0ASent to CCL by: "Gustavo L.C. Moura"= [gustavo.moura~!~ufpe.br] Dear CCL Readers,=0A=C2=A0=C2=A0=C2=A0 How are t= he exponents of the polarization functions determined in a basis set?=0A=C2= =A0=C2=A0=C2=A0 Taking carbon as an example, I know that we may determine t= he exponents of the s and p basis functions through the minimization of the= electronic energy of an atomic calculation. But, how to determine the expo= nents of the d, or even f, basis functions if they do not contribute to the= energy of the isolated atom?=0A=C2=A0=C2=A0=C2=A0 I apologize if this ques= tion sounds too basic, but I failed to find an answer to this question in t= he internet or in my books.=0A=C2=A0=C2=A0=C2=A0 Thank you very much in adv= ance for helping me with this question.=0A=C2=A0=C2=A0=C2=A0 Sincerely your= s,=0A=C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0= =C2=A0 Gustavo L.C. Mourahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehtt= p://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt=0A= =0A=0A-=3D This is automatically added to each message by the mailing scrip= t =3D-=0ATo recover the email address of the author of the message, please = change=0A= =0A=0A=0AE-mail to sub= scribers: CHEMISTRY() ccl.net or use:=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.n= et/cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-RE= QUEST() ccl.net or use=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/= send_ccl_message=0A=0A=0A=C2=A0 =C2=A0 =C2=A0 http:/= /www.ccl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time= at: http://www.ccl.net=0A=0A=0AConferences: h= ttp://server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messa= ges: http://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail b= ounces from CCL with 5.7.1 error, check:=0A=C2=A0 =C2=A0 =C2=A0 http://www.= ccl.net/spammers.txt=0A=0ARTFI: http://www.ccl.net/chemistry/aboutccl/instr= uctions/ --1073417382-1060922733-1346447883=:31984 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi Gustavo= ,

There are various algo= rithms. As Huub points out, I think this is a good one to follow:
=E2=80=9COn the Optimization of Gaussian Basis sets,=E2=80=9D G. A.= Petersson, S. Zhong, J. A. Montgomery, Jr., and M. J. Frisch, J. Chem. Phys. 118, 1101 (2003).



= From: "Van Dam, Hubertus J Hubertus= JJ.vanDam-x-pnnl.gov" <owner-chemistry() ccl.net>
To: "Austin, Amy J " <amy_jean_a= ustin() yahoo.com>
Sent:= Friday, August 31, 2012 3:56 PM
Subject: CCL: Polarization Basis Functions
=0A
Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam|*|pnn= l.gov]
Hi Gustavo,

I think the simple answer is that you are righ= t if you want to optimize the exponents with an effective 1-electron model.= However, when you introduce electron correlation (i.e. some kind of CI tre= atment) then the "unoccupied" d and f's do contribute. I think you might fi= nd some information that is useful on this point in the papers that discuss= the creation of ANO (Atomic Natural Orbital) basis sets.

I hope thi= s helps,

    Huub

-----Original Message-----
>= ; From: owner-chemistry+hubertus.vandam=3D=3Dpnnl.gov_-_ccl.net [mailto:own= er-chemistry+hubertus.vandam=3D=3Dpnnl.gov_-_ccl.net] On Behalf Of Gustavo = L.C. Moura gustavo.moura*ufpe.br
Sent: Friday, August 31, 2012 11:48 AM<= br>To: Van Dam, Hubertus J
Subject: CCL: Polarization Basis Functions

Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura~!~ufpe.br] Dea= r CCL Readers,
    How are the exponents of the polarization f= unctions determined in a basis set?
    Taking carbon as = an example, I know that we may determine the exponents of the s and p basis= functions through the minimization of the electronic energy of an atomic c= alculation. But, how to determine the exponents of the d, or even f, basis = functions if they do not contribute to the energy of the isolated atom?
=     I apologize if this question sounds too basic, but I fai= led to find an answer to this question in the internet or in my books.
&= nbsp;   Thank you very much in advance for helping me with this q= uestion.
    Sincerely yours,
     = ;           Gustavo L.C. Mourahttp:= //www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_= unsub.shtmlhttp://www.ccl.net/spammers.txt


-=3D This is automatically added to each message by the mailing script =3D-
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<= br>
--1073417382-1060922733-1346447883=:31984-- From owner-chemistry@ccl.net Fri Aug 31 17:54:00 2012 From: "Grant Hill Grant.Hill:-:glasgow.ac.uk" To: CCL Subject: CCL: Polarization Basis Functions Message-Id: <-47516-120831161000-31267-srS2Vp8m66V5TLMDE2Nu7A(a)server.ccl.net> X-Original-From: Grant Hill Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 31 Aug 2012 21:09:52 +0100 MIME-Version: 1.0 Sent to CCL by: Grant Hill [Grant.Hill=glasgow.ac.uk] Dear Gustavo, The answer to this question strongly depends on the basis set in question. The higher angular momentum functions DO contribute to the atomic energy in correlated ab initio methods (such as CISD). A popular alternative for DFT or HF based optimisations is to use symmetric homonuclear systems (often dimers). You can find a more detailed answer in the original publication for any popular basis set (e.g. correlation consistent for the former method, polarisation consistent for the latter). Best regards, Grant On 31 Aug 2012, at 19:47, "Gustavo L.C. Moura gustavo.moura*ufpe.br" wrote: > > Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura~!~ufpe.br] > Dear CCL Readers, > How are the exponents of the polarization functions determined in a basis set? > Taking carbon as an example, I know that we may determine the exponents of the s and p basis functions through the minimization of the electronic energy of an atomic calculation. But, how to determine the exponents of the d, or even f, basis functions if they do not contribute to the energy of the isolated atom? > I apologize if this question sounds too basic, but I failed to find an answer to this question in the internet or in my books. > Thank you very much in advance for helping me with this question. > Sincerely yours, > Gustavo L.C. Moura > >