From owner-chemistry@ccl.net Thu Mar 19 05:29:01 2015 From: "Cina Foroutan-Nejad canyslopus]~[yahoo.co.uk" To: CCL Subject: CCL: looking for a parameter to characterize the degree of delocalization Message-Id: <-51154-150319052619-4329-k/qoHMUWpz4ZfeJ2P4dgJw-$-server.ccl.net> X-Original-From: Cina Foroutan-Nejad Content-Type: multipart/alternative; boundary="----=_Part_397949_1795092889.1426757168595" Date: Thu, 19 Mar 2015 09:26:08 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Cina Foroutan-Nejad [canyslopus++yahoo.co.uk] ------=_Part_397949_1795092889.1426757168595 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Youhao, There is a straighforward parameter defined within the context of QTAIM (qu= antum theory of atoms in molecules). It is called delocalization index. It = measures the degree of electron sharing between two topological atoms. Many= QTAIM programs can define delocalization index between atomic pairs but us= ually they do not partition it into orbital contributions. However, if you = want you can partition DI into orbital contributions by having overlap matr= ix for each atom. Among AIM programs AIM2000 provides overlap matrix for at= oms. I am not sure if Multiwfn can do it or not but you may ask its develop= er. Once you have overlap matrix for any atom, you can measure orbital cont= ributions via a simple equation: DI(A,B) =3D - Sigma Sigma [Sij(A)Sij(B)] Where A and B are two atoms, by Sigma as you may guess I mean summation, an= d Sij(a and B) are overlap terms for each orbital. Please be careful that i= f you merely focus on pi-orbitals then a part of DI which is related to par= tial overlap between pi and sigma or delta... will be missing. For an ideal= ly symmetric system this must be zero but this is not necessarily true for = all systems. So, for non-planar/non-symmetric systems you may sum up contri= butions of pi, sigma, etc. together then compare it with total DI to have t= he contribution of mixing too. This type of computation is NOT conventional= or straightforward and I cannot refer you to a particular paper but theore= tically is possible. For more information regarding DI you may look at J. P= hys. Chem. A, 1999, 103, 304-314. On the other hand, some researchers believe that measuring current density = in the presence of magnetic fields is also a measure of pi-delocalization. = You may check some papers with the keyword current density but be aware tha= t there is a fundamental difference between DI and current density. DI is a= ground-state property but current density that is widely believed is a mea= sure of pi electron delocalization is a "response" property. This means tha= t DI is non-zero in the absence of external fields but current density is z= ero in the absence of an external magnetic field.=C2=A0 Good luck,Cina -------------------------------------------------------------------------Ci= na Foroutan-Nejad, PhD,CEITEC-Central European Institute of TechnologyMasar= yk University, Brno,Czech Republichttps://muni.academia.edu/CinaForoutanNej= ad =20 On Thursday, 19 March 2015, 3:28, Youzhao Lan lyzhao(_)aliyun.com wrote: =20 =20 Sent to CCL by: "Youzhao=C2=A0 Lan" [lyzhao]_[aliyun.com] Dear all, Is there a calculated parameter or quantity to characterize the degree of delocalization of pi-electron? Any help will be appreciated. Best regards. Youzhao Lan -=3D This is automatically added to each message by the mailing script =3D-=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20 =C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0------=_Part_397949_1795092889.1426757168595 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Youhao,

There is a straighforward parameter defined within the = context of QTAIM (quantum theory of atoms in molecules). It is called deloc= alization index. It measures the degree of electron sharing between two top= ological atoms. Many QTAIM programs can define delocalization index between= atomic pairs but usually they do not partition it into orbital contributio= ns. However, if you want you can partition DI into orbital contributions by= having overlap matrix for each atom. Among AIM programs AIM2000 provides o= verlap matrix for atoms. I am not sure if Multiwfn can do it or not but you= may ask its developer. Once you have overlap matrix for any atom, you can = measure orbital contributions via a simple equation:

DI(A,B) =3D - Sigma Sigma [Sij(A)Sij(B)]
=

Where A and B are two atoms, by Sigma as you = may guess I mean summation, and Sij(a and B) are overlap terms for each orb= ital. Please be careful that if you merely focus on pi-orbitals then a part= of DI which is related to partial overlap between pi and sigma or delta...= will be missing. For an ideally symmetric system this must be zero but thi= s is not necessarily true for all systems. So, for non-planar/non-symmetric= systems you may sum up contributions of pi, sigma, etc. together then comp= are it with total DI to have the contribution of mixing too. This type of c= omputation is NOT conventional or straightforward and I cannot refer you to= a particular paper but theoretically is possible. For more information reg= arding DI you may look at J. Phys. Chem. A, 1999, 103, 304-314.

<= /div>
On the other hand, some researchers believe= that measuring current density in the presence of magnetic fields is also = a measure of pi-delocalization. You may check some papers with the keyword = current density but be aware that there is a fundamental difference between= DI and current density. DI is a ground-state property but current density = that is widely believed is a measure of pi electron delocalization is a "re= sponse" property. This means that DI is non-zero in the absence of external= fields but current density is zero in the absence of an external magnetic = field. 

Good luck,
Cina

-= ------------------------------------------------------------------------
Cina Foroutan-Nejad, PhD,
CEITEC-Central European Institute of Technology=
Masaryk University, Brno,
Czech Repu= blic




On Thursday, 19 March 2015, 3:28, Y= ouzhao Lan lyzhao(_)aliyun.com <owner-chemistry.-$-.ccl.net> wrote:
<= /font>



Sent to CCL by: = "Youzhao  Lan" [lyzhao]_[aliyun.com]
Dear all,
Is there a calcul= ated parameter or quantity to characterize
the degree of delocalization = of pi-electron?

Any help will be appreciated.

Best regards.Youzhao Lan



-=3D This is automatically added to each messa= ge 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.-$-.ccl.net or use:
 = ;     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
<= br>E-mail to administrators: CHEMISTRY-REQUEST.-$-.ccl.net o= r use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_me= ssage
      http://www= .ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait ti= me at: http://www.ccl.net=

Job: http= ://www.ccl.net/jobs
Conferences: http://server.ccl.ne= t/chemistry/announcements/conferences/

Search Messages: h= ttp://www.ccl.net/chemistry/searchccl/index.shtml

If your mail b= ounces from CCL with 5.7.1 error, check:
      http://www.ccl.net/spam= mers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/inst= ructions/




= ------=_Part_397949_1795092889.1426757168595-- From owner-chemistry@ccl.net Thu Mar 19 08:59:01 2015 From: "=?UTF-8?B?R3JlZ29yaW8gR2FyY8OtYSBNb3Jlbm8=?= gjgarcia%ujaen.es" To: CCL Subject: CCL: looking for a parameter to characterize the degree of delocalization Message-Id: <-51155-150319051043-3585-byLwEVoDAM2ALnAUN0yz8Q[#]server.ccl.net> X-Original-From: =?UTF-8?B?R3JlZ29yaW8gR2FyY8OtYSBNb3Jlbm8=?= Content-Type: multipart/alternative; boundary="------------090508090700000905080309" Date: Thu, 19 Mar 2015 10:10:25 +0100 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?B?R3JlZ29yaW8gR2FyY8OtYSBNb3Jlbm8=?= [gjgarcia%ujaen.es] This is a multi-part message in MIME format. --------------090508090700000905080309 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit Dear Y. Lan, read this paper. I hope it could be useful Palusiak, M. and Krygowski, Tadeusz M. (2007), Application of AIM Parameters at Ring Critical Points for Estimation of π-Electron Delocalization in Six-Membered Aromatic and Quasi-Aromatic Rings. Chem. Eur. J., 13: 7996–8006. doi: 10.1002/chem.200700250 http://onlinelibrary.wiley.com/doi/10.1002/chem.200700250/abstract El 18/03/2015 a las 15:17, Youzhao Lan lyzhao(_)aliyun.com escribió: > Sent to CCL by: "Youzhao Lan" [lyzhao]_[aliyun.com] > Dear all, > Is there a calculated parameter or quantity to characterize > the degree of delocalization of pi-electron? > > Any help will be appreciated. > > Best regards. > Youzhao Lan> > > -- Gregorio García Moreno, PhD e-mail: gjgarcia_._ubu.es Department of Chemistry University of Burgos Plaza Misael Bañuelos s/n 09001 Burgos - Spain --------------090508090700000905080309 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit Dear Y. Lan, read this paper. I hope it could be useful

Palusiak, M. and Krygowski, Tadeusz M. (2007), Application of AIM Parameters at Ring Critical Points for Estimation of π-Electron Delocalization in Six-Membered Aromatic and Quasi-Aromatic Rings. Chem. Eur. J., 13: 7996–8006. doi: 10.1002/chem.200700250

http://onlinelibrary.wiley.com/doi/10.1002/chem.200700250/abstract




El 18/03/2015 a las 15:17, Youzhao Lan lyzhao(_)aliyun.com escribió:
Sent to CCL by: "Youzhao  Lan" [lyzhao]_[aliyun.com]
Dear all,
Is there a calculated parameter or quantity to characterize
the degree of delocalization of pi-electron?

Any help will be appreciated.

Best regards.
Youzhao LanE-mail to subscribers: CHEMISTRY_._ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST_._ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs 
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





-- 
Gregorio García Moreno, PhD
e-mail: gjgarcia_._ubu.es
Department of Chemistry
University of Burgos
Plaza Misael Bañuelos s/n
09001 Burgos - Spain
--------------090508090700000905080309-- From owner-chemistry@ccl.net Thu Mar 19 10:11:00 2015 From: "Youzhao Lan lyzhao.*|*.aliyun.com" To: CCL Subject: CCL: looking for a parameter to characterize the degree of delocal Message-Id: <-51156-150319091325-29018-1CZ4bmYDqnF5HypZCMZUnQ*|*server.ccl.net> X-Original-From: "Youzhao Lan" Date: Thu, 19 Mar 2015 09:13:23 -0400 Sent to CCL by: "Youzhao Lan" [lyzhao:aliyun.com] Dear Dr. Cina, Thanks for your kind help. Multiwfn can do it in terms of its manual. Best regards. -------------------------------------------------------------------------------- Youzhao Lan > From: Cina Foroutan-Nejad canyslopus]~[yahoo.co.uk Date: 2015-03-19 17:26 To: Lan, Youzhao Subject: CCL: looking for a parameter to characterize the degree of delocalization Dear Youhao, There is a straighforward parameter defined within the context of QTAIM (quantum theory of atoms in molecules). It is called delocalization index. It measures the degree of electron sharing between two topological atoms. Many QTAIM programs can define delocalization index between atomic pairs but usually they do not partition it into orbital contributions. However, if you want you can partition DI into orbital contributions by having overlap matrix for each atom. Among AIM programs AIM2000 provides overlap matrix for atoms. I am not sure if Multiwfn can do it or not but you may ask its developer. Once you have overlap matrix for any atom, you can measure orbital contributions via a simple equation: DI(A,B) = - Sigma Sigma [Sij(A)Sij(B)] Where A and B are two atoms, by Sigma as you may guess I mean summation, and Sij(a and B) are overlap terms for each orbital. Please be careful that if you merely focus on pi-orbitals then a part of DI which is related to partial overlap between pi and sigma or delta... will be missing. For an ideally symmetric system this must be zero but this is not necessarily true for all systems. So, for non-planar/non-symmetric systems you may sum up contributions of pi, sigma, etc. together then compare it with total DI to have the contribution of mixing too. This type of computation is NOT conventional or straightforward and I cannot refer you to a particular paper but theoretically is possible. For more information regarding DI you may look at J. Phys. Chem. A, 1999, 103, 304-314. On the other hand, some researchers believe that measuring current density in the presence of magnetic fields is also a measure of pi-delocalization. You may check some papers with the keyword current density but be aware that there is a fundamental difference between DI and current density. DI is a ground-state property but current density that is widely believed is a measure of pi electron delocalization is a "response" property. This means that DI is non-zero in the absence of external fields but current density is zero in the absence of an external magnetic field. Good luck, Cina ------------------------------------------------------------------------- Cina Foroutan-Nejad, PhD, CEITEC-Central European Institute of Technology Masaryk University, Brno, Czech Republic https://muni.academia.edu/CinaForoutanNejad From owner-chemistry@ccl.net Thu Mar 19 11:16:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor[*]fluor.quimica.uniovi.es" To: CCL Subject: CCL: looking for a parameter to characterize the degree of delocalization Message-Id: <-51157-150319092412-32660-kdOibE7B+4aZZ2b5t0su8w[]server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Thu, 19 Mar 2015 14:19:27 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor++fluor.quimica.uniovi.es] On Thu, Mar 19, 2015 at 09:26:08AM +0000, Cina Foroutan-Nejad canyslopus]~[yahoo.co.uk wrote: Dear Youhao, Let me continue the information provided by Cina. There are several tools to perform a QTAIM analysis: RFW Bader provided the codes of his group: Aimall is maintained by T. Keith, one of his brightest PhD's: here are other tools by some of their former collaborators, and let me stop citing codes to avoid missing some. Just search for F. Biegler-König, P. Popelier, A. Martín Pendás, A Otero-de-la-Roza, ... All of them have published QTAIM codes that you may use for your purposes. As Cina says the localization and delocalization indices provide you the information that you want. Let me not forget a chinese code specially adapted to do QTAIM analyses on molecules: multiwfn Best regards, Dr. Víctor Luaña -- . . "The hardest part in solving a problem is recognizing / `' \ its existence. Learning the causes CAN be the road to /(o)(o)\ the solution." /`. \/ .'\ -- ¿? / '`'` \ "Lo mediocre es peor que lo bueno, pero también es peor | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es una | |'`'`| | actitud" \/`'`'`'\/ -- Jorge Wasenberg, 2015 ===(((==)))==================================+========================= ! Dr.Víctor Luaña ! Mediocre is worse than ! Departamento de Química Física y Analítica ! good, but it is also ! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because ! e-mail: victor[A]fluor.quimica.uniovi.es ! mediocrity is not a grade, ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Thu Mar 19 14:21:01 2015 From: "Tian Lu sobereva ~ sina.com" To: CCL Subject: CCL: looking for a parameter to characterize the degree of delocal Message-Id: <-51158-150319134019-12566-0bJ1kYxP+TpRkE1Pru4Mow/./server.ccl.net> X-Original-From: "Tian Lu" Date: Thu, 19 Mar 2015 13:40:16 -0400 Sent to CCL by: "Tian Lu" [sobereva*sina.com] Dear Youhao, Aside from DI, you can also use fuzzy bond order (FBO) or Mayer bond order (MBO) to the evaluate electron delocalization. As shown in J. Phys. Chem. A 2005, 109, 9904-9910, the DI, FBO and MBO are closely related to each other, their key difference is the way of atomic space partition. The DI is based on AIM partition, the FBO is based on fuzzy atomic space, while the MBO is based on atomic-center basis functions. Among them the MBO is the cheapest one, the time cost is always negligible, while the DI is the most expensive one, since integrating or generating AIM basin is not a easy task. Another worthnoting quantity is condensed linear response kernel (CLRK), which is somewhat related to the above quantities and may be also used to reveal electron delocalization. For example, in Phys. Chem. Chem. Phys., 2012,14, 3960-3967, the authors replaced the DI involved in para delocalization index (PDI) by CLRK and defined para linear response index (PLR). It is shown that PLR also works well for revealing aromaticity as the well-recognized PDI. For ring systems possessing less than 12 atoms, multi-center bond order (MCBO) is a very nice tool to examine multi-center delocalization. MCBO has been prevalently used to study aromaticity, see Phys. Chem. Chem. Phys., 2000, 2, 3381-3392 for example. I suggest also paying attention to the Anisotropy of the Induced Current Density (ACID), which is a very intuitive method to exhibit electron delocalization path, see Chem. Rev. 2005, 105, 3758-3772 for a review. The last method I would like to mention is the well-known electron localization function (ELF), which has been a standard approach to investigate electron delocalization problems. The value of bifurcation point of two ELF domains is frequently used in literatures to measure the degree of electron delocalization between corresponding spatial regions, and visualizating ELF isosurfaces is helpful to identify favorable delocalization channels. Note that the localized orbital locator (LOL) is a function very analogous to ELF, some people showed that LOL sometimes works better than ELF, see Phys. Chem. Chem. Phys., 2011, 13, 2058420592. Worthnotingly, all of the above mentioned quantities can be straightforwardly decomposed into sigma and pi contributions. Except for AICD, all of them can be easily studied by Multiwfn (multiwfn.codeplex.com), many examples can be found in its manual. -------------------------------- Best wishes, Tian Lu Beijing Kein Research Center for Natural Sciences, Beijing, P. R. China ----- Original Message ----- > From: "Youzhao Lan lyzhao(_)aliyun.com" To: "Lu, Tian " Subject: CCL: looking for a parameter to characterize the degree of delocalization Date: 2015-03-18 22:17 Sent to CCL by: "Youzhao Lan" [lyzhao]_[aliyun.com] Dear all, Is there a calculated parameter or quantity to characterize the degree of delocalization of pi-electron? Any help will be appreciated. Best regards. Youzhao Lanhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt