From owner-chemistry@ccl.net Fri Jun 13 04:17:01 2014 From: "Mariusz Radon mariusz.radon~~gmail.com" To: CCL Subject: CCL: Spin Delocalization/Localization using two different functionals Message-Id: <-50203-140613041346-30039-8iaFO7EhnfK6uSQkHaYeWQ+/-server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 13 Jun 2014 10:13:35 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon~~gmail.com] On 06/13/2014 01:09 AM, Kerry Jeffry Wrighton kerry.wrighton%usach.cl wrote: > Sent to CCL by: "Kerry Jeffry Wrighton" [kerry.wrighton*usach.cl] > Dear CCL team > > I have a question related to equilibrium geometries using B3LYP (hybrid) and > BP86 (GGA) functionals using the same basis set for both methods (TZV). I have > optimized the structure of a hexavanadium cluster, which contains 4 V(IV) and > 2 V(V) atoms. When I used the B3LYP functional, spin density is perfectly > localized over 4 V(IV) atoms. In the case of the BP86 functional the spin > density is full delocalized over the 6 V atoms. In both cases, the structures > are validated through the frequency analysis and comparison with bond > distances of crystallographic data. Why did it happen? > > Best Regards > > Kerry Wrighton-Araneda > Dear Kerry: It is a known tendency of pure functionals (like BP86) to overestimate an electron delocalization due to the self interaction error. This error can be compensated, in part, by mixing an approximate exchange functional with the exact exchange (like in B3LYP). See for instance [DOI: 10.1021/ct800531s]. It is thus perfectly understandable that introducing the exact exchange in B3LYP, as compared with BP86, leads to the more localized unpaired electrons. Recently I reported the similar behavior of these two functionals for a tetravanadium cluster [DOI: 10.1016/j.inoche.2013.12.034 + Supporting Information]. Best regards, Mariusz -- Dr Mariusz Radon, Ph.D. Coordination Chemistry Group Faculty of Chemistry Jagiellonian University ul. Ingardena 3, 30-060 Krakow, Poland http://www2.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Fri Jun 13 04:51:01 2014 From: "Anastasios Papadopoulos anastp * chem.auth.gr" To: CCL Subject: CCL:G: RAM memory and Processors Combination Message-Id: <-50204-140613043903-18522-zMILTpvmv9mlYVcLy9F7tA|*|server.ccl.net> X-Original-From: "Anastasios Papadopoulos" Date: Fri, 13 Jun 2014 04:39:01 -0400 Sent to CCL by: "Anastasios Papadopoulos" [anastp##chem.auth.gr] 54124 Dear CCLer's I have a problem with Gaussian 03W. I am trying to run an optimization calculation and I have a problem with the combination of RAM memory and processors users. The only accept combination is 1512mb with 3 or 4 processors.My available memory is 8Gb and 8 processors and I can't use all the sources. Please give any idea to resolve this problem Thanks in advance. Anastasios G. Papadopoulos From owner-chemistry@ccl.net Fri Jun 13 08:45:01 2014 From: "Robert Molt Jr r.molt.chemical.physics.%%.gmail.com" To: CCL Subject: CCL: Exchange correlation Message-Id: <-50205-140612213158-17856-RWGqRAIG1WGkf0t/0fFLBw%%server.ccl.net> X-Original-From: Robert Molt Jr Content-Type: multipart/alternative; boundary="------------060507020700040900030904" Date: Thu, 12 Jun 2014 21:31:49 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt Jr [r.molt.chemical.physics ~~ gmail.com] This is a multi-part message in MIME format. --------------060507020700040900030904 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit No. The exchange refers to the energy penalty for anti-symmetrization of the wavefunction. It is a permutation operator (K) applied to the Coulomb operator (J). It is not enough to have Coulombic repulsion; QM dictates that no two fermions have the same quantum state. If you want to work with fermions, you have to represent a penalty toward having the same quantum state. Correlation is an extended euphemism to mean "everything you do not get > from the restrictions placed on the wavefunction in restricted Hartree-Fock theory." The term more precisely derives from the fact that the joint probability distribution function of the one-particle reduced density matrix shows that the there is no statistical correlation between two orbitals and their density...hence the term "correlation." On 06/12/2014 07:05 PM, William McDonald pchem=-=ucsc.edu wrote: > But isn't that a consequence of the mean-field approximation and not > an intrinsic property of the electron? > > > On Thu, Jun 12, 2014 at 2:48 PM, Susi Lehtola > susi.lehtola=alumni.helsinki.fi > > wrote: > > > Sent to CCL by: Susi Lehtola [susi.lehtola##alumni.helsinki.fi > ] > On Thu, 12 Jun 2014 11:50:09 -0700 > "William McDonald pchem]|[ucsc.edu " > > wrote: > > On Thu, Jun 12, 2014 at 3:27 AM, Sergio Manzetti sergio.manzetti:: > > outlook.com > wrote: > > > Dear all, when is it suitable to start considering Exchange > correlation > > > between Electrons, (e.g pass Oxygen, Mg, Phosporous or further > up in the > > > system)? > > > > In a system with more than one electron of the same spin. > > > > That is: in a system with more than zero electrons of the same spin. > > [Exchange is important even for a single electron, because it cancels > out (or tries to) the self-Coulomb interaction.] > > For correlation, you need at least two, but even with a single > electrons many correlation functionals yield non-zero correlation > energies... > -- > --------------------------------------------------------------- > Mr. Susi Lehtola, PhD Research Associate > susi.lehtola ~~ alumni.helsinki.fi > Department of Applied Physics > http://www.helsinki.fi/~jzlehtol > Aalto University > Finland > --------------------------------------------------------------- > Susi Lehtola, FT Tutkijatohtori > susi.lehtola ~~ alumni.helsinki.fi > Fysiikan laitos > http://www.helsinki.fi/~jzlehtol > Aalto-yliopisto > --------------------------------------------------------------- > > > > -= This is automatically added to each message by the mailing > script =- > 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/> > > > > > -- > William J. McDonald > Postdoctoral Scholar > Department of Chemistry and Biochemistry > University of California, Santa Cruz --------------060507020700040900030904 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit No.  The exchange refers to the energy penalty for anti-symmetrization of the wavefunction.  It is a permutation operator (K) applied to the Coulomb operator (J).  It is not enough to have Coulombic repulsion; QM dictates that no two fermions have the same quantum state.  If you want to work with fermions, you have to represent a penalty toward having the same quantum state.

Correlation is an extended euphemism to mean "everything you do not get from the restrictions placed on the wavefunction in restricted Hartree-Fock theory."  The term more precisely derives from the fact that the joint probability distribution function of the one-particle reduced density matrix shows that the there is no statistical correlation between two orbitals and their density...hence the term "correlation."

On 06/12/2014 07:05 PM, William McDonald pchem=-=ucsc.edu wrote:
But isn't that a consequence of the mean-field approximation and not an intrinsic property of the electron?


On Thu, Jun 12, 2014 at 2:48 PM, Susi Lehtola susi.lehtola=alumni.helsinki.fi <owner-chemistry]*[ccl.net> wrote:

Sent to CCL by: Susi Lehtola [susi.lehtola##alumni.helsinki.fi]
On Thu, 12 Jun 2014 11:50:09 -0700
"William McDonald pchem]|[ucsc.edu" <owner-chemistry ~~ ccl.net> wrote:
> On Thu, Jun 12, 2014 at 3:27 AM, Sergio Manzetti sergio.manzetti::
> outlook.com <owner-chemistry,,ccl.net> wrote:
> > Dear all, when is it suitable to start considering  Exchange correlation
> > between Electrons, (e.g pass Oxygen, Mg, Phosporous or further up in the
> > system)?
>
> In a system with more than one electron of the same spin.
>

That is: in a system with more than zero electrons of the same spin.

[Exchange is important even for a single electron, because it cancels
out (or tries to) the self-Coulomb interaction.]

For correlation, you need at least two, but even with a single
electrons many correlation functionals yield non-zero correlation
energies...
--
---------------------------------------------------------------
Mr. Susi Lehtola, PhD             Research Associate
susi.lehtola ~~ alumni.helsinki.fi   Department of Applied Physics
http://www.helsinki.fi/~jzlehtol  Aalto University
                                  Finland
---------------------------------------------------------------
Susi Lehtola, FT                  Tutkijatohtori
susi.lehtola ~~ alumni.helsinki.fi   Fysiikan laitos
http://www.helsinki.fi/~jzlehtol  Aalto-yliopisto
---------------------------------------------------------------



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--
William J. McDonald
Postdoctoral Scholar
Department of Chemistry and Biochemistry
University of California, Santa Cruz

--------------060507020700040900030904-- From owner-chemistry@ccl.net Fri Jun 13 09:20:01 2014 From: "Karthikeyan M m.karthikeyan a ncl.res.in" To: CCL Subject: CCL: Practical chemoinformatics Message-Id: <-50206-140612223022-28113-NTfR2Sm4VYtRZcv/tCiYjw**server.ccl.net> X-Original-From: Karthikeyan M Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_9439B2C7904F4BBC960BF1D2DD8F70AAnclresin_" Date: Fri, 13 Jun 2014 02:30:08 +0000 MIME-Version: 1.0 Sent to CCL by: Karthikeyan M [m.karthikeyan|a|ncl.res.in] --_000_9439B2C7904F4BBC960BF1D2DD8F70AAnclresin_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Respected CCL members I am happy to share a good news , recently I published a TextBook on "Pract= ical Chemoinformatics". please feel free to visit the urls from publishers,= and hopefully it will be made available University libraries through conso= rtiums. Today Chemoinformatics is equipped to impact our life in a big way mainly in the fields of chemical, biological, medical, Engineering and material sc= iences. About the book: This book enables the readers to practice chemoinformatics with open source tools and open source data Includes numerous step-by-step tutorials that help the reader to grasp the topics quickly Provides exposure to open source based computer programs for chemoinformatics . This book is a product of several years of experience and passion for the subject written in a simple lucid style to attract the interest of the student community who wish to master chemoinformatics as a career. The topics chosen cover the entire spectrum of chemoinformatics activities (methods, data and tools). The algorithms, open source databases, tutorials supporting theory using standard datasets, guidelines, questions and do it yourself exercises will make it valuable to the academic research community. At the same time every chapter devotes a section on development of new software tools relevant for the growing pharmaceutical, fine chemicals and life sciences industry. The book is intended to assist beginners to hone their skills and also constitute an interesting reading for the experts. Book URL: http://www.springer.com/chemistry/book/978-81-322-1779-4 List of chapters: http://www.springer.com/chemistry/book/978-81-322-1779-4?detailsPage=3Dchap= ter Front matters: http://link.springer.com/content/pdf/bfm%3A978-81-322-1780-0%2F1.pdf (Free Preview!) Table of contents from the Book includes: Open Source Tools, Techniques and Data in Chemoinformatics.- Chemoinformatics Approach for the Design and Screening of focused virtual libraries.- Machine Learning Methods in Chemoinformatics for Drug Discovery.- Docking and pharmacophore modeling for virtual screening.- Active site directed pose prediction programs for efficient filtering of molecules.- Representation, fingerprinting and modeling of chemical reactions.- Predictive methods for Organic Spectral data Simulation.- Chemical Text mining for Lead Discovery.- Integration of Automated Work flow in Chemoinformatics for drug discovery.- Cloud computing Infrastructure development for Chemoinformatics. Last but not least, please feel free to forward the details to interested colleagues, teachers and students pursuing their studies/research in the area of chemical, biological and allied sciences. This book is also suitable as a reference material in academic Libraries. Regards M. Karthikeyan Principal scientist Csir national chemical laboratory Pune. India http://moltable.ncl.res.in/ ** sorry for duplicate posting ________________________________ Disclaimer: This message and the information contained herein is proprietary and confid= ential and subject to the policy statement of the National Chemical Laborat= ory, Pune, India. You may review the policy at http://www.ncl-india.org/com= mon/webmailDisclaimer.htm --_000_9439B2C7904F4BBC960BF1D2DD8F70AAnclresin_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Respected CCL members

I am happy to share a good news , recently I published a TextBook on "= Practical Chemoinformatics". please feel free to visit the urls f= rom publishers, and hopefully it will be made available University lib= raries through consortiums.


Today Chemoinformatics is equipped to impact our life in a big way mainly&n= bsp;
in the fields of chemical, biological, medical, Engineering and material sc= iences. 

About the book: 

This book enables the readers to practice chemoinformatics with open <= br> source tools and open source data Includes numerous step-by-step 
tutorials that help the reader to grasp the topics quickly Provides  exposure to open source based computer programs for chemoinformatics . = ;
This book is a product of several years of experience and passion for =
the subject written in a simple lucid style to attract the interest of = ;
the student community who wish to master chemoinformatics as a career. = ;
The topics chosen cover the entire spectrum of chemoinformatics 
activities (methods, data and tools). The algorithms, open source 
databases, tutorials supporting theory using standard datasets, 
guidelines, questions and do it yourself exercises will make it 
valuable to the academic research community. At the same time every  chapter devotes a section on development of new software tools 
relevant for the growing pharmaceutical, fine chemicals and life 
sciences industry. The book is intended to assist beginners to hone  their skills and also constitute an interesting reading for the 
experts. 

Book URL: 
http://www.springer.com/chemist= ry/book/978-81-322-1779-4 

List of chapters: 
http://ww= w.springer.com/chemistry/book/978-81-322-1779-4?detailsPage=3Dchapter&n= bsp;

Front matters: 
http://link.springe= r.com/content/pdf/bfm%3A978-81-322-1780-0%2F1.pdf 
(Free Preview!) 


Table of contents from the Book includes: 

Open Source Tools, Techniques and Data in Chemoinformatics.- 
Chemoinformatics Approach for the Design and Screening of focused 
virtual libraries.- Machine Learning Methods in Chemoinformatics for <= br> Drug Discovery.- Docking and pharmacophore modeling for virtual 
screening.- Active site directed pose prediction programs for 
efficient filtering of molecules.- Representation, fingerprinting and =
modeling of chemical reactions.- Predictive methods for Organic 
Spectral data Simulation.- Chemical Text mining for Lead Discovery.- <= br> Integration of Automated Work flow in Chemoinformatics for drug 
discovery.- Cloud computing Infrastructure development for 
Chemoinformatics. 

Last but not least, please feel free to forward the details to 
interested colleagues, teachers and students pursuing their 
studies/research in the area of chemical, biological and allied 
sciences. This book is also suitable as a reference material in academic&nb= sp;
Libraries.


Regards

M. Karthikeyan
Principal scientist
Csir national chemical laboratory
Pune. India


** sorry for duplicate posting 



Disclaimer:

This message and the information contained herein is proprietary and confid= ential and subject to the policy statement of the National Chemical Laborat= ory, Pune, India. You may review the policy at http://www.ncl-india.org/com= mon/webmailDisclaimer.htm
 --_000_9439B2C7904F4BBC960BF1D2DD8F70AAnclresin_-- From owner-chemistry@ccl.net Fri Jun 13 09:55:01 2014 From: "Mehboob Alam mehboob.cu]*[gmail.com" To: CCL Subject: CCL: How to read data from a specific line to another specific line in a file using FORTRAN 90/95 code Message-Id: <-50207-140613021152-25794-GLcPSipGKx7OypmaUPsMYQ.@.server.ccl.net> X-Original-From: Mehboob Alam Content-Type: multipart/alternative; boundary=bcaec51ba27b67fe7504fbb18d22 Date: Fri, 13 Jun 2014 11:41:46 +0530 MIME-Version: 1.0 Sent to CCL by: Mehboob Alam [mehboob.cu_-_gmail.com] --bcaec51ba27b67fe7504fbb18d22 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello Everyone, Thanks for the fine replies. The problem is solved. With best regards, Md. Mehboob Alam Senior Research Fellow - CSIR-INDIA Department of Chemistry, University of Calcutta Kolkata - 700 009, India On Wed, Jun 11, 2014 at 2:43 PM, Javier Cerezo jcb1|a|um.es < owner-chemistry|a|ccl.net> wrote: > Hi Mehboob > > That's the way I tackle with this (maybe not too elegant but works): > > !Variable declaration > ! Unit number > integer :: unt=3D10 > ! I/O status > integer :: IOstatus > ! line string > character(len=3D240) :: line=3D"" > ! Other vars > integer :: i, n_interesting_lines > character(len=3D10) :: myvar > > !Open the file > open(unt,file=3D'myfile') > > ! First use INDEX function to identify the line that contains > "name" > do > read(unt,'(A)',IOSTAT=3DIOstatus) line > ! Two possible scenarios while reading: > ! 1) End of file > if ( IOstatus < 0 ) stop > ! 2) Target line found > if ( INDEX(line,"name") /=3D 0 ) exit > enddo > !Then, the last line can be re-read to extract any variable from = it > read(line,*) myvar > ! Now read lines of interest > do i=3D1,n_interesting_lines > read(unt,'(A)',IOSTAT=3DIOstatus) line > enddo > > Of course, this strategy needs that the target line contains a unique > pattern (i.e. "name" in this case). However, in highly structured files > (e.g. output from quantum chemistry packages) this requirement is normall= y > met. If you don't know how many lines are you going to read, you can use > another pattern (also possible to find in output from quantum chemistry > packages) to identify the last line in a similar way using INDEX again > (instead of the fixed loop: do i=3D1,n_interesting_lines). > > Javier > > > > El 11/06/14 09:49, Mehboob Alam mehboob.cu+*+gmail.com escribi=F3: > > Respected CCL members, > > I have a file containing several lines and I want to read data from 4 > continuous lines. But the condition is that the reading should be started > from a line started with a character variable "name". For example, Below,= I > have given an example input file and lines which need to read are marked > bold and blue. > > Sample input file: > > students are curious about their results > The result will be published on 10th of march this year > below is given name of the students and marks obtained by them > *name subject marks* > *krishna chemistry 85* > *Ibrahim physics 82* > *kayanuma chemistry 87* > raju maths 99 > > End of Sample input file. > > Also note that the line number containing the character variable "name" > andhow many lines are there after it are not known. > > Any help will be highly appreciated. > > With best regards, > Md. Mehboob Alam > Senior Research Fellow - CSIR-INDIA > Department of Chemistry, > University of Calcutta > Kolkata - 700 009, India > > > > -- > Javier CEREZO BASTIDA > PostDoc Researcher > ICCOM-CNR, UOS di Pisa > 56124 PISA (ITALY) > --bcaec51ba27b67fe7504fbb18d22 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello Everyone,

Thanks for the fine rep= lies. The problem is solved.

With best regards,
Md. Mehboob Alam
Se= nior Research Fellow - CSIR-INDIA
Department of Chemistry,
University of Calcutta
Ko= lkata - 700 009, India


On Wed, Jun 11, 2014 at 2:43 PM, Javier = Cerezo jcb1|a|um.es <owner-chemistry|a|cc= l.net> wrote:
=20 =20 =20
Hi Mehboob

That's the way I tackle with this (maybe not too elegant but works)= :

=A0=A0=A0=A0=A0=A0=A0 !Variable declaration
=A0=A0=A0=A0=A0=A0=A0 ! Unit number
=A0=A0=A0=A0=A0=A0=A0 integer :: unt=3D10
=A0=A0=A0=A0=A0=A0=A0 ! I/O status
=A0=A0=A0=A0=A0=A0=A0 integer :: IOstatus
=A0=A0=A0=A0=A0=A0=A0 ! line string
=A0=A0=A0=A0=A0=A0=A0 character(len=3D240) :: line=3D""
=A0=A0=A0=A0=A0=A0=A0 ! Other vars
=A0=A0=A0=A0=A0=A0=A0 integer :: i, n_interesting_lines
=A0=A0=A0=A0=A0=A0=A0 character(len=3D10) :: myvar

=A0=A0=A0=A0=A0 =A0 !Open the file
=A0=A0=A0=A0=A0=A0=A0 open(unt,file=3D'myfile')

=A0=A0=A0=A0=A0=A0=A0 ! First use INDEX function to identify the line t= hat contains "name"
=A0=A0=A0=A0=A0=A0=A0 do
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 read(unt,'(A)',IOSTAT=3DIOsta= tus) line
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ! Two possible scenarios while readin= g:
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ! 1) End of file
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 if ( IOstatus < 0 ) stop
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ! 2) Target line found
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 if ( INDEX(line,"name") /= =3D 0 ) exit
=A0=A0=A0=A0=A0=A0=A0 enddo
=A0=A0=A0=A0=A0=A0=A0 !Then, the last line can be re-read to extract an= y variable from it
=A0=A0=A0=A0=A0=A0=A0 read(line,*) myvar
=A0=A0=A0=A0=A0=A0=A0 ! Now read lines of interest
=A0=A0=A0=A0=A0=A0=A0 do i=3D1,n_interesting_lines
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 read(unt,'(A)',IOSTAT=3DIOsta= tus) line
=A0=A0=A0=A0=A0=A0=A0 enddo

Of course, this strategy needs that the target line contains a unique pattern (i.e. "name" in this case). However, in highly structured files (e.g. output from quantum chemistry packages) this requirement is normally met. If you don't know how many lines are you going to read, you can use another pattern (also possible to find in output from quantum chemistry packages) to identify the last line in a similar way using INDEX again (instead of the fixed loop: do i=3D1,n_interesting_lines).

Javier



El 11/06/14 09:49, Mehboob Alam mehboob.cu+*+gmail.com escribi=F3:
Respected CCL members,

I have a file containing several lines and I want to read data from 4 continuous lines. But the condition is that the reading should be started from a line started with a character variable "name". For example, Below, I have given an ex= ample input file and lines which need to read are marked bold and blue.

Sample input file:

students are curious about their results
The result will be published on 10th of march this year
below is given name of the students and marks obtained by them
name =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0subject =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0marks
krishna =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 chemistry =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A085
Ibrahim =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0physics =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 82
kayanuma =A0 =A0 =A0 =A0 =A0 =A0 = =A0chemistry =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 87
raju =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 maths =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A099

End of Sample input file.

Also note that the line number containing the character variable "name" andhow many lines are there after it ar= e not known.

Any help will be highly appreciated.

With best regards,
Md. Mehboob Alam
Senior Research Fellow - CSIR-INDIA
Department of Chemistry,
University of Calcutta
Kolkata - 700 009, India


--
Javier CEREZO BASTIDA
PostDoc Researcher
ICCOM-CNR, UOS di Pisa
56124 PISA (ITALY)

--bcaec51ba27b67fe7504fbb18d22-- From owner-chemistry@ccl.net Fri Jun 13 13:13:00 2014 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor() fluor.quimica.uniovi.es" To: CCL Subject: CCL: Exchange correlation Message-Id: <-50208-140613125612-21153-2b3UYca4QHxKFkGIPvDt2g^^^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: Fri, 13 Jun 2014 18:49:33 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor::fluor.quimica.uniovi.es] On Thu, Jun 12, 2014 at 09:31:49PM -0400, Robert Molt Jr r.molt.chemical.physics.**.gmail.com wrote: > No. The exchange refers to the energy penalty for anti-symmetrization > of the wavefunction. It is a permutation operator (K) applied to the > Coulomb operator (J). It is not enough to have Coulombic repulsion; QM > dictates that no two fermions have the same quantum state. If you want > to work with fermions, you have to represent a penalty toward having the > same quantum state. > > Correlation is an extended euphemism to mean "everything you do not get >> from the restrictions placed on the wavefunction in restricted > Hartree-Fock theory." The term more precisely derives from the fact > that the joint probability distribution function of the one-particle > reduced density matrix shows that the there is no statistical > correlation between two orbitals and their density...hence the term > "correlation." I absolutely agree with your position as it is the case of anybody that has read anything coming from John C. Slater. However, it is the case that the physicists in DF theory have createed their own pantheon and Slater tends to be excluded. So I'm afraid that the use of correlation or exchange-correlation will continue to declare the different formation of two different schools of people working on exactly the same field. Best regards, Dr. Víctor Luaña -- \|/ |^.^| +---!OO--\_/--OO!------------------------------+----------------------- ! Dr.Víctor Luaña ! ! Departamento de Química Física y Analítica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor**fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +----------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Fri Jun 13 14:43:00 2014 From: "sh sh shadi_shad_65{=}yahoo.com" To: CCL Subject: CCL:G: SCF done Message-Id: <-50209-140613050148-20611-Zay2eQ5fXC72GWGpVUTeMA!A!server.ccl.net> X-Original-From: "sh sh" Date: Fri, 13 Jun 2014 05:01:46 -0400 Sent to CCL by: "sh sh" [shadi_shad_65]_[yahoo.com] In gaussian output files what is SCF done abbreviated for? From owner-chemistry@ccl.net Fri Jun 13 15:18:00 2014 From: "Alberto De Petris alberto.depetris++gmail.com" To: CCL Subject: CCL:G: G03 Rerunning Thermochemical Analisys Message-Id: <-50210-140613053333-5283-Dz+DJHtOcfVy2HeHg2nswg[A]server.ccl.net> X-Original-From: "Alberto De Petris" Date: Fri, 13 Jun 2014 05:33:31 -0400 Sent to CCL by: "Alberto De Petris" [alberto.depetris::gmail.com] Hi all, I need to rerun a frequency calculation with G03 in order to have additional informations on the thermochemistry of the system. My system is a porphyrin axially coordinated to an imidazole. I found on the manual this section: Rerunning a Frequency Calculation with Different Thermochemistry Parameters. The following two-step job contains an initial frequency calculation followed by a second thermochemistry analysis using a different temperature, pressure, and selection of isotopes: %Chk=freq # HF/6-31G(d,p) Freq Test Frequencies at STP molecule specification --Link1-- %Chk=freq %NoSave # HF/6-31G(d,p) Freq(ReadIso,ReadFC) Geom=Check Test Repeat at 300 K 0,1 300.0 1.0 16 2 3 .. Note also that the freqchk utility may be used to rerun the thermochemical analysis from the frequency data stored in a Gaussian checkpoint file. But I don't have idea on how it exactly works! My input doesn't work. It is below: %chk=/home/alberto/CALCS/Hem1-ImI.chk %NoSave # b3lyp/6-31g(d) freq(ReadIso,ReadFC) geom=Check Repeat at 563 K 1,4 563.0 1.0 .. END Since I don't need to specify the isotope masses because they don't change, is correct to skip the lines dedicated to it? Is correct to insert three full stop after the Temperature Pressure section? Any advice will be greatly appreciated!!!! Alberto. From owner-chemistry@ccl.net Fri Jun 13 15:53:00 2014 From: "Sergio Manzetti sergio.manzetti a outlook.com" To: CCL Subject: CCL: Exchange correlation Message-Id: <-50211-140613101631-6194-J3jW+9AAre+vlJo1hdDM9w _ server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary="_dc91350d-178a-4703-aa46-4a01d6a51f4f_" Date: Fri, 13 Jun 2014 16:16:19 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti()outlook.com] --_dc91350d-178a-4703-aa46-4a01d6a51f4f_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Robert=2C I am not familiar with the method for applying an exchange c= orrelation. But is this applied by using perturbation on the Hamiltonian of= the multi/electron system=2C that is a perturbation Hamiltonian which appl= ied the effect from the exchange? THanks Sergio > From: owner-chemistry*|*ccl.net To: sergio.manzetti*|*gmx.com Subject: CCL: Exchange correlation Date: Thu=2C 12 Jun 2014 21:31:49 -0400 =0A= =0A= =0A= =0A= =0A= No. The exchange refers to the energy penalty for=0A= anti-symmetrization of the wavefunction. It is a permutation=0A= operator (K) applied to the Coulomb operator (J). It is not enough=0A= to have Coulombic repulsion=3B QM dictates that no two fermions have=0A= the same quantum state. If you want to work with fermions=2C you have= =0A= to represent a penalty toward having the same quantum state. =0A= =20 =0A= Correlation is an extended euphemism to mean "everything you do not=0A= get from the restrictions placed on the wavefunction in restricted=0A= Hartree-Fock theory." The term more precisely derives from the fact=0A= that the joint probability distribution function of the one-particle=0A= reduced density matrix shows that the there is no statistical=0A= correlation between two orbitals and their density...hence the term=0A= "correlation." =0A= =20 =0A= On 06/12/2014 07:05 PM=2C William=0A= McDonald pchem=3D-=3Ducsc.edu wrote: =0A= =0A= =0A= But isn't that a consequence of the mean-field=0A= approximation and not an intrinsic property of the electron?=0A= =20 =0A= =20 =0A= On Thu=2C Jun 12=2C 2014 at 2:48 PM=2C Susi=0A= Lehtola susi.lehtola=3Dalumni.helsinki.fi =0A= wrote: =0A= =20 =0A= Sent to CCL by: Susi Lehtola [susi.lehtola##alumni.helsinki.fi] =0A= On Thu=2C 12 Jun 2014 11:50:09 -0700 =0A= "William McDonald pchem]|[ucsc.edu"=0A= =0A= wrote: =0A= > On Thu=2C Jun 12=2C 2014 at 3:27 AM=2C Sergio Manzetti=0A= sergio.manzetti:: =0A= > outlook.com wrote: =0A= > > Dear all=2C when is it suitable to start considering=0A= Exchange correlation =0A= > > between Electrons=2C (e.g pass Oxygen=2C Mg=2C=0A= Phosporous or further up in the =0A= > > system)? =0A= > =0A= > In a system with more than one electron of the same=0A= spin. =0A= > =0A= =20 =0A= That is: in a system with more than zero electrons of the=0A= same spin. =0A= =20 =0A= [Exchange is important even for a single electron=2C because=0A= it cancels =0A= out (or tries to) the self-Coulomb interaction.] =0A= =20 =0A= For correlation=2C you need at least two=2C but even with a=0A= single =0A= electrons many correlation functionals yield non-zero=0A= correlation =0A= energies... =0A= -- =0A= --------------------------------------------------------------- =0A= Mr. Susi Lehtola=2C PhD Research Associate =0A= susi.lehtola ~~ alumni.helsinki.fi=0A= Department of Applied Physics =0A= http://www.helsinki.fi/~jzlehtol=0A= Aalto University =0A= Finland =0A= --------------------------------------------------------------- =0A= Susi Lehtola=2C FT Tutkijatohtori =0A= susi.lehtola ~~ alumni.helsinki.fi=0A= Fysiikan laitos =0A= http://www.helsinki.fi/~jzlehtol=0A= Aalto-yliopisto =0A= --------------------------------------------------------------- =0A= =20 =0A= =20 =0A=
Dear Robert=2C I am not familiar= with the method for applying an exchange correlation. But is this applied = by using perturbation on the Hamiltonian of the multi/electron system=2C th= at is a perturbation Hamiltonian which applied the effect from the exchange= ?
THanks

Sergio


From: own= er-chemistry*|*ccl.net
To: sergio.manzetti*|*gmx.com
Subject: CCL: Exchan= ge correlation
Date: Thu=2C 12 Jun 2014 21:31:49 -0400

=0A= =0A= =0A= =0A= =0A= No. =3B The exchange refers to the energy penalty for=0A= anti-symmetrization of the wavefunction. =3B It is a permutation=0A= operator (K) applied to the Coulomb operator (J). =3B It is not eno= ugh=0A= to have Coulombic repulsion=3B QM dictates that no two fermions have=0A= the same quantum state. =3B If you want to work with fermions=2C yo= u have=0A= to represent a penalty toward having the same quantum state.
=0A=
=0A= Correlation is an extended euphemism to mean "everything you do not=0A= get from the restrictions placed on the wavefunction in restricted=0A= Hartree-Fock theory." =3B The term more precisely derives from the = fact=0A= that the joint probability distribution function of the one-particle=0A= reduced density matrix shows that the there is no statistical=0A= correlation between two orbitals and their density...hence the term=0A= "correlation."
=0A=
=0A=
On 06/12/2014 07:05 PM=2C William=0A= McDonald pchem=3D-=3Ducsc.edu wrote:
=0A=
=0A=
=0A=
But isn't that a consequence of the mean-field=0A= approximation and not an intrinsic property of the electron?
= =0A=

=0A=
=0A=
On Thu=2C Jun 12=2C 2014 at 2:48 PM= =2C Susi=0A= Lehtola susi.lehtola=3Dalumni.helsinki.fi <=3Bowner-chemistry]*[ccl.net<= /a>>=3B=0A= wrote:
=0A=

=0A= Sent to CCL by: Susi Lehtola [susi.lehtola##alumni.helsinki.fi]
=0A= On Thu=2C 12 Jun 2014 11:50:09 -0700
=0A= "William McDonald pchem]|[ucsc.edu"=0A= <=3Bowner-chemistry ~~ ccl.net>=3B=0A= wrote:
=0A= >=3B On Thu=2C Jun 12=2C 2014 at 3:27 AM=2C Sergio Manzetti= =0A= sergio.manzetti::
=0A= >=3B outlook= .com <=3Bowner-chemistry=2C=2Cccl.net>=3B wrote:
=0A= >=3B >=3B Dear all=2C when is it suitable to start consider= ing=0A=  =3BExchange correlation
=0A= >=3B >=3B between Electrons=2C (e.g pass Oxygen=2C Mg=2C=0A= Phosporous or further up in the
=0A= >=3B >=3B system)?
=0A= >=3B
=0A= >=3B In a system with more than one electron of the same=0A= spin.
=0A= >=3B
=0A=
=0A= That is: in a system with more than zero electrons of the=0A= same spin.
=0A=
=0A= [Exchange is important even for a single electron=2C because=0A= it cancels
=0A= out (or tries to) the self-Coulomb interaction.]
=0A=
=0A= For correlation=2C you need at least two=2C but even with a=0A= single
=0A= electrons many correlation functionals yield non-zero=0A= correlation
=0A= energies...
=0A= --
=0A= ---------------------------------------------------------------
=0A= Mr. Susi Lehtola=2C PhD  =3B  =3B  =3B  =3B &nb= sp=3B  =3B Research Associate
=0A= susi.lehtola ~~ alumni.helsinki.fi=0A=  =3B Department of Applied Physics
=0A= = http://www.helsinki.fi/~jzlehtol=0A=  =3BAalto University
=0A=  =3B  =3B  =3B  =3B  =3B  =3B  =3B =  =3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B &nb= sp=3B  =3B Finland
=0A= ---------------------------------------------------------------
=0A= Susi Lehtola=2C FT  =3B  =3B  =3B  =3B  =3B=  =3B  =3B  =3B  =3BTutkijatohtori
=0A= susi.lehtola ~~ alumni.helsinki.fi=0A=  =3B Fysiikan laitos
=0A= = http://www.helsinki.fi/~jzlehtol=0A=  =3BAalto-yliopisto
=0A= ---------------------------------------------------------------
=0A=
=0A=
=0A= <=3Bbr<=3Bbr
<=3Bbr
=0A=
=0A= E-mail to subscribers: CHEMISTRY]*[ccl.net=0A= or use:
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=0A= E-mail to administrators: CHEMISTRY-REQUEST]*[ccl.net=0A= or use
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=0A=
=0A= --
=0A= William J. McDonald
=0A= Postdoctoral Scholar
=0A= Department of Chemistry and Biochemistry
=0A= University of California=2C Santa Cruz
=0A=
=0A=
=0A=
= --_dc91350d-178a-4703-aa46-4a01d6a51f4f_-- From owner-chemistry@ccl.net Fri Jun 13 16:28:00 2014 From: "William McDonald pchem]=[ucsc.edu" To: CCL Subject: CCL: Exchange correlation Message-Id: <-50212-140613125632-21230-qux4cyQyhyfP3wfFx46IzA() server.ccl.net> X-Original-From: William McDonald Content-Type: multipart/alternative; boundary=001a11c30e22252a4004fbba8e7a Date: Fri, 13 Jun 2014 09:56:14 -0700 MIME-Version: 1.0 Sent to CCL by: William McDonald [pchem]^[ucsc.edu] --001a11c30e22252a4004fbba8e7a Content-Type: text/plain; charset=UTF-8 Sorry, my previous post was totally unclear. I understand what exchange and correlation refer to. I meant to ask "isn't the self-interaction error a consequence of the mean-field approximation?" As to Dr. Lehtola's comment that "Exchange is important even for a single electron, because it cancels out (or tries to) the self-Coulomb interaction." This seems odd, because why are two-electron (Coulomb repulsion) integrals being evaluated in a one-electron system? It seems to me that for any one-electron system, one simply evaluates the electronic kinetic energy and electron-nucleus attraction; there should not be a self-Coulomb interaction. On Thu, Jun 12, 2014 at 6:31 PM, Robert Molt Jr r.molt.chemical.physics.-x-. gmail.com wrote: > No. The exchange refers to the energy penalty for anti-symmetrization of > the wavefunction. It is a permutation operator (K) applied to the Coulomb > operator (J). It is not enough to have Coulombic repulsion; QM dictates > that no two fermions have the same quantum state. If you want to work with > fermions, you have to represent a penalty toward having the same quantum > state. > > Correlation is an extended euphemism to mean "everything you do not get > from the restrictions placed on the wavefunction in restricted Hartree-Fock > theory." The term more precisely derives from the fact that the joint > probability distribution function of the one-particle reduced density > matrix shows that the there is no statistical correlation between two > orbitals and their density...hence the term "correlation." > > On 06/12/2014 07:05 PM, William McDonald pchem=-=ucsc.edu wrote: > > But isn't that a consequence of the mean-field approximation and not an > intrinsic property of the electron? > > > On Thu, Jun 12, 2014 at 2:48 PM, Susi Lehtola susi.lehtola= > alumni.helsinki.fi wrote: > >> >> Sent to CCL by: Susi Lehtola [susi.lehtola##alumni.helsinki.fi] >> On Thu, 12 Jun 2014 11:50:09 -0700 >> "William McDonald pchem]|[ucsc.edu" wrote: >> > On Thu, Jun 12, 2014 at 3:27 AM, Sergio Manzetti sergio.manzetti:: >> > outlook.com wrote: >> > > Dear all, when is it suitable to start considering Exchange >> correlation >> > > between Electrons, (e.g pass Oxygen, Mg, Phosporous or further up in >> the >> > > system)? >> > >> > In a system with more than one electron of the same spin. >> > >> >> That is: in a system with more than zero electrons of the same spin. >> >> [Exchange is important even for a single electron, because it cancels >> out (or tries to) the self-Coulomb interaction.] >> >> For correlation, you need at least two, but even with a single >> electrons many correlation functionals yield non-zero correlation >> energies... >> -- >> --------------------------------------------------------------- >> Mr. Susi Lehtola, PhD Research Associate >> susi.lehtola ~~ alumni.helsinki.fi Department of Applied Physics >> http://www.helsinki.fi/~jzlehtol Aalto University >> Finland >> --------------------------------------------------------------- >> Susi Lehtola, FT Tutkijatohtori >> susi.lehtola ~~ alumni.helsinki.fi Fysiikan laitos >> http://www.helsinki.fi/~jzlehtol Aalto-yliopisto >> --------------------------------------------------------------- >> >> >> >> E-mail to subscribers: CHEMISTRY]*[ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST]*[ccl.net or use>> >> >> > > > -- > William J. McDonald > Postdoctoral Scholar > Department of Chemistry and Biochemistry > University of California, Santa Cruz > > > -- William J. McDonald Postdoctoral Scholar Department of Chemistry and Biochemistry University of California, Santa Cruz --001a11c30e22252a4004fbba8e7a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Sorry, my previous post was totally unclear. I understand = what exchange and correlation refer to. I meant to ask "isn't the = self-interaction error a consequence of the mean-field approximation?"=
As to Dr. Lehtola's comment that "Exchange is important even for a single electron, because it cancels= =C2=A0out (or tries to) the sel= f-Coulomb interaction." This seems odd, because why are two-electron (= Coulomb repulsion) integrals being evaluated in a one-electron system? It s= eems to me that for any one-electron system, one simply evaluates the elect= ronic kinetic energy and electron-nucleus attraction; there should not be a= self-Coulomb interaction.


On Thu,= Jun 12, 2014 at 6:31 PM, Robert Molt Jr r.molt.chemical.physics.-x-.gmail.com <owner-chemistry-x-ccl.net>= wrote:
=20 =20 =20
No.=C2=A0 The exchange refers to the energy penalty for anti-symmetrization of the wavefunction.=C2=A0 It is a permutation operator (K) applied to the Coulomb operator (J).=C2=A0 It is not enoug= h to have Coulombic repulsion; QM dictates that no two fermions have the same quantum state.=C2=A0 If you want to work with fermions, you ha= ve to represent a penalty toward having the same quantum state.

Correlation is an extended euphemism to mean "everything you do no= t get from the restrictions placed on the wavefunction in restricted Hartree-Fock theory."=C2=A0 The term more precisely derives from t= he fact that the joint probability distribution function of the one-particle reduced density matrix shows that the there is no statistical correlation between two orbitals and their density...hence the term "correlation."

On 06/12/2014 07:05 PM, William McDonald pchem=3D-=3Duc= sc.edu wrote:
But isn't that a consequence of the mean-field approximation and not an intrinsic property of the electron?


On Thu, Jun 12, 2014 at 2:48 PM, Susi Lehtola susi.lehtola=3Dalumni.helsinki.fi <owner-chemistry]*[ccl.net> wrote:

Sent to CCL by: Susi Lehtola [susi.lehtola##alumni.helsinki.fi]
On Thu, 12 Jun 2014 11:50:09 -0700
"William McDonald pchem]|[ucsc.edu" <owner-chemistry ~~ ccl.net> wrote:
> On Thu, Jun 12, 2014 at 3:27 AM, Sergio Manzetti sergio.manzetti::
> outlook.c= om <owner-chemistry,,cc= l.net> wrote:
> > Dear all, when is it suitable to start considering =C2=A0Exchange correlation
> > between Electrons, (e.g pass Oxygen, Mg, Phosporous or further up in the
> > system)?
>
> In a system with more than one electron of the same spin.
>

That is: in a system with more than zero electrons of the same spin.

[Exchange is important even for a single electron, because it cancels
out (or tries to) the self-Coulomb interaction.]

For correlation, you need at least two, but even with a single
electrons many correlation functionals yield non-zero correlation
energies...
--
---------------------------------------------------------------
Mr. Susi Lehtola, PhD =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= Research Associate
susi.lehtola ~~ alumni.helsinki.fi =C2=A0 Department of Applied Physics
http://www.helsinki.fi/~jzlehtol =C2=A0Aalto University
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Finland
---------------------------------------------------------------
Susi Lehtola, FT =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0Tutkijatohtori
susi.lehtola ~~ alumni.helsinki.fi =C2=A0 Fysiikan laitos
http://www.helsinki.fi/~jzlehtol =C2=A0Aalto-yliopisto
---------------------------------------------------------------



E-mail to subscribers: CHEMISTRY]*[ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_c= cl_message

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--
William J. McDonald
Postdoctoral Scholar
Department of Chemistry and Biochemistry
University of California, Santa Cruz




--
William J. M= cDonald
Postdoctoral Scholar
Department of Chemistry and Biochemistry=
University of California, Santa Cruz
--001a11c30e22252a4004fbba8e7a-- From owner-chemistry@ccl.net Fri Jun 13 18:33:00 2014 From: "Robert Molt r.molt.chemical.physics*o*gmail.com" To: CCL Subject: CCL: Exchange correlation Message-Id: <-50213-140613164811-7276-bUUoczPft4OT4E9zPxmejg_._server.ccl.net> X-Original-From: Robert Molt Content-Type: multipart/alternative; boundary="------------070908080701040601080304" Date: Fri, 13 Jun 2014 16:48:04 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics . gmail.com] This is a multi-part message in MIME format. --------------070908080701040601080304 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Do you mean "exchange correlation" referring to a choice in an exchange-correlation /functional /(KS-DFT framework) or "exchange and correlation" referring to in a wavefunction formalism? --------------070908080701040601080304 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Do you mean "exchange correlation" referring to a choice in an exchange-correlation functional (KS-DFT framework) or "exchange and correlation" referring to in a wavefunction formalism?
--------------070908080701040601080304-- From owner-chemistry@ccl.net Fri Jun 13 19:09:00 2014 From: "Prasenjit Seal seal.prasenjit*_*gmail.com" To: CCL Subject: CCL: Prasenjit - Quering about Transition States Message-Id: <-50214-140613175650-10834-gckD6xZjvny/y/GQs9Dd1g]![server.ccl.net> X-Original-From: Prasenjit Seal Content-Type: multipart/alternative; boundary=bcaec51a7842dc03c804fbbec0cd Date: Fri, 13 Jun 2014 16:56:44 -0500 MIME-Version: 1.0 Sent to CCL by: Prasenjit Seal [seal.prasenjit ~ gmail.com] --bcaec51a7842dc03c804fbbec0cd Content-Type: text/plain; charset=UTF-8 Hi, I am having a problem dealing with transition states. For some of my systems, I have no idea what the reaction path will look like, no idea of the transition states, no idea of the reaction mechanism. What I have in hand is only the structures of the reactants and products. Is there any software available which can solve my problem? I would really appreciate if someone has some idea regarding this matter. Some of these type of reactions are 1. Si2H5(-) + SiH4 ------> Si3H7(-) + H2 2. Si2H4(-) + SiH4 ------> Si3H6(-) + H2 Please note that Si2H4(-) is silylene anions and not silene. Same goes for Si3H6(-). Si2H5(-) and Si3H7(-) are radical anions. Thanks and best regards, Prasenjit --bcaec51a7842dc03c804fbbec0cd Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi,

I am having a problem dealing with = transition states. For some of my systems, I have no idea what the reaction= path will look like, no idea of the transition states, no idea of the reac= tion mechanism.

What I have in hand is only the structures of the react= ants and products. Is there any software available which can solve my probl= em?=C2=A0

I would really appreciate if someone has= some idea regarding this matter.

Some of these type of reactions are

1. Si2H5(-) + SiH4 ------> Si3H7(-) + H2

= 2. Si2H4(-) + SiH4 ------> Si3H6(-) + H2

Please= note that Si2H4(-) is silylene anions and not silene. Same goes for Si3H6(= -). Si2H5(-) and Si3H7(-) are radical anions. =C2=A0

Thanks and best regards,
Prasenjit
--bcaec51a7842dc03c804fbbec0cd-- From owner-chemistry@ccl.net Fri Jun 13 20:59:00 2014 From: "Victor Rosas Garcia rosas.victor[]gmail.com" To: CCL Subject: CCL: Prasenjit - Quering about Transition States Message-Id: <-50215-140613204708-9917-65ssfyq1rOmbiW1KQQZ0oQ()server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=047d7bdc0a4eed1f0d04fbc121ca Date: Fri, 13 Jun 2014 19:47:03 -0500 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor,,gmail.com] --047d7bdc0a4eed1f0d04fbc121ca Content-Type: text/plain; charset=UTF-8 > From your message, I do not understant what your problem is. Do you want to know the mechanism? Do you want a transition state in particular? You say that for some of your systems you have no idea of the reaction path. Does this mean that you do have a reaction path for other systems? Those could be a starting point for the ones that lack the information. Victor 2014-06-13 16:56 GMT-05:00 Prasenjit Seal seal.prasenjit*_*gmail.com < owner-chemistry#,#ccl.net>: > Hi, > > I am having a problem dealing with transition states. For some of my > systems, I have no idea what the reaction path will look like, no idea of > the transition states, no idea of the reaction mechanism. > > What I have in hand is only the structures of the reactants and products. > Is there any software available which can solve my problem? > > I would really appreciate if someone has some idea regarding this matter. > > Some of these type of reactions are > > 1. Si2H5(-) + SiH4 ------> Si3H7(-) + H2 > > 2. Si2H4(-) + SiH4 ------> Si3H6(-) + H2 > > Please note that Si2H4(-) is silylene anions and not silene. Same goes for > Si3H6(-). Si2H5(-) and Si3H7(-) are radical anions. > > Thanks and best regards, > Prasenjit > --047d7bdc0a4eed1f0d04fbc121ca Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
From your message, I do not understant what your prob= lem is. Do you want to know the mechanism? Do you want a transition state i= n particular?

You say that for some of your systems you h= ave no idea of the reaction path.=C2=A0 Does this mean that you do have a r= eaction path for other systems? Those could be a starting point for the one= s that lack the information.

Victor


2014-06-13 16:56 GMT-05:00 Prasenjit Seal seal.prasenjit*_*gmail.com <owner-chemistry#,#ccl.net= >:
Hi,

I am= having a problem dealing with transition states. For some of my systems, I= have no idea what the reaction path will look like, no idea of the transit= ion states, no idea of the reaction mechanism.

What I have in hand is only the structures of the react= ants and products. Is there any software available which can solve my probl= em?=C2=A0

I would really appreciate if someone has= some idea regarding this matter.

Some of these type of reactions are

1. Si2H5(-) + SiH4 ------> Si3H7(-) + H2

= 2. Si2H4(-) + SiH4 ------> Si3H6(-) + H2

Please= note that Si2H4(-) is silylene anions and not silene. Same goes for Si3H6(= -). Si2H5(-) and Si3H7(-) are radical anions. =C2=A0

Thanks and best regards,
Prasenjit

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