From owner-chemistry@ccl.net Wed Mar 12 06:02:00 2014 From: "Scott Mckechnie jsm78_+_cam.ac.uk" To: CCL Subject: CCL: Sensitivity of vertical ionization energy and homo on geometry Message-Id: <-49834-140312060111-20221-+Yghi6/82995dVNDTnYIqQ||server.ccl.net> X-Original-From: "Scott Mckechnie" Date: Wed, 12 Mar 2014 06:01:09 -0400 Sent to CCL by: "Scott Mckechnie" [jsm78[#]cam.ac.uk] Dear all, I know that the vertical ionization energy and homo energy of a molecule can be quite sensitive to the molecular geometry used. I was hoping to find a more detailed discussion of this (including how the sensitivity might change with system size), can anyone point me to some relevant work? I would also welcome any comments that people might have about this. Best wishes, Scott From owner-chemistry@ccl.net Wed Mar 12 08:20:00 2014 From: "Bob Wibman teigpflaume],[hotmail.de" To: CCL Subject: CCL: Excitations in homo-dimers Message-Id: <-49835-140312041432-8228-4Rv8/p1PN7vBl3MeU3w+/A[A]server.ccl.net> X-Original-From: "Bob Wibman" Date: Wed, 12 Mar 2014 04:14:31 -0400 Sent to CCL by: "Bob Wibman" [teigpflaume+/-hotmail.de] Dear all, I have a question regarding the nature of excitations in homo-dimers of organic molecules. Previously, I have looked at hetero-dimers of molecules, in which the resulting molecular orbitals are nicely localized on either monomer. Now, for two molecules of the same type, the MOs are delocalized over both units even for very large distances and all excited states as linear combinations of these MOs will be delocalized as well. Intuitively, I'd have thought that there will be two "classes" of excitations: i) shift of the energies of the localized excitations, and ii) coupled excitations. Obviously, i) is totally missing if the start MOs delocalize. Is there anything I'm missing? Bob Wibman teigpflaume()hotmail.de From owner-chemistry@ccl.net Wed Mar 12 08:54:01 2014 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor ~~ fluor.quimica.uniovi.es" To: CCL Subject: CCL: Sensitivity of vertical ionization energy and homo on geometry Message-Id: <-49836-140312082646-32073-8+TsXXAxM91YzPNeHCEPXQ%x%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: Wed, 12 Mar 2014 12:28:53 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor__fluor.quimica.uniovi.es] On Wed, Mar 12, 2014 at 06:01:09AM -0400, Scott Mckechnie jsm78_+_cam.ac.uk wrote: > > Sent to CCL by: "Scott Mckechnie" [jsm78[#]cam.ac.uk] > I know that the vertical ionization energy and homo energy of a > molecule can be quite sensitive to the molecular geometry used. I was > hoping to find a more detailed discussion of this (including how the > sensitivity might change with system size), can anyone point me to some > relevant work? I would also welcome any comments that people might have > about this. Scott, Sorry, but I don't really understand your question. What is your level of knowledge on Molecular Spectroscopy? The IP for a molecule is the result of an experimental measurement. What do you want to know, how IPs can be calculated? Which tables of data access? Please, let us know which are your intentions. 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 Wed Mar 12 09:52:01 2014 From: "Scott McKechnie jsm78^cam.ac.uk" To: CCL Subject: CCL: Sensitivity of vertical ionization energy and homo on geometry Message-Id: <-49837-140312095050-9579-CvYc2+ae9se+8v+wRzQjBQ!A!server.ccl.net> X-Original-From: Scott McKechnie Content-Type: multipart/alternative; boundary=047d7b5da89169659304f4691f0e Date: Wed, 12 Mar 2014 13:50:42 +0000 MIME-Version: 1.0 Sent to CCL by: Scott McKechnie [jsm78 : cam.ac.uk] --047d7b5da89169659304f4691f0e Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Dr. Lua=F1a, Thank you for your reply. I am looking into comparing calculated vertical ionization energies (using orbital energies or delta-scf calculations in DFT, CCSD etc) for molecules with experimental vertical ionization energies > from photoelectron spectroscopy. I have found that the calculated ionization energies can be sensitive to changes in the geometry (i.e. from excited state geometries that are not the gas phase minimum) and was looking for references to papers which have discussed such sensitivity or some insight from ccl members. I am also interested in how this sensitivity to geometry might change with system size and the types of atoms and groups in a molecule. Best wishes, Scott On 12 March 2014 11:28, V=EDctor Lua=F1a wrote: > > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [ > victor__fluor.quimica.uniovi.es] > On Wed, Mar 12, 2014 at 06:01:09AM -0400, Scott Mckechnie jsm78_+_ > cam.ac.uk wrote: > > > > Sent to CCL by: "Scott Mckechnie" [jsm78[#]cam.ac.uk] > > I know that the vertical ionization energy and homo energy of a > > molecule can be quite sensitive to the molecular geometry used. I was > > hoping to find a more detailed discussion of this (including how the > > sensitivity might change with system size), can anyone point me to some > > relevant work? I would also welcome any comments that people might have > > about this. > > Scott, > > Sorry, but I don't really understand your question. What is your level > of knowledge on Molecular Spectroscopy? > > The IP for a molecule is the result of an experimental measurement. What > do you want to know, how IPs can be calculated? Which tables of data > access? Please, let us know which are your intentions. > > Regards, > Dr. V=EDctor Lua=F1a > -- > \|/ > |^.^| > +---!OO--\_/--OO!------------------------------+----------------------- > ! Dr.V=EDctor Lua=F1a ! > ! Departamento de Qu=EDmica F=EDsica y Anal=EDtica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: victor\a/fluor.quimica.uniovi.es ! > ! phone: +34-985-103491 fax: +34-985-103125 ! > +----------------------------------------------+ > GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > --047d7b5da89169659304f4691f0e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Dr. Lua=F1a,

Thank you for your reply. I am looking into comp= aring calculated vertical ionization energies (using orbital energies or de= lta-scf calculations in DFT, CCSD etc) for molecules with experimental vert= ical ionization energies from photoelectron spectroscopy. I have found that= the calculated ionization energies can be sensitive to changes in the geom= etry (i.e. from excited state geometries that are not the gas phase minimum= ) and was looking for references to papers which have discussed such sensit= ivity or some insight from ccl members. I am also interested in how this se= nsitivity to geometry might change with system size and the types of atoms = and groups in a molecule.

Bes= t wishes,

Scott=A0





On 12 March 2014 11:28, V=EDctor Lua=F1a <owner-chemistry.:.ccl.= net> wrote:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor__fluor.qu= imica.uniovi.es]
On Wed, Mar 12, 2014 at 06:01:09AM -0400, Scott Mckechnie j= sm78_+_cam.ac.uk wrote:<= br> >
> Sent to CCL by: "Scott =A0Mckechnie" [jsm78[#]cam.ac.uk]
> I know that the vertical ionization energy and h= omo energy of a
> molecule can be quite sensitive to the molecular geometry used. I was<= br> > hoping to find a more detailed discussion of this (including how the > sensitivity might change with system size), can anyone point me to som= e
> relevant work? I would also welcome any comments that people might hav= e
> about this.

Scott,

Sorry, but I don't really understand your question. What is your level<= br> of knowledge on Molecular Spectroscopy?

The IP for a molecule is the result of an experimental measurement. What do you want to know, how IPs can be calculated? Which tables of data
access? Please, let us know which are your intentions.

Regards,
=A0 =A0 =A0 =A0 Dr. V=EDctor Lua=F1a
--
=A0 =A0 =A0 =A0 =A0\|/
=A0 =A0 =A0 =A0 |^.^|
+---!OO--\_/--OO!------------------------------+-----------------------
! =A0 =A0 =A0 =A0 =A0 =A0Dr.V=EDctor Lua=F1a =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 !
! Departamento de Qu=EDmica F=EDsica y Anal=EDtica =A0 !
! Universidad de Oviedo, 33006-Oviedo, Spain =A0 !
! e-mail: =A0 victor\a/fluor.quimica.uniovi.es =A0 =A0 !
! phone: +34-985-10= 3491 =A0fax: +3= 4-985-103125 =A0 !
+----------------------------------------------+
=A0GroupPage : http://azufre.quimica.uniovi.es/ =A0(being reworked)



-=3D This is automatically added to each message by the mailing script =3D-=
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--047d7b5da89169659304f4691f0e-- From owner-chemistry@ccl.net Wed Mar 12 11:04:00 2014 From: "iweidlic iweidlic-$-coddes.com" To: CCL Subject: CCL: CCL announcement Message-Id: <-49838-140312102126-29832-w9w9wAyG2ckNsbf69kEQBQ!^!server.ccl.net> X-Original-From: iweidlic Content-Type: multipart/alternative; boundary="----=_Part_609151_1367355367.1394634072056" Date: Wed, 12 Mar 2014 09:21:12 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: iweidlic [iweidlic:_:coddes.com] ------=_Part_609151_1367355367.1394634072056 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Dear Colleagues, We would like to announce the release of Diversity Genie - , a small but powerful utility to analyze datasets of small organic molecules. Its features include: * Calculation and comparison of diversity of chemical sets * Sorting, slicing, and merging large SD files * Conversion between SMILES, InChI, and SDF formats * Filtering based on property values and structural uniqueness * Computation of 2D and 3D atomic coordinates * Computation of molecular properties such as molecular weight, number of rotatable bonds, number of HBO, HBA, as well as other descriptors * Export and import of data to/from CSV files * Generation and printing reports based on SD file data * Data visualization and more! A free 7 day full featured trial is available for download > from for Windows, OS X (10.8+), and Linux. We will be presenting Diversity Genie at the Dallas ACS meeting this Sunday at the afternoon CINF session. We hope you will find it a useful tool for your research! ------=_Part_609151_1367355367.1394634072056 MIME-Version: 1.0 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit
Dear Colleagues,

We would like to announce the release of Diversity Genie - www.diversitygenie.com,
a small but powerful utility to analyze datasets of small organic molecules.
Its features include:
  • Calculation and comparison of diversity of chemical sets
  • Sorting, slicing, and merging large SD files
  • Conversion between SMILES, InChI, and SDF formats
  • Filtering based on property values and structural uniqueness
  • Computation of 2D and 3D atomic coordinates
  • Computation of molecular properties such as molecular weight, number of rotatable bonds, number of HBO, HBA, as well as other descriptors
  • Export and import of data to/from CSV files
  • Generation and printing reports based on SD file data
  • Data visualization and more!
A free 7 day full featured trial is available for download from www.diversitygenie.com
for Windows, OS X (10.8+), and Linux.
We will be presenting Diversity Genie at the Dallas ACS meeting this Sunday at the afternoon CINF session. We hope you will find it a useful tool for your research!
 
 
------=_Part_609151_1367355367.1394634072056-- From owner-chemistry@ccl.net Wed Mar 12 11:38:00 2014 From: "christina msc christinamsc!A!gmail.com" To: CCL Subject: CCL:G: how to give charge and multiplicity for cation for charged complex Message-Id: <-49839-140312112137-25927-DKwUDmLUpsr5uDvFVFM7BQ*|*server.ccl.net> X-Original-From: "christina msc" Date: Wed, 12 Mar 2014 11:21:36 -0400 Sent to CCL by: "christina msc" [christinamsc|gmail.com] Dear All, I am doing DFT/TDDFT studies of certain Pd complexes using Gaussian 09 software. The overall charge of my system is +1 (charge 0, multiplicity=1). I would like to calculate cation and anion energy for this kind of charged complexes. Please let me know how to give charge and multiplicity for cation and anion for my charged complex. Thanks in advance. Yours Sincerely, Christina From owner-chemistry@ccl.net Wed Mar 12 12:25:00 2014 From: "Jim Kress jimkress35**gmail.com" To: CCL Subject: CCL: Sensitivity of vertical ionization energy and homo on geometry Message-Id: <-49840-140312115607-14293-pRTZMq1A7JzSbNsBeTwp0A^^server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0126_01CF3DEA.06942F10" Date: Wed, 12 Mar 2014 11:55:55 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35%a%gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_0126_01CF3DEA.06942F10 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Comparing vertical ionization energies with experimental data, without taking into account geometric changes that occur during the process, may = not be the best way to proceed. Frank Neese and his co-workers have = developed and implemented methodologies in their software ORCA http://cec.mpg.de/forum/ =20 that have wide-ranging capabilities in this area across the entire range = of levels of theory you might wish to apply. They also provide extensive documentation and an excellent bibliography of publications related to = most forms of spectroscopic phenomena including ionization. =20 You might want to investigate ORCA and it=92s documentation closely. =20 Jim =20 > From: owner-chemistry+jimkress35=3D=3Dgmail.com~~ccl.net [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com~~ccl.net] On Behalf Of = Scott McKechnie jsm78^cam.ac.uk Sent: Wednesday, March 12, 2014 9:51 AM To: Kress, Jim Subject: CCL: Sensitivity of vertical ionization energy and homo on = geometry =20 Dear Dr. Lua=F1a, =20 Thank you for your reply. I am looking into comparing calculated = vertical ionization energies (using orbital energies or delta-scf calculations in DFT, CCSD etc) for molecules with experimental vertical ionization = energies > from photoelectron spectroscopy. I have found that the calculated = ionization energies can be sensitive to changes in the geometry (i.e. from excited state geometries that are not the gas phase minimum) and was looking for references to papers which have discussed such sensitivity or some = insight > from ccl members. I am also interested in how this sensitivity to = geometry might change with system size and the types of atoms and groups in a molecule. =20 Best wishes, Scott=20 =20 =20 =20 =20 On 12 March 2014 11:28, V=EDctor Lua=F1a > wrote: Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor__fluor.quimica.uniovi.es = ] On Wed, Mar 12, 2014 at 06:01:09AM -0400, Scott Mckechnie = jsm78_+_cam.ac.uk wrote: > > Sent to CCL by: "Scott Mckechnie" [jsm78[#]cam.ac.uk = ] > I know that the vertical ionization energy and homo energy of a > molecule can be quite sensitive to the molecular geometry used. I was > hoping to find a more detailed discussion of this (including how the > sensitivity might change with system size), can anyone point me to = some > relevant work? I would also welcome any comments that people might = have > about this. Scott, Sorry, but I don't really understand your question. What is your level of knowledge on Molecular Spectroscopy? The IP for a molecule is the result of an experimental measurement. What do you want to know, how IPs can be calculated? Which tables of data access? Please, let us know which are your intentions. Regards, Dr. V=EDctor Lua=F1a -- \|/ |^.^| +---!OO--\_/--OO!------------------------------+----------------------- ! Dr.V=EDctor Lua=F1a ! ! Departamento de Qu=EDmica F=EDsica y Anal=EDtica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor\a/fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +----------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) -=3D This is automatically added to each message by the mailing script = =3D-
= or use:E-mail to administrators: CHEMISTRY-REQUEST+/-ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtml

Comparing vertical ionization energies with experimental data, = without taking into account geometric changes that occur during the = process, may not be the best way to proceed.=A0 Frank Neese and his = co-workers have developed and implemented methodologies in their = software ORCA

http://cec.mpg.de/forum/=

 

that have wide-ranging capabilities in this area across the entire = range of levels of theory you might wish to apply.=A0 They also provide = extensive documentation and an excellent bibliography of publications = related to most forms of spectroscopic phenomena including = ionization.

 

You might want to investigate ORCA and it’s documentation = closely.

 

Jim

 

From: = owner-chemistry+jimkress35=3D=3Dgmail.com~~ccl.net = [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com~~ccl.net] On Behalf = Of Scott McKechnie jsm78^cam.ac.uk
Sent: Wednesday, March = 12, 2014 9:51 AM
To: Kress, Jim
Subject: = CCL: Sensitivity of vertical ionization energy and homo on = geometry

 

Dear Dr. = Lua=F1a,

 

Thank you = for your reply. I am looking into comparing calculated vertical = ionization energies (using orbital energies or delta-scf calculations in = DFT, CCSD etc) for molecules with experimental vertical ionization = energies from photoelectron spectroscopy. I have found that the = calculated ionization energies can be sensitive to changes in the = geometry (i.e. from excited state geometries that are not the gas phase = minimum) and was looking for references to papers which have discussed = such sensitivity or some insight from ccl members. I am also interested = in how this sensitivity to geometry might change with system size and = the types of atoms and groups in a = molecule.

 

Best = wishes,


Scott&nbs= p;

 

 

 

 

On 12 March 2014 11:28, V=EDctor Lua=F1a <owner-chemistry+/-ccl.net> = wrote:


Sent = to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor__fluor.quimica.uniovi.es]

On Wed, Mar 12, 2014 at 06:01:09AM -0400, Scott = Mckechnie jsm78_+_cam.ac.uk wrote:
>
> Sent to CCL by: = "Scott  Mckechnie" [jsm78[#]cam.ac.uk]

> I know that the = vertical ionization energy and homo energy of a
> molecule can be = quite sensitive to the molecular geometry used. I was
> hoping to = find a more detailed discussion of this (including how the
> = sensitivity might change with system size), can anyone point me to = some
> relevant work? I would also welcome any comments that = people might have
> about this.

Scott,

Sorry, but I don't really understand = your question. What is your level
of knowledge on Molecular = Spectroscopy?

The IP for a molecule is the result of an = experimental measurement. What
do you want to know, how IPs can be = calculated? Which tables of data
access? Please, let us know which = are your intentions.

Regards,
        Dr. = V=EDctor Lua=F1a
--
        =  \|/
        = |^.^|
+---!OO--\_/--OO!------------------------------+----------------= -------
!            Dr.V=EDctor = Lua=F1a                   = !
! Departamento de Qu=EDmica F=EDsica y Anal=EDtica   !
! = Universidad de Oviedo, 33006-Oviedo, Spain   !
! e-mail:   = victor\a/fluor.quimica.uniovi.es     !
! = phone: +34-985-103491  fax: +34-985-103125   = !
+----------------------------------------------+
 GroupPage = : http://azufre.quimica.uniovi.es/  (being = reworked)

 

------=_NextPart_000_0126_01CF3DEA.06942F10-- From owner-chemistry@ccl.net Wed Mar 12 13:00:00 2014 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor,+,fluor.quimica.uniovi.es" To: CCL Subject: CCL: Sensitivity of vertical ionization energy and homo on geometry Message-Id: <-49841-140312123354-11795-+k+py3m06s2CcVTQ61kaJA_._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: Wed, 12 Mar 2014 16:36:07 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor-$-fluor.quimica.uniovi.es] On Wed, Mar 12, 2014 at 01:50:42PM +0000, Scott McKechnie jsm78^cam.ac.uk wrote: > Dear Dr. Luaña, > > Thank you for your reply. I am looking into comparing calculated vertical > ionization energies (using orbital energies or delta-scf calculations in > DFT, CCSD etc) for molecules with experimental vertical ionization energies > > from photoelectron spectroscopy. I have found that the calculated > ionization energies can be sensitive to changes in the geometry (i.e. from > excited state geometries that are not the gas phase minimum) and was > looking for references to papers which have discussed such sensitivity or > some insight from ccl members. I am also interested in how this sensitivity > to geometry might change with system size and the types of atoms and groups > in a molecule. Scott, You are asking for a very complicated problem in a forum suposedly created for professionals: CCL (Computational Chemistry List). However, the formulation of your question does not permit to identify you as a professional. At least not a CCL professional. Please, see a professor near you and interest him/her enough to take you as a student. As for an incomplete answer to the implications of your question: 1) What kind of molecule? 2) Which thermodynamic condition? 3) Effect of pressure or temperature? Or both? 4) Gas phase? Liquid? Crystal? Amorphous? ... Regards, Dr. Víctor Luaña From owner-chemistry@ccl.net Wed Mar 12 14:02:00 2014 From: "Close, David M. CLOSED*_*mail.etsu.edu" To: CCL Subject: CCL:G: how to give charge and multiplicity for cation for charged complex Message-Id: <-49842-140312125618-28173-fzTxyaCvmhbO8RD7tOGhGA{=}server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 12 Mar 2014 16:56:09 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED---mail.etsu.edu] Christina: To create the cation you must remove an electron. This will create an open shell, so the multiplicity will be 2 and the charge will be +2. For the anion you must add an electron, which will also create an open shell. This then would have charge 0 and multiplicity 2. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu.:.ccl.net [mailto:owner-chemistry+closed==etsu.edu.:.ccl.net] On Behalf Of christina msc christinamsc!A!gmail.com Sent: Wednesday, March 12, 2014 11:22 AM To: Close, David M. Subject: CCL:G: how to give charge and multiplicity for cation for charged complex Sent to CCL by: "christina msc" [christinamsc|gmail.com] Dear All, I am doing DFT/TDDFT studies of certain Pd complexes using Gaussian 09 software. The overall charge of my system is +1 (charge 0, multiplicity=1). I would like to calculate cation and anion energy for this kind of charged complexes. Please let me know how to give charge and multiplicity for cation and anion for my charged complex. Thanks in advance. Yours Sincerely, Christinahttp://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 Wed Mar 12 15:53:00 2014 From: "Abrash, Samuel sabrash(0)richmond.edu" To: CCL Subject: CCL: Sensitivity of vertical ionization energy and homo on geometry Message-Id: <-49843-140312155026-13076-bTXbk1GmsQF8sskol5MgtA:server.ccl.net> X-Original-From: "Abrash, Samuel" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_A7C78D2AEE62DB40B9CB1ADE9D5990A2C2C3B75Bquorrarichmonde_" Date: Wed, 12 Mar 2014 19:50:16 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash%richmond.edu] --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A2C2C3B75Bquorrarichmonde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable If I understand Jim's comments correctly, one of them isn't quite right. V= ertical ionization energies, both experimentally and theoretically, are bas= ed on the geometry staying unchanged during the ionization process, althoug= h of course the geometry can evolve on the ionized surface after the ioniza= tion occurs. So changes in the geometry during the process are not a consi= deration for vertical ionization energies. In contrast they are critical f= or adiabatic ionization energies which measure the energetic differences be= tween the ground state potential minima of the neutral and ionized species. On the other hand if Jim was talking about the differences in the ground st= ate geometry in different solvents (or in vacuo), and the effect that they = have on the vertical ionization energy, that would be perfectly correct. Best regards, Sam Abrash > From: owner-chemistry+sabrash=3D=3Drichmond.edu#%#ccl.net [mailto:owner-chemi= stry+sabrash=3D=3Drichmond.edu#%#ccl.net] On Behalf Of Jim Kress jimkress35**= gmail.com Sent: Wednesday, March 12, 2014 11:56 AM To: Abrash, Samuel Subject: CCL: Sensitivity of vertical ionization energy and homo on geometr= y Comparing vertical ionization energies with experimental data, without taki= ng into account geometric changes that occur during the process, may not be= the best way to proceed. Frank Neese and his co-workers have developed an= d implemented methodologies in their software ORCA http://cec.mpg.de/forum/ that have wide-ranging capabilities in this area across the entire range of= levels of theory you might wish to apply. They also provide extensive doc= umentation and an excellent bibliography of publications related to most fo= rms of spectroscopic phenomena including ionization. You might want to investigate ORCA and it's documentation closely. Jim > From: owner-chemistry+jimkress35=3D=3Dgmail.com()ccl.net [mailto:owner-chem= istry+jimkress35=3D=3Dgmail.com()ccl.net] On Behalf Of Scott McKechnie jsm7= 8^cam.ac.uk Sent: Wednesday, March 12, 2014 9:51 AM To: Kress, Jim Subject: CCL: Sensitivity of vertical ionization energy and homo on geometr= y Dear Dr. Lua=F1a, Thank you for your reply. I am looking into comparing calculated vertical i= onization energies (using orbital energies or delta-scf calculations in DFT= , CCSD etc) for molecules with experimental vertical ionization energies fr= om photoelectron spectroscopy. I have found that the calculated ionization = energies can be sensitive to changes in the geometry (i.e. from excited sta= te geometries that are not the gas phase minimum) and was looking for refer= ences to papers which have discussed such sensitivity or some insight from = ccl members. I am also interested in how this sensitivity to geometry might= change with system size and the types of atoms and groups in a molecule. Best wishes, Scott On 12 March 2014 11:28, V=EDctor Lua=F1a > wrote: Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor__fl= uor.quimica.uniovi.es] On Wed, Mar 12, 2014 at 06:01:09AM -0400, Scott Mckechnie jsm78_+_cam.ac.uk= wrote: > > Sent to CCL by: "Scott Mckechnie" [jsm78[#]cam.ac.uk] > I know that the vertical ionization energy and homo energy of a > molecule can be quite sensitive to the molecular geometry used. I was > hoping to find a more detailed discussion of this (including how the > sensitivity might change with system size), can anyone point me to some > relevant work? I would also welcome any comments that people might have > about this. Scott, Sorry, but I don't really understand your question. What is your level of knowledge on Molecular Spectroscopy? The IP for a molecule is the result of an experimental measurement. What do you want to know, how IPs can be calculated? Which tables of data access? Please, let us know which are your intentions. Regards, Dr. V=EDctor Lua=F1a -- \|/ |^.^| +---!OO--\_/--OO!------------------------------+----------------------- ! Dr.V=EDctor Lua=F1a ! ! Departamento de Qu=EDmica F=EDsica y Anal=EDtica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor\a/fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +----------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) -=3D This is automatically added to each message by the mailing script =3D-=
or u= se:E-mail to administrators: CHEMISTRY-REQUEST+/-ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtml

If I understand Jim’= ;s comments correctly, one of them isn’t quite right.  Vertical = ionization energies, both experimentally and theoretically, are based on the geometry staying unchanged during the ionization process, although of = course the geometry can evolve on the ionized surface after the ionization = occurs.  So changes in the geometry during the process are not a consi= deration for vertical ionization energies.  In contrast they are critical for adiabatic ionization energies which meas= ure the energetic differences between the ground state potential minima of = the neutral and ionized species.

 <= /p>

On the other hand if Jim = was talking about the differences in the ground state geometry in different= solvents (or in vacuo), and the effect that they have on the vertical ionization energy, that would be perfectly  correct.

 <= /p>

Best regards,<= /span>

Sam Abrash

 <= /p>

From: owner-ch= emistry+sabrash=3D=3Drichmond.edu#%#ccl.net [mailto:owner-chemistry+s= abrash=3D=3Drichmond.edu#%#ccl.net] On Behalf Of Jim Kress jimkress35**gmail.com
Sent: Wednesday, March 12, 2014 11:56 AM
To: Abrash, Samuel
Subject: CCL: Sensitivity of vertical ionization energy and homo on = geometry

 

Comparing vertical ioniza= tion energies with experimental data, without taking into account geometric= changes that occur during the process, may not be the best way to proceed.  Frank Neese and his co-workers have developed and im= plemented methodologies in their software ORCA

http://cec.mpg.de/forum/

 <= /p>

that have wide-ranging ca= pabilities in this area across the entire range of levels of theory you mig= ht wish to apply.  They also provide extensive documentation and an excellent bibliography of publications related to most forms of spe= ctroscopic phenomena including ionization.

 <= /p>

You might want to investi= gate ORCA and it’s documentation closely.

 <= /p>

Jim

 <= /p>

From: owner-= chemistry+jimkress35=3D=3Dgmail.com()ccl.net [mailto:owner-chemistry= 3;jimkress35=3D=3Dgmail.com()ccl.net] On Behalf Of Scott McKechnie jsm78^cam.ac.uk
Sent: Wednesday, March 12, 2014 9:51 AM
To: Kress, Jim
Subject: CCL: Sensitivity of vertical ionization energy and homo on = geometry

 

Dear Dr. Lua=F1a,

 

Thank you for your reply. I am looking in= to comparing calculated vertical ionization energies (using orbital energie= s or delta-scf calculations in DFT, CCSD etc) for molecules with experimental vertical ionization energies from photoelectron spectros= copy. I have found that the calculated ionization energies can be sensitive= to changes in the geometry (i.e. from excited state geometries that are no= t the gas phase minimum) and was looking for references to papers which have discussed such sensitivity or = some insight from ccl members. I am also interested in how this sensitivity= to geometry might change with system size and the types of atoms and group= s in a molecule.

 

Best wishes,


Scott 

 

 

 

 

On 12 March 2014 11:28, V=EDctor Lua=F1a <owner-chemistry= +/-ccl.net> wrote:


Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor__fluor.qu= imica.uniovi.es]

On Wed, Mar 12, 2014 at 06:01:09AM -0400, Scott Mcke= chnie jsm78_+_cam.ac.uk<= /a> wrote:
>
> Sent to CCL by: "Scott  Mckechnie" [jsm78[#]cam.ac.uk]

> I know that the = vertical ionization energy and homo energy of a
> molecule can be quite sensitive to the molecular geometry used. I was<= br> > hoping to find a more detailed discussion of this (including how the > sensitivity might change with system size), can anyone point me to som= e
> relevant work? I would also welcome any comments that people might hav= e
> about this.

Scott,

Sorry, but I don't really understand your question. What is your level
of knowledge on Molecular Spectroscopy?

The IP for a molecule is the result of an experimental measurement. What do you want to know, how IPs can be calculated? Which tables of data
access? Please, let us know which are your intentions.

Regards,
        Dr. V=EDctor Lua=F1a
--
         \|/
        |^.^|
+---!OO--\_/--OO!------------------------------+-------------------= ----
!            Dr.V=EDctor Lua=F1a    = ;               !
! Departamento de Qu=EDmica F=EDsica y Anal=EDtica   !
! Universidad de Oviedo, 33006-Oviedo, Spain   !
! e-mail:   victor\a/fluor.quimica.uniovi.es     !
! phone: +34-985-103491  fax:= +34-985-103125   !
+----------------------------------------------+
 GroupPage : http://azufre.quimica.uniovi.es/  (being reworked)




-=3D This is automatically added to each message by the mailing script =3D-= <br


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--_000_A7C78D2AEE62DB40B9CB1ADE9D5990A2C2C3B75Bquorrarichmonde_-- From owner-chemistry@ccl.net Wed Mar 12 16:28:01 2014 From: "Robert Molt r.molt.chemical.physics _ gmail.com" To: CCL Subject: CCL: Sensitivity of vertical ionization energy and homo on geometry Message-Id: <-49844-140312162056-27334-Gbv8AaAYXW+jrp71wHM5NQ,,server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 12 Mar 2014 16:20:38 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics\a/gmail.com] I echo Dr. Abrash's sentiments as correct. Dr. Robert Molt Jr., Ph.D. r.molt.chemical.physics .. gmail.com Nigel Richards Research Group Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202 On 3/12/14 3:50 PM, Abrash, Samuel sabrash(0)richmond.edu wrote: > If I understand Jim's comments correctly, one of them isn't quite right. Vertical ionization energies, both experimentally and theoretically, are based on the geometry staying unchanged during the ionization process, although of course the geometry can evolve on the ionized surface after the ionization occurs. So changes in the geometry during the process are not a consideration for vertical ionization energies. In contrast they are critical for adiabatic ionization energies which measure the energetic differences between the ground state potential minima of the neutral and ionized species. > > On the other hand if Jim was talking about the differences in the ground state geometry in different solvents (or in vacuo), and the effect that they have on the vertical ionization energy, that would be perfectly correct. > > Best regards, > Sam Abrash > >> From: owner-chemistry+sabrash==richmond.edu++ccl.net [mailto:owner-chemistry+sabrash==richmond.edu++ccl.net] On Behalf Of Jim Kress jimkress35**gmail.com > Sent: Wednesday, March 12, 2014 11:56 AM > To: Abrash, Samuel > Subject: CCL: Sensitivity of vertical ionization energy and homo on geometry > > Comparing vertical ionization energies with experimental data, without taking into account geometric changes that occur during the process, may not be the best way to proceed. Frank Neese and his co-workers have developed and implemented methodologies in their software ORCA > > http://cec.mpg.de/forum/ > > that have wide-ranging capabilities in this area across the entire range of levels of theory you might wish to apply. They also provide extensive documentation and an excellent bibliography of publications related to most forms of spectroscopic phenomena including ionization. > > You might want to investigate ORCA and it's documentation closely. > > Jim > >> From: owner-chemistry+jimkress35==gmail.com()ccl.net [mailto:owner-chemistry+jimkress35==gmail.com()ccl.net] On Behalf Of Scott McKechnie jsm78^cam.ac.uk > Sent: Wednesday, March 12, 2014 9:51 AM > To: Kress, Jim > Subject: CCL: Sensitivity of vertical ionization energy and homo on geometry > > Dear Dr. Luaña, > > Thank you for your reply. I am looking into comparing calculated vertical ionization energies (using orbital energies or delta-scf calculations in DFT, CCSD etc) for molecules with experimental vertical ionization energies from photoelectron spectroscopy. I have found that the calculated ionization energies can be sensitive to changes in the geometry (i.e. from excited state geometries that are not the gas phase minimum) and was looking for references to papers which have discussed such sensitivity or some insight from ccl members. I am also interested in how this sensitivity to geometry might change with system size and the types of atoms and groups in a molecule. > > Best wishes, > > Scott > > > > > On 12 March 2014 11:28, Víctor Luaña > wrote: > > Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor__fluor.quimica.uniovi.es] > On Wed, Mar 12, 2014 at 06:01:09AM -0400, Scott Mckechnie jsm78_+_cam.ac.uk wrote: >> Sent to CCL by: "Scott Mckechnie" [jsm78[#]cam.ac.uk] >> I know that the vertical ionization energy and homo energy of a >> molecule can be quite sensitive to the molecular geometry used. I was >> hoping to find a more detailed discussion of this (including how the >> sensitivity might change with system size), can anyone point me to some >> relevant work? I would also welcome any comments that people might have >> about this. > Scott, > > Sorry, but I don't really understand your question. What is your level > of knowledge on Molecular Spectroscopy? > > The IP for a molecule is the result of an experimental measurement. What > do you want to know, how IPs can be calculated? Which tables of data > access? Please, let us know which are your intentions. > > Regards, > Dr. Víctor Luaña > -- > \|/ > |^.^| > +---!OO--\_/--OO!------------------------------+----------------------- > ! Dr.Víctor Luaña ! > ! Departamento de Química Física y Analítica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: victor\a/fluor.quimica.uniovi.es ! > ! phone: +34-985-103491 fax: +34-985-103125 ! > +----------------------------------------------+ > GroupPage : http://azufre.quimica.uniovi.es/ (being reworked)
> > E-mail to subscribers: CHEMISTRY+/-ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST+/-ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtml Content-Type: text/html; charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > > > > > > > >
>

If I understand Jim’s comments correctly, one of them isn’t quite right.  Vertical ionization energies, both experimentally and theoretically, are based on > the geometry staying unchanged during the ionization process, although of course the geometry can evolve on the ionized surface after the ionization occurs.  So changes in the geometry during the process are not a consideration for vertical ionization energies.  > In contrast they are critical for adiabatic ionization energies which measure the energetic differences between the ground state potential minima of the neutral and ionized species.

>

 

>

On the other hand if Jim was talking about the differences in the ground state geometry in different solvents (or in vacuo), and the effect that they have on > the vertical ionization energy, that would be perfectly  correct.

>

 

>

Best regards,

>

Sam Abrash

>

 

>
>
>

From: owner-chemistry+sabrash==richmond.edu++ccl.net [mailto:owner-chemistry+sabrash==richmond.edu++ccl.net] > On Behalf Of Jim Kress jimkress35**gmail.com
> Sent: Wednesday, March 12, 2014 11:56 AM
> To: Abrash, Samuel
> Subject: CCL: Sensitivity of vertical ionization energy and homo on geometry

>
>
>

 

>

Comparing vertical ionization energies with experimental data, without taking into account geometric changes that occur during the process, may not be the best > way to proceed.  Frank Neese and his co-workers have developed and implemented methodologies in their software ORCA
>
> http://cec.mpg.de/forum/

>

 

>

that have wide-ranging capabilities in this area across the entire range of levels of theory you might wish to apply.  They also provide extensive documentation > and an excellent bibliography of publications related to most forms of spectroscopic phenomena including ionization.

>

 

>

You might want to investigate ORCA and it’s documentation closely.

>

 

>

Jim

>

 

>

From: owner-chemistry+jimkress35==gmail.com()ccl.net [mailto:owner-chemistry+jimkress35==gmail.com()ccl.net] > On Behalf Of Scott McKechnie jsm78^cam.ac.uk
> Sent: Wednesday, March 12, 2014 9:51 AM
> To: Kress, Jim
> Subject: CCL: Sensitivity of vertical ionization energy and homo on geometry

>

 

>
>

Dear Dr. Luaña,

>
>

 

>
>
>

Thank you for your reply. I am looking into comparing calculated vertical ionization energies (using orbital energies or delta-scf calculations in DFT, CCSD etc) for molecules > with experimental vertical ionization energies from photoelectron spectroscopy. I have found that the calculated ionization energies can be sensitive to changes in the geometry (i.e. from excited state geometries that are not the gas phase minimum) and was > looking for references to papers which have discussed such sensitivity or some insight from ccl members. I am also interested in how this sensitivity to geometry might change with system size and the types of atoms and groups in a molecule.

>
>
>

 

>
>
>

Best wishes,

>
>
>


> Scott 

>
>
>

 

>
>
>

 

>
>
>

 

>
>
>
>

 

>
>

On 12 March 2014 11:28, Víctor Luaña <owner-chemistry+/-ccl.net> wrote:

>
>


> Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor__fluor.quimica.uniovi.es]

>
>

On Wed, Mar 12, 2014 at 06:01:09AM -0400, Scott Mckechnie jsm78_+_cam.ac.uk wrote:
> >
> > Sent to CCL by: "Scott  Mckechnie" [jsm78[#]cam.ac.uk]

>
>
>

> I know that the vertical ionization energy and homo energy of a
> > molecule can be quite sensitive to the molecular geometry used. I was
> > hoping to find a more detailed discussion of this (including how the
> > sensitivity might change with system size), can anyone point me to some
> > relevant work? I would also welcome any comments that people might have
> > about this.

>
>

Scott,
>
> Sorry, but I don't really understand your question. What is your level
> of knowledge on Molecular Spectroscopy?
>
> The IP for a molecule is the result of an experimental measurement. What
> do you want to know, how IPs can be calculated? Which tables of data
> access? Please, let us know which are your intentions.
>
> Regards,
>         Dr. Víctor Luaña
> --
>          \|/
>         |^.^|
> +---!OO--\_/--OO!------------------------------+-----------------------
> !            Dr.Víctor Luaña                   !
> ! Departamento de Química Física y Analítica   !
> ! Universidad de Oviedo, 33006-Oviedo, Spain   !
> ! e-mail:   victor\a/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 Wed Mar 12 17:08:00 2014 From: "Gabriel Carvalho urquizagabes(_)gmail.com" To: CCL Subject: CCL: Visualizing Electron Density as Point Cloud Message-Id: <-49845-140312155403-13937-7ybO2v8PY+5DtRaY50pQDQ-$-server.ccl.net> X-Original-From: "Gabriel Carvalho" Date: Wed, 12 Mar 2014 15:54:02 -0400 Sent to CCL by: "Gabriel Carvalho" [urquizagabes]![gmail.com] Dear all, I currently have a plot of an electron density as a point cloud where each point has coordinates in space as well as a scalar describing the electron density at that point. The file consists of a bunch of lines of the form: X Y Z DENSITY I am having difficulties finding simple, easy-to-use softwares that can read and render that kind of data. I do not require it to have a lot of tools, or to render beautifully. I just need something to allow me visualization of the points and the scalar value in some way, even if a crude one. Thanks in advance for ANY suggestion, Gabriel Carvalho From owner-chemistry@ccl.net Wed Mar 12 18:13:01 2014 From: "Geoffrey Hutchison geoffh.:.pitt.edu" To: CCL Subject: CCL: Visualizing Electron Density as Point Cloud Message-Id: <-49846-140312181101-11465-bCaPOzjGcSYG1m6pFbl7xg*o*server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Wed, 12 Mar 2014 18:10:53 -0400 Mime-Version: 1.0 (Mac OS X Mail 7.2 \(1874\)) Sent to CCL by: Geoffrey Hutchison [geoffh%a%pitt.edu] > X Y Z DENSITY > > I am having difficulties finding simple, easy-to-use softwares that can read > and render that kind of data. I do not require it to have a lot of tools, or I think you want something like ParaView: http://www.paraview.org/paraview/project/imagegallery.php Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh||pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Wed Mar 12 19:50:00 2014 From: "Victor Rosas Garcia rosas.victor(a)gmail.com" To: CCL Subject: CCL: Visualizing Electron Density as Point Cloud Message-Id: <-49847-140312180814-10251-WeKqKlUJS7nlRWV2KivmJQ*|*server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=001a11c30cc86bca5c04f47012c8 Date: Wed, 12 Mar 2014 16:08:09 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor(_)gmail.com] --001a11c30cc86bca5c04f47012c8 Content-Type: text/plain; charset=ISO-8859-1 you may want to try gnuplot just my two cents Victor 2014-03-12 13:54 GMT-06:00 Gabriel Carvalho urquizagabes(_)gmail.com < owner-chemistry###ccl.net>: > > Sent to CCL by: "Gabriel Carvalho" [urquizagabes]![gmail.com] > Dear all, > > > I currently have a plot of an electron density as a point cloud where each > point has coordinates in space as well as a scalar describing the electron > density at that point. The file consists of a bunch of lines of the form: > > X Y Z DENSITY > > I am having difficulties finding simple, easy-to-use softwares that can > read > and render that kind of data. I do not require it to have a lot of tools, > or > to render beautifully. I just need something to allow me visualization of > the > points and the scalar value in some way, even if a crude one. > > Thanks in advance for ANY suggestion, > > Gabriel Carvalho> > > --001a11c30cc86bca5c04f47012c8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
you may want to try gnuplot

just my two = cents

Victor


2014-03-12 13:54 GMT-06:00 Gabriel Carvalho urquizagabes(_= )gmail.com <owner-chemistry###ccl.n= et>:

Sent to CCL by: "Gabriel =A0Carvalho" [urquizagabes]![gmail.com]
Dear all,


I currently have a plot of an electron density as a point cloud where each<= br> point has coordinates in space as well as a scalar describing the electron<= br> density at that point. The file consists of a bunch of lines of the form:
X =A0Y =A0Z =A0DENSITY

I am having difficulties finding simple, easy-to-use softwares that can rea= d
and render that kind of data. I do not require it to have a lot of tools, o= r
to render beautifully. I just need something to allow me visualization of t= he
points and the scalar value in some way, even if a crude one.

Thanks in advance for ANY suggestion,

Gabriel Carvalho



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--001a11c30cc86bca5c04f47012c8-- From owner-chemistry@ccl.net Wed Mar 12 20:25:00 2014 From: "Susi Lehtola susi.lehtola**alumni.helsinki.fi" To: CCL Subject: CCL:G: Visualizing Electron Density as Point Cloud Message-Id: <-49848-140312190502-18511-P8QXhCfBbiO9EnZx88pY0A^^^server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Thu, 13 Mar 2014 01:04:54 +0200 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola===alumni.helsinki.fi] On Wed, 12 Mar 2014 15:54:02 -0400 "Gabriel Carvalho urquizagabes(_)gmail.com" wrote: > Sent to CCL by: "Gabriel Carvalho" [urquizagabes]![gmail.com] > Dear all, > > > I currently have a plot of an electron density as a point cloud where each > point has coordinates in space as well as a scalar describing the electron > density at that point. The file consists of a bunch of lines of the form: > > X Y Z DENSITY > > I am having difficulties finding simple, easy-to-use softwares that can read > and render that kind of data. I do not require it to have a lot of tools, or > to render beautifully. I just need something to allow me visualization of the > points and the scalar value in some way, even if a crude one. I'm guessing Matlab / Octave can do this, probably gnuplot as well. If the points are on a cartesian grid, another alternative would be to write a simple script to transform the data into e.g. Gaussian cube format, which can readily be visualized by practically all molecular visualization software out there (JMol, IQMol and Avogadro come to mind). -- --------------------------------------------------------------- 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 ---------------------------------------------------------------