From owner-chemistry@ccl.net Thu May 2 11:45:00 2013 From: "Fedor Goumans goumans:-:scm.com" To: CCL Subject: CCL: ADF electronic configuration problem Message-Id: <-48641-130502103050-16298-69JaSWERz465ZJqLNQzF7g .. server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 02 May 2013 16:29:55 +0200 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans|*|scm.com] Dear Karina, I'm not sure what you want to do exactly. If you're just removing the one electron and don't do anything else, you are creating a cation (or increasing the charge by 1) and can leave everything else the same. There are different ways in ADF to get spin couplings in metallic clusters, see e.g. the advanced tutorial: http://www.scm.com/Doc/Doc2013/GUI/GUI_tutorial/page84.html Let us know at support{:}scm.com if you have any further questions or problems. We are happy to have a look at your structures and input. With kind regards, Fedor On 5/2/2013 2:48 AM, Karina Mu oz karina.munozbe- -usach.cl wrote: > Sent to CCL by: "Karina Mu oz" [karina.munozbe- -usach.cl] > Dear CCl subscribers, > > I am working with a molecule that has six vanadium (IV) centres, all having one unpaired d1 electron. I want to optimize the same fragment, but putting one of the vanadium centres with an oxidation state of (V), in which case it will present non unpaired electrons (d0 external configuration). > Anybody knows which keyword is useful to do this ? > Is not the same case in which I can use de SpinFlip keyword, which works to change the spin of the electron of the centre of interest. > > Thank you in advance > > Best regards > > Karina> > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans{:}scm.com http://www.scm.com From owner-chemistry@ccl.net Thu May 2 14:56:00 2013 From: "Brian Skinn brian.skinn]~[gmail.com" To: CCL Subject: CCL: Heterogeneous electrochemical QM-MM Message-Id: <-48642-130502124305-30005-qlcZUYMqvyBN8ftngHamMw*o*server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary=f46d043c7c58cce4a104dbbeecf0 Date: Thu, 2 May 2013 12:42:29 -0400 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [brian.skinn#gmail.com] --f46d043c7c58cce4a104dbbeecf0 Content-Type: text/plain; charset=ISO-8859-1 Markus, Thank you very much for the links. I will take a closer look at the work at Ulm, as they appear to be studying topics rather similar to my interest. The problem of localizing an 'electron deficit' in DFT/ab initio was exactly what I was wondering about. With organic species, specifying the appropriate atomic connectivity appears in the majority of cases to be sufficient for defining the oxidation state of all of the atoms. Conversely, modeling the heterogeneous electrochemical oxidation of, e.g., ferrocyanide by QM-MM would presumably be challenging because one could not 'remove an electron from an atom of the electrode,' start the atomic clock, and observe the consequences. Since removal of one electron from the system at large would likely just settle to the ferricyanide species as the ground state, it would probably be a pretty unhelpful simulation. I see what you're proposing by dividing the system into three separate QM regions, and I like the idea. The main problem that presents itself is accurate representation of the interactions between the QM regions. Can one define QM interactions between different QM regions, or only MM interactions? Very likely, some of the most interesting dynamics of the evolution of the electron density will occur at the boundaries between electrolyte and electrode and accurate simulation of that region would be critical. Thank you again, Brian (brian.skinn||gmail.com) On Sun, Apr 28, 2013 at 2:47 AM, Markus Kaukonen markus.kaukonen{:}iki.fi < owner-chemistry||ccl.net> wrote: > Dear Brian, > > One problem with the simulation of the fuel cell with standard DFT is that > electron goes where it has the lowest energy. One solution might be > dividing the device in three separate parts (anode, cathode and the > electrolyte) each treated with its own QM calculator. > > I'm slowly working along these lines: > > https://wiki.fysik.dtu.dk/ase/ase/calculators/ase_qmmm_manyqm.html#module-ase_qmmm_manyqm > > Another option: > > http://www.uni-ulm.de/nawi/nawi-thphchemie/research/theory-of-electrocatalysis.html > > Terveisin, Markus > > > On 26 April 2013 19:53, Brian Skinn brian.skinn%a%gmail.com < > owner-chemistry^_^ccl.net> wrote: > >> Hello all- >> >> I was wondering if anyone could suggest a good starting point for reading >> about the state of research on heterogeneous electrochemical QM-MM. >> Specifically, I'm interested in any frameworks that may exist for >> simulation of heterogeneous electrode reactions (metal >> dissolution/deposition, redox chemistry, etc.) and the means by which the >> 'addition' or 'removal' of electrons from the system by an applied >> electrical current is implemented. >> >> Alternatively, if such problems are known to be intractable (either >> infeasible with present hardware/software or demonstrably impossible) I am >> interested in learning in that area as well. >> >> >> Thanks, >> Brian Skinn (brian.skinn]![gmail.com) >> > > > > -- > --www=http://www.iki.fi/markus.kaukonen > --Markus.Kaukonen^_^iki.fi > --office: Karjaan lukio > --home: Viinirinne 3 F 12, 02630 Espoo, FIN > --tel: h 045-1242068 > > > --f46d043c7c58cce4a104dbbeecf0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Markus,

Thank you very mu= ch for the links.=A0 I will take a closer look at the work at Ulm, as they = appear to be studying topics rather similar to my interest.

Th= e problem of localizing an 'electron deficit' in DFT/ab initio was = exactly what I was wondering about.=A0 With organic species, specifying the= appropriate atomic connectivity appears in the majority of cases to be suf= ficient for defining the oxidation state of all of the atoms.=A0 Conversely= , modeling the heterogeneous electrochemical oxidation of, e.g., ferrocyani= de by QM-MM would presumably be challenging because one could not 'remo= ve an electron from an atom of the electrode,' start the atomic clock, = and observe the consequences. Since removal of one electron from the system= at large would likely just settle to the ferricyanide species as the groun= d state, it would probably be a pretty unhelpful simulation.

I see what you're proposing by dividing the system into three= separate QM regions, and I like the idea.=A0 The main problem that present= s itself is accurate representation of the interactions between the QM regi= ons.=A0 Can one define QM interactions between different QM regions, or onl= y MM interactions?=A0 Very likely, some of the most interesting dynamics of= the evolution of the electron density will occur at the boundaries between= electrolyte and electrode and accurate simulation of that region would be = critical.


Thank you again,
Brian (brian.skinn||gmail.com)

<= br>
On Sun, Apr 28, 2013 at 2:47 AM, Markus Kauko= nen markus.kaukonen{:}iki.fi <owner-ch= emistry||ccl.net> wrote:
Dear Brian,<= br>
One problem with the simulation of the fuel cell with standard= DFT is that electron goes where it has the lowest energy. One solution mig= ht be dividing the device in three separate parts (anode, cathode and the e= lectrolyte) each treated with its own QM calculator.

I'm slowly working along these lines:
https://wiki.fysik.dtu.dk/ase/ase/calculators/ase_= qmmm_manyqm.html#module-ase_qmmm_manyqm


Terveisin, Markus
=A0

On 26 April 2013 19:53, Brian Ski= nn brian.skinn%a%gmail.com <owner-chemistry^_^ccl.net> wrote:
Hello all-

I was wondering if anyone could suggest a good st= arting point for reading about the state of research on heterogeneous elect= rochemical QM-MM.=A0 Specifically, I'm interested in any frameworks tha= t may exist for simulation of heterogeneous electrode reactions (metal diss= olution/deposition, redox chemistry, etc.) and the means by which the '= addition' or 'removal' of electrons from the system by an appli= ed electrical current is implemented.

Alternatively, if such problems are known to be intractable (either inf= easible with present hardware/software or demonstrably impossible) I am int= erested in learning in that area as well.


Thanks,
Brian Skinn (b= rian.skinn]![gmail.com)<= br>



--
--www=3Dhttp://www.iki.fi/markus.kaukonen--Markus= .Kaukonen^_^iki.fi
--office: Karjaan lukio
--home: Viinirinne 3 F 12, 02630 Espoo, FIN
--tel: h 045-1242068

=

--f46d043c7c58cce4a104dbbeecf0--