From owner-chemistry@ccl.net Fri Apr 24 08:47:01 2015 From: "Jose Gamez Gamez-*-itmc.rwth-aachen.de" To: CCL Subject: CCL: calculate redox potential Message-Id: <-51309-150424034123-17361-tXCeYPT0Kimb7pujJM06SA(~)server.ccl.net> X-Original-From: Jose Gamez Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_8B87A03BD37C4D65A4B0E1228E1F310Ditmcrwthaachende_" Date: Fri, 24 Apr 2015 07:40:50 +0000 MIME-Version: 1.0 Sent to CCL by: Jose Gamez [Gamez=-=itmc.rwth-aachen.de] --_000_8B87A03BD37C4D65A4B0E1228E1F310Ditmcrwthaachende_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 RGVhciBBc21hYSwNCg0KSW4gYWRkaXRpb24gdG8gd2hhdCBJZ29ycyB3cm90ZToNCg0KMS4gUmVk b3ggcG90ZW50aWFscyBhcmUgcmVsYXRlZCB0aHJvdWdoIE5lcm5zdCBlcXVhdGlvbiB0byBHaWJi 4oCZcyBmcmVlIGVuZXJnaWVzLCBzbyB5b3UgbmVlZCB0byBleHByZXNzIHRoZSBlbmVyZ3kgZGlm ZmVyZW5jZXMgaW4gdGVybXMgb2YgRGVsdGFHJ3MuDQoyLiBSZWRveCByZWFjdGlvbnMgb2NjdXIg 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[bskinn%alum.mit.edu] --f46d041826e69dcb6a051478b34d Content-Type: text/plain; charset=UTF-8 CCL-ers, Provision of sufficient electronic supplementary information for published articles (molecular geometries, etc.) appears to be an ongoing challenge for computational chemists. All too often there are interesting results worth repetition and/or extension, but which are challenging to perform because the source computational files are unavailable. Further, the current journal-site-based ESI publication model is quite confining, as (I assume?) there are size limitations on what publishers wish to host on their servers. So, an idea for discussion: What about posting ESI on third-party services such as Dropbox, Github, etc? ESI is meant to be public information, so security needs are minimal. Such services are well equipped to handle the file transfer loads that ESI would likely represent, and storage costs would either be nil, or comparatively small. Further, it would be possible to deposit binary files (wavefunction information, electron density files, etc.) that might be of significant use to outside researchers wishing to analyze, repeat and/or extend a given work. Pros? Cons? I'm curious what you all think. Best regards, Brian --f46d041826e69dcb6a051478b34d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
CCL-ers,

Provision of sufficient electr= onic supplementary information for published articles (molecular geometries= , etc.) appears to be an ongoing challenge for computational chemists.=C2= =A0 All too often there are interesting results worth repetition and/or ext= ension, but which are challenging to perform because the source computation= al files are unavailable.=C2=A0 Further, the current journal-site-based ESI= publication model is quite confining, as (I assume?) there are size limita= tions on what publishers wish to host on their servers.

So, an idea for discussion: What about posting ESI on third-party ser= vices such as Dropbox, Github, etc?=C2=A0 ESI is meant to be public informa= tion, so security needs are minimal.=C2=A0 Such services are well equipped = to handle the file transfer loads that ESI would likely represent, and stor= age costs would either be nil, or comparatively small.=C2=A0 Further, it wo= uld be possible to deposit binary files (wavefunction information, electron= density files, etc.) that might be of significant use to outside researche= rs wishing to analyze, repeat and/or extend a given work.


Pros? Cons?=C2=A0 I'm curious what you all think= .


Best regards,
Brian
--f46d041826e69dcb6a051478b34d-- From owner-chemistry@ccl.net Fri Apr 24 12:00:00 2015 From: "Victor Rosas Garcia rosas.victor(0)gmail.com" To: CCL Subject: CCL: DropBox / GitHub / etc for ESI Message-Id: <-51311-150424114635-22454-Ysv47WrohPHMPL/DABJRsg]=[server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: text/plain; charset=UTF-8 Date: Fri, 24 Apr 2015 10:46:30 -0500 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor##gmail.com] I use figshare for the supplementary material on my most recent papers. Figshare will host anything, text, binary, whatever. Pretty much no size limits. Victor 2015-04-24 8:51 GMT-05:00 Brian Skinn bskinn(_)alum.mit.edu : > CCL-ers, > > Provision of sufficient electronic supplementary information for published > articles (molecular geometries, etc.) appears to be an ongoing challenge for > computational chemists. All too often there are interesting results worth > repetition and/or extension, but which are challenging to perform because > the source computational files are unavailable. Further, the current > journal-site-based ESI publication model is quite confining, as (I assume?) > there are size limitations on what publishers wish to host on their servers. > > So, an idea for discussion: What about posting ESI on third-party services > such as Dropbox, Github, etc? ESI is meant to be public information, so > security needs are minimal. Such services are well equipped to handle the > file transfer loads that ESI would likely represent, and storage costs would > either be nil, or comparatively small. Further, it would be possible to > deposit binary files (wavefunction information, electron density files, > etc.) that might be of significant use to outside researchers wishing to > analyze, repeat and/or extend a given work. > > > Pros? Cons? I'm curious what you all think. > > > Best regards, > Brian From owner-chemistry@ccl.net Fri Apr 24 12:35:01 2015 From: "Rajarshi Guha rajarshi.guha]~[gmail.com" To: CCL Subject: CCL: DropBox / GitHub / etc for ESI Message-Id: <-51312-150424115239-22936-gSlq1Z5AIowg+fgLKvNiNw]=[server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: multipart/alternative; boundary=001a113df3b672efb005147a622c Date: Fri, 24 Apr 2015 11:52:33 -0400 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha%a%gmail.com] --001a113df3b672efb005147a622c Content-Type: text/plain; charset=ISO-8859-1 Definitely agree with this - though you'd probably need something more stable than personal DropBox accounts. Alternatives include FigShare. At one point, I assume costs would be incurred, depending on how much data is being stored. How would that be handled? One possibility is for journals themselves to have GitHub or DropBox accounts - and authors push their ESI to an appropriate location. (One nice side effect would be to avoid mangling (some) data files into PDF form) On Fri, Apr 24, 2015 at 9:51 AM, Brian Skinn bskinn(_)alum.mit.edu < owner-chemistry]=[ccl.net> wrote: > CCL-ers, > > Provision of sufficient electronic supplementary information for published > articles (molecular geometries, etc.) appears to be an ongoing challenge > for computational chemists. All too often there are interesting results > worth repetition and/or extension, but which are challenging to perform > because the source computational files are unavailable. Further, the > current journal-site-based ESI publication model is quite confining, as (I > assume?) there are size limitations on what publishers wish to host on > their servers. > > So, an idea for discussion: What about posting ESI on third-party services > such as Dropbox, Github, etc? ESI is meant to be public information, so > security needs are minimal. Such services are well equipped to handle the > file transfer loads that ESI would likely represent, and storage costs > would either be nil, or comparatively small. Further, it would be possible > to deposit binary files (wavefunction information, electron density files, > etc.) that might be of significant use to outside researchers wishing to > analyze, repeat and/or extend a given work. > > > Pros? Cons? I'm curious what you all think. > > > Best regards, > Brian > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science --001a113df3b672efb005147a622c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Definitely agree with this - though you'd probably nee= d something more stable than personal DropBox accounts. Alternatives includ= e FigShare. At one point, I assume costs would be incurred, depending on ho= w much data is being stored. How would that be handled? One possibility is = for journals themselves to have GitHub or DropBox accounts - and authors pu= sh their ESI to an appropriate location.

(One nice side = effect would be to avoid mangling (some) data files into PDF form)

On Fri, Apr 24= , 2015 at 9:51 AM, Brian Skinn bskinn(_)alu= m.mit.edu <owner-chemistry]=[ccl.net> wrote:
CCL-ers,

Pro= vision of sufficient electronic supplementary information for published art= icles (molecular geometries, etc.) appears to be an ongoing challenge for c= omputational chemists.=A0 All too often there are interesting results worth= repetition and/or extension, but which are challenging to perform because = the source computational files are unavailable.=A0 Further, the current jou= rnal-site-based ESI publication model is quite confining, as (I assume?) th= ere are size limitations on what publishers wish to host on their servers.<= /div>

So, an idea for discussion: What about posting ESI= on third-party services such as Dropbox, Github, etc?=A0 ESI is meant to b= e public information, so security needs are minimal.=A0 Such services are w= ell equipped to handle the file transfer loads that ESI would likely repres= ent, and storage costs would either be nil, or comparatively small.=A0 Furt= her, it would be possible to deposit binary files (wavefunction information= , electron density files, etc.) that might be of significant use to outside= researchers wishing to analyze, repeat and/or extend a given work.


Pros? Cons?=A0 I'm curious what you al= l think.


Best regards,
Br= ian



--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Transla= tional Science
--001a113df3b672efb005147a622c-- From owner-chemistry@ccl.net Fri Apr 24 13:09:01 2015 From: "janl[*]speakeasy.net" To: CCL Subject: CCL: DropBox / GitHub / etc for ESI Message-Id: <-51313-150424120148-24230-vubtWp1KYZ30HoLa17L1tw.@.server.ccl.net> X-Original-From: janl=speakeasy.net Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary="=_2uc7ua9y0zc6" Date: Fri, 24 Apr 2015 12:01:42 -0400 MIME-Version: 1.0 Sent to CCL by: janl__speakeasy.net This message is in MIME format. --=_2uc7ua9y0zc6 Content-Type: text/plain; charset=UTF-8 Content-Description: Plaintext Version of Message Content-Disposition: inline Content-Transfer-Encoding: quoted-printable =C2=A0 This is a great idea! I am actually considering to move a Web portion (but = not the email distribution and secure pages) to the cloud. A word of cautio= n though. Allowing unattended uploads to public is a very risky proposition= . You will end up with a repository with the gigabytes of "you know what" r= ather than research data. I have been there and seen that... There are ways= to do it securely, but it is not trivial. It always requires constant moni= toring, since the scam of the Internet is always ahead and we can only reac= t. BTW, password protection is a myth with a few millions Windoz computers = with the keyboard sniffers installed. My problem is that I do not have time personally right now to work on it. I= wanted to create some upload site for Comp Chem data for a long time now, = but it will have to wait. I am getting older and I have to sleep on average= 6 hours a day and I constantly miss this "New Year Resolution". Jan CCL Maintainer. On Fri, 24 Apr 2015 09:51:45 -0400, "Brian Skinn bskinn(_)alum.mit.edu" wr= ote: CCL-ers,=C2=A0 Provision of sufficient electronic supplementary information for published = articles (molecular geometries, etc.) appears to be an ongoing challenge fo= r computational chemists.=C2=A0 All too often there are interesting results= worth repetition and/or extension, but which are challenging to perform be= cause the source computational files are unavailable.=C2=A0 Further, the cu= rrent journal-site-based ESI publication model is quite confining, as (I as= sume?) there are size limitations on what publishers wish to host on their = servers. =C2=A0 So, an idea for discussion: What about posting ESI on third-party services = such as Dropbox, Github, etc?=C2=A0 ESI is meant to be public information, = so security needs are minimal.=C2=A0 Such services are well equipped to han= dle the file transfer loads that ESI would likely represent, and storage co= sts would either be nil, or comparatively small.=C2=A0 Further, it would be= possible to deposit binary files (wavefunction information, electron densi= ty files, etc.) that might be of significant use to outside researchers wis= hing to analyze, repeat and/or extend a given work. =C2=A0 =C2=A0 Pros? Cons?=C2=A0 I'm curious what you all think. =C2=A0 =C2=A0 Best regards, Brian ----- End forwarded message ----- --=_2uc7ua9y0zc6 Content-Type: multipart/related; boundary="=_414gxteqr5ye"; start="415jkrbgghk6()wmail.speakeasy.net" Content-Transfer-Encoding: 7bit This message is in MIME format. --=_414gxteqr5ye Content-Type: text/html; charset=UTF-8 Content-Description: HTML Version of Message Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-ID: 415jkrbgghk6()wmail.speakeasy.net

=C2=A0

This is a great idea! I am actually considering to move a Web portion (b= ut not the email distribution and secure pages) to the cloud. A word of cautio= n though. Allowing unattended uploads to public is a very risky proposition. = You will end up with a repository with the gigabytes of "you know what" rather = than research data. I have been there and seen that... There are ways to do it securely, but it is not trivial. It always requires constant monitoring, si= nce the scam of the Internet is always ahead and we can only react. BTW, passwo= rd protection is a myth with a few millions Windoz computers with the keyboard sniffers installed.

My problem is that I do not have time personally right now to work on it= . I wanted to create some upload site for Comp Chem data for a long time now, b= ut it will have to wait. I am getting older and I have to sleep on average 6 hour= s a day and I constantly miss this "New Year Resolution".

Jan

CCL Maintainer.

On Fri, 24 Apr 2015 09:51:45 -0400, "Brian Skinn bskinn(_)alum.mit.edu" <owner-chemistry()ccl.net> wrote:

CCL-ers,
=C2=A0
Provision of sufficient electronic supplementary information for publi= shed articles (molecular geometries, etc.) appears to be an ongoing challenge fo= r computational chemists.=C2=A0 All too often there are interesting results w= orth repetition and/or extension, but which are challenging to perform because t= he source computational files are unavailable.=C2=A0 Further, the current journal-site-based ESI publication model is quite confining, as (I assume?) there are size limitations on what publishers wish to host on their servers.
=C2=A0
So, an idea for discussion: What about posting ESI on third-party serv= ices such as Dropbox, Github, etc?=C2=A0 ESI is meant to be public information, = so security needs are minimal.=C2=A0 Such services are well equipped to handle= the file transfer loads that ESI would likely represent, and storage costs would eit= her be nil, or comparatively small.=C2=A0 Further, it would be possible to depo= sit binary files (wavefunction information, electron density files, etc.) that = might be of significant use to outside researchers wishing to analyze, repeat and= /or extend a given work.
=C2=A0
=C2=A0
Pros? Cons?=C2=A0 I'm curious what you all think.
=C2=A0
=C2=A0
Best regards,
Brian





----- End forwarded message -----

--=_414gxteqr5ye-- --=_2uc7ua9y0zc6-- From owner-chemistry@ccl.net Fri Apr 24 13:45:01 2015 From: "Igors Mihailovs igors.mihailovs0..gmail.com" To: CCL Subject: CCL:G: calculate redox potential Message-Id: <-51314-150424120752-26434-V2kQgZIPXxkOc5ivzEB3lw||server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=089e0158b8e8c967a105147a9812 Date: Fri, 24 Apr 2015 19:07:25 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0-x-gmail.com] --089e0158b8e8c967a105147a9812 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Dr. G=C3=A1mez, Is it possible to evaluate Gibbs energy correctly in Gaussian 09? Frequency job yields Gibbs energy, but I am currently reluctant of using it, because as I understood it is simply computed from all vibrational modes, while there are often low-frequency (below 200=E2=80=93300 cm=E2=81=BB=E2=81=A0= =C2=B9) modes, which, as far as I know, are considered to be unreliable, and every molecule would require Your personal involvement to "separate the sheep from the goats" because this is structure-dependent question (or?). In addition, this Gibbs energy obviously does not account for weak bond with the solvent molecules, if we use PCM description of it=E2=80=A6 Am I wrong in these considerations? P.S. Thank You for pointing to that quite recent review. With best wishes, Igors Mihailovs (engineer) Institute of Solid State Physics University of Latvia 2015-04-24 10:40 GMT+03:00 Jose Gamez Gamez-*-itmc.rwth-aachen.de < owner-chemistry#ccl.net>: > Dear Asmaa, > > In addition to what Igors wrote: > > 1. Redox potentials are related through Nernst equation to Gibb=E2=80=99= s free > energies, so you need to express the energy differences in terms of > DeltaG's. > 2. Redox reactions occur usually in solution, so you'll probably need to > estimate the solvation energy. > > This review should be useful for you: http://doi.org/10.1039/c4cp01572j > > Cheers, > > Dr. Jos=C3=A9 A. G=C3=A1mez [image: ITMC-RWTH] Institute > of Technical and Macromolecular Chemistry. Division of Technical Chemistr= y > and Petrol Chemistry. RWTH Aachen University. Worringerweg 1, 52074 > Aachen, Germany Phone: +49 241 8026510 Fax: +49 241 8022177 > > On 23 Apr 2015, at 20:21, Igors Mihailovs igors.mihailovs0()gmail.com < > owner-chemistry#ccl.net> wrote: > > Dear Asmaa, > > Redox potential is the equilibrium property of many-molecules system in > solution, the potential of electrode at which oxidation and reduction rat= e > is equal. On the other hand, what we usually calculate in ab initio metho= ds > is the property of a single molecule, maybe with solvation shells or usin= g > some continuum solvation model. For example, for ionization of a molecule > > IP(vertical) =3D E(cation) |-| R (neutral) =E2=80=93 E(neutral) |-| R(neu= tral); > IP(adiabatic) =3D E(cation) |-| R (cation) =E2=80=93 E(neutral) |-| R(neu= tral); > > where E stands for energy and R =E2=80=93 for geometry. Assuming that the= redox > potential corresponds to zero thermodynamical barrier between the molecul= e > and the electrode, it seems that adiabatic IP is more related to the redo= x > potential than the vertical one, me trying to apply Marcus=E2=80=93Hush t= heory > here. So, this is the quantity You need to compare Your excited state > ionization (oxidation) potential with. > > In Gaussian, You should then simply run geometry optimizations for both > neutral molecule and the cation, and then subtract their energies, as the > formula above states. On how to perform these calculations, please refer = to > the Gaussian online manual at > http://www.gaussian.com/g_tech/g_ur/g09help.htm and, in case You have > some troubles, feel free to contact Gaussian vendor via help "at" > gaussian.com, they are usually very helpful and open to any questions > (really). > > With best wishes, > Igors Mihailovs (engineer) > Institute of Solid State Physics > University of Latvia > > > 2015-04-14 20:34 GMT+03:00 asmaa el-sayed asmaaphys88 . gmail.com < > owner-chemistry|-|ccl.net>: > >> >> Sent to CCL by: "asmaa el-sayed" [asmaaphys88~!~gmail.com] >> Dear, all >> Does anyone know how to calculate the redox potential for compound in t= he >> ground state using gausssian? i need this redox potential to calculate t= he >> oxidation potential of the compound on the excited state. >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> >> >> E-mail to subscribers: CHEMISTRY|-|ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST|-|ccl.net or use>> >> >> > > --089e0158b8e8c967a105147a9812 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Dr. G=C3=A1mez,

Is it possible= to evaluate Gibbs energy correctly in Gaussian 09? Frequency job yields Gi= bbs energy, but I am currently reluctant of using it, because as I understo= od it is simply computed from all vibrational modes, while there are often = low-frequency (below 200=E2=80=93300 cm=E2=81=BB=E2=81=A0=C2=B9) modes, whi= ch, as far as I know, are considered to be unreliable, and every molecule w= ould require Your personal involvement to "separate the sheep from the= goats" because this is structure-dependent question (or?). In additio= n, this Gibbs energy obviously does not account for weak bond with the solv= ent molecules, if we use PCM description of it=E2=80=A6

Am I wrong i= n these considerations?

P.S. Thank You for pointing to that qu= ite recent review.

With best wishes,
Igors Mihailovs (engineer)
Institute of Solid State Physics<= br>
University of Latvia


2015-04-24 10:40 GMT+03:00 Jose Gamez Gamez-= *-itmc.rwth-aachen.de <o= wner-chemistry#ccl.net>:
Dear Asmaa,

In addition to what Igors wrote:

1. Redox potentials are related through Nernst equation to Gibb=E2=80= =99s free energies, so you need to express the energy differences in terms = of DeltaG's.
2. Redox reactions occur usually in solution, so you'll probably n= eed to estimate the solvation energy.

This review should be useful for you: http://doi.org/10.1039/c4cp01572j

Cheers,
=C2=A0
Dr. Jos=C3=A9 A.= G=C3=A1mez
3D"= Institute of Tec= hnical and Macromolecular Chemistry. Division of Technical Chemistry and Pe= trol Chemistry.
RWTH Aachen Univ= ersity.
Worringerweg 1, = 52074 Aachen, Germany
Phone: +49 241 8= 026510
Fax: +49 241 802= 2177

On 23 Apr 2015, at 20:21, Igors Mihailovs igors.mihailovs0()gmail.com <owner-chemistry#ccl.net> wr= ote:

Dear Asmaa,

Redox potential is the equilibrium property of many-molecules system in sol= ution, the potential of electrode at which oxidation and reduction rate is = equal. On the other hand, what we usually calculate in ab initio methods is= the property of a single molecule, maybe with solvation shells or using some continuum solvation model. For e= xample, for ionization of a molecule

IP(vertical) =3D E(cation) |-| R (neutral) =E2=80=93 E(neutral) |-| R(neutr= al);
IP(adiabatic) =3D E(cation) |-| R (cation) =E2=80=93 E(neutral) |-| R(neutr= al);

where E stands for energy and R =E2=80=93 for geometry. Assuming that the r= edox potential corresponds to zero thermodynamical barrier between the mole= cule and the electrode, it seems that adiabatic IP is more related to the r= edox potential than the vertical one, me trying to apply Marcus=E2=80=93Hush theory here. So, this is the quantity = You need to compare Your excited state ionization (oxidation) potential wit= h.

In Gaussian, You should then simply run geometry optimizations for both neu= tral molecule and the cation, and then subtract their energies, as the form= ula above states. On how to perform these calculations, please refer to the= Gaussian online manual at http://www.gaussian.com/g_tech/g_ur/g09help.htm and, in case You hav= e some troubles, feel free to contact Gaussian vendor via help "at&quo= t; gaussian.com, they a= re usually very helpful and open to any questions (really).

With best wishes,
Igors Mihailovs (engineer)
Institute of Solid State Physics
University of Latvia


2015-04-14 20:34 GMT+03:00 asmaa el-sayed asmaap= hys88 . gmail.com <owner-chemistry|-|ccl.net>:

Sent to CCL by: "asmaa=C2=A0 el-sayed" [asmaaphys88~!~gmail.com]
Dear, all
=C2=A0Does anyone know how to calculate the redox potential for compound in= the
ground state using gausssian? i need this redox potential to calculate the<= br> oxidation potential of the compound on the excited state.



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


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--089e0158b8e8c967a105147a9812-- From owner-chemistry@ccl.net Fri Apr 24 14:20:00 2015 From: "Bennion, Brian bennion1(!)llnl.gov" To: CCL Subject: CCL: DropBox / GitHub / etc for ESI Message-Id: <-51315-150424122953-2862-Xepe/52SZEji7/uTnHkX+A/a\server.ccl.net> X-Original-From: "Bennion, Brian" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_2FD898B2B3ACB44289F398FACE042B4ADA43C720PRDEXMBX01thela_" Date: Fri, 24 Apr 2015 16:29:47 +0000 MIME-Version: 1.0 Sent to CCL by: "Bennion, Brian" [bennion1*llnl.gov] --_000_2FD898B2B3ACB44289F398FACE042B4ADA43C720PRDEXMBX01thela_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello Brian, I agree that this is a neglected part of our work. I know that PLOSone requires that information to repeat the calculations be= deposited on a server provided by the author. If that is not possible the= y work with you to find another site to host the data. Putting data on dropbox etc is a tempting idea and should be explored. How= ever, unless all journals require deposition of electronic structure data f= iles then there is no carrot/stick to make this happen. The pdbdatabank is= a good example of balancing the needs of the researcher vs the rights of o= thers to reproduce/extend structural experiments. You mentioned security is not needed, i disagree slightly. Yes the data sh= ould not sit behind a password that is handed out in single interactions. However, it is important that the supplementary data is not altered/removed= /blocked/hacked etc as it is sitting out in the public. These issues can b= e partially ameliorated with dedicated websites that have dedicated staff a= nd checksums as employed on other websites that offer code to download. Ho= w will that be supported? I don't know. Brian Bennion ________________________________ > From: owner-chemistry+bennion1=3D=3Dllnl.gov.:.ccl.net [owner-chemistry+benni= on1=3D=3Dllnl.gov.:.ccl.net] on behalf of Brian Skinn bskinn(_)alum.mit.edu [= owner-chemistry.:.ccl.net] Sent: Friday, April 24, 2015 6:51 AM To: Bennion, Brian Subject: CCL: DropBox / GitHub / etc for ESI CCL-ers, Provision of sufficient electronic supplementary information for published = articles (molecular geometries, etc.) appears to be an ongoing challenge fo= r computational chemists. All too often there are interesting results wort= h repetition and/or extension, but which are challenging to perform because= the source computational files are unavailable. Further, the current jour= nal-site-based ESI publication model is quite confining, as (I assume?) the= re are size limitations on what publishers wish to host on their servers. So, an idea for discussion: What about posting ESI on third-party services = such as Dropbox, Github, etc? ESI is meant to be public information, so se= curity needs are minimal. Such services are well equipped to handle the fi= le transfer loads that ESI would likely represent, and storage costs would = either be nil, or comparatively small. Further, it would be possible to de= posit binary files (wavefunction information, electron density files, etc.)= that might be of significant use to outside researchers wishing to analyze= , repeat and/or extend a given work. Pros? Cons? I'm curious what you all think. Best regards, Brian --_000_2FD898B2B3ACB44289F398FACE042B4ADA43C720PRDEXMBX01thela_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello Brian,

I agree that this is a neglected part of our work.

I know that PLOSone requires that information to repeat the calculations be= deposited on a server provided by the author.  If that is not possibl= e they work with you to find another site to host the data.

Putting data on dropbox etc is a tempting idea and should be explored. = ; However, unless all journals require deposition of electronic structure d= ata files then there is no carrot/stick to make this happen.  The pdbd= atabank is a good example of balancing the needs of the researcher vs the rights of others to reproduce/extend struct= ural experiments.

You mentioned security is not needed, i disagree slightly.  Yes the da= ta should not sit behind a password that is handed out in single interactio= ns. 

However, it is important that the supplementary data is not altered/removed= /blocked/hacked etc as it is sitting out in the public.  These issues = can be partially ameliorated with dedicated websites that have dedicated st= aff and checksums as employed on other websites that offer code to download.  How will that be supported?&nb= sp; I don't know.

Brian Bennion



From: owner-chemistry+bennion1=3D=3Dl= lnl.gov.:.ccl.net [owner-chemistry+bennion1=3D=3Dllnl.gov.:.ccl.net] on beh= alf of Brian Skinn bskinn(_)alum.mit.edu [owner-chemistry.:.ccl.net]
Sent: Friday, April 24, 2015 6:51 AM
To: Bennion, Brian
Subject: CCL: DropBox / GitHub / etc for ESI

CCL-ers,

Provision of sufficient electronic supplementary information for publi= shed articles (molecular geometries, etc.) appears to be an ongoing challen= ge for computational chemists.  All too often there are interesting re= sults worth repetition and/or extension, but which are challenging to perform because the source computational file= s are unavailable.  Further, the current journal-site-based ESI public= ation model is quite confining, as (I assume?) there are size limitations o= n what publishers wish to host on their servers.

So, an idea for discussion: What about posting ESI on third-party serv= ices such as Dropbox, Github, etc?  ESI is meant to be public informat= ion, so security needs are minimal.  Such services are well equipped t= o handle the file transfer loads that ESI would likely represent, and storage costs would either be nil, or comparat= ively small.  Further, it would be possible to deposit binary files (w= avefunction information, electron density files, etc.) that might be of sig= nificant use to outside researchers wishing to analyze, repeat and/or extend a given work.


Pros? Cons?  I'm curious what you all think.


Best regards,
Brian
--_000_2FD898B2B3ACB44289F398FACE042B4ADA43C720PRDEXMBX01thela_-- From owner-chemistry@ccl.net Fri Apr 24 14:55:00 2015 From: "Carles Bo cbo ~~ iciq.cat" To: CCL Subject: CCL: DropBox / GitHub / etc for ESI Message-Id: <-51316-150424123700-7278-lDmkbPf4jz+sqI9ah9uoVA- -server.ccl.net> X-Original-From: Carles Bo Content-Language: ca-ES Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 24 Apr 2015 16:36:48 +0000 MIME-Version: 1.0 Sent to CCL by: Carles Bo [cbo#,#iciq.cat] Hi all, We figured out such a problem time ago and decided to react. After some years working, a nice piece of software is out there: http://www.iochem-bd.org This is our "almost-ready-to-lunch" computational chemistry results repository. Demo server and demo users accounts available. Just try. Sup Info PDF files automatically generated from raw output files. We'd appreciate to receive your feedback. Cheers, Carles El 24/04/2015, a les 17:25, Brian Skinn bskinn(_)alum.mit.edu va escriure: > CCL-ers, > > Provision of sufficient electronic supplementary information for published articles (molecular geometries, etc.) appears to be an ongoing challenge for computational chemists. All too often there are interesting results worth repetition and/or extension, but which are challenging to perform because the source computational files are unavailable. Further, the current journal-site-based ESI publication model is quite confining, as (I assume?) there are size limitations on what publishers wish to host on their servers. > > So, an idea for discussion: What about posting ESI on third-party services such as Dropbox, Github, etc? ESI is meant to be public information, so security needs are minimal. Such services are well equipped to handle the file transfer loads that ESI would likely represent, and storage costs would either be nil, or comparatively small. Further, it would be possible to deposit binary files (wavefunction information, electron density files, etc.) that might be of significant use to outside researchers wishing to analyze, repeat and/or extend a given work. > > > Pros? Cons? I'm curious what you all think. > > > Best regards, > Brian From owner-chemistry@ccl.net Fri Apr 24 15:30:01 2015 From: "James Buchwald buchwj],[rpi.edu" To: CCL Subject: CCL: DropBox / GitHub / etc for ESI Message-Id: <-51317-150424131511-31071-gMbwaR/kkwxAvQSw39PSgw|*|server.ccl.net> X-Original-From: James Buchwald Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Fri, 24 Apr 2015 13:15:02 -0400 MIME-Version: 1.0 Sent to CCL by: James Buchwald [buchwj-.-rpi.edu] I think one of the challenges for such an approach will be long-term availability of the ESI data. The current model of "publisher hosts the ESI" has the advantage that the publisher is responsible for ensuring that the data continues to be available for as long as the article is available. Moving to an external host could (would?) lead to situations where the site goes out of business/suffers irrecoverable data loss/etc and the ESI is potentially lost (and then you get broken links in the original paper). Obviously this is less of a potential issue (in the short term) for large sites such as GitHub, but there is still a question of how such methods will persist in the long (30+ years) term. I think there is a need for publishers to develop their own new ESI storage and retrieval mechanisms for large data sets, etc., such that the publisher can ensure the long-term availability of the data on the same timeframe as the manuscript itself. Best, James On 04/24/2015 09:51 AM, Brian Skinn bskinn(_)alum.mit.edu wrote: > CCL-ers, > > Provision of sufficient electronic supplementary information for > published articles (molecular geometries, etc.) appears to be an > ongoing challenge for computational chemists. All too often there are > interesting results worth repetition and/or extension, but which are > challenging to perform because the source computational files are > unavailable. Further, the current journal-site-based ESI publication > model is quite confining, as (I assume?) there are size limitations on > what publishers wish to host on their servers. > > So, an idea for discussion: What about posting ESI on third-party > services such as Dropbox, Github, etc? ESI is meant to be public > information, so security needs are minimal. Such services are well > equipped to handle the file transfer loads that ESI would likely > represent, and storage costs would either be nil, or comparatively > small. Further, it would be possible to deposit binary files > (wavefunction information, electron density files, etc.) that might be > of significant use to outside researchers wishing to analyze, repeat > and/or extend a given work. > > > Pros? Cons? I'm curious what you all think. > > > Best regards, > Brian -- James R. Buchwald Graduate Student, Dept. of Chemistry and Chemical Biology Rensselaer Polytechnic Institute Graduate Research Assistant, Dinolfo Laboratory Teaching Assistant, Experimental Chemistry IV From owner-chemistry@ccl.net Fri Apr 24 16:04:01 2015 From: "Arthur Zalevsky aozalevsky:-:gmail.com" To: CCL Subject: CCL: DropBox / GitHub / etc for ESI Message-Id: <-51318-150424145423-1835-Qrg2V0RhFNRIqpGcbg/OAQ..server.ccl.net> X-Original-From: Arthur Zalevsky Content-Type: multipart/alternative; boundary=001a11c38a2229b13705147ceca9 Date: Fri, 24 Apr 2015 21:54:14 +0300 MIME-Version: 1.0 Sent to CCL by: Arthur Zalevsky [aozalevsky:+:gmail.com] --001a11c38a2229b13705147ceca9 Content-Type: text/plain; charset=UTF-8 Great idea in all means. Also p2p networks can be considered. Though BioTorrents ( http://blogs.nature.com/news/2010/04/improving_the_portability_of_d_1.html) eventually died it was a nice try. Regards, Arthur 2015-04-24 16:51 GMT+03:00 Brian Skinn bskinn(_)alum.mit.edu < owner-chemistry..ccl.net>: > CCL-ers, > > Provision of sufficient electronic supplementary information for published > articles (molecular geometries, etc.) appears to be an ongoing challenge > for computational chemists. All too often there are interesting results > worth repetition and/or extension, but which are challenging to perform > because the source computational files are unavailable. Further, the > current journal-site-based ESI publication model is quite confining, as (I > assume?) there are size limitations on what publishers wish to host on > their servers. > > So, an idea for discussion: What about posting ESI on third-party services > such as Dropbox, Github, etc? ESI is meant to be public information, so > security needs are minimal. Such services are well equipped to handle the > file transfer loads that ESI would likely represent, and storage costs > would either be nil, or comparatively small. Further, it would be possible > to deposit binary files (wavefunction information, electron density files, > etc.) that might be of significant use to outside researchers wishing to > analyze, repeat and/or extend a given work. > > > Pros? Cons? I'm curious what you all think. > > > Best regards, > Brian > --001a11c38a2229b13705147ceca9 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Great idea in all means. Also p2p networks can be consider= ed. Though BioTorrents (http://blogs.nature.com/news/2010/04/im= proving_the_portability_of_d_1.html) eventually died it was a nice try.=

Regards,
Arthur

2015-04-24 16:51 GMT+03:00 Brian Sk= inn bskinn(_)alum.mit.edu <owner= -chemistry..ccl.net>:
CCL-ers,

Provision of sufficient electronic s= upplementary information for published articles (molecular geometries, etc.= ) appears to be an ongoing challenge for computational chemists.=C2=A0 All = too often there are interesting results worth repetition and/or extension, = but which are challenging to perform because the source computational files= are unavailable.=C2=A0 Further, the current journal-site-based ESI publica= tion model is quite confining, as (I assume?) there are size limitations on= what publishers wish to host on their servers.

So= , an idea for discussion: What about posting ESI on third-party services su= ch as Dropbox, Github, etc?=C2=A0 ESI is meant to be public information, so= security needs are minimal.=C2=A0 Such services are well equipped to handl= e the file transfer loads that ESI would likely represent, and storage cost= s would either be nil, or comparatively small.=C2=A0 Further, it would be p= ossible to deposit binary files (wavefunction information, electron density= files, etc.) that might be of significant use to outside researchers wishi= ng to analyze, repeat and/or extend a given work.

=
Pros? Cons?=C2=A0 I'm curious what you all think.
<= div>

Best regards,
Brian

--001a11c38a2229b13705147ceca9-- From owner-chemistry@ccl.net Fri Apr 24 16:40:01 2015 From: "Brian Skinn brian.skinn],[gmail.com" To: CCL Subject: CCL: DropBox / GitHub / etc for ESI Message-Id: <-51319-150424145852-6745-oM8B6P496kcJxgu3dWEZbA]^[server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary=f46d0444ed39456df405147cfc1a Date: Fri, 24 Apr 2015 14:58:24 -0400 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [brian.skinn!A!gmail.com] --f46d0444ed39456df405147cfc1a Content-Type: text/plain; charset=UTF-8 Jan, I wasn't thinking of something for unattended public uploads; more that, say, each research group would have its own space for ESI uploads and would be responsible for ensuring nothing 'untoward' was deposited there. I wasn't thinking of a central, interconnected repository; more just something that each researcher or research group might consider as an alternative/augmentation to the ESI hosted by the journal publishers. But, your email prompted a realization: the security question is actually quite acute, since it would be *highly* problematic if a 'black hat' accessed the material and, say, garbled it, or edited it such that various numbers were made to be incorrect. It would defeat the entire point of the system if no one could trust in the correctness of the ESI! Not so trivial a thing after all, I guess. -Brian On Fri, Apr 24, 2015 at 12:01 PM, janl[*]speakeasy.net < owner-chemistry,,ccl.net> wrote: > > > This is a great idea! I am actually considering to move a Web portion (but > not the email distribution and secure pages) to the cloud. A word of > caution though. Allowing unattended uploads to public is a very risky > proposition. You will end up with a repository with the gigabytes of "you > know what" rather than research data. I have been there and seen that... > There are ways to do it securely, but it is not trivial. It always requires > constant monitoring, since the scam of the Internet is always ahead and we > can only react. BTW, password protection is a myth with a few millions > Windoz computers with the keyboard sniffers installed. > > My problem is that I do not have time personally right now to work on it. > I wanted to create some upload site for Comp Chem data for a long time now, > but it will have to wait. I am getting older and I have to sleep on average > 6 hours a day and I constantly miss this "New Year Resolution". > > Jan > > CCL Maintainer. > > On Fri, 24 Apr 2015 09:51:45 -0400, "Brian Skinn bskinn(_)alum.mit.edu" > wrote: > > CCL-ers, > > Provision of sufficient electronic supplementary information for published > articles (molecular geometries, etc.) appears to be an ongoing challenge > for computational chemists. All too often there are interesting results > worth repetition and/or extension, but which are challenging to perform > because the source computational files are unavailable. Further, the > current journal-site-based ESI publication model is quite confining, as (I > assume?) there are size limitations on what publishers wish to host on > their servers. > > So, an idea for discussion: What about posting ESI on third-party services > such as Dropbox, Github, etc? ESI is meant to be public information, so > security needs are minimal. Such services are well equipped to handle the > file transfer loads that ESI would likely represent, and storage costs > would either be nil, or comparatively small. Further, it would be possible > to deposit binary files (wavefunction information, electron density files, > etc.) that might be of significant use to outside researchers wishing to > analyze, repeat and/or extend a given work. > > > Pros? Cons? I'm curious what you all think. > > > Best regards, > Brian > > > > > > ----- End forwarded message ----- > > --f46d0444ed39456df405147cfc1a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Jan,
I wasn't thinking of something for unattended publ= ic uploads; more that, say, each research group would have its own space fo= r ESI uploads and would be responsible for ensuring nothing 'untoward&#= 39; was deposited there.=C2=A0 I wasn't thinking of a central, intercon= nected repository; more just something that each researcher or research gro= up might consider as an alternative/augmentation to the ESI hosted by the j= ournal publishers.

But, your email prompted a realizatio= n: the security question is actually quite acute, since it would be=C2=A0highly=C2=A0problematic if a 'black hat' accessed the material= and, say, garbled it, or edited it such that various numbers were made to = be incorrect.=C2=A0 It would defeat the entire point of the system if no on= e could trust in the correctness of the ESI!


<= /div>
Not so trivial a thing after all, I guess.


-Brian


On Fri, Apr 24, 2015 at 12:01 PM, j= anl[*]speakeasy.net = <owner-chem= istry,,ccl.net> wrote:

=C2=A0

This is a great idea! I am actually considering to move a Web portion (b= ut not the email distribution and secure pages) to the cloud. A word of cautio= n though. Allowing unattended uploads to public is a very risky proposition. = You will end up with a repository with the gigabytes of "you know what&quo= t; rather than research data. I have been there and seen that... There are ways to do it securely, but it is not trivial. It always requires constant monitoring, si= nce the scam of the Internet is always ahead and we can only react. BTW, passwo= rd protection is a myth with a few millions Windoz computers with the keyboard sniffers installed.

My problem is that I do not have time personally right now to work on it= . I wanted to create some upload site for Comp Chem data for a long time now, b= ut it will have to wait. I am getting older and I have to sleep on average 6 hour= s a day and I constantly miss this "New Year Resolution".

Jan

CCL Maintainer.

On Fri, 24 Apr 2015 09:51:45 -04= 00, "Brian Skinn bskinn(_)alum.mit.edu= " <owner-chemistry#%#c= cl.net> wrote:

CCL-ers,
=C2=A0
Provision of sufficient electronic supplementary information for publi= shed articles (molecular geometries, etc.) appears to be an ongoing challenge fo= r computational chemists.=C2=A0 All too often there are interesting results w= orth repetition and/or extension, but which are challenging to perform because t= he source computational files are unavailable.=C2=A0 Further, the current journal-site-based ESI publication model is quite confining, as (I assume?) there are size limitations on what publishers wish to host on their servers.
=C2=A0
So, an idea for discussion: What about posting ESI on third-party serv= ices such as Dropbox, Github, etc?=C2=A0 ESI is meant to be public information, = so security needs are minimal.=C2=A0 Such services are well equipped to handle= the file transfer loads that ESI would likely represent, and storage costs would eit= her be nil, or comparatively small.=C2=A0 Further, it would be possible to depo= sit binary files (wavefunction information, electron density files, etc.) that = might be of significant use to outside researchers wishing to analyze, repeat and= /or extend a given work.
=C2=A0
=C2=A0
Pros? Cons?=C2=A0 I'm curious what you all think.
=C2=A0
=C2=A0
Best regards,
Brian





----- End forwarded message -----


--f46d0444ed39456df405147cfc1a-- From owner-chemistry@ccl.net Fri Apr 24 17:15:00 2015 From: "Dr. Robert Molt Jr. r.molt.chemical.physics * gmail.com" To: CCL Subject: CCL:G: calculate redox potential Message-Id: <-51320-150424152234-27351-cjurB8JNzss1Ykx9cqOyPg###server.ccl.net> X-Original-From: "Dr. Robert Molt Jr." Content-Type: multipart/alternative; boundary="------------030109000102070809000004" Date: Fri, 24 Apr 2015 15:22:26 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Robert Molt Jr." [r.molt.chemical.physics[*]gmail.com] This is a multi-part message in MIME format. --------------030109000102070809000004 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit There are many factors that go into calculating Gibbs energies correctly. For one, it's not what "Gaussian" can do. Gaussian is a software with many methods in it. For two, describing the electronic wavefunction has its own challenges. There are many reviews discussing the difficulty in being "accurate." You have to know how accurate you need to be, pick an appropriate method. DFT errors range from qualitatively wrong to +/- 5kcal/mol (common) to accurate to +/- 1.5 kcal/mol. That's a big range. Every method has a lot that goes into it to determine how accurate it is. Gibbs energies rely on partition functions. How accurately one calculates a partition function is its own question ( the errors you spoke of in vibrational modes cancel /to some extent/...then again, everything cancels out /to some extent/...how accurately do you need things?). Not to mention solvation. My point: there are many sources of error at many different points. It's not the software, it's the methods and the intelligence of the user. Dr. Robert Molt Jr. r.molt.chemical.physics]|[gmail.com On 04/24/2015 12:07 PM, Igors Mihailovs igors.mihailovs0..gmail.com wrote: > Dear Dr. Gámez, > > Is it possible to evaluate Gibbs energy correctly in Gaussian 09? > Frequency job yields Gibbs energy, but I am currently reluctant of > using it, because as I understood it is simply computed from all > vibrational modes, while there are often low-frequency (below 200–300 > cm⁻⁠¹) modes, which, as far as I know, are considered to be > unreliable, and every molecule would require Your personal involvement > to "separate the sheep from the goats" because this is > structure-dependent question (or?). In addition, this Gibbs energy > obviously does not account for weak bond with the solvent molecules, > if we use PCM description of it… > > Am I wrong in these considerations? > > P.S. Thank You for pointing to that quite recent review. > > With best wishes, > Igors Mihailovs (engineer) > Institute of Solid State Physics > University of Latvia > > > 2015-04-24 10:40 GMT+03:00 Jose Gamez Gamez-*-itmc.rwth-aachen.de > >: > > Dear Asmaa, > > In addition to what Igors wrote: > > 1. Redox potentials are related through Nernst equation to Gibb’s > free energies, so you need to express the energy differences in > terms of DeltaG's. > 2. Redox reactions occur usually in solution, so you'll probably > need to estimate the solvation energy. > > This review should be useful for you: > http://doi.org/10.1039/c4cp01572j > > Cheers, > Dr. José A. Gámez > ITMC-RWTH Institute of Technical and > Macromolecular Chemistry. Division of Technical Chemistry and > Petrol Chemistry. > RWTH Aachen University. > Worringerweg 1, 52074 Aachen, Germany > Phone: +49 241 8026510 > > Fax: +49 241 8022177 > > >> On 23 Apr 2015, at 20:21, Igors Mihailovs >> igors.mihailovs0()gmail.com >> > wrote: >> >> Dear Asmaa, >> >> Redox potential is the equilibrium property of many-molecules >> system in solution, the potential of electrode at which oxidation >> and reduction rate is equal. On the other hand, what we usually >> calculate in ab initio methods is the property of a single >> molecule, maybe with solvation shells or using some continuum >> solvation model. For example, for ionization of a molecule >> >> IP(vertical) = E(cation) |-| R (neutral) – E(neutral) |-| R(neutral); >> IP(adiabatic) = E(cation) |-| R (cation) – E(neutral) |-| R(neutral); >> >> where E stands for energy and R – for geometry. Assuming that the >> redox potential corresponds to zero thermodynamical barrier >> between the molecule and the electrode, it seems that adiabatic >> IP is more related to the redox potential than the vertical one, >> me trying to apply Marcus–Hush theory here. So, this is the >> quantity You need to compare Your excited state ionization >> (oxidation) potential with. >> >> In Gaussian, You should then simply run geometry optimizations >> for both neutral molecule and the cation, and then subtract their >> energies, as the formula above states. On how to perform these >> calculations, please refer to the Gaussian online manual at >> http://www.gaussian.com/g_tech/g_ur/g09help.htm and, in case You >> have some troubles, feel free to contact Gaussian vendor via help >> "at" gaussian.com , they are usually very >> helpful and open to any questions (really). >> >> With best wishes, >> Igors Mihailovs (engineer) >> Institute of Solid State Physics >> University of Latvia >> >> >> 2015-04-14 20:34 GMT+03:00 asmaa el-sayed asmaaphys88 . gmail.com >> > >: >> >> >> Sent to CCL by: "asmaa el-sayed" [asmaaphys88~!~gmail.com >> ] >> Dear, all >> Does anyone know how to calculate the redox potential for >> compound in the >> ground state using gausssian? i need this redox potential to >> calculate the >> oxidation potential of the compound on the excited state. >> >> >> >> -= 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>> >> >> Before posting, check wait time at: >> http://www.ccl.net >> > Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> Search Messages: >> http://www.ccl.net/chemistry/searchccl/index.shtml>> >> >> > > --------------030109000102070809000004 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit There are many factors that go into calculating Gibbs energies correctly.

For one, it's not what "Gaussian" can do. Gaussian is a software with many methods in it.

For two, describing the electronic wavefunction has its own challenges. There are many reviews discussing the difficulty in being "accurate." You have to know how accurate you need to be, pick an appropriate method. DFT errors range from qualitatively wrong to +/- 5kcal/mol (common) to accurate to +/- 1.5 kcal/mol. That's a big range. Every method has a lot that goes into it to determine how accurate it is.

Gibbs energies rely on partition functions. How accurately one calculates a partition function is its own question ( the errors you spoke of in vibrational modes cancel to some extent...then again, everything cancels out to some extent...how accurately do you need things?).

Not to mention solvation.

My point: there are many sources of error at many different points. It's not the software, it's the methods and the intelligence of the user.
Dr. Robert Molt Jr.
r.molt.chemical.physics]|[gmail.com
On 04/24/2015 12:07 PM, Igors Mihailovs igors.mihailovs0..gmail.com wrote:
Dear Dr. Gámez,

Is it possible to evaluate Gibbs energy correctly in Gaussian 09? Frequency job yields Gibbs energy, but I am currently reluctant of using it, because as I understood it is simply computed from all vibrational modes, while there are often low-frequency (below 200–300 cm⁻⁠¹) modes, which, as far as I know, are considered to be unreliable, and every molecule would require Your personal involvement to "separate the sheep from the goats" because this is structure-dependent question (or?). In addition, this Gibbs energy obviously does not account for weak bond with the solvent molecules, if we use PCM description of it…

Am I wrong in these considerations?

P.S. Thank You for pointing to that quite recent review.

With best wishes,
Igors Mihailovs (engineer)
Institute of Solid State Physics
University of Latvia


2015-04-24 10:40 GMT+03:00 Jose Gamez Gamez-*-itmc.rwth-aachen.de <owner-chemistry[a]ccl.net>:
Dear Asmaa,

In addition to what Igors wrote:

1. Redox potentials are related through Nernst equation to Gibb’s free energies, so you need to express the energy differences in terms of DeltaG's.
2. Redox reactions occur usually in solution, so you'll probably need to estimate the solvation energy.

This review should be useful for you: http://doi.org/10.1039/c4cp01572j

Cheers,
 
Dr. José A. Gámez
ITMC-RWTH Institute of Technical and Macromolecular Chemistry. Division of Technical Chemistry and Petrol Chemistry.
RWTH Aachen University.
Worringerweg 1, 52074 Aachen, Germany
Phone: +49 241 8026510

Fax: +49 241 8022177

On 23 Apr 2015, at 20:21, Igors Mihailovs igors.mihailovs0()gmail.com <owner-chemistry[a]ccl.net> wrote:

Dear Asmaa,

Redox potential is the equilibrium property of many-molecules system in solution, the potential of electrode at which oxidation and reduction rate is equal. On the other hand, what we usually calculate in ab initio methods is the property of a single molecule, maybe with solvation shells or using some continuum solvation model. For example, for ionization of a molecule

IP(vertical) = E(cation) |-| R (neutral) – E(neutral) |-| R(neutral);
IP(adiabatic) = E(cation) |-| R (cation) – E(neutral) |-| R(neutral);

where E stands for energy and R – for geometry. Assuming that the redox potential corresponds to zero thermodynamical barrier between the molecule and the electrode, it seems that adiabatic IP is more related to the redox potential than the vertical one, me trying to apply Marcus–Hush theory here. So, this is the quantity You need to compare Your excited state ionization (oxidation) potential with.

In Gaussian, You should then simply run geometry optimizations for both neutral molecule and the cation, and then subtract their energies, as the formula above states. On how to perform these calculations, please refer to the Gaussian online manual at http://www.gaussian.com/g_tech/g_ur/g09help.htm and, in case You have some troubles, feel free to contact Gaussian vendor via help "at" gaussian.com, they are usually very helpful and open to any questions (really).

With best wishes,
Igors Mihailovs (engineer)
Institute of Solid State Physics
University of Latvia


2015-04-14 20:34 GMT+03:00 asmaa el-sayed asmaaphys88 . gmail.com <owner-chemistry|-|ccl.net>:

Sent to CCL by: "asmaa  el-sayed" [asmaaphys88~!~gmail.com]
Dear, all
 Does anyone know how to calculate the redox potential for compound in the
ground state using gausssian? i need this redox potential to calculate the
oxidation potential of the compound on the excited state.




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