From owner-chemistry@ccl.net Sun Jul 22 11:57:01 2018 From: "J C Womack jw5533^my.bristol.ac.uk" To: CCL Subject: CCL: PBE for inorganic chemistry Message-Id: <-53403-180722060721-20736-N3WZIqGVr1dGbTtPpoKNhw:_:server.ccl.net> X-Original-From: J C Womack Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Sun, 22 Jul 2018 11:07:09 +0100 MIME-Version: 1.0 Sent to CCL by: J C Womack [jw5533]^[my.bristol.ac.uk] To add to the list of resources for comparing XC functionals, I have found this recent review by Mardirossian and Head-Gordon to be quite informative: "Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals" N. Mardirossian and M. Head-Gordon, Molecular Physics, 2017 http://dx.doi.org/10.1080/00268976.2017.1333644 They compared 200 functionals against a very large set of reference data (nearly 5000 data points). The functional compared include PBE, B3LYP and their dispersion-corrected versions. I hope this helps, James On 18/07/18 16:33, Víctor Luaña Cabal victor|*|fluor.quimica.uniovi.es wrote: > > Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor=-=fluor.quimica.uniovi.es] > * Yury Minenkov yury.minenkov ~ gmail.com [2018-07-18 11:29:07 +0300]: >> >> Sent to CCL by: Yury Minenkov [yury.minenkov]~[gmail.com] >> Dear Grigoriy, >> >> First of all, I am not sure whether this statement is entirely >> correct. Perhaps, in the majority of cases PBE will outperform B3LYP >> for inorganic species, and B3LYP will provide better results for >> organic molecules. But, in general, it is hard to say a priori whether >> B3LYP or PBE is going to perform better for your system. I am sure >> this topic has been discussed many times. Unfortunately, I remember no >> references apart from my own/my colleagues works (sorry for >> self-promotion). Perhaps something can be found in "A Chemist's Guide >> to Density Functional Theory, " 2nd Edition by Wolfram Koch, Max C. >> Holthausen. > > Grigoriy, Yury, > > Nice book. Try also: "The ABC of DFT" by Kieron Burke et al. This is a > free and excellent book written from the point of view of physicicts. > emember that in DFT Physicits and Chemist finally found a true > conection. > > Once a year we receive information from ¿Girona, Barcelona? (Spain, > anyway) about which functionals perform better for each kind of > property. The basis of that report is that practitioners vote their > preferences. In young Internet times it was assumed that market, social > media, whatever in which a huge amount of people participated was a true > way to discovery. The finantial crisis has made evident that such a > trick has many problems, but .... You can check. In the Girona polling > only quantum authors participate, if I remember correctly. > > Look for Prof. Marcel Swart at ICREA. The 2017 results: > > > > Marcel, > > Do your poll includes solid state properties? Many physicits participate > in the poll? I just don't remember. > > Cheers, > Víctor Luaña > -- > . . One should not treat others in ways that one would not like > / `' \ to be treated > /(o)(o)\ (Golden rule of ethics) > /`. \/ .'\ > / '`'` \ "Freedom!, freedom!, freedom! After that put whatever > | \'`'`/ | term you like" > | |'`'`| | --Largo Caballero (socialist, spanish president in the exile, > \/`'`'`'\/ shortly before dying) > ==(((==)))===================================+ A person is slave of his words > ! Dr.Víctor Luaña, in silico chemist & prof. ! and owner of his silences. > ! Departamento de Química Física y Analítica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! "Never let your sense of morals > ! e-mail: ! prevent you from doing what is > ! phone: +34-984080927 fax: +34-985103125 ! right." > +--------------------------------------------+ -- Salvor Hardin, "Foundation" > GroupPage: > Articles: > git-hub: > ORCID: 0000-0003-4585-4627; RID: H-2045-2015> > -- James C. Womack Email: jw5533(!)my.bristol.ac.uk Web: https://jcwomack.com From owner-chemistry@ccl.net Sun Jul 22 23:23:00 2018 From: "Lars Goerigk lars.goerigk:-:unimelb.edu.au" To: CCL Subject: CCL: PBE for inorganic chemistry Message-Id: <-53404-180722213549-30501-SAsFFDOgJIc8n708ZniT8Q:server.ccl.net> X-Original-From: Lars Goerigk Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_DCFE5517D0CA437DB7E0695BB940DE90unimelbeduau_" Date: Mon, 23 Jul 2018 01:35:31 +0000 MIME-Version: 1.0 Sent to CCL by: Lars Goerigk [lars.goerigk%%unimelb.edu.au] --_000_DCFE5517D0CA437DB7E0695BB940DE90unimelbeduau_ Content-Type: text/plain; charset=WINDOWS-1252 Content-Transfer-Encoding: quoted-printable Hi Grigory, the big problem of having a zoo of DFT approximations is that it=92s hard t= o follow the literature for some and that many users therefore rely on popu= lar approaches. B3LYP and PBE are definitely two examples of the latter str= ategy. While the aforementioned =93Chemist=92s guide to DFT" is definitely a must-= read for people new to the field, the applications in the second half of th= at book are based on what people knew in the early 2000s. A lot has changed= since then and a lot of progress has been made. I therefore recommend these two papers from last year that can be considere= d as some of the largest DFT benchmark studies conducted for thermochemistr= y, kinetics and noncovalent interactions. I suggest to use them for guidanc= e. 1) Mol. Phys. 2017, 115, 2315. (Open Access) 2) Phys. Chem. Chem. Phys. 2017, 19, 32184 (Open Access) In a nutshell, there is no reason why PBE or B3LYP should be used in routin= e thermochemistry applications any more. If possible, double hybrids should= be used and if that is not feasible, any of the hybrids recommended in the= aforementioned papers. The story may be a bit different for transition met= al complexes, but overall the above recommendations could be used as a star= ting point in my opinion. Regarding double hybrids, most programs have effi= cient implementations of the resolution-of-the-identity MP2, and we run dou= ble hybrid applications routinely with large basis sets (usually QZ) and sy= stems with up to 50-80 atoms without any real problems. Some double hybrids= even scale N^4 is a Laplace transform algorithm is used. It is also important to use approaches that properly describe London disper= sion (even for geometries, reaction energies etc.), and I recommend DFT-D3(= BJ) or any of VV10-type van-der-Waals variants (sometimes called DFT-NL, so= metimes used with the suffix =93-V=94 as in Head-Gordon=92s B97M-V etc.). Note that despite popular belief, dispersion corrections should also be use= d for Minnesota functionals (both for equilibrium and non-equilibrium struc= tures): 3) J. Phys. Chem. Lett. 2015, 6, 3891. 4) J. Chem. Theory Comput. 2016, 12, 4303. 5) Ref. 2 from above Finally, do not fall into the B3LYP/6-31G* =93trap" as many DFT users still= do in joint experimental-computational collaborations: 6) J. Org. Chem. 2012, 77, 10824. I hope this helped. Cheers, Lars Dr Lars Goerigk | Lecturer Melbourne Centre for Theoretical & Computational Chemistry School of Chemistry | The University of Melbourne Victoria 3010 | Australia Website: http://goerigk.chemistry.unimelb.edu.au Follow me on Twitter: https://twitter.com/lgoer_compchem On 18 Jul 2018, at 3:51 am, Grigoriy Zhurko reg_zhurko.=-=.chemcraftprog.com<= http://chemcraftprog.com> > wrote: Sent to CCL by: Grigoriy Zhurko [reg_zhurko**chemcraftprog.com] I have heard that the PBE functional is often appropriate for inorganic che= mistry, while the B3LYP one is usually better for organic chemistry. Can yo= u help me find publications, in which the advantages of PBE for computing i= norganic molecules is described (for citing)? Grigoriy Zhurko https://chemcraftprog.com/ -=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 Job: http://www.ccl.net/jobs --_000_DCFE5517D0CA437DB7E0695BB940DE90unimelbeduau_ Content-Type: text/html; charset=WINDOWS-1252 Content-ID: Content-Transfer-Encoding: quoted-printable Hi Grigory,

the big problem of having a zoo of DF= T approximations is that it=92s hard to follow the literature for some and = that many users therefore rely on popular approaches. B3LYP and PBE are def= initely two examples of the latter strategy.
While the aforementioned =93Chemist= =92s guide to DFT" is definitely a must-read for people new to the fie= ld, the applications in the second half of that book are based on what= people knew in the early 2000s. A lot has changed since then and a lot of progress has been made.

I therefore recommend these two paper= s from last year that can be considered as some of the largest DFT benchmar= k studies conducted for thermochemistry, kinetics and noncovalent interacti= ons. I suggest to use them for guidance.

1) Mol. Phys. 201= 7, 115, 2315. (Open Access)
2)
In a nutshell, there is no reason why= PBE or B3LYP should be used in routine thermochemistry applications any mo= re. If possible, double hybrids should be used and if that is not feasible,= any of the hybrids recommended in the aforementioned papers. The story may be a bit different for trans= ition metal complexes, but overall the above recommendations could be used = as a starting point in my opinion. Regarding double hybrids, most programs = have efficient implementations of the resolution-of-the-identity MP2, and we run double hybrid applications = ;routinely with large basis sets (usually QZ) and systems with up= to 50-80 atoms without any real problems. Some double hybrids even sc= ale N^4 is a Laplace transform algorithm is used.

It is also important to use approache= s that properly describe London dispersion (even for geometries, reaction e= nergies etc.), and I recommend DFT-D3(BJ) or any of VV10-type van-der-Waals= variants (sometimes called DFT-NL, sometimes used with the suffix =93-V=94 as in Head-Gordon=92s B97M-V etc.)= .
Note that despite popular belief, dis= persion corrections should also be used for Minnesota functionals (both for= equilibrium and non-equilibrium structures):

3) J. Phys. Chem. Lett.&n= bsp;2015, 6, 3891. 
4) J. Chem. Theory Comput. 2016, 12, 4303.
5) Ref. 2 from above

Finally, do not fall into the B3= LYP/6-31G* =93trap" as many DFT users still do in joint experimen= tal-computational collaborations:
6) J. Org. Chem. <= strong>2012, 77, 10824.

I hope this helped.

Cheers,
Lars

Dr Lars Goerigk | Lecturer 
Melbourne Centre for Theoretical & Computational Chemistry
School of Chemistry | The University of Melbourne
Victoria 3010 | Australia
Follow me on Twitter: https://twitter.com/lgoer_compchem



On 18 Jul 2018, at 3:51 am, Grigoriy Zhurko reg_zhurko.=-=.chemcraftprog.com <owner-chemistry=-=ccl.net> wrote:


Sent to CCL by: Grigoriy Zhurko [reg_zhurko**chemcraftprog.com]
I have heard that the PBE functional is often appropriate for inorganic che= mistry, while the B3LYP one is usually better for organic chemistry. Can yo= u help me find publications, in which the advantages of PBE for computing i= norganic molecules is described (for citing)?

Grigoriy Zhurko
https://chemcraftprog.com/



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