From owner-chemistry@ccl.net Sun Jul 8 21:14:00 2018 From: "Robert Molt r.molt.chemical.physics],[gmail.com" To: CCL Subject: CCL: thoughts on computational chemistry course Message-Id: <-53376-180708092022-31748-uwJjxEtvE2mKvXIJ7Xrolw||server.ccl.net> X-Original-From: Robert Molt Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Sun, 8 Jul 2018 09:20:12 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics(~)gmail.com] Claiming that no real world chemistry is done without solvation is rather insulting to all the people who have careers in atmospheric chemistry or surface science (or the many government agencies which fund both because of the extreme practical importance of air quality and catalysis). On 7/7/18 10:09 PM, 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] > * Andreas Klamt klamt**cosmologic.de [2018-07-07 18:44:15 +0200]: >> Sent to CCL by: Andreas Klamt [klamt^-^cosmologic.de] >> ... If you like to enable your students to do any real world >> computational chemistry, don't forget to teach them a little bit about >> solvation. > Andreas, > > An important observation. As solvation is not my field of expertise I > would appreciate a short actualization. What method is curently assumed > to be the most advanced form of treating solvation? > > I am currently interested in old 1920's experiments regarding alcaline > metals in liquid NH_3. I was thinking on a mixed method: describe the > alcaline metal plus the first solvation shell as an explicit quantum > cluster model and represent the rest of the liquid as a continuous > dielectric using a cosmo or similar model. What do you think? > > This is not an exercise for students, just something for learning > myself. At least right now. > > Best regards, > 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> > -- Dr. Robert Molt Jr. r.molt.chemical.physics^-^gmail.com From owner-chemistry@ccl.net Sun Jul 8 21:49:00 2018 From: "Andreas Klamt klamt|*|cosmologic.de" To: CCL Subject: CCL: thoughts on computational chemistry course Message-Id: <-53377-180708154656-30589-ea5Dt9q/HLqFTCtdMK6FSw*_*server.ccl.net> X-Original-From: Andreas Klamt Content-Language: de-DE Content-Type: multipart/alternative; boundary="------------771540A50848A66672EEE236" Date: Sun, 8 Jul 2018 21:46:36 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt+*+cosmologic.de] This is a multi-part message in MIME format. --------------771540A50848A66672EEE236 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Victor, I am afraid that I have to say that my COSMO-RS method is currently the most accurate method for predicting free energies in solution. This is based on the following arguments: 1) Accuracy (kcal/mol) on 2343 data from Minnesota DB, see A. Klamt, B. Mennucci, J. Tomasi, V. Barone, C. Curutchet, M. Orozco and F. Javier Luque, Acc. Chem. Res., 2009, 42 (4), pp 489):     COSMOtherm 0.48 (latest COSMOtherm version 0.40)     SM8                 0.52 (fitted on this data set!)     PCM             ~ 0.9    (only 3 solvents) 2) relative to force fields: Two benchmarks vs.Force-Field-MD show that the error on DGsolv is only about half of the error of force-field methods. Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation by Jin Zhang†‡, Badamkhatan Tuguldur§‡, and David van der Spoel J. Chem. Inf. Model., 2015, 55 (6), pp 1192–1201  (see also the erratum): ~230 DGsolv RMSD: MD 3.7 kJ/mol, ADF-COSMO-RS 2.3 kJ/mol, COSMOtherm 1.7 kJ/mol. see also: Current Status of the AMOEBA Polarizable Force Field    Ponder et al., J Phys Chem B. 2010; 114(8): 2549:  22 DGsolv RMSD: AMOEBA 2.7 kJ/mol, COSMOtherm has 1.6 kJ/mol RMSD on this small dataset. 3)Blind challenges: COSMO-RS is winner of all the 3 IFPSCs (Industrial Fluid Property Simulation Challenges; AICHE/NIST)   which were on free energy of transfer (e.g. activity coefficients) and on which COSMO-RS was allowed to participate. 4)Blind challenges: COSMOlogicclearlyis best in theSAMPL5 blind challengeon alkane-waterlogDsof53 demandingdrugsand isbetterthantheexperimental values. J ComputAidedMol Des (2016). doi:10.1007/s10822-016-9927-y 5)Blind challenges: SAMPL6 on pKa prediction: TwoCOSMOthermusersachieverank 1 and 4 (Grimme et al., and a Novartis group). Rank 2 and 3 were data driven increment methods. Summarizing, SMx methods and COSMO-RS are close to each other on the dGsolv database, but COSMO-RS has a much broader validation, especially in blind challenges. Force-field based methods seem to have twice the error bars than COSMO-RS. This also applies to the 3D-RSIM and other methods, which require force-fields as input. Regarding alkaline metals in NH3: It is surely wise to describe the first solvation shell explicitly! What I do not understand: Are the alkaline atoms neutral? Or what is the counterion? Best Andreas > Andreas, > > An important observation. As solvation is not my field of expertise I > would appreciate a short actualization. What method is curently assumed > to be the most advanced form of treating solvation? > > I am currently interested in old 1920's experiments regarding alcaline > metals in liquid NH_3. I was thinking on a mixed method: describe the > alcaline metal plus the first solvation shell as an explicit quantum > cluster model and represent the rest of the liquid as a continuous > dielectric using a cosmo or similar model. What do you think? > > This is not an exercise for students, just something for learning > myself. At least right now. > > Best regards, > 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" > Prof. Dr. Andreas Klamt > CEO / Geschäftsführer > COSMOlogic GmbH & Co. KG > Imbacher Weg 46 > D-51379 Leverkusen, Germany > > phone +49-2171-731681 > fax +49-2171-731689 > e-mail klamt*cosmologic.de > web www.cosmologic.de > > [University address: Inst. of Physical and > Theoretical Chemistry, University of Regensburg] > > HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt > > --------------771540A50848A66672EEE236 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Victor,

I am afraid that I have to say that my COSMO-RS method is currently the most accurate method for predicting free energies in solution.

This is based on the following arguments:
1) Accuracy (kcal/mol) on 2343 data from Minnesota DB, see A. Klamt, B. Mennucci, J. Tomasi, V. Barone, C. Curutchet, M. Orozco and F. Javier Luque, Acc. Chem. Res., 2009, 42 (4), pp 489):
    COSMOtherm 0.48 (latest COSMOtherm version 0.40)
    SM8                 0.52 (fitted on this data set!)
    PCM             ~ 0.9    (only 3 solvents)
2) relative to force fields: Two benchmarks vs.Force-Field-MD show that the error on DGsolv is only about half of the error of force-field methods.
Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation by Jin Zhang†‡, Badamkhatan Tuguldur§‡, and David van der Spoel J. Chem. Inf. Model., 2015, 55 (6), pp 1192–1201  (see also the erratum):
~230 DGsolv RMSD: MD 3.7 kJ/mol, ADF-COSMO-RS 2.3 kJ/mol, COSMOtherm 1.7 kJ/mol.
see also: Current Status of the AMOEBA Polarizable Force Field    Ponder et al., J Phys Chem B. 2010; 114(8): 2549:
 22 DGsolv RMSD: AMOEBA 2.7 kJ/mol, COSMOtherm has 1.6 kJ/mol RMSD on this small dataset.

3) Blind challenges: COSMO-RS is winner of all the 3 IFPSCs (Industrial Fluid Property Simulation Challenges; AICHE/NIST)

  which were on free energy of transfer (e.g. activity coefficients) and on which COSMO-RS was allowed to participate.

4) Blind challenges: COSMOlogic clearly is best in the SAMPL5 blind challenge on alkane-water logDs of 53 demanding drugs and is better than the experimental values. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9927-y
5) Blind challenges: SAMPL6 on pKa prediction: Two COSMOtherm users achieve rank 1 and 4 (Grimme et al., and a Novartis group). Rank 2 and 3 were data driven increment methods.

Summarizing, SMx methods and COSMO-RS are close to each other on the dGsolv database, but COSMO-RS has a much broader validation, especially in blind challenges.
Force-field based methods seem to have twice the error bars than COSMO-RS. This also applies to the 3D-RSIM and other methods, which require force-fields as input.

Regarding alkaline metals in NH3: It is surely wise to describe the first solvation shell explicitly! What I do not understand: Are the alkaline atoms neutral? Or what is the counterion?

Best

Andreas


Andreas,

An important observation. As solvation is not my field of expertise I
would appreciate a short actualization. What method is curently assumed
to be the most advanced form of treating solvation?

I am currently interested in old 1920's experiments regarding alcaline
metals in liquid NH_3. I was thinking on a mixed method: describe the
alcaline metal plus the first solvation shell as an explicit quantum
cluster model and represent the rest of the liquid as a continuous
dielectric using a cosmo or similar model. What do you think?

This is not an exercise for students, just something for learning
myself. At least right now.

Best regards,
             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:  <victor^fluor.quimica.uniovi.es>  ! prevent you from doing what is
! phone: +34-984080927    fax: +34-985103125 ! right." 
+--------------------------------------------+ -- Salvor Hardin, "Foundation"


Prof. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Imbacher Weg 46
D-51379 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt*cosmologic.de
web    	www.cosmologic.de

[University address:      Inst. of Physical and
Theoretical Chemistry, University of Regensburg]

HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
--------------771540A50848A66672EEE236--