From owner-chemistry@ccl.net Sat Sep 12 08:16:01 2015 From: "Mohan maruthi sena maruthi.sena,,gmail.com" To: CCL Subject: CCL:G: Symmetry constraint during scan calculation Message-Id: <-51725-150912073425-24282-NY27tO5Q59gzTll3edI9WA . server.ccl.net> X-Original-From: Mohan maruthi sena Content-Type: multipart/alternative; boundary=94eb2c03536ca32834051f8b36c8 Date: Sat, 12 Sep 2015 17:04:21 +0530 MIME-Version: 1.0 Sent to CCL by: Mohan maruthi sena [maruthi.sena^_^gmail.com] --94eb2c03536ca32834051f8b36c8 Content-Type: text/plain; charset=UTF-8 Hi all, I am trying to perform a scan calculation for SF6 molecule using Gaussian09. I have optimized the molecule and the symmetry of the molecule is octahedral. I want to perform scan of angle [FSF] calculation by imposing D3h symmetry constraint on the molecule [and also keeping bond length fixed]. How can I do this g09? [option in input file]. Thanks for a reply in advance, Regards, Mohan --94eb2c03536ca32834051f8b36c8 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi all,
=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 I am trying to perform a scan calculation= for SF6 molecule using Gaussian09. I have optimized the molecule and the s= ymmetry of the molecule is octahedral. I want to perform scan of angle [FSF= ] calculation by imposing D3h symmetry constraint on the molecule [and also= keeping bond length fixed].=C2=A0=C2=A0 How can I do this g09? [option in = input file].

Thanks for a reply in advance,

Regar= ds,
Mohan
--94eb2c03536ca32834051f8b36c8-- From owner-chemistry@ccl.net Sat Sep 12 09:47:01 2015 From: "Andreas Hans Goeller agoeller]^[live.de" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51726-150912094456-29248-lWH5YcGkJhbc1LcamlUB4A[]server.ccl.net> X-Original-From: "Andreas Hans Goeller" Date: Sat, 12 Sep 2015 09:44:55 -0400 Sent to CCL by: "Andreas Hans Goeller" [agoeller[*]live.de] Dear all, just to come back to the original topic about QM with relevance to the real life. I work in Pharma, I have a QM background from Erlangen. I worked with Tim Clark and Paul Schleyer who always combined theory and practise. I did 3-4 studies on reactivity in my 15 years now, which gives you an idea of how important reactivity modelling is in pharma. Those studies are not published and I can not share them with you. They dealt with the understanding of reactions that did not work or with the decision if to spend high effort on a new reaction scheme. It was not important to get exact numbers but to understand stereo- or regioselectivity or the side of attack. Nevertheless, I want to get the right answer for the right reason and therefore use the best methods applicable for the specific problem. And there are good benchmarks on what to use, e.g. from the Grimme group. Since our molecules are about 400-500 Da and have at least 5 rotatable bonds, CCSDT is no option obviously. And our reactions are not in gas phase. The real problems for us are binding affinity to proteins (compared to protein catalysis most of the QM papers deal with) conformer energies hydrogen bonding weak lipophilic interactions tautomer equilibria pKa changes in charge distribution for core hopping atrop isomerism .. And we need to apply those methods to sets of eg 20 to 1000 molecules. We are happy with reliable relative numbers, because as Andreas Klamt already pointed out, we are often concerned with filtering out the molecules which will not work anyhow. The biggest hurdle for QM in industry still is the zoo of methods hindering people with modelling and pharmaceutical background from even trying to use QM, softwares with non-intuitive input and chaotic output files (end of the 90s there were already attempts with chemical markup language to standardize outputs), stability, how to run multiple jobs etc. At the Lugano conference 2013 there was a discussion session organized bei Peter Luethi where three us us from industry tried to provide some understanding on our needs and problems. My feeling was that there was little interest, understanding and willingness to listen, and there were just 2 professors in the audience. The big issue I see also in this discussion is unwillingness to cross borders. There is computational chemstry outside QM development, and those work contributes to market products which help ill people and rescue lives. Finally, I can add 2 publications dealing with successful applications of QM in the widest sense. We have developed a software called CypScore (ChemMedChem, 2009, 657) which is QSAR based on atomic descriptors derived from AM1 and predits metabolic labile sites in molecules. There is a Nature publication from 2015 which shows one application example. Use of this software probably ruled out sythesis of hundreds of metabolically labile molecules. And though it is very approximate QM with known problems this software is an important part of our daily work. best regards From owner-chemistry@ccl.net Sat Sep 12 10:28:01 2015 From: "Thomas Manz thomasamanz]_[gmail.com" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51727-150911174953-16896-I8dEooJQW3EUaemJ9cfTrQ()server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a1135cf24c263e5051f7fb1a3 Date: Fri, 11 Sep 2015 15:49:47 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz..gmail.com] --001a1135cf24c263e5051f7fb1a3 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Gerald, You wrote "Once you fix the basis set" The Hohenberg-Kohn theorems do not state that the basis is set is a functional of the electron distribution. Therefore, from a purely theoretical viewpoint, the basis set does not correspond to a physical observable. There is no experiment that can be done to measure the "basis set" of a sodium chloride crystal in nature, for example. This means only quantities with a well-defined basis set limit can be physical observables. Yes, this follows directly from the Hohenberg-Kohn theorems, but perhaps you don't have to invoke those to make the same point. Sincerely, Tom On Fri, Sep 11, 2015 at 12:30 PM, Gerald Knizia knizia{} theochem.uni-stuttgart.de wrote: > > Sent to CCL by: Gerald Knizia [knizia!^!theochem.uni-stuttgart.de] > Dear Tom, > yes, you can, in principle, get a mapping from the density to the > Hamiltonian. But what is your point? You do not need the density to get > the Hamiltonian---it is well known how the Hamiltonian of a molecular or > crystalline system looks. > > Besides, based on this argument (density determines Hamiltonian > determines everything else, thus everything else is observable, too, in > some sense), you can just as well defend Mulliken and L=C3=B6wdin charges= : > Once you fix the basis set, you have a one-to-one mapping from the > density (which's poles tell you where the nuclei are and which charges > they have), and thus the Hamiltonian, and thus the Mulliken/L=C3=B6wdin > charges. The qualitatively important aspect here has nothing to do with > DFT, but just with the fact that the Mulliken/L=C3=B6wdin charges depend = on > arbitrary calculation parameters (the basis set), and have no > well-defined physical limit. > > Now, there are some reasons to consider "generalized" observability (in > the sense defined by Cioslowski and Surjan: > http://dx.doi.org/10.1016/0166-1280(92)85003-4 ), but the fact remains > that this kind observability has a quite different quality than a > quantity which can actually be measured. And atomic charge is most > definitely not one of them. In order to define atomic charges, you HAVE > to put in some amount of empirical information (e.g., where you draw the > boundaries between atoms (like in Hirshfeld, VDD, or AIM) or how you > make atomic reference states (in IAOs). > > Best wishes, > Gerald > > > On Fri, 2015-09-11 at 06:58 -0600, Thomas Manz thomasamanz|a|gmail.com > wrote: > > Stefan, > > > > > > You wrote: "the HK theorems simply do not apply here." > > > > > > You are very incorrect! > > The Hohenberg-Kohn theorems always apply to a non-degenerate, > > non-relativistic chemical ground state. > > > > That is the whole point of these theorems! They establish that there > > is a one-to-one mapping between the > > system's Hamiltonian (up to an arbitrary constant potential offset) > > and its ground state electron density distribution. > > Because the system's Hamiltonian determines its wavefunction, this > > establishes that all physical properties of the system, not just its > > energy are functionals of the ground state electron density > > distribution. > > > > > > It is true that there is some flexibility in how to define net atomic > > charges, but owing to the Hohenberg-Kohn theorems all methods that are > > not functionals of the electron density distribution are ruled out up > > front. This means that Mulliken and Lowdin populations cannot > > represent physical properties, because they are not functionals of the > > ground state electron distribution. This does not mean that net atomic > > charges are not physical properties, because it is possible to > > construct definitions of net atomic charges that are functionals of > > the electron density distribution. > > > > > > Sincerely, > > > > > > Tom > > > > On Fri, Sep 11, 2015 at 2:54 AM, Stefan Grimme grimme*| > > *thch.uni-bonn.de wrote: > > > > Sent to CCL by: "Stefan Grimme" [grimme^thch.uni-bonn.de] > > Dear Tom, > > to this: > > >I wanted to address one more of your comments. You wrote: "I > > don't want to defend orbital based partitionings (I prefer > > observables) but making the mathematical limit to the > > encompassing requirement seem nonsense to me." Actually, this > > has already been proved in Nobel prize winning work. In 1998, > > Walter Kohn received the Nobel prize in chemistry for his > > development of density functional theory. This theory proved > > that all ground state properties of a non-relativistic, > > non-degenerate quantum chemical system can be represented as a > > functional of the ground state electron density distribution. > > A direct corollary is that since net atomic charges are a > > property of a chemical system, for a non-degenerate chemical > > ground state the net atomic charges have to be a functional of > > the ground state electron distribution. When I and others say > > that the net atomic charges should approach a well-defined > > basis set limit, because they are functionals of the electron > > density distribution, we! > > are simply stating a direct corollary of the Hohenberg-Kohn > > theorems. This has already been proved and received a Nobel > > prize. > > > > the HK theorems simply do not apply here. They establish a > > relation between two observables in a strict QM sense (energy > > and density). Because there is no atomic charge operator as I > > already said, the statement > > "atomic charges are a functional of the ground state density" > > is just empty. > > What you probably mean is that some operational definitions > > of atomic charge like AIM or Hirshfeld are functionals of the > > density. > > This is true but does not eliminate the arbitrariness in their > > definition > > (usually artificial boundaries in the molecule). > > > > Best wishes > > Stefan > > > > > > > > -=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> > Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/ > > > > Search Messages: > > http://www.ccl.net/chemistry/searchccl/index.shtml> > > > > > > > > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a1135cf24c263e5051f7fb1a3 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Gerald,

You wrote "Once you fix the basis set"

The Hohenberg-Kohn theorems d= o not state that the basis is set is a functional of the electron distribut= ion.
Therefor= e, from a purely theoretical viewpoint, the basis set does not correspond t= o a physical observable.
There is no experiment that can be done to measure the "ba= sis set" of a sodium chloride crystal in nature, for example.
This means only quant= ities with a well-defined basis set limit can be physical observables.
Yes, this follows= directly from the Hohenberg-Kohn theorems, but perhaps you don't have = to invoke those to make the same point.

Sin= cerely,

Tom
=
On Fri, Sep 11, 2015 at 12:30 PM, Gerald Kni= zia knizia{}theochem.uni-stutt= gart.de <owner-chemistry],[ccl.net> wrote:

Sent to CCL by: Gerald Knizia [knizia!^!theochem.uni-stuttgart.de]
Dear Tom,
yes, you can, in principle, get a mapping from the density to the
Hamiltonian. But what is your point? You do not need the density to get
the Hamiltonian---it is well known how the Hamiltonian of a molecular or crystalline system looks.

Besides, based on this argument (density determines Hamiltonian
determines everything else, thus everything else is observable, too, in
some sense), you can just as well defend Mulliken and L=C3=B6wdin charges:<= br> Once you fix the basis set, you have a one-to-one mapping from the
density (which's poles tell you where the nuclei are and which charges<= br> they have), and thus the Hamiltonian, and thus the Mulliken/L=C3=B6wdin
charges. The qualitatively important aspect here has nothing to do with
DFT, but just with the fact that the Mulliken/L=C3=B6wdin charges depend on=
arbitrary calculation parameters (the basis set), and have no
well-defined physical limit.

Now, there are some reasons to consider "generalized" observabili= ty (in
the sense defined by Cioslowski and Surjan:
http://dx.doi.org/10.1016/0166-1280(92)85003-4 ), = but the fact remains
that this kind observability has a quite different quality than a
quantity which can actually be measured. And atomic charge is most
definitely not one of them. In order to define atomic charges, you HAVE
to put in some amount of empirical information (e.g., where you draw the boundaries between atoms (like in Hirshfeld, VDD, or AIM) or how you
make atomic reference states (in IAOs).

Best wishes,
Gerald


On Fri, 2015-09-11 at 06:58 -0600, Thomas Manz thomasamanz|a|gmail.com
wrote:
> Stefan,
>
>
> You wrote: "the HK theorems simply do not apply here."
>
>
> You are very incorrect!
> The Hohenberg-Kohn theorems always apply to a non-degenerate,
> non-relativistic chemical ground state.
>
> That is the whole point of these theorems! They establish that there > is a one-to-one mapping between the
> system's Hamiltonian (up to an arbitrary constant potential offset= )
> and its ground state electron density distribution.
> Because the system's Hamiltonian determines its wavefunction, this=
> establishes that all physical properties of the system, not just its > energy are functionals of the ground state electron density
> distribution.
>
>
> It is true that there is some flexibility in how to define net atomic<= br> > charges, but owing to the Hohenberg-Kohn theorems all methods that are=
> not functionals of the electron density distribution are ruled out up<= br> > front. This means that Mulliken and Lowdin populations cannot
> represent physical properties, because they are not functionals of the=
> ground state electron distribution. This does not mean that net atomic=
> charges are not physical properties, because it is possible to
> construct definitions of net atomic charges that are functional= s of
> the electron density distribution.
>
>
> Sincerely,
>
>
> Tom
>
> On Fri, Sep 11, 2015 at 2:54 AM, Stefan Grimme grimme= *|
> *thch.uni-bonn.de <owner-chemistry+/-ccl.net> wrote:
>
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Sent to CCL by: "Stefan=C2=A0 Gr= imme" [grimme^thch.uni-bonn.de]
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Dear Tom,
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0to this:
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0>I wanted to address one more of y= our comments. You wrote:=C2=A0 "I
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0don't want to defend orbital base= d partitionings (I prefer
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0observables) but making the mathemati= cal limit to the
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0encompassing requirement seem nonsens= e to me." Actually, this
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0has already been proved in Nobel priz= e winning work. In 1998,
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Walter Kohn received the Nobel prize = in chemistry for his
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0development of density functional the= ory. This theory proved
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0that all ground state properties of a= non-relativistic,
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0non-degenerate quantum chemical syste= m can be represented as a
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0functional of the ground state electr= on density distribution.
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0A direct corollary is that since net = atomic charges are a
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0property of a chemical system, for a = non-degenerate chemical
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0ground state the net atomic charges h= ave to be a functional of
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0the ground state electron distributio= n. When I and others say
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0that the net atomic charges sh= ould approach a well-defined
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0basis set limit, because they are fun= ctionals of the electron
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0density distribution= , we!
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0are simply stating a direct co= rollary of the Hohenberg-Kohn
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0theorems. This has already been prove= d and received a Nobel
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0prize.
>
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0the HK theorems simply do not apply h= ere. They establish a
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0relation between two observables in a= strict QM sense (energy
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0and density). Because there is no ato= mic charge operator as I
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0already said, the statement
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0"atomic charges are a functional= of the ground state density"
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0is just empty.
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0What you probably mean is that some o= perational definitions
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0of atomic charge like AIM or Hirshfel= d are functionals of the
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0density.
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0This is true but does not eliminate t= he arbitrariness in their
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0definition
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(usually artificial boundaries in the= molecule).
>
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Best wishes
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Stefan
>
>
>
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0-=3D This is = automatically added to each message by the mailing
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0script =3D-
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0E-mail to sub= scribers: CHEMISTRY+/-ccl.net or use:>
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0E-mail to administrators: CHEM= ISTRY-REQUEST+/-ccl.net or use>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Conferences:
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0http://server.ccl.net/chemistry/announc= ements/conferences/
>
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Search Messages:
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0http://www.c= cl.net/chemistry/searchccl/index.shtml>
>
>
>
>



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--001a1135cf24c263e5051f7fb1a3-- From owner-chemistry@ccl.net Sat Sep 12 11:03:00 2015 From: "Thomas Manz thomasamanz * gmail.com" To: CCL Subject: CCL: net atomic charges Message-Id: <-51728-150911190016-12250-n1MHFmEV2EcKQBGe4PDqaA]^[server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a1149a21e73f784051f80adc3 Date: Fri, 11 Sep 2015 17:00:09 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz-#-gmail.com] --001a1149a21e73f784051f80adc3 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Robert, > from the Merriam-Webster dictionary: arbitrary (adjective) - (a) not planned or chosen for a particular reason, (b) not based on reason or evidence, (c) done without concern for what is fair or right (http://www.merriam-webster.com/dictionary/arbitrary) Saying the partitioning is "arbitrary" is not quite accurate. It is more accurate to say there is some flexibility in how to partition the electron density among atoms. The reason it is not arbitrary is because several candidates are proposed and then comparisons to experiments are made to determine which algorithms perform the best. This does allow for some flexibility in the partitioning, but "arbitrary" is clearly not the right word since experimental comparisons rule out the poor performing algorithms. In this sense the development of charge assignment methods is a scientific process. My example of an airplane mentioned early on is a good analogy. It is certainly true that there is some flexibility in the design of an airplane. One can make the airplane lighter, heavier, longer, taller, with two or four wings, etc. There is certainly flexibility here. But, it is not quite correct to say that airplane design is "arbitrary". The notion of arbitrariness somehow misses the point that airplane designs are subjected to scientific testing and their performance is evaluated and refined over time. My charge assignment schemes go through a similar development and rigorous testing phase. Therefore, it would not be quite to correct to say that they are "arbitrary" since they have been subjected to rigorous testing and refinement via the scientific method. You can apply this same kind of reasoning to any kind of technical product. Usually when developing software or methods, there is testing and evaluation that goes on. So it is somewhat unfair, for example, to say that design of an automobile is "arbitrary". Yes, there is some flexibility in the design of an automobile and that is why we have different models and so forth. But, the automobiles have been designed to perform in certain ways, to meet certain safety features, to meet emission standards, to meet minimum fuel efficiency requirements, to have certain comforts, to look good, and so forth. These designs are put through rigorous testing and go through refinements and improvements. It isn't quite fair to dismiss the enormous amount of development, design, testing, and optimization as "arbitrary". Somehow the word "arbitrary" doesn't capture the essence of the extensive testing and development involved. It doesn't give due and fair credit to those who put in the extensive work to develop and test a method in order to make it accurate, broadly applicable, computationally efficient, and robustly convergent. I have found through experience that those who characterize the properties of atoms in materials as "arbitrary" are almost universally using seriously defective methods. It is somewhat ironic, since they are using the worst methods available and yet they extend these criticisms to reliable methods. By analogy to my discussion above, it is if they are claiming that automobile designs are "arbitrary" and then they go out and drive a 50 year old broken car and then criticize all automobile manufactures for the "arbitrariness" of their car designs. They would have a much different experience and impression if they tried driving a new car instead of a 50 year old broken one. By the way, diborane is one of the easiest molecules to compute net atomic charges for. It is somewhat trickier to compute bond orders for. Here are my calculations for the net atomic charges and bond orders of diborane: B atomic charge: -0.0221 bridging H atomic charge: 0.131 outer H atomic charge: -0.054 B-H(bridging) bond order: 0.423 B-B bond order: 0.627 B-H(outer) bond order: 0.940 sum of bond orders for B atom: 3.39 sum of bond orders for bridging H atom: 0.91 sum of bond orders for outer H atom: 1.01 Sincerely, Tom On Fri, Sep 11, 2015 at 2:25 PM, Robert Molt r.molt.chemical.physics%x% gmail.com wrote: > There is nothing problematic with saying "there is no such thing as the > quantum mechanical operator for atomic charge." Any atomic charge model > requires an *arbitrary *partitioning of density as "belonging" to certain > atoms. None of the laws of physics are written in terms of atoms! We don'= t > write the force between atoms, we write the force between charges. > Trivializing the problem of partitioning is brushing under the rug the > inherent problem: we cannot partition it without arbitrary choices. > > An atomic charge model is especially problematic when the electron densit= y > is delocalized. There is no way to say to "whom" the density "belongs" in > diborane or a metal conducting a current. > > Moreover, this is the accepted view of the community. See Cramer, chapter > 9; see Jensen's book (don't recall the chapter; see Szabo and Ostlund, > chapters 1-3. > > > On 9/11/15 1:57 PM, V=C3=ADctor Lua=C3=B1a Cabal victor- -fluor.quimica.u= niovi.es > wrote: > > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor%f= luor.quimica.uniovi.es] > On Fri, Sep 11, 2015 at 06:25:07AM -0400, Robert Molt r.molt.chemical.phy= sics-*-gmail.com wrote: > > Atomic charges, as a computational model, are an approximation which is > completely independent of DFT. No Nobel Prize has been given for atomic > charges (and never will be, because there is no such thing as the > quantum mechanical operator for atomic charge). > > > To all, > > $ > Q =3D \int \rho(\bm{r}) d\bm{r} > =3D \int \abs{\Psi}^2 d\bm{x}. > $ > The quantum mechanical operator involved is \hat{1}. No problem > with its definition or properties (analytic, hermitic, ...). > > The question of atomic charges is completely different and it is not > related with the existence or not or an operator, but with the definition > of the boundary of an atom in a molecule or solid. The problem is here > $ > Q =3D \sum_i Q_i > =3D \sum_i \int_{\Omega_i} rho(\bm{r}) d\bm{r} > $ > What is $\Omega_i$? It is a problem of partitioning. > > Can we partition the bulk modulus of a crystal into ionic components? > Elastic constants, energ=C3=ADes, multipolar moments, ...? Yes, we and > others did ... if you accept the QTAIM concepts. Can we partition any > property? The QTAIM concepts assumes that, and there is a large school > of people working on it. > > The e-mail by Stephan Grimme on this discussion mentioned clearly and > appropriately the point. I believe in the QTAIM ideas, but they are > not the only ones and they are not the ultimate and exclusive truth. > > So the sentence "there is no such thing as the quantum mechanical > operator for atomic charge" is quite problematic and I can say with > absolute property that "there is a perfectly defined operator of the > atomic charge ... if you are studying an atom". And, believe me, there > are also chemists studying atoms ... and solids ... and liquids ... and > materials ... and ... > > So, please, calm down and do not jump to defend a person that is present > in the discussiond and can defend his opinions by himself. > > Peace (Shalom, Salam, Paz, ...), > V=C3=ADctor Lua=C3=B1a > -- > . . "In science a person can be convinced by a good argument. > / `' \ That is almost impossible in politics or religion" > /(o)(o)\ (Adapted from Carl Sagan) > /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero tambi=C3=A9n es peo= r > / '`'` \ que lo malo, porque la mediocridad no es un grado, es una > | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 > | |'`'`| | (Mediocre is worse than good, but it is also worse than > \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) > =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !"I have two kinds= of problems, > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! the urgent = and the important. > ! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not importa= nt, > ! e-mail: victor:-:fluor.quimica.uniovi.es ! and the important are ne= ver > ! phone: +34-985-103491 fax: +34-985-103125 ! urgent. > +----------------------------- > ---------------+ (Dwight D. Eisenhower) > GroupPage : http://azufre.quimica.uniovi.es/CHEMISTRY*o*ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST*o*ccl.net or usehttp://www.ccl.net/c= hemistry/sub_unsub.shtml > > -- > Dr. Robert Molt Jr. > Visiting Associate Professor of Chemistry > Department of Chemistry & Chemical Biology > Indiana University-Purdue University Indianapolis > LD 326 > 402 N. Blackford St. > Indianapolis, IN 46202 > > > On Fri, Sep 11, 2015 at 9:06 AM, Thomas Manz thomasamanz##gmail.com < owner-chemistry*o*ccl.net> wrote: > Hi Robert, > > > I'm copying this discussion on net atomic charges to a new thread. > > From the Nobel prize website: "The Nobel Prize in Chemistry 1998 was > divided equally between Walter Kohn "for his development of the > density-functional theory" and John A. Pople "for his development of > computational methods in quantum chemistry"." From my email: "In 1998, > Walter Kohn received the Nobel prize in chemistry for his development of > density functional theory." From your email: "Your comment is a very > incorrect characterization of the 1998 Nobel Prize." > > My point is that the Hohenberg-Kohn theorems tell us what types of > computations can give us meaningful physical properties. As stated in the > Hohenberg-Kohn theorems, the Hamiltonian of a non-degenerate ground state > system is determined by the ground-state electron density distribution up > to an arbitrary constant potential offset. Since the Hamiltonian determin= es > the system's wavefunction, and the wavefunction determines the system's > properties, it directly follows from the Hohenberg-Kohn Theorems that all > of the observable properties of a non-degenerate ground state quantum > chemical system are functionals of the ground state electron distribution= . > This is what the Hohenberg-Kohn theorems state. The energy is included as > one of the observables, but the Hohenberg-Kohn theorems are not limited t= o > the system=E2=80=99s energy alone. > > Therefore, it is a direct corollary of the Hohenberg-Kohn theorems that a > physically valid definition of net atomic charges must be constructed to > give values that are a functional of the electron density distribution. A= ny > definition that is constructed in such a way as to lack a complete basis > set limit is therefore physically invalid. This follows directly from the > Hohenberg-Kohn theorems. > > It is true that after ruling out such unphysical methodologies as Mullike= n > and Lowdin populations, that flexibility in how to define the net atomic > charges as functionals of the electron distribution still remains. Yes, t= he > possibility of overlap of three-dimensional electron distributions betwee= n > the atoms is a challenge to sort out, but it is not a problem that cannot > be studied. This is where application of the scientific method comes into > play. By comparing different proposals to experimental data across a wide > variety of systems, it is possible to draw meaningful scientific > conclusions about which methods for assigning net atomic charges give > closer agreement to experimental data and are therefore more scientifical= ly > accurate. This does not mean we will be able to compute net atomic charge= s > with the same level of precision as we can measure system energies, but i= t > still means that net atomic charges are a valid scientific concept and th= at > they follow known theorems and obey the scientific method. > > > > Sincerely, > > > > Tom > > > > ----------- > > > Dr. Manz: > > > Your comment is a very incorrect characterization of the 1998 Nobel > Prize. > > > a.) You're addressing Stephen Grimme, a leader of DFT in computational > chemistry in the world; trust me, he is well aware of DFT. This is like > lecturing Newton on a new subject called "trigonometry." > > > b.) DFT's contribution to science is NOT "The density is an observable.= " > This has been known since the days of classical electromagnetics that you > can write all the entire theory of classical EM in terms of density. It's > what we spend every day of classical EM classes solving for. Wavefunction > people defined and were using the electron density of chemical systems LO= NG > before there was a DFT; just read Szabo and Ostlund. Rather, DFT is a > statement about being able to calculate the energy as a function of densi= ty > directly practically, with no calculation of the wavefunction necessary > (there is more to it than this, but as a bird's eye-view statement). > > > c.) Your statement has a huge assumption in it that is in no way > associated with DFT. You wrote: > > > "A direct corollary is that since net atomic charges are a property of = a > chemical system..." > > > This is NOT a direct corollary. There is no such thing as atomic > charges, that's the point of another thread. The TOTAL charge of a system > is well-defined, but defining the charge of an arbitrary subsystem is not > always possible. There are many reasons you cannot do this rigorously. On= e > is that you are trying to represent a function of 3 variables (the densit= y, > a real observable) by ONE number (the "atomic charge"); this is impossibl= e. > The change in the density, spatially, at different points on a 3D grid (l= et > alone the fact we have spin!) cannot be represent by one number. > > > Atomic charges, as a computational model, are an approximation which is > completely independent of DFT. No Nobel Prize has been given for atomic > charges (and never will be, because there is no such thing as the quantum > mechanical operator for atomic charge). > > > > > *Robert Molt r.molt.chemical.physics-*-gmail.com * < > owner-chemistry*_*ccl.net> > --001a1149a21e73f784051f80adc3 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Robert,

from the Merriam-Webster dic= tionary: arbitrary (adjective) - (a) not planned or chosen for a particular= reason, (b) not based on reason or evidence, (c) done without concern for = what is fair or right
(http://www.merriam-webster.com/dictionary/arbitrary)

Saying the partitioning is "arbitrary"= is not quite accurate. It is more accurate to say there is some flexibilit= y in how to partition the electron density among atoms.
The reaso= n it is not arbitrary is because several candidates are proposed and then c= omparisons to experiments are made to determine which algorithms perform th= e best.
This does allow for some flexibility in the partitioning,= but "arbitrary" is clearly not the right word since experimental= comparisons rule out the poor performing algorithms.=C2=A0
In th= is sense the development of charge assignment methods is a scientific proce= ss.

My example of an airplane mentioned early on i= s a good analogy. It is certainly true that there is some flexibility in th= e design of an airplane. One can make the airplane
lighter, heavi= er, longer, taller, with two or four wings, etc. There is certainly flexibi= lity here. But, it is not quite correct to say that airplane design is &quo= t;arbitrary".
The notion of arbitrariness somehow misses the= point that airplane designs are subjected to scientific testing and their = performance is evaluated and refined over time.
My charge assignm= ent schemes go through a similar development and rigorous testing phase. Th= erefore, it would not be quite to correct to say that they are "arbitr= ary" since
they have been subjected to rigorous testing and = refinement via the scientific method.

You can appl= y this same kind of reasoning to any kind of technical product. Usually whe= n developing software or methods, there is testing and evaluation that goes= on.
So it is somewhat unfair, for example, to say that design of= an automobile is "arbitrary". Yes, there is some flexibility in = the design of an automobile and that is why we
have different mod= els and so forth. But, the automobiles have been designed to perform in cer= tain ways, to meet certain safety features, to meet emission standards, to<= /div>
meet minimum fuel efficiency requirements, to have certain comfor= ts, to look good, and so forth. These designs are put through rigorous test= ing and go through refinements and=C2=A0
improvements. It isn'= ;t quite fair to dismiss the enormous amount of development, design, testin= g, and optimization as "arbitrary". Somehow the word "arbitr= ary" doesn't capture
the essence of the extensive testin= g and development involved. It doesn't give due and fair credit to thos= e who put in the extensive work to develop and test a method in order
=
to make it accurate, broadly applicable, computationally efficient, an= d robustly convergent.

I have found through experi= ence that those who characterize the properties of atoms in materials as &q= uot;arbitrary" are almost universally using seriously defective method= s.
It is somewhat ironic, since they are using the worst methods = available and yet they extend these criticisms to reliable methods. By anal= ogy to my discussion above,
it is if they are claiming that autom= obile designs are "arbitrary" and then they go out and drive a 50= year old broken car and then criticize all automobile manufactures
for the "arbitrariness" of their car designs. They would have = a much different experience and impression if they tried driving a new car = instead of a 50 year old broken one.

By the way, d= iborane is one of the easiest molecules to compute net atomic charges for. = It is somewhat trickier to compute bond orders for.
Here are my c= alculations for the net atomic charges and bond orders of diborane:



<= div>sum of bond orders for outer H atom: 1.01




O= n Fri, Sep 11, 2015 at 2:25 PM, Robert Molt r.molt.chemical.physics%x%gmail.com=C2=A0<owner-chemistry*o*ccl.net<= /a>>=C2=A0wrote:
There is nothing problematic with saying "there is no su= ch thing as the quantum mechanical operator for atomic charge." Any at= omic charge model requires an=C2=A0arbitrary=C2=A0partitioning of de= nsity as "belonging" to certain atoms. None of the laws of physic= s are written in terms of atoms! We don't write the force between atoms= , we write the force between charges. Trivializing the problem of partition= ing is brushing under the rug the inherent problem: we cannot partition it = without arbitrary choices.

An atomic charge model is especially prob= lematic when the electron density is delocalized. There is no way to say to= "whom" the density "belongs" in diborane or a metal co= nducting a current.

Moreover, this is the accepted view of the commu= nity. See Cramer, chapter 9; see Jensen's book (don't recall the ch= apter; see Szabo and Ostlund, chapters 1-3.
Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cab=
al [victor%fl=
uor.quimica.uniovi.es]
On Fri, Sep 11, 2015 at 06:25:07AM -0400, Robert Molt r.molt.chemical.physi=
cs-*-gmail.com wrote:

Atomic charges, as a computational mod=
el, are an approximation which is =20
completely independent of DFT. No Nobel Prize has been given for atomic =20
charges (and never will be, because there is no such thing as the =20
quantum mechanical operator for atomic charge).


To all,

$
Q =3D \int \rho(\bm{r}) d\bm{r}
  =3D \int \abs{\Psi}^2 d\bm{x}.
$
The quantum mechanical operator involved is \hat{1}. No problem
with its definition or properties (analytic, hermitic, ...).

The question of atomic charges is completely different and it is not
related with the existence or not or an operator, but with the definition
of the boundary of an atom in a molecule or solid. The problem is here
$
Q =3D \sum_i Q_i
  =3D \sum_i \int_{\Omega_i} rho(\bm{r}) d\bm{r}
$
What is $\Omega_i$? It is a problem of partitioning.

Can we partition the bulk modulus of a crystal into ionic components?
Elastic constants, energ=C3=ADes, multipolar moments, ...?  Yes, we and
others did ... if you accept the QTAIM concepts. Can we partition any
property? The QTAIM concepts assumes that, and there is a large school
of people working on it.

The e-mail by Stephan Grimme on this discussion mentioned clearly and
appropriately the point. I believe in the QTAIM ideas, but they are
not the only ones and they are not the ultimate and exclusive truth.

So the sentence "there is no such thing as the quantum mechanical
operator for atomic charge" is quite problematic and I can say with
absolute property that "there is a perfectly defined operator of the
atomic charge ... if you are studying an atom". And, believe me, there
are also chemists studying atoms ... and solids ... and liquids ... and
materials ... and ...

So, please, calm down and do not jump to defend a person that is present
in the discussiond and can defend his opinions by himself.

Peace (Shalom, Salam, Paz, ...),
                                V=C3=ADctor Lua=C3=B1a
--
     .  .    "In science a person can be convinced by a good argument.
    / `' \   That is almost impossible in politics or religion"
   /(o)(o)\  (Adapted from Carl Sagan)
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero tambi=C3=A9n=
 es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es=
 una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse th=
an
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an =
attitude)
=3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !"I have tw=
o kinds of problems,
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! the urgent an=
d the important.
! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important=
,
! e-mail:   victor:-:fluor.quimica.uniovi.es   ! and the important are never
! phone: +34-985-103491  fax: +34-985-103125 ! urgent.
+-----------------------------
---------------+        (Dwight D=
. Eisenhower)
 GroupPage : http://azufre.quimica.uniovi.es/CHEMISTRY*o*ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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<= span class=3D"">
--=20
Dr. Robert Molt Jr.
Visiting Associate Professor of Chemistry
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202


On Fri, Sep 11, 2015 at 9:06 AM, Thomas Manz thomasamanz##gmail.com <owner-chemistry*o*ccl.net>= wrote:

Hi Rob= ert,

=C2=A0

I'm copying this discussion on net atomic charges to a new thread.=

From the Nob= el prize website: "The Nobel Prize in Chemistry 1998 was divided equal= ly between Walter Kohn "for his development of the density-functional = theory" and John A. Pople "for his development of computational m= ethods in quantum chemistry"." From my email: "In 1998, Walt= er Kohn received the Nobel prize in chemistry for his development of densit= y functional theory." From your email: "Your comment is a very in= correct characterization of the 1998 Nobel Prize."

My point is that the Hohenberg-K= ohn theorems tell us what types of computations can give us meaningful phys= ical properties. As stated in the Hohenberg-Kohn theorems, the Hamiltonian = of a non-degenerate ground state system is determined by the ground-state e= lectron density distribution up to an arbitrary constant potential offset. = Since the Hamiltonian determines the system's wavefunction, and the wav= efunction determines the system's properties, it directly follows from = the Hohenberg-Kohn Theorems that all of the observable properties of a non-= degenerate ground state quantum chemical system are functionals of the grou= nd state electron distribution. This is what the Hohenberg-Kohn theorems st= ate. The energy is included as one of the observables, but the Hohenberg-Ko= hn theorems are not limited to the system=E2=80=99s energy alone.
Therefore, it is a dir= ect corollary of the Hohenberg-Kohn theorems that a physically valid defini= tion of net atomic charges must be constructed to give values that are a fu= nctional of the electron density distribution. Any definition that is const= ructed in such a way as to lack a complete basis set limit is therefore phy= sically invalid. This follows directly from the Hohenberg-Kohn theorems.

It is true that= after ruling out such unphysical methodologies as Mulliken and Lowdin popu= lations, that flexibility in how to define the net atomic charges as functi= onals of the electron distribution still remains. Yes, the possibility of o= verlap of three-dimensional electron distributions between the atoms is a c= hallenge to sort out, but it is not a problem that cannot be studied. This = is where application of the scientific method comes into play. By comparing= different proposals to experimental data across a wide variety of systems,= it is possible to draw meaningful scientific conclusions about which metho= ds for assigning net atomic charges give closer agreement to experimental d= ata and are therefore more scientifically accurate. This does not mean we w= ill be able to compute net atomic charges with the same level of precision = as we can measure system energies, but it still means that net atomic charg= es are a valid scientific concept and that they follow known theorems and o= bey the scientific method.

=C2=A0

Sincerely,

=C2=A0

Tom

=C2=A0

------= -----

> Dr. Manz:

> Your co= mment is a very incorrect characterization of the 1998 Nobel Prize.<= br>
&= gt; a.) You're addressing Stephen Grimme, a leader of DFT in computatio= nal chemistry in the world; trust me, he is well aware of DFT. This is like= lecturing Newton on a new subject called "trigonometry."<= br>
&= gt; b.) DFT's contribution to science is NOT "The density is an ob= servable." This has been known since the days of classical electromagn= etics that you can write all the entire theory of classical EM in terms of = density. It's what we spend every day of classical EM classes solving f= or. Wavefunction people defined and were using the electron density of chem= ical systems LONG before there was a DFT; just read Szabo and Ostlund. Rath= er, DFT is a statement about being able to calculate the energy as a functi= on of density directly practically, with no calculation of the wavefunction= necessary (there is more to it than this, but as a bird's eye-view sta= tement).

> c.) Your statement has a huge assumption in it that is = in no way associated with DFT. You wrote:

> "A direct corolla= ry is that since net atomic charges are a property of a chemical system...&= quot;

> This is NOT a direct corollary. There is no such thing as = atomic charges, that's the point of another thread. The TOTAL charge of= a system is well-defined, but defining the charge of an arbitrary subsyste= m is not always possible. There are many reasons you cannot do this rigorou= sly. One is that you are trying to represent a function of 3 variables (the= density, a real observable) by ONE number (the "atomic charge");= this is impossible. The change in the density, spatially, at different poi= nts on a 3D grid (let alone the fact we have spin!) cannot be represent by = one number.=C2=A0

> Atomic charges, as a computational model, are = an approximation which is completely independent of DFT. No Nobel Prize has= been given for atomic charges (and never will be, because there is no such= thing as the quantum mechanical operator for atomic charge).=

=C2=A0

>=C2=A0Ro= bert Molt r.molt.chemical.physics-*-gmail.com=C2= =A0<owner-chemistry*_*ccl.net>


--001a1149a21e73f784051f80adc3-- From owner-chemistry@ccl.net Sat Sep 12 11:38:01 2015 From: "Susi Lehtola susi.lehtola:alumni.helsinki.fi" To: CCL Subject: CCL: net atomic charges Message-Id: <-51729-150911190604-14417-xSBAqeddbpZMjKFMAsW+tg{}server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Fri, 11 Sep 2015 16:05:52 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola:+:alumni.helsinki.fi] On 09/11/2015 08:06 AM, Thomas Manz thomasamanz##gmail.com wrote: > By comparing different proposals to experimental data across a wide > variety of systems, it is possible to draw meaningful scientific > conclusions about which methods for assigning net atomic charges give > closer agreement to experimental data and are therefore more scientifically > accurate. This does not mean we will be able to compute net atomic charges > with the same level of precision as we can measure system energies, but it > still means that net atomic charges are a valid scientific concept and that > they follow known theorems and obey the scientific method. But the point is that *there is no way* to unequivocally define partial charges. You *can* measure the electron density, which is a 3D distribution. You *cannot* boil the 3D distribution down into a set of N numbers that represent the partial charges on the nuclei in the system. The values you get all depend on how you want to define the partial charges. Barring methods that lack a mathematical limit like Mulliken and Löwdin charges, you still have a zoo of methods to assign partial charges that you cannot rank against each other, since each of them is consistent in its own definition. For instance you have Bader, Voronoi or Hirshfeld charges (and a large variation of schemes that build upon Hirshfeld), which give different values for the partial charges. You have electrostatic potential derived charges that depend on the set of points at which you want to reproduce the value of the electric potential. And so on. All of these are mathematically well defined and have a meaningful complete basis set limit, but they all give different answers. Each of them are "correct" for the property they have been defined for, but really none of them are correct, since *there is no unequivocal way* of dividing a smeared electron distribution between nuclei, because a partial charge is not an observable. -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola+*+alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA ----------------------------------------------------------------------- From owner-chemistry@ccl.net Sat Sep 12 12:13:00 2015 From: "Thomas Manz thomasamanz]-[gmail.com" To: CCL Subject: CCL: atomic population analysis Message-Id: <-51730-150912092430-21158-gZsqE3CAJG5HlSDknGdafA(0)server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a11400d6a38c32d051f8cc055 Date: Sat, 12 Sep 2015 07:24:24 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz###gmail.com] --001a11400d6a38c32d051f8cc055 Content-Type: text/plain; charset=UTF-8 Hi Robert, The notion of atomic population analysis methods as being arbitrary reflects the practical state of affairs in decades past. It is certainly true that the earliest methods such as Mulliken and Lowdin populations are inherently arbitrary because they lack a basis set limit. But, the notion of arbitrariness doesn't accurately characterize the most recently developed methods which not only have a well-defined basis set limit but also have been developed with extensive and rigorous comparisons to experimental data. At the time the textbooks you mentioned were written, things had only begun to improve in the area of atomic population analysis. I'm sure the authors of those textbooks did the best they could with the information available at that time. Since those textbooks were written, newer methods have been developed that are at least an order of magnitude more accurate in comparisons to experiments than the crude, early methods. If one were going to write a textbook today, it would be appropriate to say that many of the early atomic population analysis methods were arbitrary but that some of the most recent ones have been developed through a legitimate scientific design process. This is an area in which I currently do research. In my research group, atomic population analysis methods are developed using scientific methods. The procedure we use is not unlike the one used to design airplanes. Yes, there is some flexibility in the design of an airplane. One could make it longer or shorter, for example. Yet, it is not quite accurate to say the design of an airplane is arbitrary. Airplanes, like my atomic population analysis methods, are designed to meet certain performance criteria. An airplane should fly, for example. Not only should it fly, but it should have stable control, take off and land smoothly, etc. There is some flexibility when choosing the shape of airplane, but it is not quite accurate to say the shape of an airplane is arbitrary. Proposed airplane shapes are tested in wind tunnels to see how they react to air turbulence, how much drag they produce, etc. There is a real engineering design element involved with scientific process of engineering and testing prototypes to continuously improve the design. Saying that airplane designs are arbitrary somehow doesn't do justice to the enormous amount of design work, prototype building, and scientific testing that goes into producing an efficient airplane. The same principle applies to the development of accurate atomic population analysis methods in my research group. We use a legitimate and rigorous process that involves engineering design, prototype building and scientific testing with comparisons to experimental data. I realize that many other research groups do not use such a rigorous process, but if you are going to say that atomic population analysis methods are arbitrary, please restrict this designation to those that actually are arbitrary and mention that some of the recent efforts use a legitimate scientific design process. The diborane molecule you mentioned does present an interesting example. Please find below the net atomic charges and bond orders I computed for this molecule: B atomic charge: -0.0221 bridging H atomic charge: 0.131 outer H atomic charge: -0.054 B-H(bridging) bond order: 0.423 B-B bond order: 0.627 B-H(outer) bond order: 0.940 sum of bond orders for B atom: 3.39 sum of bond orders for bridging H atom: 0.91 sum of bond orders for outer H atom: 1.01 Sincerely, Tom On Fri, Sep 11, 2015 at 2:25 PM, Robert Molt r.molt.chemical.physics%x% gmail.com wrote: > There is nothing problematic with saying "there is no such thing as the > quantum mechanical operator for atomic charge." Any atomic charge model > requires an *arbitrary *partitioning of density as "belonging" to certain > atoms. None of the laws of physics are written in terms of atoms! We don't > write the force between atoms, we write the force between charges. > Trivializing the problem of partitioning is brushing under the rug the > inherent problem: we cannot partition it without arbitrary choices. > > An atomic charge model is especially problematic when the electron density > is delocalized. There is no way to say to "whom" the density "belongs" in > diborane or a metal conducting a current. > > Moreover, this is the accepted view of the community. See Cramer, chapter > 9; see Jensen's book (don't recall the chapter; see Szabo and Ostlund, > chapters 1-3. > > --001a11400d6a38c32d051f8cc055 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Robert,

The notion of ato= mic population analysis methods as being arbitrary reflects the practical s= tate of affairs in decades past. It is certainly true that the earliest met= hods such as Mulliken and Lowdin populations are inherently arbitrary becau= se they lack a basis set limit. But, the notion of arbitrariness doesn'= t accurately characterize the most recently developed methods which not onl= y have a well-defined basis set limit but also have been developed with ext= ensive and rigorous comparisons to experimental data.

<= div>At the time the textbooks you mentioned were written, things had only b= egun to improve in the area of atomic population analysis. I'm sure the= authors of those textbooks did the best they could with the information av= ailable at that time. Since those textbooks were written, newer methods hav= e been developed that are at least an order of magnitude more accurate in c= omparisons to experiments than the crude, early methods. If one were going = to write a textbook today, it would be appropriate to say that many of the = early atomic population analysis methods were arbitrary but that some of th= e most recent ones have been developed through a legitimate scientific desi= gn process.

This is an area in which I currently d= o research. In my research group, atomic population analysis methods are de= veloped using scientific methods. The procedure we use is not unlike the on= e used to design airplanes. Yes, there is some flexibility in the design of= an airplane. One could make it longer or shorter, for example. Yet, it is = not quite accurate to say the design of an airplane is arbitrary. Airplanes= , like my atomic population analysis methods, are designed to meet certain = performance criteria. An airplane should fly, for example. Not only should = it fly, but it should have stable control, take off and land smoothly, etc.= There is some flexibility when choosing the shape of airplane, but it is n= ot quite accurate to say the shape of an airplane is arbitrary. Proposed ai= rplane shapes are tested in wind tunnels to see how they react to air turbu= lence, how much drag they produce, etc. There is a real engineering design = element involved with scientific process of engineering and testing prototy= pes to continuously improve the design. Saying that airplane designs are ar= bitrary somehow doesn't do justice to the enormous amount of design wor= k, prototype building, and scientific testing that goes into producing an e= fficient airplane.=C2=A0

The same principle applie= s to the development of accurate atomic population analysis methods in my r= esearch group. We use a legitimate and rigorous process that involves engin= eering design, prototype building and scientific testing with comparisons t= o experimental data. I realize that many other research groups do not use s= uch a rigorous process, but if you are going to say that atomic population = analysis methods are arbitrary, please restrict this designation to those t= hat actually are arbitrary and mention that some of the recent efforts use = a legitimate scientific design process.

The dibora= ne molecule you mentioned does present an interesting example. Please find = below the net atomic charges and bond orders I computed for this molecule:= =C2=A0

B atomi= c charge: -0.0221
bridging H atomic ch= arge: 0.131
outer H atomic charge: -0.= 054

B-H(bridging) bond order: 0.423
B-B bond order: 0.627
B-H(outer) bon= d order: 0.940

sum of bond orders for B atom: 3.39
sum of bond orders for bridging H atom: 0.91
sum of bond orders for outer H atom: 1.01

Sincerely,

Tom=C2=A0


On Fri, Sep 11, 2015 at 2:25 PM, Robert Mol= t r.molt.chemical.physics%x%gmail.com=C2=A0<owner-chemistry^ccl.net>=C2=A0wro= te:
There is nothing problematic with saying "ther= e is no such thing as the quantum mechanical operator for atomic charge.&qu= ot; Any atomic charge model requires an=C2=A0arbitrary=C2=A0partitioning of = density as "belonging" to certain atoms. None of the laws of phys= ics are written in terms of atoms! We don't write the force between ato= ms, we write the force between charges. Trivializing the problem of partiti= oning is brushing under the rug the inherent problem: we cannot partition i= t without arbitrary choices.

An atomic charge mod= el is especially problematic when the electron density is delocalized. Ther= e is no way to say to "whom" the density "belongs" in d= iborane or a metal conducting a current.

Moreover= , this is the accepted view of the community. See Cramer, chapter 9; see Je= nsen's book (don't recall the chapter; see Szabo and Ostlund, chapt= ers 1-3.

--001a11400d6a38c32d051f8cc055-- From owner-chemistry@ccl.net Sat Sep 12 12:48:00 2015 From: "Robert Molt r.molt.chemical.physics%gmail.com" To: CCL Subject: CCL:G: Symmetry constraint during scan calculation Message-Id: <-51731-150912102142-10695-i6jXQklpo4Z3ElW31calJw%server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Sat, 12 Sep 2015 10:21:34 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics#gmail.com] if you start in a symmetry point group in Gaussian, you tend to follow it by default. You can make this more explicit by using the symmetry keyword in Gaussian (check the manual for details). On 9/12/15 7:34 AM, Mohan maruthi sena maruthi.sena,,gmail.com wrote: > Hi all, > I am trying to perform a scan calculation for SF6 molecule > using Gaussian09. I have optimized the molecule and the symmetry of > the molecule is octahedral. I want to perform scan of angle [FSF] > calculation by imposing D3h symmetry constraint on the molecule [and > also keeping bond length fixed]. How can I do this g09? [option in > input file]. > > Thanks for a reply in advance, > > Regards, > Mohan -- Dr. Robert Molt Jr. Visiting Associate Professor of Chemistry Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202 From owner-chemistry@ccl.net Sat Sep 12 21:16:00 2015 From: "Thomas Manz thomasamanz#%#gmail.com" To: CCL Subject: CCL: net atomic charges Message-Id: <-51732-150912162309-3197-Mu5sKuZJlgGKCSgVAFyT8g..server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a1136e03a727bbc051f929925 Date: Sat, 12 Sep 2015 14:23:03 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz:_:gmail.com] --001a1136e03a727bbc051f929925 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Susi, I understand your point and it is an important consideration. Among the methods you mentioned, the original Hirshfeld method systematically gives charge magnitudes that are much too small. Sure, there will still be alternative methodologies such as APT, Bader's quantum chemical topology, DDEC, etc. that provide different definitions of the charge partitioning optimized for different goals. For example, the APT method is appropriate for studying infrared spectra intensities (i.e., dynamic dipole moment changes), but not good for reproducing static electric potentials or static dipole moments. Yet here we can speak to the comparisons of these charge methods to experiments and to their accuracy for reproducing the electrostatic potential surrounding the material or to molecular dipole moments or to core electron binding energy shifts. This is wholly scientific. These schemes, which are formulated with well-defined basis set limits, are not altogether unlike our different exchange-correlation methods for computing system energies and geometries in DFT. Generally, because these methods have clear definitions, it is possible to make some reasonable choices of which is best for a particular kind of application. One would probably want to use APT charges not Bader or DDEC charges for studying IR spectra intensity. If one were studying electrides, Bader's quantum chemical topology would be the natural choice. If it is desired to construct a point-charge model for a flexible force-field, the DDEC charges would be well-suited for this, while the Bader charges would generally not be. Both the Bader and DDEC schemes would also fall under the category of "general-purpose" methods that can be used to study practically any material of interest, including charge transfer between atoms in dense materials. But my overall point is that it is possible to make scientific study of atomic population analysis methods and the notion that these are arbitrary is not accurate. Yes, there are different schemes and methodologies, but these are constructed for defined reasons not arbitrary ones. To put this in perspective would most quantum chemists describe different exchange-correlation functionals as "arbitrary"? Would most quantum chemists say "constructing exchange-correlation functionals is an arbitrary process"? There shouldn't be a double standard here. If we are not going to describe exchange-correlation functionals as arbitrary we shouldn't use this term for atomic population analysis methods (except those which truly are arbitrary because they are malformed such as lacking a basis set limit or having other gross defects). Sincerely, Tom On Fri, Sep 11, 2015 at 5:05 PM, Susi Lehtola susi.lehtola: alumni.helsinki.fi wrote: > > Sent to CCL by: Susi Lehtola [susi.lehtola:+:alumni.helsinki.fi] > On 09/11/2015 08:06 AM, Thomas Manz thomasamanz##gmail.com wrote: > >> By comparing different proposals to experimental data across a wide >> variety of systems, it is possible to draw meaningful scientific >> conclusions about which methods for assigning net atomic charges give >> closer agreement to experimental data and are therefore more >> scientifically >> accurate. This does not mean we will be able to compute net atomic charg= es >> with the same level of precision as we can measure system energies, but = it >> still means that net atomic charges are a valid scientific concept and >> that >> they follow known theorems and obey the scientific method. >> > > But the point is that *there is no way* to unequivocally define partial > charges. You *can* measure the electron density, which is a 3D > distribution. You *cannot* boil the 3D distribution down into a set of N > numbers that represent the partial charges on the nuclei in the system. T= he > values you get all depend on how you want to define the partial charges. > > Barring methods that lack a mathematical limit like Mulliken and L=C3=B6w= din > charges, you still have a zoo of methods to assign partial charges that y= ou > cannot rank against each other, since each of them is consistent in its o= wn > definition. For instance you have Bader, Voronoi or Hirshfeld charges (an= d > a large variation of schemes that build upon Hirshfeld), which give > different values for the partial charges. You have electrostatic potentia= l > derived charges that depend on the set of points at which you want to > reproduce the value of the electric potential. And so on. > > All of these are mathematically well defined and have a meaningful > complete basis set limit, but they all give different answers. Each of th= em > are "correct" for the property they have been defined for, but really non= e > of them are correct, since *there is no unequivocal way* of dividing a > smeared electron distribution between nuclei, because a partial charge is > not an observable. > -- > ----------------------------------------------------------------------- > Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow > susi.lehtola_._alumni.helsinki.fi Lawrence Berkeley National Laboratory > http://www.helsinki.fi/~jzlehtol USA > ----------------------------------------------------------------------- > > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --001a1136e03a727bbc051f929925 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Susi,

I understand your point and it= is an important consideration. Among the methods you mentioned, the origin= al Hirshfeld method systematically gives charge magnitudes that are much to= o small.=C2=A0
Sure, there will still be alternative methodologie= s such as APT, Bader's quantum chemical topology, DDEC, etc. that provi= de different definitions of the charge partitioning optimized for different= goals.
For example, the APT method is appropriate for studying i= nfrared spectra intensities (i.e., dynamic dipole moment changes), but not = good for reproducing static electric potentials or static dipole moments.= =C2=A0
Yet here we can speak to the comparisons of these charge m= ethods to experiments and to their accuracy for reproducing the electrostat= ic potential surrounding the material or to molecular dipole moments
<= div>or to core electron binding energy shifts. This is wholly scientific. T= hese schemes, which are formulated with well-defined basis set limits, are = not altogether unlike our different exchange-correlation=C2=A0
me= thods for computing system energies and geometries in DFT. Generally, becau= se these methods have clear definitions, it is possible to make some reason= able choices of which is best for a=C2=A0
particular kind of appl= ication. One would probably want to use APT charges not Bader or DDEC charg= es for studying IR spectra intensity. If one were studying electrides, Bade= r's quantum chemical topology
would be the natural choice. If= it is desired to construct a point-charge model for a flexible force-field= , the DDEC charges would be well-suited for this, while the Bader charges w= ould generally not be.=C2=A0
Both the Bader and DDEC schemes woul= d also fall under the category of "general-purpose" methods that = can be used to study practically any material of interest,=C2=A0
= including charge transfer between atoms in dense materials.=C2=A0

But my overall point is that it is possible to make scienti= fic study of atomic population analysis methods and the notion that these a= re arbitrary is not accurate.
Yes, there are different schemes an= d methodologies, but these are constructed for defined reasons not arbitrar= y ones.

To put this in perspective would most quan= tum chemists describe different exchange-correlation functionals as "a= rbitrary"? Would most quantum chemists say
"constructin= g exchange-correlation functionals is an arbitrary process"? There sho= uldn't be a double standard here. If we are not going to describe=C2=A0=
exchange-correlation functionals as arbitrary we shouldn't u= se this term for atomic population analysis methods (except those which tru= ly are arbitrary
because they are malformed such as lacking a bas= is set limit or having other gross defects).

Since= rely,

Tom
On Fri, Sep 11, 2015 at 5:05 PM, Susi Lehtola = susi.lehtola:alumni.helsinki.fi <= span dir=3D"ltr"><owner-chemistry=ccl.net> wrote:

Sent to CCL by: Susi Lehtola [susi.lehtola:+:alumni.helsinki.fi]
On 09/11/2015 08:06 AM, Thomas Manz thomasamanz##gmail.com wrote:
By comparing different proposals to experimental data across a wide
variety of systems, it is possible to draw meaningful scientific
conclusions about which methods for assigning net atomic charges give
closer agreement to experimental data and are therefore more scientifically=
accurate. This does not mean we will be able to compute net atomic charges<= br> with the same level of precision as we can measure system energies, but it<= br> still means that net atomic charges are a valid scientific concept and that=
they follow known theorems and obey the scientific method.

But the point is that *there is no way* to unequivocally define partial cha= rges. You *can* measure the electron density, which is a 3D distribution. Y= ou *cannot* boil the 3D distribution down into a set of N numbers that repr= esent the partial charges on the nuclei in the system. The values you get a= ll depend on how you want to define the partial charges.

Barring methods that lack a mathematical limit like Mulliken and L=C3=B6wdi= n charges, you still have a zoo of methods to assign partial charges that y= ou cannot rank against each other, since each of them is consistent in its = own definition. For instance you have Bader, Voronoi or Hirshfeld charges (= and a large variation of schemes that build upon Hirshfeld), which give dif= ferent values for the partial charges. You have electrostatic potential der= ived charges that depend on the set of points at which you want to reproduc= e the value of the electric potential. And so on.

All of these are mathematically well defined and have a meaningful complete= basis set limit, but they all give different answers. Each of them are &qu= ot;correct" for the property they have been defined for, but really no= ne of them are correct, since *there is no unequivocal way* of dividing a s= meared electron distribution between nuclei, because a partial charge is no= t an observable.
--
-----------------------------------------------------------------------
Mr. Susi Lehtola, PhD=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Chemis= t Postdoctoral Fellow
susi.lehtola_._alumni.helsinki.fi=C2=A0 =C2=A0Lawrence Berkeley Nationa= l Laboratory
http://www.helsinki.fi/~jzlehtol=C2=A0 USA
-----------------------------------------------------------------------



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