From owner-chemistry@ccl.net Fri Sep 11 00:35:00 2015 From: "N. Sukumar nagams^rpi.edu" To: CCL Subject: CCL:G: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51705-150911000952-21409-TL7fmqAOlz/iGNJ0A+nVDw..server.ccl.net> X-Original-From: "N. Sukumar" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Fri, 11 Sep 2015 09:37:54 +0530 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams]![rpi.edu] Since this list includes a large number of non-specialists, one should be careful to avoid making sweeping statements like "While we may not be able to measure atomic charges as precisely as energies in experiments, it is not true to say atomic charges are not experimentally observable. They can be observed and measured through spectroscopy experiments, albeit with much less precision than we are able to measure energies." "Atomic charges" are about as measurable as the divinity of an orbital! Both are entirely theoretical properties of theoretical objects. I joint Stefan in asking how to "measure atomic charges" - and before that please also clarify what you mean by "atomic." -- N. SUKUMAR Professor & Head, Department of Chemistry Director, Center for Informatics Shiv Nadar University, India On 2015-09-11 05:32, Thomas Manz thomasamanz-*-gmail.com wrote: > Hi Stefan, > > In regards to your questions about MP2, one has to be extremely > careful with such an approach, because the denominator is of the form > (energy_1 - energy_2) which causes the denominator to become zero when > energy_1 = energy_2. This can cause perturbation methods to blow up. > For this reason, I generally prefer non-perturbative methods such as > CCSD, when a higher-level calculation result is needed. I would > recommend CCSD as opposed to MP2, simply because CCSD has a more > well-defined mathematical limit on the results of the calculation. > Personally, I don't use MP2 calculations for this reason, but this > doesn't necessarily mean others can't. However, I wouldn't go so far > as to say that MP2 calculations don't have a well-defined basis set > limit. I believe that for most systems the complete basis set limit > would be well-defined for MP2 calculations. In this sense, the MP2 > calculations are much more well-defined than Mulliken or Lowdin > populations, which definitely do not have a basis set limit. > >> If the set is small (minimal) the derived atomic charges are > chemically reasonable and correlate well with those from other methods > for well understood reasons. > > The populations of the density matrix projected onto a smaller basis > set is usually referred to by a different name. At least in Gaussian > programs, it is called Pop=MBS. In Gaussian programs, this is a > different algorithm than Pop=Regular which performs Mulliken analysis > in the current basis set. In my experience, the Pop=MBS method is not > very useful and tends to crash a large percentage of the time. It > seems to crash especially often for heavier atoms and for those with > pseudopotentials. Also, people have tested the idea to project > plane-wave basis sets onto minimal localized atomic orbital basis > sets, but this results in charge leakage where the density matrix in > the smaller basis set does not accurately represent the true density > matrix. In general, the small basis sets do not represent the density > matrix with high accuracy. Therefore, in general, I cannot recommend > the approach you mentioned. There are certainly much better approaches > if the goal is to compute net atomic charges. > > Best, > > Tom > > On Thu, Sep 10, 2015 at 2:04 PM, Stefan Grimme > grimme,,thch.uni-bonn.de [1] wrote: > >> Sent to CCL by: "Stefan  Grimme" [grimme|*|thch.uni-bonn.de [1]] >> Dear Tom, >> I followed this discussion quietly for some time but now can't >> resist to >> comment on this too extreme viewpoint: >> >> 1. Methods can be useful and reasonable without a definite >> mathematical limit. A Mulliken or Loewdin population analysis gives >> a definite result for a given well-defined AO basis set. If the set >> is small (minimal) the derived atomic charges are chemically >> reasonable and correlate well with those from other methods for well >> understood reasons. I don't want to defend orbital based >> partitionings (I prefer observables) but making the mathematical >> limit >> to the encompassing requirement seems nonsense to me. >> There are other useful and widely used QC methods like >> Moeller-Plesset >> perturbation theory which are often divergent (or at least >> convergence is >> unlcear) in large one-particle basis sets and hence also do not >> have a >> definite mathematical limit. Is this a good reason to abandon all >> MP2 >> calculations? >> >> 2. The word "observe" in our context can only mean "observable" in >> a QM >> sense. Hence, because there is no operator for "atomic charge" an >> observable atomic charge does not exist in a strict sense. You >> probably mean >> correlations of spectroscopic signatures with atomic charges when >> writing >> "They can be observed and measured through spectroscopy >> experiments". >> If you have another opinion on that I would like to know more >> details on >> how to measure atomic charges. >> >> Best wishes >> Stefan >> >>> Hi Peeter, >> >>> There is a fundamental distinction between the current >> conversation focused on exchange-correlation theories and basis sets >> and the earlier discussion focused on atomic properties. If one >> increases the basis set size, exchange-correlation functionals such >> as B3LYP, M06, or whatever one you care to use will approach a >> well-defined mathematical limit. We can then discuss what the >> relative accuracy of that mathematical limit is in comparison to >> experimental properties and also discuss how close we are to that >> mathematical limit with a particular basis set. Thus, it is >> meaningful to discuss how adequate an exchange-correlation theory or >> basis set are for a particular research problem. Of course, the goal >> is to choose an adequate level that is not too computationally >> expensive for the particular research question being studied. >> >>> In contrast, Mulliken and Lowdin population analysis schemes do >> not have any defined mathematical limits. As the basis set is >> increased and the energy and electron density approach the complete >> basis set limit, the Mulliken and Lowdin populations behave >> erratically and blow up. This is how we know for sure that Mulliken >> and Lowdin population analysis schemes are utter nonsense and should >> never be used for publication results. As pointed out by one person, >> their only purpose is for debugging calculations to see if the >> symmetry or other basic features of the input geometry are >> malformed. >> >>> It is not the earlier discussion on atomic charges that is >> "nonsense" but rather the Mulliken and Lowdin populations that are >> nonsense, because they have no defined mathematical limits. This has >> nothing to do with atomic charges, per se. The Mulliken and Lowdin >> populations do not measure anything physical. They do not measure >> atomic charges. Probably the confusion has been propagated by >> calling Mulliken and Lowdin populations as types of "atomic >> charges", but really the Mulliken and Lowdin populations cannot be >> atomic charges, because they have no defined mathematical limits. In >> the future, I shall try to avoid referring to Mulliken and Lowdin >> populations as types of atomic charges, because I think this error >> is responsible for the confusion surrounding the definition of >> atomic charges. While we may not be able to measure atomic charges >> as precisely as energies in experiments, it is not true to say >> atomic charges are not experimentally observable. They can be >> observed and m! >>  easured through spectroscopy experiments, albeit with much less >> precision than we are able to measure energies. I could go into more >> extensive details and examples if you are interested. >> >> -= This is automatically added to each message by the mailing >> script =- > > > > Links: > ------ > [1] http://thch.uni-bonn.de > [2]> [3]> [4] http://www.ccl.net > [5] http://www.ccl.net/jobs > [6] http://server.ccl.net/chemistry/announcements/conferences/ > [7] http://www.ccl.net/chemistry/searchccl/index.shtml > [8]> [9] http://www.ccl.net/chemistry/aboutccl/instructions/ -- N. SUKUMAR Professor & Head, Department of Chemistry Director, Center for Informatics Shiv Nadar University, India From owner-chemistry@ccl.net Fri Sep 11 01:10:00 2015 From: "Thomas Manz thomasamanz**gmail.com" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51706-150910235058-11179-dWTTvNmCVsFNdr8SMR68KQ##server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a114763541c1926051f709fc5 Date: Thu, 10 Sep 2015 21:50:49 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz|,|gmail.com] --001a114763541c1926051f709fc5 Content-Type: text/plain; charset=UTF-8 Stephen, 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. One of the main problems with the Mulliken and Lowdin populations is that they violate the Hohenberg-Kohn theorems, because they are not functionals of the total electron density distribution. Therefore, it is physically impossible for the Mulliken and Lowdin populations to represent a true physical property. This is why I and others have taken the position that these quantities are nonsense in the sense that it is mathematically impossible (via the Hohenberg-Kohn Theorems) for them to correspond to a physical property. Sincerely, Tom On Thu, Sep 10, 2015 at 2:04 PM, Stefan Grimme grimme,,thch.uni-bonn.de < owner-chemistry**ccl.net> wrote: > > Sent to CCL by: "Stefan Grimme" [grimme|*|thch.uni-bonn.de] > Dear Tom, > I followed this discussion quietly for some time but now can't resist to > comment on this too extreme viewpoint: > > 1. Methods can be useful and reasonable without a definite mathematical > limit. A Mulliken or Loewdin population analysis gives a definite result > for a given well-defined AO basis set. If the set is small (minimal) the > derived atomic charges are chemically reasonable and correlate well with > those from other methods for well understood reasons. I don't want to > defend orbital based partitionings (I prefer observables) but making the > mathematical limit > to the encompassing requirement seems nonsense to me. > There are other useful and widely used QC methods like Moeller-Plesset > perturbation theory which are often divergent (or at least convergence is > unlcear) in large one-particle basis sets and hence also do not have a > definite mathematical limit. Is this a good reason to abandon all MP2 > calculations? > > 2. The word "observe" in our context can only mean "observable" in a QM > sense. Hence, because there is no operator for "atomic charge" an > observable atomic charge does not exist in a strict sense. You probably > mean > correlations of spectroscopic signatures with atomic charges when writing > "They can be observed and measured through spectroscopy experiments". > If you have another opinion on that I would like to know more details on > how to measure atomic charges. > > > Best wishes > Stefan > > >Hi Peeter, > > >There is a fundamental distinction between the current conversation > focused on exchange-correlation theories and basis sets and the earlier > discussion focused on atomic properties. If one increases the basis set > size, exchange-correlation functionals such as B3LYP, M06, or whatever one > you care to use will approach a well-defined mathematical limit. We can > then discuss what the relative accuracy of that mathematical limit is in > comparison to experimental properties and also discuss how close we are to > that mathematical limit with a particular basis set. Thus, it is meaningful > to discuss how adequate an exchange-correlation theory or basis set are for > a particular research problem. Of course, the goal is to choose an adequate > level that is not too computationally expensive for the particular research > question being studied. > > >In contrast, Mulliken and Lowdin population analysis schemes do not have > any defined mathematical limits. As the basis set is increased and the > energy and electron density approach the complete basis set limit, the > Mulliken and Lowdin populations behave erratically and blow up. This is how > we know for sure that Mulliken and Lowdin population analysis schemes are > utter nonsense and should never be used for publication results. As pointed > out by one person, their only purpose is for debugging calculations to see > if the symmetry or other basic features of the input geometry are malformed. > > >It is not the earlier discussion on atomic charges that is "nonsense" but > rather the Mulliken and Lowdin populations that are nonsense, because they > have no defined mathematical limits. This has nothing to do with atomic > charges, per se. The Mulliken and Lowdin populations do not measure > anything physical. They do not measure atomic charges. Probably the > confusion has been propagated by calling Mulliken and Lowdin populations as > types of "atomic charges", but really the Mulliken and Lowdin populations > cannot be atomic charges, because they have no defined mathematical limits. > In the future, I shall try to avoid referring to Mulliken and Lowdin > populations as types of atomic charges, because I think this error is > responsible for the confusion surrounding the definition of atomic charges. > While we may not be able to measure atomic charges as precisely as energies > in experiments, it is not true to say atomic charges are not experimentally > observable. They can be observed and m! > easured through spectroscopy experiments, albeit with much less precision > than we are able to measure energies. I could go into more extensive > details and examples if you are interested.> > > --001a114763541c1926051f709fc5 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable 
Stephen,

I wanted to address one more of your comments. You wrote:  "I don'=
t want to defend orbital based partitionings (I prefer observables) but mak=
ing the mathematical limit to the encompassing requirement seem nonsense to=
 me." Actually, this has already been proved in Nobel prize winning wo=
rk. In 1998, Walter Kohn received the Nobel prize in chemistry for his deve=
lopment of density functional theory. This theory proved that all ground st=
ate properties of a non-relativistic, non-degenerate quantum chemical syste=
m can be represented as a functional of the ground state electron density d=
istribution. A direct corollary is that since net atomic charges are a prop=
erty of a chemical system, for a non-degenerate chemical ground state the n=
et atomic charges have to be a functional of the ground state electron dist=
ribution. When I and others say that the net atomic charges should approach=
 a well-defined basis set limit, because they are functionals of the electr=
on density distribution, we are simply stating a direct corollary of the Ho=
henberg-Kohn theorems. This has already been proved and received a Nobel pr=
ize.
One of the main problems with the=
 Mulliken and Lowdin populations is that they violate the Hohenberg-Kohn th=
eorems, because they are not functionals of the total electron density dist=
ribution. Therefore, it is physically impossible for the Mulliken and Lowdi=
n populations to represent a true physical property. This is why I and othe=
rs have taken the position that these quantities are nonsense in the sense =
that it is mathematically impossible (via the Hohenberg-Kohn Theorems) for =
them to correspond to a physical property.
Sincerely,

Tom

On= Thu, Sep 10, 2015 at 2:04 PM, Stefan Grimme grimme,,thch.uni-bonn.de <owner-chemistry**ccl.net><= /span> wrote:

Sent to CCL by: "Stefan=C2=A0 Grimme" [grimme|*|thch.uni-bonn.de]
Dear Tom,
I followed this discussion quietly for some time but now can't resist t= o
comment on this too extreme viewpoint:

1. Methods can be useful and reasonable without a definite mathematical lim= it. A Mulliken or Loewdin population analysis gives a definite result for a= given well-defined AO basis set. If the set is small (minimal) the derived= atomic charges are chemically reasonable and correlate well with those fro= m other methods for well understood reasons. I don't want to defend orb= ital based partitionings (I prefer observables) but making the mathematical= limit
to the encompassing requirement seems nonsense to me.
There are other useful and widely used QC methods like Moeller-Plesset
perturbation theory which are often divergent (or at least convergence is unlcear) in large one-particle basis sets and hence also do not have a
definite mathematical limit. Is this a good reason to abandon all MP2
calculations?

2. The word "observe" in our context can only mean "observab= le" in a QM
sense. Hence, because there is no operator for "atomic charge" an=
observable atomic charge does not exist in a strict sense. You probably mea= n
correlations of spectroscopic signatures with atomic charges when writing "They can be observed and measured through spectroscopy experiments&qu= ot;.
If you have another opinion on that I would like to know more details on how to measure atomic charges.


Best wishes
Stefan

>Hi Peeter,

>There is a fundamental distinction between the current conversation foc= used on exchange-correlation theories and basis sets and the earlier discus= sion focused on atomic properties. If one increases the basis set size, exc= hange-correlation functionals such as B3LYP, M06, or whatever one you care = to use will approach a well-defined mathematical limit. We can then discuss= what the relative accuracy of that mathematical limit is in comparison to = experimental properties and also discuss how close we are to that mathemati= cal limit with a particular basis set. Thus, it is meaningful to discuss ho= w adequate an exchange-correlation theory or basis set are for a particular= research problem. Of course, the goal is to choose an adequate level that = is not too computationally expensive for the particular research question b= eing studied.

>In contrast, Mulliken and Lowdin population analysis schemes do not hav= e any defined mathematical limits. As the basis set is increased and the en= ergy and electron density approach the complete basis set limit, the Mullik= en and Lowdin populations behave erratically and blow up. This is how we kn= ow for sure that Mulliken and Lowdin population analysis schemes are utter = nonsense and should never be used for publication results. As pointed out b= y one person, their only purpose is for debugging calculations to see if th= e symmetry or other basic features of the input geometry are malformed.

>It is not the earlier discussion on atomic charges that is "= ;nonsense" but rather the Mulliken and Lowdin populations that are non= sense, because they have no defined mathematical limits. This has nothing t= o do with atomic charges, per se. The Mulliken and Lowdin populations do no= t measure anything physical. They do not measure atomic charges. Probably t= he confusion has been propagated by calling Mulliken and Lowdin populations= as types of "atomic charges", but really the Mulliken and Lowdin= populations cannot be atomic charges, because they have no defined mathema= tical limits. In the future, I shall try to avoid referring to Mulliken and= Lowdin populations as types of atomic charges, because I think this error = is responsible for the confusion surrounding the definition of atomic charg= es. While we may not be able to measure atomic charges as precisely as ener= gies in experiments, it is not true to say atomic charges are not experimen= tally observable. They can be observed and m!
=C2=A0easured through spectroscopy experiments, albeit wit= h much less precision than we are able to measure energies. I could go into= more extensive details and examples if you are interested.



-=3D This is automatically added to each message by= the mailing script =3D-
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--001a114763541c1926051f709fc5-- From owner-chemistry@ccl.net Fri Sep 11 03:57:00 2015 From: "Peter Jarowski peterjarowski{:}gmail.com" To: CCL Subject: CCL:G: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51707-150911035615-14294-D0CHp55iRhu+KC01Y8W4Kg^^server.ccl.net> X-Original-From: Peter Jarowski Content-Type: multipart/alternative; boundary=001a113ac3426f7406051f740c3a Date: Fri, 11 Sep 2015 09:56:08 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Jarowski [peterjarowski[-]gmail.com] --001a113ac3426f7406051f740c3a Content-Type: text/plain; charset=UTF-8 Hi All: Can I ask that the population discussion be moved to a new thread. Very interesting but much more theoretical than the original question. Thanks. Peter On Friday, September 11, 2015, N. Sukumar nagams^rpi.edu < owner-chemistry**ccl.net> wrote: > > Sent to CCL by: "N. Sukumar" [nagams]![rpi.edu] > Since this list includes a large number of non-specialists, one should be > careful to avoid making sweeping statements like "While we may not be able > to measure atomic charges as precisely as energies in experiments, it is > not true to say atomic charges are not experimentally observable. They can > be observed and measured through spectroscopy experiments, albeit with much > less precision than we are able to measure energies." > > "Atomic charges" are about as measurable as the divinity of an orbital! > Both are entirely theoretical properties of theoretical objects. I joint > Stefan in asking how to "measure atomic charges" - and before that please > also clarify what you mean by "atomic." > > -- > N. SUKUMAR > Professor & Head, Department of Chemistry > Director, Center for Informatics > Shiv Nadar University, India > > On 2015-09-11 05:32, Thomas Manz thomasamanz-*-gmail.com wrote: > >> Hi Stefan, >> >> In regards to your questions about MP2, one has to be extremely >> careful with such an approach, because the denominator is of the form >> (energy_1 - energy_2) which causes the denominator to become zero when >> energy_1 = energy_2. This can cause perturbation methods to blow up. >> For this reason, I generally prefer non-perturbative methods such as >> CCSD, when a higher-level calculation result is needed. I would >> recommend CCSD as opposed to MP2, simply because CCSD has a more >> well-defined mathematical limit on the results of the calculation. >> Personally, I don't use MP2 calculations for this reason, but this >> doesn't necessarily mean others can't. However, I wouldn't go so far >> as to say that MP2 calculations don't have a well-defined basis set >> limit. I believe that for most systems the complete basis set limit >> would be well-defined for MP2 calculations. In this sense, the MP2 >> calculations are much more well-defined than Mulliken or Lowdin >> populations, which definitely do not have a basis set limit. >> >> If the set is small (minimal) the derived atomic charges are >>> >> chemically reasonable and correlate well with those from other methods >> for well understood reasons. >> >> The populations of the density matrix projected onto a smaller basis >> set is usually referred to by a different name. At least in Gaussian >> programs, it is called Pop=MBS. In Gaussian programs, this is a >> different algorithm than Pop=Regular which performs Mulliken analysis >> in the current basis set. In my experience, the Pop=MBS method is not >> very useful and tends to crash a large percentage of the time. It >> seems to crash especially often for heavier atoms and for those with >> pseudopotentials. Also, people have tested the idea to project >> plane-wave basis sets onto minimal localized atomic orbital basis >> sets, but this results in charge leakage where the density matrix in >> the smaller basis set does not accurately represent the true density >> matrix. In general, the small basis sets do not represent the density >> matrix with high accuracy. Therefore, in general, I cannot recommend >> the approach you mentioned. There are certainly much better approaches >> if the goal is to compute net atomic charges. >> >> Best, >> >> Tom >> >> On Thu, Sep 10, 2015 at 2:04 PM, Stefan Grimme >> grimme,,thch.uni-bonn.de [1] wrote: >> >> Sent to CCL by: "Stefan Grimme" [grimme|*|thch.uni-bonn.de [1]] >>> Dear Tom, >>> I followed this discussion quietly for some time but now can't >>> resist to >>> comment on this too extreme viewpoint: >>> >>> 1. Methods can be useful and reasonable without a definite >>> mathematical limit. A Mulliken or Loewdin population analysis gives >>> a definite result for a given well-defined AO basis set. If the set >>> is small (minimal) the derived atomic charges are chemically >>> reasonable and correlate well with those from other methods for well >>> understood reasons. I don't want to defend orbital based >>> partitionings (I prefer observables) but making the mathematical >>> limit >>> to the encompassing requirement seems nonsense to me. >>> There are other useful and widely used QC methods like >>> Moeller-Plesset >>> perturbation theory which are often divergent (or at least >>> convergence is >>> unlcear) in large one-particle basis sets and hence also do not >>> have a >>> definite mathematical limit. Is this a good reason to abandon all >>> MP2 >>> calculations? >>> >>> 2. The word "observe" in our context can only mean "observable" in >>> a QM >>> sense. Hence, because there is no operator for "atomic charge" an >>> observable atomic charge does not exist in a strict sense. You >>> probably mean >>> correlations of spectroscopic signatures with atomic charges when >>> writing >>> "They can be observed and measured through spectroscopy >>> experiments". >>> If you have another opinion on that I would like to know more >>> details on >>> how to measure atomic charges. >>> >>> Best wishes >>> Stefan >>> >>> Hi Peeter, >>>> >>> >>> There is a fundamental distinction between the current >>>> >>> conversation focused on exchange-correlation theories and basis sets >>> and the earlier discussion focused on atomic properties. If one >>> increases the basis set size, exchange-correlation functionals such >>> as B3LYP, M06, or whatever one you care to use will approach a >>> well-defined mathematical limit. We can then discuss what the >>> relative accuracy of that mathematical limit is in comparison to >>> experimental properties and also discuss how close we are to that >>> mathematical limit with a particular basis set. Thus, it is >>> meaningful to discuss how adequate an exchange-correlation theory or >>> basis set are for a particular research problem. Of course, the goal >>> is to choose an adequate level that is not too computationally >>> expensive for the particular research question being studied. >>> >>> In contrast, Mulliken and Lowdin population analysis schemes do >>>> >>> not have any defined mathematical limits. As the basis set is >>> increased and the energy and electron density approach the complete >>> basis set limit, the Mulliken and Lowdin populations behave >>> erratically and blow up. This is how we know for sure that Mulliken >>> and Lowdin population analysis schemes are utter nonsense and should >>> never be used for publication results. As pointed out by one person, >>> their only purpose is for debugging calculations to see if the >>> symmetry or other basic features of the input geometry are >>> malformed. >>> >>> It is not the earlier discussion on atomic charges that is >>>> >>> "nonsense" but rather the Mulliken and Lowdin populations that are >>> nonsense, because they have no defined mathematical limits. This has >>> nothing to do with atomic charges, per se. The Mulliken and Lowdin >>> populations do not measure anything physical. They do not measure >>> atomic charges. Probably the confusion has been propagated by >>> calling Mulliken and Lowdin populations as types of "atomic >>> charges", but really the Mulliken and Lowdin populations cannot be >>> atomic charges, because they have no defined mathematical limits. In >>> the future, I shall try to avoid referring to Mulliken and Lowdin >>> populations as types of atomic charges, because I think this error >>> is responsible for the confusion surrounding the definition of >>> atomic charges. While we may not be able to measure atomic charges >>> as precisely as energies in experiments, it is not true to say >>> atomic charges are not experimentally observable. They can be >>> observed and m! >>> easured through spectroscopy experiments, albeit with much less >>> precision than we are able to measure energies. I could go into more >>> extensive details and examples if you are interested. >>> >>> -= This is automatically added to each message by the mailing >>> script =- >>> >> >> >> >> Links: >> ------ >> [1] http://thch.uni-bonn.de >> [2]> [3]> [4] http://www.ccl.net >> [5] http://www.ccl.net/jobs >> [6] http://server.ccl.net/chemistry/announcements/conferences/ >> [7] http://www.ccl.net/chemistry/searchccl/index.shtml >> [8]> [9] http://www.ccl.net/chemistry/aboutccl/instructions/ >> > > -- > N. SUKUMAR > Professor & Head, Department of Chemistry > Director, Center for Informatics > Shiv Nadar University, Indiahttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --001a113ac3426f7406051f740c3a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi All:=C2=A0

Can I ask that the population discussion b= e moved to a new thread. Very interesting but much more theoretical than th= e original question.

Thanks.

<= div>Peter

On Friday, September 11, 2015, N. Sukumar nagams^rpi.edu <owner-chemistry**ccl.net> wrote:
rpi.edu]
Since this list includes a large number of non-specialists, one should be c= areful to avoid making sweeping statements like "While we may not be a= ble to measure atomic charges as precisely as energies in experiments, it i= s not true to say atomic charges are not experimentally observable. They ca= n be observed and measured through spectroscopy experiments, albeit with mu= ch less precision than we are able to measure energies."

"Atomic charges" are about as measurable as the divinity of an or= bital! Both are entirely theoretical properties of theoretical objects. I j= oint Stefan in asking how to "measure atomic charges" - and befor= e that please also clarify what you mean by "atomic."

--
N. SUKUMAR
Professor & Head, Department of Chemistry
Director, Center for Informatics
Shiv Nadar University, India

On 2015-09-11 05:32, Thomas Manz thomasamanz-*-gmail.com wrote:
Hi Stefan,

In regards to your questions about MP2, one has to be extremely
careful with such an approach, because the denominator is of the form
(energy_1 - energy_2) which causes the denominator to become zero when
energy_1 =3D energy_2. This can cause perturbation methods to blow up.
For this reason, I generally prefer non-perturbative methods such as
CCSD, when a higher-level calculation result is needed. I would
recommend CCSD as opposed to MP2, simply because CCSD has a more
well-defined mathematical limit on the results of the calculation.
Personally, I don't use MP2 calculations for this reason, but this
doesn't necessarily mean others can't. However, I wouldn't go s= o far
as to say that MP2 calculations don't have a well-defined basis set
limit. I believe that for most systems the complete basis set limit
would be well-defined for MP2 calculations. In this sense, the MP2
calculations are much more well-defined than Mulliken or Lowdin
populations, which definitely do not have a basis set limit.

If the set is small (minimal) the derived atomic charges are
chemically reasonable and correlate well with those from other methods
for well understood reasons.

The populations of the density matrix projected onto a smaller basis
set is usually referred to by a different name. At least in Gaussian
programs, it is called Pop=3DMBS. In Gaussian programs, this is a
different algorithm than Pop=3DRegular which performs Mulliken analysis
in the current basis set. In my experience, the Pop=3DMBS method is not
very useful and tends to crash a large percentage of the time. It
seems to crash especially often for heavier atoms and for those with
pseudopotentials. Also, people have tested the idea to project
plane-wave basis sets onto minimal localized atomic orbital basis
sets, but this results in charge leakage where the density matrix in
the smaller basis set does not accurately represent the true density
matrix. In general, the small basis sets do not represent the density
matrix with high accuracy. Therefore, in general, I cannot recommend
the approach you mentioned. There are certainly much better approaches
if the goal is to compute net atomic charges.

Best,

Tom

On Thu, Sep 10, 2015 at 2:04 PM, Stefan Grimme
grimme,,thch.uni-bonn= .de [1] <owner-chemistry]~[ccl.net> wrote:

Sent to CCL by: "Stefan=C2=A0 Grimme" [grimme|*|thch.uni-bonn.de [1]]
Dear Tom,
I followed this discussion quietly for some time but now can't
resist to
comment on this too extreme viewpoint:

1. Methods can be useful and reasonable without a definite
mathematical limit. A Mulliken or Loewdin population analysis gives
a definite result for a given well-defined AO basis set. If the set
is small (minimal) the derived atomic charges are chemically
reasonable and correlate well with those from other methods for well
understood reasons. I don't want to defend orbital based
partitionings (I prefer observables) but making the mathematical
limit
to the encompassing requirement seems nonsense to me.
There are other useful and widely used QC methods like
Moeller-Plesset
perturbation theory which are often divergent (or at least
convergence is
unlcear) in large one-particle basis sets and hence also do not
have a
definite mathematical limit. Is this a good reason to abandon all
MP2
calculations?

2. The word "observe" in our context can only mean "observab= le" in
a QM
sense. Hence, because there is no operator for "atomic charge" an=
observable atomic charge does not exist in a strict sense. You
probably mean
correlations of spectroscopic signatures with atomic charges when
writing
"They can be observed and measured through spectroscopy
experiments".
If you have another opinion on that I would like to know more
details on
how to measure atomic charges.

Best wishes
Stefan

Hi Peeter,

There is a fundamental distinction between the current
conversation focused on exchange-correlation theories and basis sets
and the earlier discussion focused on atomic properties. If one
increases the basis set size, exchange-correlation functionals such
as B3LYP, M06, or whatever one you care to use will approach a
well-defined mathematical limit. We can then discuss what the
relative accuracy of that mathematical limit is in comparison to
experimental properties and also discuss how close we are to that
mathematical limit with a particular basis set. Thus, it is
meaningful to discuss how adequate an exchange-correlation theory or
basis set are for a particular research problem. Of course, the goal
is to choose an adequate level that is not too computationally
expensive for the particular research question being studied.

In contrast, Mulliken and Lowdin population analysis schemes do
not have any defined mathematical limits. As the basis set is
increased and the energy and electron density approach the complete
basis set limit, the Mulliken and Lowdin populations behave
erratically and blow up. This is how we know for sure that Mulliken
and Lowdin population analysis schemes are utter nonsense and should
never be used for publication results. As pointed out by one person,
their only purpose is for debugging calculations to see if the
symmetry or other basic features of the input geometry are
malformed.

It is not the earlier discussion on atomic charges that is
"nonsense" but rather the Mulliken and Lowdin populations that ar= e
nonsense, because they have no defined mathematical limits. This has
nothing to do with atomic charges, per se. The Mulliken and Lowdin
populations do not measure anything physical. They do not measure
atomic charges. Probably the confusion has been propagated by
calling Mulliken and Lowdin populations as types of "atomic
charges", but really the Mulliken and Lowdin populations cannot be
atomic charges, because they have no defined mathematical limits. In
the future, I shall try to avoid referring to Mulliken and Lowdin
populations as types of atomic charges, because I think this error
is responsible for the confusion surrounding the definition of
atomic charges. While we may not be able to measure atomic charges
as precisely as energies in experiments, it is not true to say
atomic charges are not experimentally observable. They can be
observed and m!
=C2=A0easured through spectroscopy experiments, albeit with much less
precision than we are able to measure energies. I could go into more
extensive details and examples if you are interested.

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



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--001a113ac3426f7406051f740c3a-- From owner-chemistry@ccl.net Fri Sep 11 04:32:01 2015 From: "Jean-Pierre DJUKIC djukic__unistra.fr" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51708-150911040809-18901-j6cwM3Xrki6uLi9AYzjLEA],[server.ccl.net> X-Original-From: Jean-Pierre DJUKIC Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Fri, 11 Sep 2015 10:08:06 +0200 MIME-Version: 1.0 Sent to CCL by: Jean-Pierre DJUKIC [djukic^_^unistra.fr] Tom is right. I wonder how this very example that Tom quotes would be treated with modern DFT methods. The rotational barrier of Cr(CO)3 is in benzene[Cr(CO)3] around 1 kcal/mol. In substitued systems, say anilineCr(CO)3 it rises a bit for various reasons, but not that much and nonetheless there exist rotamers of very close energy the statistical weight of which is thought to be different for each rotamer. This statistical distribution is indeed temperature dependent, it explains why a nucleophile will prefer attacking at the meta position relative to some nucleofuge and not ortho like intuition could suggest at a first glance under "some" conditions. We are talking about kinetic discrimination of states close in energy. The same stands for enantioselective processes where the differences of TS energies may challenge common accuracy in DFT, then add solvation issues ... and the fact that in reality molecules are animated and flexible indeed and not static like we generally see them in most published studies. Le 10/09/2015 18:58, Tom Albright talbright1234-$-gmail.com a écrit : > Furthermore the orientation of the Cr(CO)3 group directs attack by > nucleophiles on the arene. All this at the (almost, but I am sure in > your mind, totally) unreliable EHT level. The energy differences are > small but one can formulate a coherent explanation of the > regioselectivity. This is useful. -- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr Jean-Pierre DJUKIC (Đukić)(DR CNRS) Laboratoire de Chimie et Systémique OrganoMétalliques (LCSOM) http://lcsom.u-strasbg.fr Adresse postale: LCSOM, Institut de Chimie de Strasbourg UMR 7177 CNRS / Université de Strasbourg 4, rue Blaise Pascal 67000 Strasbourg Cedex. me joindre: Institut Le bel, aile nord, 9ème étage, pièce 942b, tel: +33 (0)368851523 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Conseil Scientifique de l'Institut de Chimie du CNRS http://www.cnrs.fr/comitenational/csi/inc.htm ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-chemistry@ccl.net Fri Sep 11 07:06:01 2015 From: "Peter Jarowski peterjarowski^_^gmail.com" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51709-150911014322-15289-dzJt3c2fwOsfLWm6SuBJdw:_:server.ccl.net> X-Original-From: Peter Jarowski Content-Type: multipart/alternative; boundary=001a113ac3422ccca5051f723153 Date: Fri, 11 Sep 2015 07:43:15 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Jarowski [peterjarowski ~~ gmail.com] --001a113ac3422ccca5051f723153 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hello: Thanks for the post. I see your logic, especially if you are considering a range of different reagents for example. However, what if you are trying to optimize a given reaction. I have found, despite error, elementary steps in a mechanism are readily comparable in terms of barrier. Any examples of fine tuning equilibrium or selectivity for different products simply by changing environmental conditions? What about small perturbations in structure, that should be fairly consistent? Obviously we are dealing with needed sub kcal accuracy in TS energy with a bit more flexibility in intermediate relative energies. Either way, if this is important we can use a compound CBS method etc. to get the needed accuracy, no? Best, Peter On Fri, Sep 11, 2015 at 3:46 AM, Andreas Klamt klamt*|*cosmologic.de < owner-chemistry(-)ccl.net> wrote: > > Sent to CCL by: Andreas Klamt [klamt,cosmologic.de] > Hi all, > > now let me put my 5 cents into the discussion, having spent 12 years as > computational chemist at Bayer, finally as head of the group, an being > in close contact with many comp. chem. group in industry all over the > world since more than 25 years now: > > I consider it as one of the greatest successes and values of > computational chemistry in industry to rule out the impossible and leave > a smaller set of potentially doable alternatives. We can rarely decide > whether a reaction will really be feasible, because our error bars are > much too large for that. But we can often decide that a reaction will be > impossible in the proposed way, because the barrier is much to high, > even taking into account the computational uncertainties. And such a > decision can save a lot of time and money in industry. But such success > will not be published or communicated as big successes, because the > colleague who came to you with the question, will not be enthusiastic if > you post the fact, that he came with an idea to you that turned out to > be completely unrealistic. > > Therefore industrial success cases often are of the kind: Within a set > of alternatives, find those which we should try in the lab and rule out > those which are clearly impossible, e.g. suggest a ranked list of > solvents for a certain reaction or separation, so that the > experimentalist can focus on the top 20 or so. If you are lucky, there > may be an unexpected candidate under the top 20, and the experimentalist > then test it and finds it as very good. That would be considered as a > success case. But most often you are just narrowing the choices for the > experimentalist. If the colleague is fair he will admit that this was > helpful. Or he may say that he new those candidates upfront. > > Andreas > > > Am 10.09.2015 um 15:50 schrieb Jerome Kieffer > Jerome.Kieffer....terre-adelie.org: > > > > Sent to CCL by: Jerome Kieffer [Jerome.Kieffer*o*terre-adelie.org] > > On Thu, 10 Sep 2015 07:26:41 +0100 > > "Peter Jarowski peterjarowski=3D=3D=3Dgmail.com" > wrote: > > > >> I ask a simple question and further ask everyone to pretend they are a= t > an > >> interview outside of an academic environment where you will find willi= ng > >> and interested parties who enjoy the alphabet soup of DFT. what exampl= e > and > >> what statistics would you present to justify your work. Clearly, you a= re > >> talking to experimentalists, as theory does not exist without them. > >> > >> How does theory drive experiment? > >> How much money does it save? > >> How much revenue can it produce? > >> How reliable is it? > >> How essential is it and what can it do that experiment can not? > > > > Hi all, > > > > I had the opportunity to do computational chemistry as part of a > > (large) industrial group, a decade ago. > > Such questions were often asked and it was not easy to be honest. > > > > When speaking of reactivity, everything is about the energy barrier > > between two (or more) path which leads to different products. > > Some critical steps may be mono, the other bi-molecular, so it is > > harder to compare them... > > Then comes the enthalpic and entropic contribution, not speaking about > > solvatation for spices that do not exist per-se as they are transition > > states. > > > > I left this job a while ago and I have to admit the "correctness" of > > most result I obtained at that time were mainly "lucky error > cancelation": > > Concidering : > > A --> B > > A --> C > > in kinetic condition, let AB and AC be the transition states: > > [C]/[B] =3D exp(-(G[AC*]-G[AB*])/RT) > > > > The error in the exponential is 2x the error in calculating the free > > energy of one TS, one ends with a huge error bars which is anything but > > conclusive at that time (one error was about 6kcal/mol ... while with > > ony 1kcal/mol error, no conclusion was possible) . > > > > Cheers, > > > > > -- > -------------------------------------------------- > > Prof. Dr. Andreas Klamt > CEO / Gesch=C3=A4ftsf=C3=BChrer > 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 > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a113ac3422ccca5051f723153 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello:

Thanks for the post. I = see your logic, especially if you are considering a range of different reag= ents for example. However, what if you are trying to optimize a given react= ion. I have found, despite error, elementary steps in a mechanism are readi= ly comparable in terms of barrier. Any examples of fine tuning equilibrium = or selectivity for different products simply by changing environmental cond= itions? What about small perturbations in structure, that should be fairly = consistent? Obviously we are dealing with needed sub kcal accuracy in TS en= ergy with a bit more flexibility in intermediate relative energies. Either = way, if this is important we can use a compound CBS method etc. to get the = needed accuracy, no?

Best,

Peter

On Fri, Sep 11, 2015 at = 3:46 AM, Andreas Klamt klamt*|*cosmologic.= de <owner-chemistry(-)ccl.net> wrote:

Sent to CCL by: Andreas Klamt [klamt,cosmologic.de]
Hi all,

now let me put my 5 cents into the discussion, having spent 12 years as
computational chemist at Bayer, finally as head of the group, an being
in close contact with many comp. chem. group in industry all over the
world since more than 25 years now:

I consider it as one of the greatest successes and values of
computational chemistry in industry to rule out the impossible and leave a smaller set of potentially doable alternatives. We can rarely decide
whether a reaction will really be feasible, because our error bars are
much too large for that. But we can often decide that a reaction will be impossible in the proposed way, because the barrier is much to high,
even taking into account the computational uncertainties. And such a
decision can save a lot of time and money in industry. But such success
will not be published or communicated as big successes, because the
colleague who came to you with the question, will not be enthusiastic if you post the fact, that he came with an idea to you that turned out to
be completely unrealistic.

Therefore industrial success cases often are of the kind: Within a set
of alternatives, find those which we should try in the lab and rule out
those which are clearly impossible, e.g. suggest a ranked list of
solvents for a certain reaction or separation, so that the
experimentalist can focus on the top 20 or so. If you are lucky, there
may be an unexpected candidate under the top 20, and the experimentalist then test it and finds it as very good. That would be considered as a
success case. But most often you are just narrowing the choices for the
experimentalist. If the colleague is fair he will admit that this was
helpful. Or he may say that he new those candidates upfront.

Andreas


Am 10.09.2015 um 15:50 schrieb Jerome Kieffer
Jerome.Kieffer....terre-adelie.org:
>
> Sent to CCL by: Jerome Kieffer [Jerome.Kieffer*o*terre-adelie.org] > On Thu, 10 Sep 2015 07:26:41 +0100
> "Peter Jarowski peterjarowski=3D=3D=3Dgmail.com" <owner-chemis= try~!~ccl.n= et> wrote:
>
>> I ask a simple question and further ask everyone to pretend they a= re at an
>> interview outside of an academic environment where you will find w= illing
>> and interested parties who enjoy the alphabet soup of DFT. what ex= ample and
>> what statistics would you present to justify your work. Clearly, y= ou are
>> talking to experimentalists, as theory does not exist without them= .
>>
>> How does theory drive experiment?
>> How much money does it save?
>> How much revenue can it produce?
>> How reliable is it?
>> How essential is it and what can it do that experiment can not? >
> Hi all,
>
> I had the opportunity to do computational chemistry as part of a
> (large) industrial group, a decade ago.
> Such questions were often asked and it was not easy to be honest.
>
> When speaking of reactivity, everything is about the energy barrier > between two (or more) path which leads to different products.
> Some critical steps may be mono, the other bi-molecular, so it is
> harder to compare them...
> Then comes the enthalpic and entropic contribution, not speaking about=
> solvatation for spices that do not exist per-se as they are transition=
> states.
>
> I left this job a while ago and I have to admit the "correctness&= quot; of
> most result I obtained at that time were mainly "lucky error canc= elation":
> Concidering :
> A --> B
> A --> C
> in kinetic condition, let AB and AC be the transition states:
> [C]/[B] =3D exp(-(G[AC*]-G[AB*])/RT)
>
> The error in the exponential is 2x the error in calculating the free > energy of one TS, one ends with a huge error bars which is anything bu= t
> conclusive at that time (one error was about 6kcal/mol ... while with<= br> > ony 1kcal/mol error, no conclusion was possible) .
>
> Cheers,
>


--
--------------------------------------------------

Prof. Dr. Andreas Klamt
CEO / Gesch=C3=A4ftsf=C3=BChrer
COSMOlogic GmbH & Co. KG
Imbacher Weg 46
D-51379 Leverkusen, Germany

phone=C2=A0 =C2=A0+49-2171-731681
fax=C2=A0 =C2=A0 =C2=A0+49-2171-731689
e-mail=C2=A0 klamt..cosmologic.de
web=C2=A0 =C2=A0 =C2=A0www.cosmologic.de

[University address:=C2=A0 =C2=A0 =C2=A0 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



-=3D This is automatically added to each message by the mailing script =3D-=
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--001a113ac3422ccca5051f723153-- From owner-chemistry@ccl.net Fri Sep 11 07:41:01 2015 From: "mann........... navu1989mann++gmail.com" To: CCL Subject: CCL:G: regarding bpw91 funtional Message-Id: <-51710-150911032920-11435-LX5aV4xwimDbvA+RIKWjJQ()server.ccl.net> X-Original-From: "mann..........." Content-Type: multipart/alternative; boundary=001a1141236042ef80051f73ac8b Date: Fri, 11 Sep 2015 12:59:15 +0530 MIME-Version: 1.0 Sent to CCL by: "mann..........." [navu1989mann],[gmail.com] --001a1141236042ef80051f73ac8b Content-Type: text/plain; charset=UTF-8 Respected sir, I am using gaussian 03 and getting problem in optimizing oxygen atom by using dft/bpw91/d95v level of theory. As bpw91 funtional is not present as default in gaussian 03. d95v basis set can be put as additional keyword but i am not getting how to give input for additional funtional . kindly help my in solving this problem. i will be highly oblized. With Regards Navjot kaur Research Scholar Panjab university Chandigarh --001a1141236042ef80051f73ac8b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Respected sir,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0I am using gaussian 03 and getting problem i= n optimizing oxygen atom by using dft/bpw91/d95v level of theory. As bpw91 = funtional is not present as default in gaussian 03. =C2=A0d95v basis set ca= n be put as additional keyword but i am not getting how to give input for a= dditional funtional . kindly help my in =C2=A0solving this problem. =C2=A0i= will be highly oblized.
=C2=A0
With Regards
= Navjot kaur
=C2=A0Research Scholar
Panjab university
Chandigarh

--001a1141236042ef80051f73ac8b-- From owner-chemistry@ccl.net Fri Sep 11 08:16:01 2015 From: "Stefan Grimme grimme*|*thch.uni-bonn.de" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51711-150911045433-16888-pSW5TVuO/oW7WPUf2+M8+Q*|*server.ccl.net> X-Original-From: "Stefan Grimme" Date: Fri, 11 Sep 2015 04:54:31 -0400 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 From owner-chemistry@ccl.net Fri Sep 11 08:51:01 2015 From: "Robert Molt r.molt.chemical.physics-*-gmail.com" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51712-150911062515-25169-EFcMnbdllmmg9CbWVzhLCA-*-server.ccl.net> X-Original-From: Robert Molt Content-Type: multipart/alternative; boundary="------------090100050507070404010602" Date: Fri, 11 Sep 2015 06:25:07 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics#,#gmail.com] This is a multi-part message in MIME format. --------------090100050507070404010602 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable Dr. Manz: Your comment is a very incorrect characterization of the 1998 Nobel Prize= =2E a.) You're addressing Stephen Grimme, a leader of DFT in computational=20 chemistry in the world; trust me, he is well aware of DFT. This is like=20 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=20 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.=20 Wavefunction people defined and were using the electron density of=20 chemical systems LONG before there was a DFT; just read Szabo and=20 Ostlund. Rather, DFT is a statement about being able to calculate the=20 energy as a function of density directly practically, with no=20 calculation of the wavefunction necessary (there is more to it than=20 this, but as a bird's eye-view statement). c.) Your statement has a huge assumption in it that is in no way=20 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=20 charges, that's the point of another thread. The TOTAL charge of a=20 system is well-defined, but defining the charge of an arbitrary=20 subsystem is not always possible. There are many reasons you cannot do=20 this rigorously. One is that you are trying to represent a function of 3 = variables (the density, a real observable) by ONE number (the "atomic=20 charge"); this is impossible. The change in the density, spatially, at=20 different points on a 3D grid (let alone the fact we have spin!) cannot=20 be represent by one number. Atomic charges, as a computational model, 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). On 9/10/15 11:50 PM, Thomas Manz thomasamanz**gmail.com wrote: > Stephen, > > I wanted to address one more of your comments. You wrote: "I don't wan= t 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 develo= pment of density functional theory. This theory proved that all ground st= ate properties of a non-relativistic, non-degenerate quantum chemical sys= tem can be represented as a functional of the ground state electron densi= ty distribution. A direct corollary is that since net atomic charges are = a property of a chemical system, for a non-degenerate chemical ground sta= te the net atomic charges have to be a functional of the ground state ele= ctron distribution. When I and others say that the net atomic charges sho= uld approach a well-defined basis set limit, because they are functionals= of the electron density distribution, we are simply stating a direct cor= ollary of the Hohenberg-Kohn theorems. This has already been proved and r= eceived a Nobel prize. > One of the main problems with the Mulliken and Lowdin populations is th= at they violate the Hohenberg-Kohn theorems, because they are not functio= nals of the total electron density distribution. Therefore, it is physica= lly impossible for the Mulliken and Lowdin populations to represent a tru= e physical property. This is why I and others have taken the position tha= t these quantities are nonsense in the sense that it is mathematically im= possible (via the Hohenberg-Kohn Theorems) for them to correspond to a ph= ysical property. > Sincerely, > > Tom > > On Thu, Sep 10, 2015 at 2:04 PM, Stefan Grimme=20 > grimme,,thch.uni-bonn.de =20 > > wrote: > > > Sent to CCL by: "Stefan Grimme" [grimme|*|thch.uni-bonn.de > ] > Dear Tom, > I followed this discussion quietly for some time but now can't > resist to > comment on this too extreme viewpoint: > > 1. Methods can be useful and reasonable without a definite > mathematical limit. A Mulliken or Loewdin population analysis > gives a definite result for a given well-defined AO basis set. If > the set is small (minimal) the derived atomic charges are > chemically reasonable and correlate well with those from other > methods for well understood reasons. I don't want to defend > orbital based partitionings (I prefer observables) but making the > mathematical limit > to the encompassing requirement seems nonsense to me. > There are other useful and widely used QC methods like Moeller-Ples= set > perturbation theory which are often divergent (or at least > convergence is > unlcear) in large one-particle basis sets and hence also do not hav= e a > definite mathematical limit. Is this a good reason to abandon all M= P2 > calculations? > > 2. The word "observe" in our context can only mean "observable" in > a QM > sense. Hence, because there is no operator for "atomic charge" an > observable atomic charge does not exist in a strict sense. You > probably mean > correlations of spectroscopic signatures with atomic charges when > writing > "They can be observed and measured through spectroscopy experiments= ". > If you have another opinion on that I would like to know more > details on > how to measure atomic charges. > > > Best wishes > Stefan > > >Hi Peeter, > > >There is a fundamental distinction between the current > conversation focused on exchange-correlation theories and basis > sets and the earlier discussion focused on atomic properties. If > one increases the basis set size, exchange-correlation functionals > such as B3LYP, M06, or whatever one you care to use will approach > a well-defined mathematical limit. We can then discuss what the > relative accuracy of that mathematical limit is in comparison to > experimental properties and also discuss how close we are to that > mathematical limit with a particular basis set. Thus, it is > meaningful to discuss how adequate an exchange-correlation theory > or basis set are for a particular research problem. Of course, the > goal is to choose an adequate level that is not too > computationally expensive for the particular research question > being studied. > > >In contrast, Mulliken and Lowdin population analysis schemes do > not have any defined mathematical limits. As the basis set is > increased and the energy and electron density approach the > complete basis set limit, the Mulliken and Lowdin populations > behave erratically and blow up. This is how we know for sure that > Mulliken and Lowdin population analysis schemes are utter nonsense > and should never be used for publication results. As pointed out > by one person, their only purpose is for debugging calculations to > see if the symmetry or other basic features of the input geometry > are malformed. > > >It is not the earlier discussion on atomic charges that is > "nonsense" but rather the Mulliken and Lowdin populations that are > nonsense, because they have no defined mathematical limits. This > has nothing to do with atomic charges, per se. The Mulliken and > Lowdin populations do not measure anything physical. They do not > measure atomic charges. Probably the confusion has been propagated > by calling Mulliken and Lowdin populations as types of "atomic > charges", but really the Mulliken and Lowdin populations cannot be > atomic charges, because they have no defined mathematical limits. > In the future, I shall try to avoid referring to Mulliken and > Lowdin populations as types of atomic charges, because I think > this error is responsible for the confusion surrounding the > definition of atomic charges. While we may not be able to measure > atomic charges as precisely as energies in experiments, it is not > true to say atomic charges are not experimentally observable. They > can be observed and m! > easured through spectroscopy experiments, albeit with much less > precision than we are able to measure energies. I could go into > more extensive details and examples if you are interested. > > > > -=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/=> > > --=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 --------------090100050507070404010602 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit 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 LONG 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 density 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. 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 points on a 3D grid (let 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).

On 9/10/15 11:50 PM, Thomas Manz thomasamanz**gmail.com wrote:
Stephen,

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.
One of the main problems with the Mulliken and Lowdin populations is that they violate the Hohenberg-Kohn theorems, because they are not functionals of the total electron density distribution. Therefore, it is physically impossible for the Mulliken and Lowdin populations to represent a true physical property. This is why I and others have taken the position that these quantities are nonsense in the sense that it is mathematically impossible (via the Hohenberg-Kohn Theorems) for them to correspond to a physical property.
Sincerely,

Tom

On Thu, Sep 10, 2015 at 2:04 PM, Stefan Grimme grimme,,thch.uni-bonn.de <owner-chemistry,+,ccl.net> wrote:

Sent to CCL by: "Stefan  Grimme" [grimme|*|thch.uni-bonn.de]
Dear Tom,
I followed this discussion quietly for some time but now can't resist to
comment on this too extreme viewpoint:

1. Methods can be useful and reasonable without a definite mathematical limit. A Mulliken or Loewdin population analysis gives a definite result for a given well-defined AO basis set. If the set is small (minimal) the derived atomic charges are chemically reasonable and correlate well with those from other methods for well understood reasons. I don't want to defend orbital based partitionings (I prefer observables) but making the mathematical limit
to the encompassing requirement seems nonsense to me.
There are other useful and widely used QC methods like Moeller-Plesset
perturbation theory which are often divergent (or at least convergence is
unlcear) in large one-particle basis sets and hence also do not have a
definite mathematical limit. Is this a good reason to abandon all MP2
calculations?

2. The word "observe" in our context can only mean "observable" in a QM
sense. Hence, because there is no operator for "atomic charge" an
observable atomic charge does not exist in a strict sense. You probably mean
correlations of spectroscopic signatures with atomic charges when writing
"They can be observed and measured through spectroscopy experiments".
If you have another opinion on that I would like to know more details on
how to measure atomic charges.


Best wishes
Stefan

>Hi Peeter,

>There is a fundamental distinction between the current conversation focused on exchange-correlation theories and basis sets and the earlier discussion focused on atomic properties. If one increases the basis set size, exchange-correlation functionals such as B3LYP, M06, or whatever one you care to use will approach a well-defined mathematical limit. We can then discuss what the relative accuracy of that mathematical limit is in comparison to experimental properties and also discuss how close we are to that mathematical limit with a particular basis set. Thus, it is meaningful to discuss how adequate an exchange-correlation theory or basis set are for a particular research problem. Of course, the goal is to choose an adequate level that is not too computationally expensive for the particular research question being studied.

>In contrast, Mulliken and Lowdin population analysis schemes do not have any defined mathematical limits. As the basis set is increased and the energy and electron density approach the complete basis set limit, the Mulliken and Lowdin populations behave erratically and blow up. This is how we know for sure that Mulliken and Lowdin population analysis schemes are utter nonsense and should never be used for publication results. As pointed out by one person, their only purpose is for debugging calculations to see if the symmetry or other basic features of the input geometry are malformed.

>It is not the earlier discussion on atomic charges that is "nonsense" but rather the Mulliken and Lowdin populations that are nonsense, because they have no defined mathematical limits. This has nothing to do with atomic charges, per se. The Mulliken and Lowdin populations do not measure anything physical. They do not measure atomic charges. Probably the confusion has been propagated by calling Mulliken and Lowdin populations as types of "atomic charges", but really the Mulliken and Lowdin populations cannot be atomic charges, because they have no defined mathematical limits. In the future, I shall try to avoid referring to Mulliken and Lowdin populations as types of atomic charges, because I think this error is responsible for the confusion surrounding the definition of atomic charges. While we may not be able to measure atomic charges as precisely as energies in experiments, it is not true to say atomic charges are not experimentally observable. They can be observed and m!
 easured through spectroscopy experiments, albeit with much less precision than we are able to measure energies. I could go into more extensive details and examples if you are interested.
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-- 
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
--------------090100050507070404010602-- From owner-chemistry@ccl.net Fri Sep 11 09:26:00 2015 From: "Sebastian Kozuch seb.kozuch:+:gmail.com" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51713-150911063218-27735-Wpgipmyx3+CiMsQCIO1NCw(0)server.ccl.net> X-Original-From: Sebastian Kozuch Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=windows-1255 Date: Fri, 11 Sep 2015 13:31:50 +0300 MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [seb.kozuch+/-gmail.com]
Dear friends,

Obviously this thread went off on a tangent (and at some point it went ballistic). Coming back to the original question:

http://onlinelibrary.wiley.com/doi/10.1002/ijch.201400170/abstract

"The Unpredictability of Research Directions and the Synergy between Theory and Experiment in Physical-Organic Chemistry", a review by Wes Borden that recently appeared in Isr J Chem.

Regarding the second topic, about the suitability of methods to obtain meaningful results, remember the wise words of Coulson: "Give me insight, not numbers". But also consider the wise words of Leibniz: "When there are disputes among persons, we can simply say: Calculemus". There is a time for everything, and a season for every activity under the heavens.

Best,
Sebastian

On 7/9/2015 10:39 AM, Peter Damian Jarowski peterjarowski[-]gmail.com wrote:
Sent to CCL by: "Peter Damian Jarowski" [peterjarowski : gmail.com]
Dear All:

I am looking to collect case studies of how computational chemistry (specifically QM) has been able to predict or refine/optimize chemical reactions, especially cases where experimental work has followed this theoretical work up to achieve higher yields or selectivity. Any references or descriptions would be much appreciated and I would use them to build an argument for QM. I would of course give references and credit and then I will share a report here.

A good example would be my own work where we were able to predict the existence of an isolable intermediate and then prove this with experiment and XRD:

Wu, Y.-L.; Jarowski, P. D.; Schweizer, W. B.; Diederich, F. "Mechanistic Investigation of the Formal [2+2] Cycloaddition-Cycloreversion Reaction between 4-(N,N-Dimethylamino)phenylacetylene and Arylated 1,1-Dicyanovinyl Derivatives to Form Intramolecular Charge-Transfer Chromophores." Chem. Eur. J. 2009, 16, 202-211.

However, I am looking for industry relevant examples. I would love to hear from the community about this and I think it would benefit everyone to have at hand such examples.

Best Regards,

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From owner-chemistry@ccl.net Fri Sep 11 10:00:01 2015 From: "Renier Dreyer renier.dreyer^_^crunchyard.com" To: CCL Subject: CCL: ADF on CrunchYard's New HPC facility Message-Id: <-51714-150911081000-2858-/o8P1ibP953CLaG6M4rXRw..server.ccl.net> X-Original-From: "Renier Dreyer" Date: Fri, 11 Sep 2015 08:09:59 -0400 Sent to CCL by: "Renier Dreyer" [renier.dreyer]|[crunchyard.com] CrunchYard is pleased to announce that ADF is now available on our new HPC facility. Access thousands of true cores instantly using our easy website submission portal. The new HPC system makes use of Xeon based CPU's with 4GB ECC RAM per core and infiniband interconnects. Please contact SCM or Dr. Renier Dreyer (renier.dreyer],[crunchyard.com) at CrunchYard to find out how to access ADF on CrunchYard. From owner-chemistry@ccl.net Fri Sep 11 10:36:01 2015 From: "Thomas Manz tmanz^nmsu.edu" To: CCL Subject: CCL: net atomic charges Message-Id: <-51715-150911083939-25835-yGGP5e/bi0doIbpsrsHzoQ^server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a1136e03a07c505051f780234 Date: Fri, 11 Sep 2015 06:39:34 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [tmanz|-|nmsu.edu] --001a1136e03a07c505051f780234 Content-Type: text/plain; charset=UTF-8 Hi N. Sukumar, You wrote: >Since this list includes a large number of non-specialists, one should be careful to avoid making sweeping statements like "While we may not be able to measure atomic charges as precisely as energies in experiments, it is not true to say atomic charges are not experimentally observable. They can be observed and measured through spectroscopy experiments, albeit with much less precision than we are able to measure energies." This is one of the reasons that such statements need to be made. Non-specialists need to learn to. We shouldn't withhold knowledge from people simply because they are non-specialists. >"Atomic charges" are about as measurable as the divinity of an orbital! Both are entirely theoretical properties of theoretical objects. I joint Stefan in asking how to "measure atomic charges" - and before that please also clarify what you mean by "atomic." Please refer to my earlier reply discussing the N__C60 endohedral complex example. The short answer is that we learn information about the net atomic charges from spectroscopic signatures and related experimental data. These experiments do provide a basis for testing theories of net atomic charge via the scientific method. However, as I pointed out we are not able to measure net atomic charges with the same degree of precision as we can measure system energies. By atomic, we mean the properties assigned to each atom in a material. It is true that these properties are not determined with the same precision as the overall energy of the system. But it is also a misconception to say properties of atoms in a material do not exist. In the case of atomic spin moments, for example, these can be clearly measured via polarized neutron diffraction experiments. The average position of each atom in a crystal can be measured via x-ray diffraction experiments. There is therefore a real sense in which the properties of atoms in a material are a useful concept not only theoretically but also experimentally. Regarding net atomic charges, it is certainly true that in the DNA molecule, the oxygen atoms in the phosphate groups carry negative net atomic charges and are attracted to Na+, H+, or other cations in solution. It is also certainly true that ion transport (e.g., Na+, K+, Cl-, etc) through cell membranes is a well-established biological process. It is certainly true that Na atoms are positively charged in the standard NaCl crystal phase. While we may legitimately argue whether the charge of the Na atom in the standard NaCl crystal is +0.8 or +0.9 or + 1.0, this is simply a question of precision. In many cases, we can only quantify the net atomic charges to a precision of within perhaps ~+/- 0.1 electrons, or in some cases even less precisely to within ~ +/- 0.3 electrons. But, this doesn't mean that such charges are non-existent or that we can't get experimental information about them. Sincerely, Tom --001a1136e03a07c505051f780234 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi N. Sukumar,

You wrote:

>Since this list includes a large num= ber of non-specialists, one should be careful to avoid making sweeping stat= ements like "While we may not be able to measure atomic charges as pre= cisely as energies in experiments, it is not true to say atomic charges are= not experimentally observable. They can be observed and measured through s= pectroscopy experiments, albeit with much less precision than we are able t= o measure energies."


T= his is one of the reasons that such statements need to be made. Non-special= ists need to learn to. We shouldn't withhold knowledge from people simp= ly because they are non-specialists.


>"Atomic char= ges" are about as measurable as the divinity of an orbital! Both are e= ntirely theoretical properties of theoretical objects. I joint Stefan in as= king how to "measure atomic charges" - and before that please als= o clarify what you mean by "atomic."


Please refer to my earlier reply discussing the N__C60 endohedral comple= x example. The short answer is that we learn information about the net atom= ic charges from spectroscopic signatures and related experimental data. The= se experiments do provide a basis for testing theories of net atomic charge= via the scientific method. However, as I pointed out we are not able to me= asure net atomic charges with the same degree of precision as we can measur= e system energies.


<= /span>

By atomic, we mean the p= roperties assigned to each atom in a material. It is true that these proper= ties are not determined with the same precision as the overall energy of th= e system. But it is also a misconception to say properties of atoms in a ma= terial do not exist. In the case of atomic spin moments, for example, these= can be clearly measured via polarized neutron diffraction experiments. The= average position of each atom in a crystal can be measured via x-ray diffr= action experiments. There is therefore a real sense in which the properties= of atoms in a material are a useful concept not only theoretically but als= o experimentally.=C2=A0

=

Regarding net atomi= c charges, it is certainly true that in the DNA molecule, the oxygen atoms = in the phosphate groups carry negative net atomic charges and are attracted= to Na+, H+, or other cations in solution. It is also certainly true that i= on transport (e.g., Na+, K+, Cl-, etc) through cell membranes is a well-est= ablished biological process. It is certainly true that Na atoms are positiv= ely charged in the standard NaCl crystal phase. While we may legitimately a= rgue whether the charge of the Na atom in the standard NaCl crystal is +0.8= or +0.9 or + 1.0, this is simply a question of precision. In many cases, w= e can only quantify the net atomic charges to a precision of within perhaps= ~+/- 0.1 electrons, or in some cases even less precisely to within ~ +/- 0= .3 electrons. But, this doesn't mean that such charges are non-existent= or that we can't get experimental information about =C2=A0them.=


Sincerely,


Tom

--001a1136e03a07c505051f780234-- From owner-chemistry@ccl.net Fri Sep 11 11:11:00 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor : fluor.quimica.uniovi.es" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51716-150911084043-26769-LaNhtwLaTIqlVkRZUdcqrQ!=!server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Fri, 11 Sep 2015 14:23:55 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor,fluor.quimica.uniovi.es] On Thu, Sep 10, 2015 at 09:50:49PM -0600, Thomas Manz thomasamanz**gmail.com wrote: Tom, May I add a point to your excellent statement of the problem? There is a perfectly well defined functional for the charge of the full system at hand. Some sentences by the participants in this discussion may have induced some to think otherwise. The charge of a fragment of a system is what is being discussed. The problem is not limited to the charge and is clearly extensible to the contribution of a fragment to the peoperties of the system. A different but related point is that describing the fragments that we assume independent as non interacting is clearly not enough, as fragments too far apart can mantain important electrostatic interaction energies. I prefer to use the description of weakly correlated fragments, but my point of view is probably not so popular. I'm alone in thinking that this discussion, and others similar, elevates back the level of CCL to the original intentions for this forum? Best regards and peace, Vctor -- . . "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 tambin 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 than \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) ===(((==)))==================================+========================= ! Dr.Vctor Luaa, in silico chemist & prof. !"I have two kinds of problems, ! Departamento de Qumica Fsica y Analtica ! the urgent and 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/ From owner-chemistry@ccl.net Fri Sep 11 11:45:00 2015 From: "Thomas Manz thomasamanz|a|gmail.com" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51717-150911085833-11345-YnMH7SrytD1H++CQ9PnXyA---server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a114903a6932283051f7845f7 Date: Fri, 11 Sep 2015 06:58:27 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz~!~gmail.com] --001a114903a6932283051f7845f7 Content-Type: text/plain; charset=UTF-8 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 < owner-chemistry(_)ccl.net> 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> > > --001a114903a6932283051f7845f7 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Stefan,

You wrote: "the HK theorems simply do not apply here."

You are very incorrect!
The Hohenberg-Kohn theorems always apply to a non-deg= enerate, non-relativistic chemical ground state.=C2=A0
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 a= rbitrary constant potential offset) and its ground state electron density d= istribution.=C2=A0
Becaus= e the system's Hamiltonian determines its wavefunction, this establishe= s that all physical properties of the=C2=A0system, not just its energy are functionals of the ground state ele= ctron density distribution.=C2=A0

It is true that there is some flexibility in how to= define net atomic charges, but owing to the Hohenberg-Kohn theorems all me= thods that are not functionals of the electron density distribution are rul= ed out up front. This means that Mulliken and Lowdin populations cannot rep= resent 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 o= f net atomic charges that are functionals of the electron density distribut= ion.

Sincerely,

Tom

On Fri, Sep 11, 2015 at 2:54 AM, Stefan Grimme grimme*|*thch.uni-bonn.de <owner-chemistry(_)ccl.n= et> wrote:

Sent to CCL by: "Stefan=C2=A0 Grimme" [grimme^thch.uni-bonn.de]=
Dear Tom,
to this:
>I wanted to address one more of your comments. You wrote:=C2=A0 "I= don't want to defend orbital based partitionings (I prefer observables= ) but making the mathematical limit to the encompassing requirement seem no= nsense to me." Actually, this has already been proved in Nobel prize w= inning 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 chemi= cal system can be represented as a functional of the ground state electron = density distribution. A direct corollary is that since net atomic charges a= re a property of a chemical system, for a non-degenerate chemical ground st= ate the net atomic charges have to be a functional of the ground state elec= tron distribution. When I and others say that the net atomic charges should= approach a well-defined basis set limit, because they are functionals of t= he electron density distribution, we!
=C2=A0 are simply stating a direct corollary of the Hohenb= erg-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



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--001a114903a6932283051f7845f7-- From owner-chemistry@ccl.net Fri Sep 11 12:20:00 2015 From: "Ambrish K Srivastava ambrishphysics.|-|.gmail.com" To: CCL Subject: CCL:G: regarding bpw91 funtional Message-Id: <-51718-150911092448-16928-IGWnYIicdIUBLUY+548zzA|-|server.ccl.net> X-Original-From: Ambrish K Srivastava Content-Type: text/plain; charset=UTF-8 Date: Fri, 11 Sep 2015 18:54:43 +0530 MIME-Version: 1.0 Sent to CCL by: Ambrish K Srivastava [ambrishphysics,gmail.com] Dear Navjot you can simply put the functional to be used somewhere in the route section: For e.g. # opt freq gen m06 specifies m06 functional which is not available as default in Gaussian. However, I still don't understand that what do you mean by "optimizing" oxygen atom?? Best, AKS On 9/11/15, mann........... navu1989mann++gmail.com wrote: > Respected sir, > I am using gaussian 03 and getting problem in optimizing > oxygen atom by using dft/bpw91/d95v level of theory. As bpw91 funtional is > not present as default in gaussian 03. d95v basis set can be put as > additional keyword but i am not getting how to give input for additional > funtional . kindly help my in solving this problem. i will be highly > oblized. > > With Regards > Navjot kaur > Research Scholar > Panjab university > Chandigarh > -- *Ambrish K. Srivastava CSIR Senior Research Fellow Department of Physics University of Lucknow Lucknow, India-226007* Google Scholar: http://scholar.google.co.in/citations?user=XTcgp1EAAAAJ Research Gate: https://www.researchgate.net/profile/Ambrish_K_Srivastava From owner-chemistry@ccl.net Fri Sep 11 12:56:00 2015 From: "Robert Molt r.molt.chemical.physics#gmail.com" To: CCL Subject: CCL:G: regarding bpw91 funtional Message-Id: <-51719-150911101229-31224-mfz0FcwEvghhJ6438YYXrw[-]server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Fri, 11 Sep 2015 10:12:21 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics^_^gmail.com] What do you mean when you say you are "optimizing" an oxygen atom? "Optimizing" usually refers to a geometry (there is no geometry to an atom). Have you consulted the Gaussian manual on functionals? On 9/11/15 3:29 AM, mann........... navu1989mann++gmail.com wrote: > Respected sir, > I am using gaussian 03 and getting problem in > optimizing oxygen atom by using dft/bpw91/d95v level of theory. As > bpw91 funtional is not present as default in gaussian 03. d95v basis > set can be put as additional keyword but i am not getting how to give > input for additional funtional . kindly help my in solving this > problem. i will be highly oblized. > With Regards > Navjot kaur > Research Scholar > Panjab university > Chandigarh > -- 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 Fri Sep 11 13:30:01 2015 From: "Thomas Manz thomasamanz##gmail.com" To: CCL Subject: CCL: net atomic charges Message-Id: <-51720-150911110642-22111-G8zJQe1fF5fM8it41CrSKg .. server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a114903a60c269b051f7a0e3e Date: Fri, 11 Sep 2015 09:06:05 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz[-]gmail.com] --001a114903a60c269b051f7a0e3e Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable 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 determines 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 to 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. Any 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 Mulliken and Lowdin populations, that flexibility in how to define the net atomic charges as functionals of the electron distribution still remains. Yes, the possibility of overlap of three-dimensional electron distributions between 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 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. 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 LONG 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 density 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. 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 points on a 3D grid (let 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> --001a114903a60c269b051f7a0e3e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Hi Robert,

=C2=A0

I'm copying this discussion on net atomic= charges to a new thread.
=
From the Nobel prize website: "The Nobel Prize in Chemist= ry 1998 was divided equally between Walter Kohn "for his development o= f the density-functional theory" and John A. Pople "for his devel= opment of computational methods in quantum chemistry"." From my e= mail: "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.&= quot;

My poin= t is that the Hohenberg-Kohn theorems tell us what types of computations ca= n give us meaningful physical properties. As stated in the Hohenberg-Kohn t= heorems, the Hamiltonian of a non-degenerate ground state system is determi= ned by the ground-state electron density distribution up to an arbitrary co= nstant potential offset. Since the Hamiltonian determines the system's = wavefunction, and the wavefunction determines the system's properties, = it directly follows from the Hohenberg-Kohn Theorems that all of the observ= able properties of a non-degenerate ground state quantum chemical system ar= e functionals of the ground state electron distribution. This is what the H= ohenberg-Kohn theorems state. The energy is included as one of the observab= les, but the Hohenberg-Kohn theorems are not limited to the system=E2=80=99= s 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. An= y 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 H= ohenberg-Kohn theorems.
It is true that after ruling out such unphysical methodologies a= s Mulliken and Lowdin populations, that flexibility in how to define the ne= t atomic charges as functionals of the electron distribution still remains.= Yes, the possibility of overlap of three-dimensional electron distribution= s between the atoms is a challenge to sort out, but it is not a problem tha= t cannot be studied. This is where application of the scientific method com= es into play. By comparing different proposals to experimental data across = a wide variety of systems, it is possible to draw meaningful scientific con= clusions about which methods for assigning net atomic charges give closer a= greement to experimental data and are therefore more scientifically accurat= e. This does not mean we will be able to compute net atomic charges with th= e same level of precision as we can measure system energies, but it still m= eans that net atomic charges are a valid scientific concept and that they f= ollow known theorems and obey the scientific method.

=C2=A0=

Sincerely,

=C2=A0

Tom

=C2=A0

-----------

> Dr. Manz:

> Your comment is a very incorrect characterization of t= he 1998 Nobel Prize.

> a.) You're addressing Stephen Grimme, a= leader of DFT in computational chemistry in the world; trust me, he is wel= l aware of DFT. This is like lecturing Newton on a new subject called "= ;trigonometry."

> b.) DFT's contribution to science is NO= T "The density is an observable." This has been known since the d= ays 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 cl= assical EM classes solving for. Wavefunction people defined and were using = the electron density of chemical systems LONG before there was a DFT; just = read Szabo and Ostlund. Rather, DFT is a statement about being able to calc= ulate the energy as a function of density directly practically, with no cal= culation of the wavefunction necessary (there is more to it than this, but = as a bird's eye-view statement).

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

> "A direct corollary is that since net atomic charges are a prope= rty 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 cha= rge of an arbitrary subsystem is not always possible. There are many reason= s you cannot do this rigorously. 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 points on a 3D grid (let alone the fact we have sp= in!) cannot be represent by one number.=C2=A0

> Atomic charges, as= a computational model, are an approximation which is completely independen= t 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 a= tomic charge).

=C2=A0

>=C2=A0Robert Molt r.molt.chemical.physics-*-gmail.com=C2=A0&l= t;owner-chemis= try _ ccl.net>

--001a114903a60c269b051f7a0e3e-- From owner-chemistry@ccl.net Fri Sep 11 14:23:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor- -fluor.quimica.uniovi.es" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51721-150911141448-17978-Q6UvJ+YqjsiEB0bIjY13Nw**server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Fri, 11 Sep 2015 19:57:41 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor%fluor.quimica.uniovi.es] On Fri, Sep 11, 2015 at 06:25:07AM -0400, Robert Molt r.molt.chemical.physics-*-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 = \int \rho(\bm{r}) d\bm{r} = \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 = \sum_i Q_i = \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, energes, 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, ...), Vctor Luaa -- . . "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 tambin 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 than \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) ===(((==)))==================================+========================= ! Dr.Vctor Luaa, in silico chemist & prof. !"I have two kinds of problems, ! Departamento de Qumica Fsica y Analtica ! the urgent and 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/ From owner-chemistry@ccl.net Fri Sep 11 16:31:01 2015 From: "Gerald Knizia knizia{}theochem.uni-stuttgart.de" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51722-150911143032-12418-TFFOtA69IGbKYDknWEsSPA===server.ccl.net> X-Original-From: Gerald Knizia Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Fri, 11 Sep 2015 14:30:12 -0400 Mime-Version: 1.0 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 Löwdin 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/Löwdin charges. The qualitatively important aspect here has nothing to do with DFT, but just with the fact that the Mulliken/Löwdin 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 > > > > -= This is automatically added to each message by the mailing > script =- > E-mail to subscribers: CHEMISTRY+/-ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST+/-ccl.net or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: > http://www.ccl.net/chemistry/searchccl/index.shtml> > > > > From owner-chemistry@ccl.net Fri Sep 11 17:06:01 2015 From: "Robert Molt r.molt.chemical.physics%x%gmail.com" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51723-150911162545-3566-AxwW0lPcefvwQOuucvsVgg+*+server.ccl.net> X-Original-From: Robert Molt Content-Type: multipart/alternative; boundary="------------090408000501060307080304" Date: Fri, 11 Sep 2015 16:25:36 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics%gmail.com] This is a multi-part message in MIME format. --------------090408000501060307080304 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit 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. On 9/11/15 1:57 PM, Vctor Luaa 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] > On Fri, Sep 11, 2015 at 06:25:07AM -0400, Robert Molt r.molt.chemical.physics-*-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 = \int \rho(\bm{r}) d\bm{r} > = \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 = \sum_i Q_i > = \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, energes, 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, ...), > Vctor Luaa > -- > . . "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 tambin 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 than > \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) > ===(((==)))==================================+========================= > ! Dr.Vctor Luaa, in silico chemist & prof. !"I have two kinds of problems, > ! Departamento de Qumica Fsica y Analtica ! the urgent and 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/> > -- 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 --------------090408000501060307080304 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: 8bit 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.

On 9/11/15 1:57 PM, Vctor Luaa 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]
On Fri, Sep 11, 2015 at 06:25:07AM -0400, Robert Molt r.molt.chemical.physics-*-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 = \int \rho(\bm{r}) d\bm{r}
  = \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 = \sum_i Q_i
  = \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, energes, 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, ...),
                                Vctor Luaa
--
     .  .    "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 tambin 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 than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==================================+=========================
! Dr.Vctor Luaa, in silico chemist & prof. !"I have two kinds of problems,
! Departamento de Qumica Fsica y Analtica ! the urgent and 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)
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-- 
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
--------------090408000501060307080304-- From owner-chemistry@ccl.net Fri Sep 11 18:48:01 2015 From: "Lars Goerigk lars.goerigk a unimelb.edu.au" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51724-150911182415-30617-eHfa3kw6oqYy1fFTFAObag__server.ccl.net> X-Original-From: "Lars Goerigk" Date: Fri, 11 Sep 2015 18:24:14 -0400 Sent to CCL by: "Lars Goerigk" [lars.goerigk() unimelb.edu.au] Hi Peter, >>Obviously we are dealing with needed sub kcal accuracy in TS energy with a bit more flexibility in intermediate relative energies. >>Either way, if this is important we can use a compound CBS method etc. to get the needed accuracy, no? Composite methods with sub-kcal accuracy would actually be Wn-Theory or Wn-F12 Theory, which can be costly of course. As for, CBS-QB3 and TS-energies, Amir Karton and I have recently shown that CBS-QB3 should not be trusted for this: J. Comput. Chem. 2015, 36, 622-632. http://onlinelibrary.wiley.com/doi/10.1002/jcc.23837/abstract As to my previous post, you mentioned you would also like to use MRCI if you could. I just wanted to clarify that my comment was not about any costly WFT methods, but simply about DFT strategies that were shown to be more reliable than B3LYP/6-31G* at almost negligible additional cost on standard hardware with an efficient QM code (that uses the RI-approximation, for instance). For example, when tested over a large database covering different chemical problems, B3LYP was worse than the average of all tested hybrids: PCCP 2011, 13, 6670-6688. http://pubs.rsc.org/en/content/articlelanding/2011/cp/c0cp02984j#!divAbstract About unforeseeable error cancellation in B3LYP/6-31G* for thermochemistry (lack of London dispersion and basis-set superposition error due to the small basis set) and how to solve this problem efficiently: JOC 2012, 77, 10824-10834 http://pubs.acs.org/doi/abs/10.1021/jo302156p About structural optimisation of polypeptides and comparison to experiment data with DFT/6-31G* (BP86 and B3LYP are normally popular here): J. Phys. Chem. B 2014, 118, 14612-14626 http://pubs.acs.org/doi/abs/10.1021/jp510148h I entirely understand that one has to be pragmatic in applications, particularly when it comes to big systems. Nevertheless, one can still try to minimise the possibility of artifacts without compromising the efficiency of the approach. However, I also want to reemphasise that for a true comparison with experiment, relying on a good method for the electronic energy is only the first step, and one needs equally good approaches to also cover other effects (solvation, enthalpic, entropic effects etc.) That means if a popular method gave you relative electronic energies that agree well with experiment without having calculated any of these corrections, that would just be a lucky hit, and sadly this is something that one sees very frequently in the literature (even sometimes in high-impact journals). Cheers, Lars --- Dr. Lars Goerigk ARC DECRA Fellow School of Chemistry The University of Melbourne VIC 3010 Australia Research profile: http://www.chemistry.unimelb.edu.au/dr-lars-goerigk List of my publications: http://www.researcherid.com/rid/D-3717-2009 Follow me on Twitter: https://twitter.com/lgoer_compchem