From owner-chemistry@ccl.net Wed Sep 2 01:16:00 2015 From: "Xin Wang xwchem85%gmail.com" To: CCL Subject: CCL: NBO vs Loewdin Charges Message-Id: <-51655-150902011422-21361-JU78qJ+Oc2NfKQXR8nUM1Q=-=server.ccl.net> X-Original-From: "Xin Wang" Date: Wed, 2 Sep 2015 01:14:21 -0400 Sent to CCL by: "Xin Wang" [xwchem85]*[gmail.com] Dear all, Thank you very much for your inputs. What surprised me was the very large negative values predicted by Loewdin charges and according to ORCA manual, Loewdin charges are preferred over Mulliken. Just to answer Jim Kress, SARC-ZORA is an all electron basis set for Pu and I haven't used any ECPs. I also would like to thank Gerald Knizia and John McKelvey for suggesting the basis set independent methodologies. with kind regards Xin > "Gerald Knizia knizia__theochem.uni-stuttgart.de" wrote: > > Sent to CCL by: Gerald Knizia [knizia()theochem.uni-stuttgart.de] > Dear Robert, > sorry, but this question is completely beside the point. Of course no > method can predict anything accurately if you use a horribly inadequate > basis set[1]. However, as Susi pointed out, many Hilbert space partial > charge assignment methods (in particular both Mulliken and Lwdin > charges) contain an unphysical dependence on the basis set, which makes > their values arbitrary also when using perfectly adequate basis sets. > Mulliken and Lwdin charges have no basis set limit! > And *this* kind of basis set dependence---which is what people speak > about when talking about the problematic basis set dependence of partial > charge methods---is absolutely avoidable. > > Best wishes, > Gerald > > > [1] And just for the record: No one should ever use STO-3G for anything. > Not because it is a minimal basis set, but because it very, very bad > minimal basis set. > > On Tue, 2015-09-01 at 13:50 -0400, Dr. Robert Molt Jr. > r.molt.chemical.physics]*[gmail.com wrote: > > Sent to CCL by: "Dr. Robert Molt Jr." [r.molt.chemical.physics~~gmail.com] > > Can it predict properties accurately of a system composed of fluoride > > ions and negatively charged oxygens with the STO-3G basis set? > > > > Dr. Robert Molt Jr. > > r.molt.chemical.physics|*|gmail.com > > > > On 09/01/2015 11:10 AM, Gerald Knizia kniziaa/theochem.uni-stuttgart.de > > wrote: > > > Sent to CCL by: Gerald Knizia [knizia[*]theochem.uni-stuttgart.de] > > > Dear Robert, > > > in this generality saying "all atomic charge models are not basis > > > independent" is not true. It is absolutely possible to make up > > > Hilbert-space partial charge models which have a well-defined basis set > > > limit. See for example the Intrinsic Atomic Orbitals: > > > > > > http://pubs.acs.org/doi/abs/10.1021/ct400687b > > > > > > (yes, this is my paper. I also link to it because I think this could > > > have been what John meant). If anyone is interested in those charges: > > > They can also be computed with IboView (an free, open source program > > > with pre-compiled binaries for Windows and source for linux), which can > > > make simple KS wave functions itself, and otherwise import wave > > > functions from Orca, Turbomole, and Molpro: > > > > > > http://www.iboview.org > > > > > > Best wishes, > > > Gerald > > > > > > > > > On Tue, 2015-09-01 at 01:06 -0400, Dr. Robert Molt Jr. > > > r.molt.chemical.physics+/-gmail.com wrote: > > >> Atomic charge models are not basis independent; see Chris Cramer's > > >> book, chapter 9, p.314. Some models give charges which are consistent > > >> with increasing basis set size, some are not, but all depend on the > > >> basis. > > >> > > >> If you have anions, you cannot describe the density correctly without > > >> diffuse functions; this is a basis set dependence. > > >> Dr. Robert Molt Jr. > > >> r.molt.chemical.physics]-[gmail.com > > >> On 08/31/2015 11:14 PM, John McKelvey jmmckel(a)gmail.com wrote: > > >> > > >>> Hello, > > >>> > > >>> > > >>> There is a paper from a group in Germany demonstrating essentially > > >>> basis set independence of atomic charges.... Terrible to say that > > >>> while I remember the paper, and that the method has been installed > > >>> in ORCA for the next release, I will have to search for the paper... > > >>> just moved from Indiana to Missouri so things are in a bit of > > >>> disarray. > > >>> > > >>> > > >>> Maybe someone has seen this paper? > > >>> > > >>> > > >>> > > >>> John > > >>> > > >>> > > >>> On Mon, Aug 31, 2015 at 5:47 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 Mon, Aug 31, 2015 at 04:22:51PM -0400, Jim Kress > > >>> jimkress35-x-gmail.com wrote: > > >>> > > > >>> > Sent to CCL by: "Jim Kress" [jimkress35]-[gmail.com] > > >>> > Did you use an ECP for Plutonium and if so, was it > > >>> properly represented in > > >>> > the AIM analysis? > > >>> > > >>> Jim, > > >>> > > >>> QTAIM should refer to the all electron density. However > > >>> there have > > >>> been explorations of using ECP valence densities and they > > >>> can work if > > >>> you do it carefully. You can either add the core > > >>> contributions to the > > >>> valence density (it works) or be advise that your electron > > >>> density is > > >>> not complete, so there are properties of the real QTAIM > > >>> analysis that > > >>> can not work. > > >>> > > >>> For instance, the basins and the topological partition of > > >>> the full > > >>> electron density (rho) is not equivalent if you are using > > >>> only the > > >>> valence component (val-rho). > > >>> > > >>> However, if the basins are well defined there is no problem > > >>> in > > >>> integrating the valence density within the full electron > > >>> rho. The same > > >>> can be said for the analysis of spin components, and so on. > > >>> Using the critic2 code a lot of strange numerical > > >>> experiments of > > >>> this kind can be easily performed. The code also has > > >>> techniques to > > >>> fulfill the valence density with core components. > > >>> > > >>> Read on critic2 in this ref. > > >>> > > >>> A. Otero-de-la-Roza et al, Comput phys Commun 182 (2013) > > >>> 2232--2248 > > >>> > > >>> An updated version of the code and manual can be found on > > >>> > > >>> > > >>> > > >>> > > >>> I may look for old work published on this subject, if you > > >>> are truly > > >>> interested. > > >>> > > >>> Best regards, > > >>> 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 hate the > > >>> bureaucracy > > >>> ! Departamento de Qumica Fsica y Analtica ! imposed by > > >>> companies to > > >>> ! Universidad de Oviedo, 33006-Oviedo, Spain ! which I owe > > >>> nothing: > > >>> ! e-mail: victor(a)fluor.quimica.uniovi.es ! amazon, > > >>> ResearchGATE and > > >>> ! phone: +34-985-103491 fax: +34-985-103125 ! the like. > > >>> +--------------------------------------------+ > > >>> GroupPage : http://azufre.quimica.uniovi.es/ > > >>> (being reworked) > > >>> > > >>> > > >>> > > >>> > > >>> E-mail to subscribers: CHEMISTRY/a\ccl.net or use:> > > > >>> E-mail to administrators: CHEMISTRY-REQUEST/a\ccl.net or use> > Conferences: > > >>> http://server.ccl.net/chemistry/announcements/conferences/ > > >>> > > >>> Search Messages: > > >>> http://www.ccl.net/chemistry/searchccl/index.shtml> > > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> -- > > >>> John McKelvey > > >>> 545 Legacy Pointe Dr > > >>> O'Fallon, MO 63376 > > >>> 636-294-5302 > > >>> jmmckel/a\gmail.com> > > > > From owner-chemistry@ccl.net Wed Sep 2 02:12:00 2015 From: "Irena Efremenko irena.efremenko*weizmann.ac.il" To: CCL Subject: CCL: NBO vs Loewdin Charges Message-Id: <-51656-150902021116-8975-1iJvv1j9FPGvfoONVQZ6Zg]|[server.ccl.net> X-Original-From: Irena Efremenko Content-Language: en-US Content-Type: multipart/signed; boundary="Apple-Mail=_B3EE1C62-91EE-44AA-8CD4-17841670E1EB"; protocol="application/pkcs7-signature"; micalg=sha1 Date: Wed, 2 Sep 2015 06:11:04 +0000 MIME-Version: 1.0 Sent to CCL by: Irena Efremenko [irena.efremenko__weizmann.ac.il] --Apple-Mail=_B3EE1C62-91EE-44AA-8CD4-17841670E1EB Content-Type: multipart/alternative; boundary="Apple-Mail=_D76449B4-5C79-4E27-AAB0-3B9B0CDFA725" --Apple-Mail=_D76449B4-5C79-4E27-AAB0-3B9B0CDFA725 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Thanks, Tom, agree. But my main idea is that atomic charges derived from = QC calculations is a kind of fiction. I would recommend not to use it at = all, especially for transition metals, and even more for such heavy = atoms as Pu. =20 ****** Dr. Irena Efremenko Department of Organic Chemistry Weizmann Institute of Science 76100 Rehovot, Israel Phone: +972 8 9343680 FAX: +972 8 9343029 Email: irena.efremenko-x-weizmann.ac.il ****** > On Sep 1, 2015, at 22:37 , Thomas Manz thomasamanz__gmail.com = wrote: >=20 > Irena, >=20 > You said "the basis set dependence of atomic charges arises from the = basis set dependence of the spatial distribution of the electron = density". This is only true for charge assignment methods that are = functionals of the electron density. >=20 > It is profoundly violated by Mulliken, Lowden, and other charge = assignment methods that have explicit basis set dependence. This is why = Mulliken and Lowden charges are not generally considered useful. >=20 > Tom >=20 > On Tue, Sep 1, 2015 at 8:47 AM, Irena Efremenko = irena.efremenko---weizmann.ac.il = > wrote: > The initial question is lost in the discussion of technical problems.=20= >=20 > In my opinion, the answer is that ATOMS IN MOLECULES is not a physical = observable. (corollary: partial atomic charges are not physical = observables.) The partitioning of the electron density according to the = definition of atoms in each specific scheme is what determines atomic = charges, and this can be somewhat arbitrary. For example, in the = Mulliken partitioning scheme the electron density between two bonded = atoms is divided half-and-half, while in QTAIM atoms are divided by = surfaces of zero flux in the gradient vector field of the electron = density. Thus, corresponding charges should be different.=20 >=20 > Again, the basis set dependence of atomic charges arises from the = basis set dependence of the spatial distribution of the electron = density, especially in the range of diffuse functions. Usually, it = influences calculated charges to a lesser degree than the partitioning = scheme. > =20 > ****** > Dr. Irena Efremenko > Department of Organic Chemistry > Weizmann Institute of Science > 76100 Rehovot, Israel > Phone: +972 8 9343680 > FAX: +972 8 9343029 > Email: irena.efremenko,weizmann.ac.il = > ****** >=20 >> On Sep 1, 2015, at 08:06 , Dr. Robert Molt Jr. = r.molt.chemical.physics+/-gmail.com = > wrote: >>=20 >> Atomic charge models are not basis independent; see Chris Cramer's = book, chapter 9, p.314. Some models give charges which are consistent = with increasing basis set size, some are not, but all depend on the = basis. >>=20 >> If you have anions, you cannot describe the density correctly without = diffuse functions; this is a basis set dependence. >> Dr. Robert Molt Jr. >> r.molt.chemical.physics]-[gmail.com = >> On 08/31/2015 11:14 PM, John McKelvey jmmckel(a)gmail.com = wrote: >>> Hello, >>>=20 >>> There is a paper from a group in Germany demonstrating essentially = basis set independence of atomic charges.... Terrible to say that while = I remember the paper, and that the method has been installed in ORCA for = the next release, I will have to search for the paper... just moved = > from Indiana to Missouri so things are in a bit of disarray. >>>=20 >>> Maybe someone has seen this paper? >>>=20 >>>=20 >>> John >>> =20 >>>=20 >>> On Mon, Aug 31, 2015 at 5:47 PM, V=C3=ADctor Lua=C3=B1a Cabal = victor_-_fluor.quimica.uniovi.es = > wrote: >>>=20 >>> Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal = [victor ~~ fluor.quimica.uniovi.es ] >>> On Mon, Aug 31, 2015 at 04:22:51PM -0400, Jim Kress = jimkress35-x-gmail.com wrote: >>> > >>> > Sent to CCL by: "Jim Kress" [jimkress35]-[gmail.com = ] >>> > Did you use an ECP for Plutonium and if so, was it properly = represented in >>> > the AIM analysis? >>>=20 >>> Jim, >>>=20 >>> QTAIM should refer to the all electron density. However there have >>> been explorations of using ECP valence densities and they can work = if >>> you do it carefully. You can either add the core contributions to = the >>> valence density (it works) or be advise that your electron density = is >>> not complete, so there are properties of the real QTAIM analysis = that >>> can not work. >>>=20 >>> For instance, the basins and the topological partition of the full >>> electron density (rho) is not equivalent if you are using only the >>> valence component (val-rho). >>>=20 >>> However, if the basins are well defined there is no problem in >>> integrating the valence density within the full electron rho. The = same >>> can be said for the analysis of spin components, and so on. >>> Using the critic2 code a lot of strange numerical experiments of >>> this kind can be easily performed. The code also has techniques to >>> fulfill the valence density with core components. >>>=20 >>> Read on critic2 in this ref. >>>=20 >>> A. Otero-de-la-Roza et al, Comput phys Commun 182 (2013) 2232--2248 >>>=20 >>> An updated version of the code and manual can be found on >>>=20 >>> > >>> > >>>=20 >>> I may look for old work published on this subject, if you are truly >>> interested. >>>=20 >>> Best regards, >>> V=C3=ADctor Lua=C3=B1a >>> -- >>> . . "In science a person can be convinced by a good = argument. >>> / `' \ That is almost impossible in politics or religion" >>> /(o)(o)\ (Adapted from Carl Sagan) >>> /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero tambi=C3=A9n = es peor >>> / '`'` \ que lo malo, porque la mediocridad no es un grado, es = una >>> | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 >>> | |'`'`| | (Mediocre is worse than good, but it is also worse = than >>> \/`'`'`'\/ bad, because mediocrity is not a grade, it is an = attitude) >>> = =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D >>> ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. ! I hate the = bureaucracy >>> ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! = imposed by companies to >>> ! Universidad de Oviedo, 33006-Oviedo, Spain ! which I owe nothing: >>> ! e-mail: victor(a)fluor.quimica.uniovi.es = ! amazon, ResearchGATE and >>> ! phone: +34-985-103491 fax: +34-985-103125 = ! the like. >>> +--------------------------------------------+ >>> GroupPage : http://azufre.quimica.uniovi.es/ = >>> (being reworked) >>>=20 >>>=20 >>>=20 >>>=20 >>>=20 >>> E-mail to subscribers: CHEMISTRY/a\ccl.net = or use:= >>>=20 >>> E-mail to administrators: CHEMISTRY-REQUEST/a\ccl.net = or use= >>>=20= >>>=20= >>>=20 >>> Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ = >>>=20= >>>=20 >>>=20= >>>=20= >>>=20 >>>=20 >>>=20 >>>=20 >>>=20 >>>=20 >>>=20 >>>=20 >>>=20 >>>=20 >>> --=20 >>> John McKelvey >>> 545 Legacy Pointe Dr >>> O'Fallon, MO 63376 >>> 636-294-5302 >>> jmmckel/a\gmail.com >=20 >=20 --Apple-Mail=_D76449B4-5C79-4E27-AAB0-3B9B0CDFA725 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Thanks, Tom, agree. But my main idea is that atomic charges = derived from QC calculations is a kind of fiction. I would recommend not = to use it at all, especially for transition metals, and even more for = such heavy atoms as Pu.   
******
Dr. Irena Efremenko
Department of Organic Chemistry
Weizmann = Institute of Science
76100 Rehovot, Israel
Phone: +972 8 9343680
FAX:   +972 8 = 9343029
Email: irena.efremenko-x-weizmann.ac.il
******

On Sep 1, 2015, at 22:37 , Thomas Manz thomasamanz__gmail.com = <owner-chemistry-x-ccl.net> wrote:

Irena,

You said "the basis set = dependence of atomic charges arises from the basis set dependence of the = spatial distribution of the electron density". This is only true for = charge assignment methods that are functionals of the electron = density.

It is profoundly = violated by Mulliken, Lowden, and other charge assignment methods that = have explicit basis set dependence. This is why Mulliken and Lowden = charges are not generally considered useful.

Tom

On Tue, Sep 1, 2015 at 8:47 AM, = Irena Efremenko irena.efremenko---weizmann.ac.il <owner-chemistry,+,ccl.net> = wrote:
The initial = question is lost in the discussion of technical = problems. 

In my opinion, the answer is that ATOMS IN MOLECULES is not a = physical observable. (corollary: partial atomic charges are not physical = observables.) The partitioning of the electron density according to the = definition of atoms in each specific scheme is what determines atomic = charges, and this can be somewhat arbitrary. For example, in the = Mulliken partitioning scheme the electron density between two bonded = atoms is divided half-and-half, while in QTAIM atoms are divided by = surfaces of zero flux in the gradient vector field of the electron = density. Thus, corresponding charges should be = different. 

Again, the basis set dependence of atomic charges arises from = the basis set dependence of the spatial distribution of the electron = density, especially in the range of diffuse functions. Usually, it = influences calculated charges to a lesser degree than the partitioning = scheme.
  
******
Dr. Irena Efremenko
Department of Organic = Chemistry
Weizmann Institute of Science
76100 = Rehovot, Israel
Phone: +972 8 = 9343680
FAX:   +972 8 = 9343029
Email: irena.efremenko,weizmann.ac.il
******

On Sep 1, 2015, at 08:06 , Dr. Robert Molt Jr. = r.molt.chemical.physics+/-gmail.com <owner-chemistry,ccl.net> = wrote:

=20
Atomic charge models are not basis independent; see Chris Cramer's book, chapter 9, p.314. Some models give charges which are consistent with increasing basis set size, some are not, but all depend on the basis.

If you have anions, you cannot describe the density correctly without diffuse functions; this is a basis set dependence.
Dr. Robert Molt Jr.
r.molt.chemical.physics]-[gmail.com
On 08/31/2015 11:14 PM, John McKelvey jmmckel(a)gmail.com wrote:
Hello,

There is a paper from a group in Germany demonstrating essentially basis set independence of atomic charges....  Terrible to say that while I remember the paper, and that the method has been installed in ORCA for the next release, I will have to search for the paper...  just moved from Indiana = to Missouri so things are in a bit of disarray.

Maybe someone has seen this paper?


John
 

On Mon, Aug 31, 2015 at 5:47 PM, = V=C3=ADctor Lua=C3=B1a Cabal victor_-_fluor.quimica.uniovi.es <owner-chemistry/a\ccl.net> wrote:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D = Cabal [victor ~~ fluor.quimica.uniovi.es]
On Mon, Aug 31, 2015 at 04:22:51PM -0400, Jim Kress jimkress35-x-gmail.com= wrote:
>
> Sent to CCL by: "Jim Kress" [jimkress35]-[gmail.com]
> Did you use an ECP for Plutonium and if so, was it properly represented in
> the AIM analysis?

Jim,

QTAIM should refer to the all electron density. However there have
been explorations of using ECP valence densities and they can work if
you do it carefully. You can either add the core contributions to the
valence density (it works) or be advise that your electron density is
not complete, so there are properties of the real QTAIM analysis that
can not work.

For instance, the basins and the topological partition of the full
electron density (rho) is not equivalent if you are using only the
valence component (val-rho).

However, if the basins are well defined there is no problem in
integrating the valence density within the full electron rho. The same
can be said for the analysis of spin components, and so = on.
Using the critic2 code a lot of strange numerical experiments of
this kind can be easily performed. The code also has techniques to
fulfill the valence density with core components.

Read on critic2 in this ref.

A. Otero-de-la-Roza et al, Comput phys Commun 182 (2013) 2232--2248

An updated version of the code and manual can be found on

<http://azufre.quimica.uniovi.es/software.html#critic2> <http://schooner.chem.dal.ca/wiki/Critic2>
=
I may look for old work published on this subject, if you are truly
interested.

Best regards,
            =  V=C3=ADctor Lua=C3=B1a
--
     .  .    "In science a = person can be convinced by a good argument.
    / `' \   That is almost impossible = in politics or religion"
   /(o)(o)\  (Adapted from Carl Sagan)
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, = pero tambi=C3=A9n es peor
 /   '`'`   \ que lo malo, porque = la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, = 2015
 |  |'`'`|  | (Mediocre is worse than good, = but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a = grade, it is an attitude)
= =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. = ! I hate the bureaucracy
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica = ! imposed by companies to
! Universidad de Oviedo, 33006-Oviedo, Spain ! which I owe nothing:
! e-mail:   victor(a)fluor.quimica.uniovi.es   ! = amazon, ResearchGATE and
! phone: +34-985-103491  fax: +34-985-103125 ! the like.
+--------------------------------------------+
 GroupPage : http://azufre.quimica.uniovi.es/
             (being = reworked)


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--
John McKelvey
545 Legacy Pointe Dr
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636-294-5302
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The log r integrals can be easily computed by a 2d fft. Regards, Ulf From owner-chemistry@ccl.net Wed Sep 2 04:50:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor{=}fluor.quimica.uniovi.es" To: CCL Subject: CCL: NBO vs Loewdin Charges Message-Id: <-51658-150902044826-25122-uKxuO21mT4w7naKs8bEBYw,+,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: Wed, 02 Sep 2015 10:32:24 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor_-_fluor.quimica.uniovi.es] On Wed, Sep 02, 2015 at 06:11:04AM +0000, Irena Efremenko irena.efremenko*weizmann.ac.il wrote: > Thanks, Tom, agree. But my main idea is that atomic charges derived > from QC calculations is a kind of fiction. I would recommend not to > use it at all, especially for transition metals, and even more for such > heavy atoms as Pu. Irena, Your position is wise and many quantum chemists would agree, in principle. On the other hand, neglecting the possibility of fragmenting a molecule or solid into components means rejecting some of the most powerful ideas in chemistry. What is important to take home is that any splitting of a system into atoms, functional groups, or weakly interacting portions is an approximation and introduces errors. Compounds containg transition metals must deal with the strong correlation problem, and heavy systems like Pu enforce to consider relativistic terms, but neither of both aspects precludes fragmentation methods. On the other hand notice that there are two main fragmentation trends: (1) fragment a system into components, and (2) form a large system > from weakly correlated components. All the recent discussion was based on a type-(1) problem, but type-(2) methods are key for biomolecules and molecular solids, just to mention two important problems. Let's not throw the baby with the bath water, Víctor -- . . "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 también 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.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems, ! Departamento de Química Física y Analítica ! 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 Wed Sep 2 09:42:01 2015 From: "Thomas Exner texner##gmx.net" To: CCL Subject: CCL: OpenTox Euro 2015 meeting, 30 Sept - 2 Oct in Dublin Message-Id: <-51659-150902083522-27508-jAiet2lyfzGXj4h0LyTvpQ||server.ccl.net> X-Original-From: Thomas Exner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 02 Sep 2015 14:35:04 +0200 MIME-Version: 1.0 Sent to CCL by: Thomas Exner [texner-.-gmx.net] Dear CCLers: One topic of the OpenTox Euro conference will be the future activities of the OpenTox working groups on APIs (WG1), AOPs (WG2), Standards (WG3), and Deployment (WG4). Please note that we start the working groups completely from scratch. Therefore, contributions of people not yet associated with OpenTox are highly appreciated. We are searching for people interested in providing new services using OpenTox standards and especially experimentalists sharing their views on how to best organize data and make them accessible in the most useful way. To get a head start, we will organize virtual meetings previous to the conference. These meetings will be used for a general introduction and for planning the working group sessions on Wed. Sept. 30. They will take place Wed. Sep. 9, 3pm CEST for WG2 (AOPs) and WG3 (data standards) Wed. Sep. 9, 4pm CEST for WG1 (API) and WG4 (deployment) Please contact me if you are interested in participating so that I can send you the login information. Best regards. Thomas Thomas Exner schrieb: > The OpenTox Euro 2015 meeting takes place 30 Sept - 2 Oct in Dublin, > Ireland. The conference theme is Reproducible High Quality Safety > Science on Complex Systems and will include conference sessions on > Information Requirements & Standards, Characterisation of Systems, High > Content Screening, Metabolism, Modelling Cellular Perturbations & > Responses, Linking Parameters & Evidence across Scales, Simulation, > Systems Biology and Knowledge Integration Supporting Decision Making. > > OpenTox Association Working group meetings will be held on the topics of > Application Programming Interfaces, Adverse Outcome Pathways, Data and > Metadata Standards and Resource Deployment on the first day of the > conference. Persons interested in these working groups but not able to > come to the conference please contact Thomas Exner > (thomas.exner+*+douglasconnect.com) for information on how to participate > virtually. The meeting will also include a General Assembly of the > Association in addition to hands-on modelling and analysis sessions, > poster session and knowledge cafes. > > We are still accepting posters until 31 August. To submit an abstract > for the meeting: > http://www.opentox.net/submit-abstract-poster-or-chair > > Information and updates on the program will be posted at: > http://www.opentox.net/events/opentox-euro-2015 > > best regards > Barry Hardy > > President, OpenTox Association > On behalf of the Organising Committee > > On the OpenTox Association > Following up on the initial OpenTox project which was funded by the EU > under FP7, OpenTox has developed as an open standards platform > supporting application and infrastructure development in predictive > toxicology and safety assessment. The OpenTox Association was founded 27 > March this year as an international member-based non-profit association. > > The purpose of the Association is to promote the community-based > exchange and use of open knowledge, software, methods, tools, data, > reference resources, and standards in the scientific activities of > predictive toxicology, safety assessment and risk management, including > the 3Rs goal of the Reduction, Refinement and Replacement of Animal > Testing. > > More information on the Association: > http://www.opentox.net/the-opentox-association > From owner-chemistry@ccl.net Wed Sep 2 10:17:01 2015 From: "Irena Efremenko irena.efremenko_-_weizmann.ac.il" To: CCL Subject: CCL: NBO vs Loewdin Charges Message-Id: <-51660-150902093859-16734-3e7b5ZZ+GUO2rkFqeRYjGA|,|server.ccl.net> X-Original-From: Irena Efremenko Content-Language: en-US Content-Type: multipart/signed; boundary="Apple-Mail=_40AAA846-7B25-4EC2-A658-59DEFB47CD49"; protocol="application/pkcs7-signature"; micalg=sha1 Date: Wed, 2 Sep 2015 13:38:47 +0000 MIME-Version: 1.0 Sent to CCL by: Irena Efremenko [irena.efremenko:-:weizmann.ac.il] --Apple-Mail=_40AAA846-7B25-4EC2-A658-59DEFB47CD49 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Victor,=20 I have nothing against partitioning of molecules or solids into = fragments. We often use quantities not well-defined in QC in order to = interpret computational results in terms of general theory. In my = opinion, trends in atomic charges obtained by the same method for = similar systems could be informative, but atomic charges themselves have = a physical meaning only in the framework of each specific partitioning = scheme. In your type-(1) systems the error introduced by partitioning = often leads to meaningless results, such as negative charges on metal = atoms in complexes. Charges calculated by different methods could easily = differ 2-3 times.=20 I suppose type-(2) systems show more reasonable behaviour. Anyway, I suggest to keep the baby separately from the bath water and to = use atomic charges with care. Irena =20 > On Sep 2, 2015, at 11:32 , V=EDctor Lua=F1a Cabal = victor{=3D}fluor.quimica.uniovi.es wrote: >=20 >=20 > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal = [victor_-_fluor.quimica.uniovi.es] > On Wed, Sep 02, 2015 at 06:11:04AM +0000, Irena Efremenko = irena.efremenko*weizmann.ac.il wrote: >> Thanks, Tom, agree. But my main idea is that atomic charges derived >> from QC calculations is a kind of fiction. I would recommend not to >> use it at all, especially for transition metals, and even more for = such >> heavy atoms as Pu. >=20 > Irena, >=20 > Your position is wise and many quantum chemists would agree, in = principle. >=20 > On the other hand, neglecting the possibility of fragmenting a = molecule > or solid into components means rejecting some of the most powerful = ideas > in chemistry. What is important to take home is that any splitting of > a system into atoms, functional groups, or weakly interacting portions > is an approximation and introduces errors. >=20 > Compounds containg transition metals must deal with the strong = correlation > problem, and heavy systems like Pu enforce to consider relativistic = terms, > but neither of both aspects precludes fragmentation methods. >=20 > On the other hand notice that there are two main fragmentation trends: > (1) fragment a system into components, and (2) form a large system >> from weakly correlated components. All the recent discussion was = based > on a type-(1) problem, but type-(2) methods are key for biomolecules > and molecular solids, just to mention two important problems. >=20 > Let's not throw the baby with the bath water, > V=EDctor > -- > . . "In science a person can be convinced by a good argument. > / `' \ That is almost impossible in politics or religion" > /(o)(o)\ (Adapted from Carl Sagan) > /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero tambi=E9n 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) > = =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > ! Dr.V=EDctor Lua=F1a, in silico chemist & prof. !"I have two kinds of = problems, > ! Departamento de Qu=EDmica F=EDsica y Anal=EDtica ! the urgent and = the important. > ! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not = important, > ! e-mail: victor.*o*.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/ >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail=_40AAA846-7B25-4EC2-A658-59DEFB47CD49 Content-Disposition: attachment; filename="smime.p7s" Content-Type: application/pkcs7-signature; name="smime.p7s" Content-Transfer-Encoding: base64 MIAGCSqGSIb3DQEHAqCAMIACAQExCzAJBgUrDgMCGgUAMIAGCSqGSIb3DQEHAQAAoIIG5zCCBuMw ggXLoAMCAQICCmVTQC8AAAAABhswDQYJKoZIhvcNAQEFBQAwcDESMBAGCgmSJomT8ixkARkWAklM MRIwEAYKCZImiZPyLGQBGRYCQUMxGDAWBgoJkiaJk/IsZAEZFghXRUlaTUFOTjEbMBkGCgmSJomT 8ixkARkWC1dJRkktQ0EtRE9NMQ8wDQYDVQQDEwZXSVMtQ0EwHhcNMTMxMTEyMTEyODU3WhcNMTcx MTExMTEyODU3WjCBwjESMBAGCgmSJomT8ixkARkWAklMMRIwEAYKCZImiZPyLGQBGRYCQUMxGDAW BgoJkiaJk/IsZAEZFghXRUlaTUFOTjEbMBkGCgmSJomT8ixkARkWC1dJRkktQ0EtRE9NMQwwCgYD VQQLEwNXSVMxEjAQBgNVBAsTCVdJQ0NVc2VyczEQMA4GA1UEAxMHY29pcmVuYTEtMCsGCSqGSIb3 DQEJARYeaXJlbmEuZWZyZW1lbmtvQHdlaXptYW5uLmFjLmlsMIGfMA0GCSqGSIb3DQEBAQUAA4GN ADCBiQKBgQCxhrzVJdc7FYqS++QNix5vn7cuTiw3WGW+1KH//QlvgUcmgEdkhliZnHNCqt7BBgw4 idHBbOlZyEzkOMaegPHs/bLViUdQz9SpE+QXYC+9Q1BZPbqUg2rgvKptKDGpIFStu+2gnNqhvCej k63PZoQvC8eTE+d579nnuWZOCccOWwIDAQABo4IDrjCCA6owHQYDVR0OBBYEFJaZQjeJSbfjOuyR +uJE6fVMU9t3MB8GA1UdIwQYMBaAFDi0crqR+2s+8VNlAGJP7Sk0cXyyMIIBHwYDVR0fBIIBFjCC ARIwggEOoIIBCqCCAQaGgcJsZGFwOi8vL0NOPVdJUy1DQSxDTj13aWZpLWNhLENOPUNEUCxDTj1Q dWJsaWMlMjBLZXklMjBTZXJ2aWNlcyxDTj1TZXJ2aWNlcyxDTj1Db25maWd1cmF0aW9uLERDPVdJ RkktQ0EtRE9NLERDPVdFSVpNQU5OLERDPUFDLERDPUlMP2NlcnRpZmljYXRlUmV2b2NhdGlvbkxp c3Q/YmFzZT9vYmplY3RDbGFzcz1jUkxEaXN0cmlidXRpb25Qb2ludIY/aHR0cDovL3dpZmktY2Eu d2lmaS1jYS1kb20ud2Vpem1hbm4uYWMuaWwvQ2VydEVucm9sbC9XSVMtQ0EuY3JsMIIBPwYIKwYB BQUHAQEEggExMIIBLTCBugYIKwYBBQUHMAKGga1sZGFwOi8vL0NOPVdJUy1DQSxDTj1BSUEsQ049 UHVibGljJTIwS2V5JTIwU2VydmljZXMsQ049U2VydmljZXMsQ049Q29uZmlndXJhdGlvbixEQz1X SUZJLUNBLURPTSxEQz1XRUlaTUFOTixEQz1BQyxEQz1JTD9jQUNlcnRpZmljYXRlP2Jhc2U/b2Jq ZWN0Q2xhc3M9Y2VydGlmaWNhdGlvbkF1dGhvcml0eTBuBggrBgEFBQcwAoZiaHR0cDovL3dpZmkt Y2Eud2lmaS1jYS1kb20ud2Vpem1hbm4uYWMuaWwvQ2VydEVucm9sbC93aWZpLWNhLldJRkktQ0Et RE9NLldFSVpNQU5OLkFDLklMX1dJUy1DQS5jcnQwFwYJKwYBBAGCNxQCBAoeCABVAHMAZQByMAwG A1UdEwEB/wQCMAAwCwYDVR0PBAQDAgWgMCkGA1UdJQQiMCAGCisGAQQBgjcKAwQGCCsGAQUFBwME BggrBgEFBQcDAjBdBgNVHREEVjBUoDIGCisGAQQBgjcUAgOgJAwiY29pcmVuYUBXSUZJLUNBLURP TS5XRUlaTUFOTi5BQy5JTIEeaXJlbmEuZWZyZW1lbmtvQHdlaXptYW5uLmFjLmlsMEQGCSqGSIb3 DQEJDwQ3MDUwDgYIKoZIhvcNAwICAgCAMA4GCCqGSIb3DQMEAgIAgDAHBgUrDgMCBzAKBggqhkiG 9w0DBzANBgkqhkiG9w0BAQUFAAOCAQEAE0Se9gaAx+jctlE+k5YgtGTeaWxlZ/JZ7PN0D/KfciTh IKmKbZ64lbh6p2qEFoonDJlpvPhhn38TrAckOexq84b0RrNsGFdMAkKgsf9cYQxrfv8fAuvPrjsw 6OkYyiDYwsVtrZs3mJEUOwwxhgaIYsV7SXw1QFpgdPctl3NOwIjhJxOpWoPTdAWL6jX1BpYl82uZ wP7V++Q1gll44AuIYrAN1Bklm5us9egL5cs1pc2hktT3oJD+d6FvJNHkRRq/W241rf4wJh8FJsGp CA0ypZcSN3nU3xN/+AVqPDYpzReLrKz9l25knCy3KUcFOZI4n4TH8nuGOjFw5FA4qwTRfzGCAqkw ggKlAgEBMH4wcDESMBAGCgmSJomT8ixkARkWAklMMRIwEAYKCZImiZPyLGQBGRYCQUMxGDAWBgoJ kiaJk/IsZAEZFghXRUlaTUFOTjEbMBkGCgmSJomT8ixkARkWC1dJRkktQ0EtRE9NMQ8wDQYDVQQD EwZXSVMtQ0ECCmVTQC8AAAAABhswCQYFKw4DAhoFAKCCAYEwGAYJKoZIhvcNAQkDMQsGCSqGSIb3 DQEHATAcBgkqhkiG9w0BCQUxDxcNMTUwOTAyMTMzODQ2WjAjBgkqhkiG9w0BCQQxFgQUzp/o8AM5 WwyEkVpZWGkuEPZDarQwgY4GCSsGAQQBgjcQBDGBgDB+MHAxEjAQBgoJkiaJk/IsZAEZFgJJTDES MBAGCgmSJomT8ixkARkWAkFDMRgwFgYKCZImiZPyLGQBGRYIV0VJWk1BTk4xGzAZBgoJkiaJk/Is ZAEZFgtXSUZJLUNBLURPTTEPMA0GA1UEAxMGV0lTLUNBAgplU0AvAAAAAAYbMIGQBgsqhkiG9w0B CRACCzGBgKB+MHAxEjAQBgoJkiaJk/IsZAEZFgJJTDESMBAGCgmSJomT8ixkARkWAkFDMRgwFgYK CZImiZPyLGQBGRYIV0VJWk1BTk4xGzAZBgoJkiaJk/IsZAEZFgtXSUZJLUNBLURPTTEPMA0GA1UE AxMGV0lTLUNBAgplU0AvAAAAAAYbMA0GCSqGSIb3DQEBAQUABIGAfzGQLTDZEmCsL/KLWXYMlLwu dJ29b242CHm/rUj1iYg9CMeB927s4a+mhUiBncSbBOZmoFnrQBZAgnun7Lsn+ZaeITanEIY74uWn jeupoCXEw7uv2H3aHo7GSjSsTSfs+HDNFleUWecOOc95gJ2t7Fi/hp6YbtyZxdZkAgUNMOcAAAAA AAA= --Apple-Mail=_40AAA846-7B25-4EC2-A658-59DEFB47CD49-- From owner-chemistry@ccl.net Wed Sep 2 11:08:01 2015 From: "Thomas Manz thomasamanz(-)gmail.com" To: CCL Subject: CCL:G: analytic Coulomb and Exchange integrals for 2-dimensional Gaussian functions confined to a plane Message-Id: <-51661-150902110712-32414-UZ+ZVduTPs1kn/8Vf0PwNg[-]server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a11353f1ef04db2051ec50447 Date: Wed, 2 Sep 2015 09:07:03 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz]-[gmail.com] --001a11353f1ef04db2051ec50447 Content-Type: text/plain; charset=UTF-8 Hi Ulf, Thanks for your response. I'm not familiar with analytic forms for the 1/r the anisotropic Gaussian integrals. Do you have a reference for these? Sincerely, Tom On Wed, Sep 2, 2015 at 12:54 AM, uekstrom#%#gmail.com uekstrom#%#gmail.com < owner-chemistry],[ccl.net> wrote: > > Sent to CCL by: "uekstrom=-=gmail.com" [uekstrom=-=gmail.com] > If you want the 1/r form you can take the expressions for anisotropic > gaussian integrals and take the planar limit, but I am not sure that > you will end up with a closed expression, there might be one integral > that you have to approximate. The log r integrals can be easily > computed by a 2d fft. > > Regards, > Ulf> > > --001a11353f1ef04db2051ec50447 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Ulf,

Thanks for your response. I'= ;m not familiar with analytic forms for the 1/r the anisotropic Gaussian in= tegrals.
Do you have a reference for these?

<= div>Sincerely,

Tom

On Wed, Sep 2, 2015 at 12:54 AM, ueks= trom#%#gmail.com uekstrom#%#gmail.com <owner-chemistry],[ccl.net>= wrote:

Sent to CCL by: "uekstrom=3D-=3Dgmail.com" [uekstrom=3D-=3Dgmail.com]
If you want the 1/r form you can take the expressions for anisotropic
gaussian integrals and take the planar limit, but I am not sure that
you will end up with a closed expression, there might be one integral
that you have to approximate. The log r integrals can be easily
computed by a 2d fft.

Regards,
Ulf



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--001a11353f1ef04db2051ec50447-- From owner-chemistry@ccl.net Wed Sep 2 12:23:01 2015 From: "Thomas Manz thomasamanz###gmail.com" To: CCL Subject: CCL: NBO vs Loewdin Charges Message-Id: <-51662-150902121600-11201-1rivS2WCoojV8OKI6LgONA.:.server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a1136e03a1581db051ec5fb32 Date: Wed, 2 Sep 2015 10:15:53 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz.:.gmail.com] --001a1136e03a1581db051ec5fb32 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi, The difficulty with charge assignment schemes is largely due to historical artifacts. All of the earliest schemes for assigning net atomic charges were seriously flawed: Mulliken, Lowden, Hirshfeld, etc. Even Bader's AIM theory, which has many beautiful theoretical properties, can give non-nuclear attractors in some materials. The persistent use of methods like Mulliken and Lowden, which have been known for decades (longer than most of us have been alive) to be highly unstable and have no well-defined basis set limit, has contributed to the confusion. > From a historical perspective, this is similar to people's early aversion to "flying machines". For many decades, the concept of heavier than air flying machines (what we now call airplanes) was considered a crackpot idea (a "fiction"). This is because early attempts to build "flying machines" were dismal failures. It was only after people were able to construct successful demonstrations that the societal resistance to airplanes began to reverse. Nowadays, it is hard for us to imagine or justify the profound societal resistance to building airplanes that existed around 1900. Some of the modern charge assignment methods are getting much better than the earliest ones. There is mounting experimental and computational evidence that some of the most recent schemes are orders of magnitude more reliable than those developed decades ago. Hopefully, this recent progress will go a long way towards convincing computational chemistry researchers that the limitations we have become accustomed to can be reversed after all. I realize all of this will take time, but as a computational chemistry community we need to make an effort for progress. The continual use of explicitly basis set dependent methods like Mulliken and Lowden is a bit weary at times, and comes off as a serious shame in the face of better available recent methods. As a computational chemistry community what can we do to support progress? Do you think it is appropriate at this time for computational chemistry journals to develop standards that Mulliken and Lowden populations are not considered to be of publishable quality and that published populations should be from methods with a well-defined basis set limit? One could argue that it is important for published articles to show the fundamental limitations of Mulliken and Lowden schemes, but this has been established in countless papers over the past 50 years. I recall that my master's thesis advisor, who is a purely experimental catalysis researcher, warned us many years ago about the limitations of Mulliken charges. If experimentalists knew about this all the way back then, why as a leading computational chemistry community are we still fighting the obvious decades later? It may be that the computational chemistry community has been slow to develop better alternatives. I believe the continued use of Mulliken and Lowden schemes as default methods in some quantum chemistry programs is due to the inherent limitations of other available charge assignment schemes. Until recently, the NPA/NBO scheme, which has many great properties, was non-convergent for many systems near the complete basis set limit. My experience and tests have shown this improved within the last year. The NBO website and manual says that recently they have improved the projection algorithm to make it more reliable. So, at least until very recently, the convergence of the NPA/NBO scheme was not sufficiently reliable to use it as a default charge assignment method. The issue of non-nuclear attractors has precluded using Bader's scheme as a default method for assigning net atomic charges. The Hirshfeld method assigns net atomic charges that are too small in magnitude. Methods such as CHELP, CHELPG, ESP, etc. do not work for dense nonporous materials that lack a van der Waals surface. Computing the APT and Born effective charges requires a computationally expensive frequency (first-order perturbation theory) computation or a series of energy calculations with various atomic displacements. Thus, it seems that until recently the computational chemistry community has been stuck with seriously flawed methods such as Mulliken and Lowden as defaults in popular quantum chemistry programs. For the past couple of years, I and one of my Ph.D. students have been developing a better alternative. The goal of our project is to develop a general-purpose atomic population analysis method that works nearly flawlessly across a broad range of diverse material classes, including both molecular and solid-state materials. We have made extensive comparisons to experimental properties across diverse materials. Our objective is to develop a method that converges reliably and efficiently and would be ideally suited for use as a default atomic population analysis method in popular quantum chemistry programs irrespective of the basis set type. We currently have a manuscript on this new method under review. We are hoping that it is not too late for the computational chemistry community to improve. We earnestly solicit your support to enable the computational chemistry community to make progress in the important area of atomic population analysis methods. Sincerely, Tom On Wed, Sep 2, 2015 at 12:11 AM, Irena Efremenko irena.efremenko* weizmann.ac.il wrote: > Thanks, Tom, agree. But my main idea is that atomic charges derived from > QC calculations is a kind of fiction. I would recommend not to use it at > all, especially for transition metals, and even more for such heavy atoms > as Pu. > ****** > Dr. Irena Efremenko > Department of Organic Chemistry > Weizmann Institute of Science > 76100 Rehovot, Israel > Phone: +972 8 9343680 > FAX: +972 8 9343029 > Email: irena.efremenko[*]weizmann.ac.il > ****** > > On Sep 1, 2015, at 22:37 , Thomas Manz thomasamanz__gmail.com < > owner-chemistry[*]ccl.net> wrote: > > Irena, > > You said "the basis set dependence of atomic charges arises from the > basis set dependence of the spatial distribution of the electron density"= . > This is only true for charge assignment methods that are functionals of t= he > electron density. > > It is profoundly violated by Mulliken, Lowden, and other charge assignmen= t > methods that have explicit basis set dependence. This is why Mulliken and > Lowden charges are not generally considered useful. > > Tom > > On Tue, Sep 1, 2015 at 8:47 AM, Irena Efremenko > irena.efremenko---weizmann.ac.il wrote: > >> The initial question is lost in the discussion of technical problems. >> >> In my opinion, the answer is that ATOMS IN MOLECULES is not a physical >> observable. (corollary: partial atomic charges are not physical >> observables.) The partitioning of the electron density according to the >> definition of atoms in each specific scheme is what determines atomic >> charges, and this can be somewhat arbitrary. For example, in the Mullike= n >> partitioning scheme the electron density between two bonded atoms is >> divided half-and-half, while in QTAIM atoms are divided by surfaces of z= ero >> flux in the gradient vector field of the electron density. Thus, >> corresponding charges should be different. >> >> Again, the basis set dependence of atomic charges arises from the basis >> set dependence of the spatial distribution of the electron density, >> especially in the range of diffuse functions. Usually, it influences >> calculated charges to a lesser degree than the partitioning scheme. >> >> ****** >> Dr. Irena Efremenko >> Department of Organic Chemistry >> Weizmann Institute of Science >> 76100 Rehovot, Israel >> Phone: +972 8 9343680 >> FAX: +972 8 9343029 >> Email: irena.efremenko,weizmann.ac.il >> ****** >> >> On Sep 1, 2015, at 08:06 , Dr. Robert Molt Jr. r.molt.chemical.physics+/= - >> gmail.com wrote: >> >> Atomic charge models are not basis independent; see Chris Cramer's book, >> chapter 9, p.314. Some models give charges which are consistent with >> increasing basis set size, some are not, but all depend on the basis. >> >> If you have anions, you cannot describe the density correctly without >> diffuse functions; this is a basis set dependence. >> >> Dr. Robert Molt Jr.r.molt.chemical.physics]-[gmail.com >> >> On 08/31/2015 11:14 PM, John McKelvey jmmckel(a)gmail.com wrote: >> >> Hello, >> >> There is a paper from a group in Germany demonstrating essentially basis >> set independence of atomic charges.... Terrible to say that while I >> remember the paper, and that the method has been installed in ORCA for t= he >> next release, I will have to search for the paper... just moved from >> Indiana to Missouri so things are in a bit of disarray. >> >> Maybe someone has seen this paper? >> >> >> John >> >> >> On Mon, Aug 31, 2015 at 5:47 PM, V=C3=ADctor Lua=C3=B1a Cabal >> victor_-_fluor.quimica.uniovi.es wrote: >> >>> >>> Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor= ~~ >>> fluor.quimica.uniovi.es] >>> On Mon, Aug 31, 2015 at 04:22:51PM -0400, Jim Kress >>> jimkress35-x-gmail.com wrote: >>> > >>> > Sent to CCL by: "Jim Kress" [jimkress35]-[gmail.com] >>> > Did you use an ECP for Plutonium and if so, was it properly >>> represented in >>> > the AIM analysis? >>> >>> Jim, >>> >>> QTAIM should refer to the all electron density. However there have >>> been explorations of using ECP valence densities and they can work if >>> you do it carefully. You can either add the core contributions to the >>> valence density (it works) or be advise that your electron density is >>> not complete, so there are properties of the real QTAIM analysis that >>> can not work. >>> >>> For instance, the basins and the topological partition of the full >>> electron density (rho) is not equivalent if you are using only the >>> valence component (val-rho). >>> >>> However, if the basins are well defined there is no problem in >>> integrating the valence density within the full electron rho. The same >>> can be said for the analysis of spin components, and so on. >>> Using the critic2 code a lot of strange numerical experiments of >>> this kind can be easily performed. The code also has techniques to >>> fulfill the valence density with core components. >>> >>> Read on critic2 in this ref. >>> >>> A. Otero-de-la-Roza et al, Comput phys Commun 182 (2013) 2232--2248 >>> >>> An updated version of the code and manual can be found on >>> >>> >>> >>> >>> I may look for old work published on this subject, if you are truly >>> interested. >>> >>> Best regards, >>> V=C3=ADctor Lua=C3=B1a >>> -- >>> . . "In science a person can be convinced by a good argument. >>> / `' \ That is almost impossible in politics or religion" >>> /(o)(o)\ (Adapted from Carl Sagan) >>> /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero tambi=C3=A9n es p= eor >>> / '`'` \ que lo malo, porque la mediocridad no es un grado, es una >>> | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 >>> | |'`'`| | (Mediocre is worse than good, but it is also worse than >>> \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude= ) >>> =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D >>> ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. ! I hate the bur= eaucracy >>> ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! imposed b= y companies to >>> ! Universidad de Oviedo, 33006-Oviedo, Spain ! which I owe nothing: >>> ! e-mail: victor(a)fluor.quimica.uniovi.es ! amazon, ResearchGATE >>> and >>> ! phone: +34-985-103491 fax: +34-985-103125 ! the like. >>> +--------------------------------------------+ >>> GroupPage : http://azufre.quimica.uniovi.es/ >>> (being reworked) >>> >>> >>> >>> >>> >>> E-mail to subscribers: CHEMISTRY/a\ccl.net or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST/a\ccl.net or use>>> >>> >>> >>> >>> >>> >>> >>> >> >> >> -- >> John McKelvey >> 545 Legacy Pointe Dr >> O'Fallon, MO 63376 >> 636-294-5302 >> jmmckel/a\gmail.com >> >> >> >> > > --001a1136e03a1581db051ec5fb32 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi,

The difficulty with charge assignme= nt schemes is largely due to historical artifacts.=C2=A0
All of t= he earliest schemes for assigning net atomic charges were seriously flawed:= Mulliken, Lowden, Hirshfeld, etc.
Even Bader's AIM theory, w= hich has many beautiful theoretical properties, can give non-nuclear attrac= tors in some materials.
The persistent use of methods like Mullik= en and Lowden, which have been known for decades (longer than most of us ha= ve been alive)
to be highly unstable and have no well-defined bas= is set limit, has contributed to the confusion.

Fr= om a historical perspective, this is similar to people's early aversion= to "flying machines".
For many decades, the concept of= heavier than air flying machines (what we now call airplanes) was consider= ed a crackpot idea (a "fiction").
This is because early= attempts to build "flying machines" were dismal failures.
<= div>It was only after people were able to construct successful demonstratio= ns that the societal resistance to airplanes began to reverse.
No= wadays, it is hard for us to imagine or justify the profound societal resis= tance to building airplanes that existed around 1900.

<= div>Some of the modern charge assignment methods are getting much better th= an the earliest ones.
There is mounting experimental and computat= ional evidence that some of the most recent schemes
are orders of= magnitude more reliable than those developed decades ago.
Hopefu= lly, this recent progress will go a long way towards convincing computation= al chemistry researchers that=C2=A0
the limitations we have becom= e accustomed to can be reversed after all.
I realize all of this = will take time, but as a computational chemistry community we need to make = an effort for progress.

The continual use of expli= citly basis set dependent methods like Mulliken and Lowden is a bit weary a= t times, and comes off as a=C2=A0
serious shame in the face of be= tter available recent methods. As a computational chemistry community what = can we do to support progress?
Do you think it is appropriate at = this time for computational chemistry journals to develop standards that Mu= lliken and Lowden
populations are not considered to be of publish= able quality and that published populations should be from methods with a= =C2=A0
well-defined basis set limit? One could argue that it is i= mportant for published articles to show the fundamental limitations of
Mulliken and Lowden schemes, but this has been established in countle= ss papers over the past 50 years.=C2=A0
I recall that my master&#= 39;s thesis advisor, who is a purely experimental catalysis researcher, war= ned us many years ago
about the limitations of Mulliken charges. = If experimentalists knew about this all the way back then, why as a leading=
computational chemistry community are we still fighting the obvi= ous decades later?

It may be that the computationa= l chemistry community has been slow to develop better alternatives.
I believe the continued use of Mulliken and Lowden schemes as default me= thods in some
quantum chemistry programs is due to the inherent l= imitations of other available charge assignment schemes.
Until re= cently, the NPA/NBO scheme, which has many great properties, was non-conver= gent for many systems
near the complete basis set limit. My exper= ience and tests have shown this improved within the last year.
Th= e NBO website and manual says that recently they have improved the projecti= on algorithm to make it
more reliable. So, at least until very re= cently, the convergence of the NPA/NBO scheme was not sufficiently
reliable to use it as a default charge assignment method. The issue of no= n-nuclear attractors has precluded
using Bader's scheme as a = default method for assigning net atomic charges. The Hirshfeld method assig= ns
net atomic charges that are too small in magnitude. Methods su= ch as CHELP, CHELPG, ESP, etc. do not work
for dense nonporous ma= terials that lack a van der Waals surface. Computing the APT and Born effec= tive charges=C2=A0
requires a computationally expensive frequency= (first-order perturbation theory) computation or a series of energy calcul= ations with
various atomic displacements. Thus, it seems that unt= il recently the computational chemistry community has been stuck with=C2=A0=
seriously flawed methods such as Mulliken and Lowden as defaults= in popular quantum chemistry programs.

For the pa= st couple of years, I and one of my Ph.D. students have been developing a b= etter alternative.
The goal of our project is to develop a genera= l-purpose atomic population analysis method that works
nearly fla= wlessly across a broad range of diverse material classes, including both mo= lecular and solid-state
materials. We have made extensive compari= sons to experimental properties across diverse materials.
Our obj= ective is to develop a method that converges reliably and efficiently and w= ould be ideally suited
for use as a default atomic population ana= lysis method in popular quantum chemistry programs
irrespective o= f the basis set type. We currently have a manuscript on this new method und= er review.
We are hoping that it is not too late for the computat= ional chemistry community to improve.
We earnestly solicit your s= upport to enable the computational chemistry community to make progress in = the important
area of atomic population analysis methods.

Sincerely,

Tom

On Wed, Se= p 2, 2015 at 12:11 AM, Irena Efremenko irena.efremenko*weizmann.ac.il <owner-chemistry\a/ccl.net> wrote:
Thanks, Tom, agree. But my main idea is that atomic charges derived = > from QC calculations is a kind of fiction. I would recommend not to use it = at all, especially for transition metals, and even more for such heavy atom= s as Pu. =C2=A0=C2=A0
******
Dr. Irena Efremenko
Depa= rtment of Organic Chemistry
Weizmann Institute of Science
76100 Rehov= ot, Israel
Phone: +972 8 9343680
FAX: =C2=A0 +972 8 9343029=
Email:=C2=A0irena.efremenko[*]weizmann.ac.il
******

On Sep 1, 2015, at= 22:37 , Thomas Manz thomasamanz__gmail.com <owner-chemistry[*]ccl.net> wrote:

=
Irena,

You= said "the basis set depe= ndence of atomic charges arises from the basis set dependence of the spatia= l distribution of the electron density". This is only true for charge = assignment methods that are functionals of the electron density.

<= span style=3D"font-size:12.8000001907349px">It is profoundly violated by Mu= lliken, Lowden, and other charge assignment methods that have explicit basi= s set dependence. This is why Mulliken and Lowden charges are not generally= considered useful.

T= om

On Tue, Sep 1, 2015 at 8:47 AM, Irena Efremenko= ire= na.efremenko---weizmann.ac.il <owner-chemistry,+,ccl.net&g= t; wrote:
The initial question is lost in th= e discussion of technical problems.=C2=A0

In my op= inion, the answer is that ATOMS IN MOLECULES is not a physical observable. = (corollary: partial atomic charges are not physical observables.) The parti= tioning of the electron density according to the definition of atoms in eac= h specific scheme is what determines atomic charges, and this can be somewh= at arbitrary. For example, in the Mulliken partitioning scheme the electron= density between two bonded atoms is divided half-and-half, while in QTAIM = atoms are divided by surfaces of zero flux in the gradient vector field of = the electron density. Thus, corresponding charges should be different.=C2= =A0

Again, the basis set dependence of atomic char= ges arises from the basis set dependence of the spatial distribution of the= electron density, especially in the range of diffuse functions. Usually, i= t influences calculated charges to a lesser degree than the partitioning sc= heme.
=C2=A0=C2=A0
******
Dr. Irena Efremenko
Department of Organic= Chemistry
Weizmann Institute of Science
76100 Rehovot, Israel
Pho= ne: +972 8 9343680
FAX: =C2=A0 +972 8 9343029
Email:=C2= =A0iren= a.efremenko,weizmann.ac.il
******

On Sep 1, 2015, at= 08:06 , Dr. Robert Molt Jr. r.molt.chemical.physics+/-gmail.com <owner-chemistry,ccl.net> wrote:
=20
Atomic charge models are not basis independent; see Chris Cramer's book, chapter 9, p.314. Some models give charges which are consistent with increasing basis set size, some are not, but all depend on the basis.

If you have anions, you cannot describe the density correctly without diffuse functions; this is a basis set dependence.
Dr. Robert Molt Jr.
r.=
molt.chemical.physics]-[gmail.com
On 08/31/2015 11:14 PM, John McKelvey jmmckel(a)gmail.com wrote:
Hello,

There is a paper from a group in Germany demonstrating essentially basis set independence of atomic charges....=C2=A0 Terrible to say that while I remember the paper, and that the method has been installed in ORCA for the next release, I will have to search for the paper...=C2=A0 just moved from Indiana to Missouri so things are in a bit of disarray.

Maybe someone has seen this paper?


John
=C2=A0


Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cab= al [victor ~~ fluor.quimica.uniovi.es]
On Mon, Aug 31, 2015 at 04:22:51PM -0400, Jim Kress jimkress35-x-gmail.com wrote:
>
> Sent to CCL by: "Jim Kress" [jimkress35]-[gmail.com]
> Did you use an ECP for Plutonium and if so, was it properly represented in
> the AIM analysis?

Jim,

QTAIM should refer to the all electron density. However there have
been explorations of using ECP valence densities and they can work if
you do it carefully. You can either add the core contributions to the
valence density (it works) or be advise that your electron density is
not complete, so there are properties of the real QTAIM analysis that
can not work.

For instance, the basins and the topological partition of the full
electron density (rho) is not equivalent if you are using only the
valence component (val-rho).

However, if the basins are well defined there is no problem in
integrating the valence density within the full electron rho. The same
can be said for the analysis of spin components, and so on.
Using the critic2 code a lot of strange numerical experiments of
this kind can be easily performed. The code also has techniques to
fulfill the valence density with core components.

Read on critic2 in this ref.

A. Otero-de-la-Roza et al, Comput phys Commun 182 (2013) 2232--2248

An updated version of the code and manual can be found on

<http://azufre.quimica.uniovi.es= /software.html#critic2>
<http://schooner.chem.dal.ca/wiki/Critic2= >

I may look for old work published on this subject, if you are truly
interested.

Best regards,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0V=C3=ADctor Lua=C3=B1a
--
=C2=A0 =C2=A0 =C2=A0.=C2=A0 .=C2=A0 =C2=A0 "In science a= person can be convinced by a good argument.
=C2=A0 =C2=A0 / `' \=C2=A0 =C2=A0That is almost impossibl= e in politics or religion"
=C2=A0 =C2=A0/(o)(o)\=C2=A0 (Adapted from Carl Sagan)
=C2=A0 /`. \/ .'\=C2=A0 "Lo mediocre es peor que lo = bueno, pero tambi=C3=A9n es peor
=C2=A0/=C2=A0 =C2=A0'`'`=C2=A0 =C2=A0\ que lo malo, p= orque la mediocridad no es un grado, es una
=C2=A0|=C2=A0 \'`'`/=C2=A0 | actitud" -- Jorge W= asenberg, 2015
=C2=A0|=C2=A0 |'`'`|=C2=A0 | (Mediocre is worse than = good, but it is also worse than
=C2=A0 \/`'`'`'\/=C2=A0 bad, because mediocrity i= s not a grade, it is an attitude)
=3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. ! = I hate the bureaucracy
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica != imposed by companies to
! Universidad de Oviedo, 33006-Oviedo, Spain ! which I owe nothing:
! e-mail:=C2=A0 =C2=A0victor(a)<= a href=3D"http://fluor.quimica.uniovi.es/" rel=3D"noreferrer" target=3D"_bl= ank">fluor.quimica.uniovi.es=C2=A0 =C2=A0! amazon, ResearchGATE and
! phone: +34-985-103491=C2=A0 fax: +34-985-103125 ! the like.
+--------------------------------------------+
=C2=A0GroupPage : http://azufre.quimica.uniovi.es/=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(being rework= ed)



--
John McKelvey
545 Legacy Pointe Dr




--001a1136e03a1581db051ec5fb32-- From owner-chemistry@ccl.net Wed Sep 2 15:48:01 2015 From: "Susi Lehtola susi.lehtola^alumni.helsinki.fi" To: CCL Subject: CCL: NBO vs Loewdin Charges Message-Id: <-51663-150902124524-13613-XXiFdHqVaMe+ozY+RWhnQg . server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 2 Sep 2015 09:45:11 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola%x%alumni.helsinki.fi] On 09/01/2015 10:14 PM, Xin Wang xwchem85%gmail.com wrote: > Sent to CCL by: "Xin Wang" [xwchem85]*[gmail.com] > Dear all, > > Thank you very much for your inputs. > > What surprised me was the very large negative > values predicted by Loewdin charges and according > to ORCA manual, Loewdin charges are preferred > over Mulliken. I believe I have also read this somewhere (maybe it was indeed the ORCA manual, or maybe it was somewhere else). However, I have not been able to find any citation which would actually support this claim. In my own personal experience, Löwdin typically gives charages that are opposite to common chemical knowledge. -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola[a]alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA ----------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Sep 2 16:23:01 2015 From: "Susi Lehtola susi.lehtola/./alumni.helsinki.fi" To: CCL Subject: CCL: analytic Coulomb and Exchange integrals for 2-dimensional Gaussian functions confined to a plane Message-Id: <-51664-150902150720-4388-DtAmMLLO0lDDc3/R3Evatg|*|server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Wed, 2 Sep 2015 12:07:07 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola|a|alumni.helsinki.fi] On 08/31/2015 10:45 PM, uekstrom=-=gmail.com uekstrom=-=gmail.com wrote: > > Sent to CCL by: "uekstrom\a/gmail.com" [uekstrom\a/gmail.com] > Do you want the 1/r or log(r) form of the interaction? (the latter is > the right one when also the electric field is confined to the plane). .. but you only get the log(r) form when you're looking at something like an infinite charged wire on the z-axis and examining the electric field on the (x,y) plane, which I doubt is the case here since z is assumed to be a vanishingly small dimension...? -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola|*|alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA ----------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Sep 2 18:10:00 2015 From: "Salter-Duke, Brian James - brian.james.duke],[gmail.com" To: CCL Subject: CCL: NBO vs Loewdin Charges Message-Id: <-51665-150902180210-16466-kJMVXZPj5AA4c2iGG6pciw() server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 3 Sep 2015 07:55:18 +1000 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke-*-gmail.com] I entirely agree with Thomas about Mulliken and Lowden charges. There is a case for removing them from all quantum chemistry software. It is a bit like the case for removing STO-nG basis sets from such software. In my opinion, neither those basis sets or those charges should be used in publications. However I do not support removing them from our programs. Mulliken charges are computationally cheap and they give a quick indication whether one has stuffed up in giving a geometry that does not have the expected symmetry. Similarly STO-3G calculations give a good test of ones basis data. They should be used only for testing data. Brian. On Wed, Sep 02, 2015 at 10:15:53AM -0600, Thomas Manz thomasamanz###gmail.com wrote: > Hi, > > The difficulty with charge assignment schemes is largely due to historical > artifacts. > All of the earliest schemes for assigning net atomic charges were seriously > flawed: Mulliken, Lowden, Hirshfeld, etc. > Even Bader's AIM theory, which has many beautiful theoretical properties, > can give non-nuclear attractors in some materials. > The persistent use of methods like Mulliken and Lowden, which have been > known for decades (longer than most of us have been alive) > to be highly unstable and have no well-defined basis set limit, has > contributed to the confusion. > > > From a historical perspective, this is similar to people's early aversion > to "flying machines". > For many decades, the concept of heavier than air flying machines (what we > now call airplanes) was considered a crackpot idea (a "fiction"). > This is because early attempts to build "flying machines" were dismal > failures. > It was only after people were able to construct successful demonstrations > that the societal resistance to airplanes began to reverse. > Nowadays, it is hard for us to imagine or justify the profound societal > resistance to building airplanes that existed around 1900. > > Some of the modern charge assignment methods are getting much better than > the earliest ones. > There is mounting experimental and computational evidence that some of the > most recent schemes > are orders of magnitude more reliable than those developed decades ago. > Hopefully, this recent progress will go a long way towards convincing > computational chemistry researchers that > the limitations we have become accustomed to can be reversed after all. > I realize all of this will take time, but as a computational chemistry > community we need to make an effort for progress. > > The continual use of explicitly basis set dependent methods like Mulliken > and Lowden is a bit weary at times, and comes off as a > serious shame in the face of better available recent methods. As a > computational chemistry community what can we do to support progress? > Do you think it is appropriate at this time for computational chemistry > journals to develop standards that Mulliken and Lowden > populations are not considered to be of publishable quality and that > published populations should be from methods with a > well-defined basis set limit? One could argue that it is important for > published articles to show the fundamental limitations of > Mulliken and Lowden schemes, but this has been established in countless > papers over the past 50 years. > I recall that my master's thesis advisor, who is a purely experimental > catalysis researcher, warned us many years ago > about the limitations of Mulliken charges. If experimentalists knew about > this all the way back then, why as a leading > computational chemistry community are we still fighting the obvious decades > later? > > It may be that the computational chemistry community has been slow to > develop better alternatives. > I believe the continued use of Mulliken and Lowden schemes as default > methods in some > quantum chemistry programs is due to the inherent limitations of other > available charge assignment schemes. > Until recently, the NPA/NBO scheme, which has many great properties, was > non-convergent for many systems > near the complete basis set limit. My experience and tests have shown this > improved within the last year. > The NBO website and manual says that recently they have improved the > projection algorithm to make it > more reliable. So, at least until very recently, the convergence of the > NPA/NBO scheme was not sufficiently > reliable to use it as a default charge assignment method. The issue of > non-nuclear attractors has precluded > using Bader's scheme as a default method for assigning net atomic charges. > The Hirshfeld method assigns > net atomic charges that are too small in magnitude. Methods such as CHELP, > CHELPG, ESP, etc. do not work > for dense nonporous materials that lack a van der Waals surface. Computing > the APT and Born effective charges > requires a computationally expensive frequency (first-order perturbation > theory) computation or a series of energy calculations with > various atomic displacements. Thus, it seems that until recently the > computational chemistry community has been stuck with > seriously flawed methods such as Mulliken and Lowden as defaults in popular > quantum chemistry programs. > > For the past couple of years, I and one of my Ph.D. students have been > developing a better alternative. > The goal of our project is to develop a general-purpose atomic population > analysis method that works > nearly flawlessly across a broad range of diverse material classes, > including both molecular and solid-state > materials. We have made extensive comparisons to experimental properties > across diverse materials. > Our objective is to develop a method that converges reliably and > efficiently and would be ideally suited > for use as a default atomic population analysis method in popular quantum > chemistry programs > irrespective of the basis set type. We currently have a manuscript on this > new method under review. > We are hoping that it is not too late for the computational chemistry > community to improve. > We earnestly solicit your support to enable the computational chemistry > community to make progress in the important > area of atomic population analysis methods. > > Sincerely, > > Tom > > > On Wed, Sep 2, 2015 at 12:11 AM, Irena Efremenko irena.efremenko* > weizmann.ac.il wrote: > > > Thanks, Tom, agree. But my main idea is that atomic charges derived from > > QC calculations is a kind of fiction. I would recommend not to use it at > > all, especially for transition metals, and even more for such heavy atoms > > as Pu. > > ****** > > Dr. Irena Efremenko > > Department of Organic Chemistry > > Weizmann Institute of Science > > 76100 Rehovot, Israel > > Phone: +972 8 9343680 > > FAX: +972 8 9343029 > > Email: irena.efremenko[*]weizmann.ac.il > > ****** > > > > On Sep 1, 2015, at 22:37 , Thomas Manz thomasamanz__gmail.com < > > owner-chemistry[*]ccl.net> wrote: > > > > Irena, > > > > You said "the basis set dependence of atomic charges arises from the > > basis set dependence of the spatial distribution of the electron density". > > This is only true for charge assignment methods that are functionals of the > > electron density. > > > > It is profoundly violated by Mulliken, Lowden, and other charge assignment > > methods that have explicit basis set dependence. This is why Mulliken and > > Lowden charges are not generally considered useful. > > > > Tom > > > > On Tue, Sep 1, 2015 at 8:47 AM, Irena Efremenko > > irena.efremenko---weizmann.ac.il wrote: > > > >> The initial question is lost in the discussion of technical problems. > >> > >> In my opinion, the answer is that ATOMS IN MOLECULES is not a physical > >> observable. (corollary: partial atomic charges are not physical > >> observables.) The partitioning of the electron density according to the > >> definition of atoms in each specific scheme is what determines atomic > >> charges, and this can be somewhat arbitrary. For example, in the Mulliken > >> partitioning scheme the electron density between two bonded atoms is > >> divided half-and-half, while in QTAIM atoms are divided by surfaces of zero > >> flux in the gradient vector field of the electron density. Thus, > >> corresponding charges should be different. > >> > >> Again, the basis set dependence of atomic charges arises from the basis > >> set dependence of the spatial distribution of the electron density, > >> especially in the range of diffuse functions. Usually, it influences > >> calculated charges to a lesser degree than the partitioning scheme. > >> > >> ****** > >> Dr. Irena Efremenko > >> Department of Organic Chemistry > >> Weizmann Institute of Science > >> 76100 Rehovot, Israel > >> Phone: +972 8 9343680 > >> FAX: +972 8 9343029 > >> Email: irena.efremenko,weizmann.ac.il > >> ****** > >> > >> On Sep 1, 2015, at 08:06 , Dr. Robert Molt Jr. r.molt.chemical.physics+/- > >> gmail.com wrote: > >> > >> Atomic charge models are not basis independent; see Chris Cramer's book, > >> chapter 9, p.314. Some models give charges which are consistent with > >> increasing basis set size, some are not, but all depend on the basis. > >> > >> If you have anions, you cannot describe the density correctly without > >> diffuse functions; this is a basis set dependence. > >> > >> Dr. Robert Molt Jr.r.molt.chemical.physics]-[gmail.com > >> > >> On 08/31/2015 11:14 PM, John McKelvey jmmckel(a)gmail.com wrote: > >> > >> Hello, > >> > >> There is a paper from a group in Germany demonstrating essentially basis > >> set independence of atomic charges.... Terrible to say that while I > >> remember the paper, and that the method has been installed in ORCA for the > >> next release, I will have to search for the paper... just moved from > >> Indiana to Missouri so things are in a bit of disarray. > >> > >> Maybe someone has seen this paper? > >> > >> > >> John > >> > >> > >> On Mon, Aug 31, 2015 at 5:47 PM, Víctor Luaña Cabal > >> victor_-_fluor.quimica.uniovi.es wrote: > >> > >>> > >>> Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor ~~ > >>> fluor.quimica.uniovi.es] > >>> On Mon, Aug 31, 2015 at 04:22:51PM -0400, Jim Kress > >>> jimkress35-x-gmail.com wrote: > >>> > > >>> > Sent to CCL by: "Jim Kress" [jimkress35]-[gmail.com] > >>> > Did you use an ECP for Plutonium and if so, was it properly > >>> represented in > >>> > the AIM analysis? > >>> > >>> Jim, > >>> > >>> QTAIM should refer to the all electron density. However there have > >>> been explorations of using ECP valence densities and they can work if > >>> you do it carefully. You can either add the core contributions to the > >>> valence density (it works) or be advise that your electron density is > >>> not complete, so there are properties of the real QTAIM analysis that > >>> can not work. > >>> > >>> For instance, the basins and the topological partition of the full > >>> electron density (rho) is not equivalent if you are using only the > >>> valence component (val-rho). > >>> > >>> However, if the basins are well defined there is no problem in > >>> integrating the valence density within the full electron rho. The same > >>> can be said for the analysis of spin components, and so on. > >>> Using the critic2 code a lot of strange numerical experiments of > >>> this kind can be easily performed. The code also has techniques to > >>> fulfill the valence density with core components. > >>> > >>> Read on critic2 in this ref. > >>> > >>> A. Otero-de-la-Roza et al, Comput phys Commun 182 (2013) 2232--2248 > >>> > >>> An updated version of the code and manual can be found on > >>> > >>> > >>> > >>> > >>> I may look for old work published on this subject, if you are truly > >>> interested. > >>> > >>> Best regards, > >>> Víctor Luaña > >>> -- > >>> . . "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 también 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.Víctor Luaña, in silico chemist & prof. ! I hate the bureaucracy > >>> ! Departamento de Química Física y Analítica ! imposed by companies to > >>> ! Universidad de Oviedo, 33006-Oviedo, Spain ! which I owe nothing: > >>> ! e-mail: victor(a)fluor.quimica.uniovi.es ! amazon, ResearchGATE > >>> and > >>> ! phone: +34-985-103491 fax: +34-985-103125 ! the like. > >>> +--------------------------------------------+ > >>> GroupPage : http://azufre.quimica.uniovi.es/ > >>> (being reworked) > >>> > >>> > >>> > >>> > >>> > >>> E-mail to subscribers: CHEMISTRY/a\ccl.net or use:>>> > >>> E-mail to administrators: CHEMISTRY-REQUEST/a\ccl.net or use>>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >> > >> > >> -- > >> John McKelvey > >> 545 Legacy Pointe Dr > >> O'Fallon, MO 63376 > >> 636-294-5302 > >> jmmckel/a\gmail.com > >> > >> > >> > >> > > > > -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke(!)monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia From owner-chemistry@ccl.net Wed Sep 2 23:29:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor(0)fluor.quimica.uniovi.es" To: CCL Subject: CCL: NBO vs Loewdin Charges Message-Id: <-51666-150902232100-31391-wtyylTaIwjENN9asqUvHDA:_: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: Thu, 03 Sep 2015 05:04:58 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor_+_fluor.quimica.uniovi.es] On Wed, Sep 02, 2015 at 10:15:53AM -0600, Thomas Manz thomasamanz###gmail.com wrote: > Hi, > > The difficulty with charge assignment schemes is largely due to historical > artifacts. > All of the earliest schemes for assigning net atomic charges were seriously > flawed: Mulliken, Lowden, Hirshfeld, etc. > Even Bader's AIM theory, which has many beautiful theoretical properties, > can give non-nuclear attractors in some materials. > The persistent use of methods like Mulliken and Lowden, which have been > known for decades (longer than most of us have been alive) > to be highly unstable and have no well-defined basis set limit, has > contributed to the confusion. Sorry, but I *must* intervene. Non nuclear attractors (NNA) aka NNM (non nuclear maxima) *are real* an have a well known meaning [6]. In my opinion hey have a "well-defined basis set limit", but I don't really known if we agree on what that means. Using good enough basis sets and xc treatments are essential, and it is easy to agree on that. By other names NNA'shave been known as electrides [1], solved electrons [2], color centers [3], solids under high pressure conditions [4] ... and many other well accepted physical known properties. Many are known since one century or more to any solid state physicists. It is true that the issue was plenty of confusion and wrong seminal ideas. For instance, it proved to be wrong that metellicity was due to the existence of NNA's. The true result is that a metal may have NNA's (Li, Na, ...) [5] or it may not have NNA's (Cs, many 3d pure metals ...). Metalic character and NNA are different properties, each responding to different characteristics. There are other real causes to the confussion on this subject. The carbon-carbon bond exemplifies many. In the case of triple C#C bonds the interatomic distances are closer to the border of occurence or not occurrence of NNA's. Details on basis set, electron correlation treatment, embeding, ... can produce that real or spurious NNA's appear in your calculation. My advise (and this has been given *many times* by any good in sillico chemists: never trust an apparent software result before examining the variables that control it). Remember the old saying: 'garbage in garbage out' (GIGO). In the case of NNA's: explore well the effect of the interatomic distances and then anything that influences the geometry. This is a particular subject in which I have worked and published for a long time. I hoped that the issue would be clear after Phys. Rev. Lett. 83 (1999) 1930 [6], but I should have know best. Peace and success, Víctor [1] Density-functional description of electrides SG Dale, A Otero-de-la-Roza, ER Johnson Physical Chemistry Chemical Physics 16 (2014) 14584-14593 [2] Na solved in NH3 produces solved electrons that give a nice blue color to the solution. This is explained in many general chemistry courses (Chemistry 101, if you prefer te USA terms). [3] Rigorous characterization of oxygen vacancies in ionic oxides Paula Mori-Sánchez et al Phys. Rev. B 66 (2002) 075103-1--6 [4] Non-nuclear maxima of the electron density on alkaline metals V Luaña, P Mori-Sánchez, A Costales, MA Blanco, AM Pendás The Journal of chemical physics 119 (2003) 6341-6350 [5] Polarity inversion in the electron density of BP crystal, Paula Mori-Sánchez, Ángel Martín Pendás, Víctor Luaña Phys. Rev. B 63 (2001) 125103-1--4 [6] Non-nuclear maxima of the electron density AM Pendás, MA Blanco, A Costales, P Mori-Sánchez, V Luaña Physical review letters 83 (1999) 1930 -- . . "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 también 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.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems, ! Departamento de Química Física y Analítica ! 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/