From owner-chemistry "-at-" ccl.net Wed Aug 18 13:14:01 2021 From: "Mark Zottola mzottola]|[gmail.com" To: CCL Subject: CCL:G: QTAIM Delocalisation Index and NNA Message-Id: <-54439-210818131102-16678-+j7chJ6BvDaCdGL6LQKV+w : server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary="0000000000003b71de05c9d8848d" Date: Wed, 18 Aug 2021 13:10:41 -0400 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola++gmail.com] --0000000000003b71de05c9d8848d Content-Type: text/plain; charset="UTF-8" Would it be possible for you to read the basis set information from formats other than Gaussian and Molden files? Reading in a PUNCH file from Firefly or a dat file from GAMESS would be helpful. OpenBabel does not convert into fck format nor does it read from dat files. MultiWFN is extraordinarily helpful and eliminating this limitation would make it even more valuable. On Tue, Aug 17, 2021 at 3:07 PM Tian Lu sobereva * sina.com < owner-chemistry+*+ccl.net> wrote: > > Sent to CCL by: "Tian Lu" [sobereva|a|sina.com] > Dear Tobias, > > Mayer bond order and Fuzzy bond order are essentially equivalent to DI, see > J. Phys. Chem. A, 109, 9904 (2005) for comparison and detailed discussion, > the only difference between them is the partition of atomic spaces. Their > values are fairly close to each other especially for homonuclear bonds. > > So, I suggest you to employ Mayer bond order or fuzzy bond order instead, > they can be easily calculated using options 1 and 7 respectively in main > function 9 of Multiwfn code (http://sobereva.com/multiwfn). In this case > you > do not need to worry about the presence of NNA. Another advantage is that > their calculations are significantly cheaper than calculating DI based on > the > expensive AIM paritition. > > -------------------------------- > > Best regards, > Dr. Tian Lu > Beijing Kein Research Center for Natural Sciences, Beijing, P. R. China > > > ----- Original Message ----- > > From: "Tobias Kraemer tobias.kraemer/a\mu.ie" > To: "Lu, Tian " > Subject: CCL: QTAIM Delocalisation Index and NNA > Date: 2021-08-17 04:01 > Sent to CCL by: "Tobias Kraemer" [tobias.kraemer[-]mu.ie] > Dear CCLers, > I am currently running some QTAIM topology analyses of main group dimers > (AlAl, SiSi...) to elucidate > their electronic structures. What has become a frequent occurrence is the > presence of non-nuclear attractors at the centre of the E-E linkages, and > this causes some issues > regarding the interpretation of QTAIM parameters. In particular I would > like > to use delocalisation > indices (DI) to quantify the amount of single- or double bond character in > these species. In the > presence of a NNA there is no bond-critical point and associated DI, but > two > bcps between each atom > and the NNA (and I am not sure how to interpret this situation yet). I have > found a paper by Chesnut in > this area, and in one paper (Heteroatom Chemistry 2002, 13, 53) I came > across > this footnote in a table > summarising QTAIM DI values: > "A non-nuclear attractor (NNA) is found in the Si Si bond midpoint in this > molecule. An effective Si Si > delocalization index is determined by presuming that half of the NNA > belongs > to each silicon atom. > This removes the NNA from the picture while preserving the sum of the Fii > and > Fij terms." > So, it seems to be possible to calculate an "effective" delocalisation > index > for the two atoms that are > bonded but in the presence of an NNA. I am a bit stuck at the moment, > trying > to reproduce the > numbers from the referenced paper for some of the compounds. The above > seems > to be implying that > the NNA basin population of the NNA is divided equally between the two > neighbouring centres but I > am not quite sure whether this also involves the DI(E,NNA) values. I was > wondering whether anyone > here has experience with these situations, and would be able to provide > some > more detail or a protocol > on how to exactly obtain these effective DIs when a NNA is present. I have > looked at the original > literature by Bader, but so far had little success combining various > parameters from the (AIMALL) > output in order to reproduce these values. It's not clear which numbers I > am > looking for in the output, > or rather, how to combine the right numbers. > You help would be much appreciated. Thanks in advance. > Kind regards, > Tobias> > > --0000000000003b71de05c9d8848d Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Wou= ld it be possible for you to read the basis set information from formats ot= her than Gaussian and Molden files?
Reading in a PUNCH file from Firefly or a dat file fro= m GAMESS would be helpful.=C2=A0 OpenBabel does not convert into fck format= nor does it read from dat files.=C2=A0 MultiWFN is extraordinarily helpful= and eliminating this limitation would make it even more valuable.

On = Tue, Aug 17, 2021 at 3:07 PM Tian Lu sobereva * sina.com <owner-chemistr= y+*+ccl.net> wrote:

Sent to CCL by: "Tian=C2=A0 Lu" [sobereva|a|sina.com]
Dear Tobias,

Mayer bond order and Fuzzy bond order are essentially equivalent to DI, see=
J. Phys. Chem. A, 109, 9904 (2005) for comparison and detailed discussion,<= br> the only difference between them is the partition of atomic spaces. Their values are fairly close to each other especially for homonuclear bonds.

So, I suggest you to employ Mayer bond order or fuzzy bond order instead, they can be easily calculated using options 1 and 7 respectively in main function 9 of Multiwfn code (http://sobereva.com/multiwfn). In thi= s case you
do not need to worry about the presence of NNA. Another advantage is that their calculations are significantly cheaper than calculating DI based on t= he
expensive AIM paritition.

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

Best regards,
Dr. Tian Lu
Beijing Kein Research Center for Natural Sciences, Beijing, P. R. China


----- Original Message -----
> From: "Tobias Kraemer tobias.kraemer/a\mu.ie" <owner-chemistry~~ccl.net&g= t;
To: "Lu, Tian " <sobereva~~sina.com>
Subject: CCL: QTAIM Delocalisation Index and NNA
Date: 2021-08-17 04:01
Sent to CCL by: "Tobias Kraemer" [tobias.kraemer[-]mu.ie]
Dear CCLers,
I am currently running some QTAIM topology analyses of main group dimers (AlAl, SiSi...) to elucidate
their electronic structures. What has become a frequent occurrence is the presence of non-nuclear attractors at the centre of the E-E linkages, and this causes some issues
regarding the interpretation of QTAIM parameters. In particular I would lik= e
to use delocalisation
indices (DI) to quantify the amount of single- or double bond character in<= br> these species. In the
presence of a NNA there is no bond-critical point and associated DI, but tw= o
bcps between each atom
and the NNA (and I am not sure how to interpret this situation yet). I have=
found a paper by Chesnut in
this area, and in one paper (Heteroatom Chemistry 2002, 13, 53) I came acro= ss
this footnote in a table
summarising QTAIM DI values:
"A non-nuclear attractor (NNA) is found in the Si Si bond midpoint in = this
molecule. An effective Si Si
delocalization index is determined by presuming that half of the NNA belong= s
to each silicon atom.
This removes the NNA from the picture while preserving the sum of the Fii a= nd
Fij terms."
So, it seems to be possible to calculate an "effective" delocalis= ation index
for the two atoms that are
bonded but in the presence of an NNA. I am a bit stuck at the moment, tryin= g
to reproduce the
numbers from the referenced paper for some of the compounds. The above seem= s
to be implying that
the NNA basin population of the NNA is divided equally between the two
neighbouring centres but I
am not quite sure whether this also involves the DI(E,NNA) values. I was wondering whether anyone
here has experience with these situations, and would be able to provide som= e
more detail or a protocol
on how to exactly obtain these effective DIs when a NNA is present. I have<= br> looked at the original
literature by Bader, but so far had little success combining various
parameters from the (AIMALL)
output in order to reproduce these values. It's not clear which numbers= I am
looking for in the output,
or rather, how to combine the right numbers.
You help would be much appreciated. Thanks in advance.
Kind regards,
Tobias



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