From owner-chemistry@ccl.net Wed Feb 19 01:36:00 2020 From: "Peter Kraus peter.kraus##geeksonbikes.net" To: CCL Subject: CCL: Isosurface representation of VSCC Message-Id: <-53981-200219013142-21547-ZJRwhxFR3RiONkS4qUwa5w*|*server.ccl.net> X-Original-From: Peter Kraus Content-Type: multipart/alternative; boundary="00000000000086da6e059ee7f0fb" Date: Wed, 19 Feb 2020 14:31:28 +0800 MIME-Version: 1.0 Sent to CCL by: Peter Kraus [peter.kraus\a/geeksonbikes.net] --00000000000086da6e059ee7f0fb Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Tymofii, thank you for the article. I have to admit, that I have never used QTAIM, despite finding the theory rather elegant ever since Prof. Farrugia mentioned it in my undergrad... My take away message from the paper you mentioned is rather different, however: rather than sticking to Bader's original intention of doing away with the hazy concept of "chemical bond" altogether, it might be easier to rename the (3, -1) critical points (and associated paths) as "line critical points" (or paths). The idea that the MG's of a structure derived from the optimized density and from the "promolecule" density are rather similar is not surprising to anyone who looked at how accurate the superposition of atomic densities is as a guess for QM calculations! As a final point, if we assume the H=C2=B7=C2=B7=C2=B7H line paths to be "a= rtefacts" due to distorted structure, I wonder whether simply re-optimizing the structures with dispersion corrections (the authors used plain B3LYP) would provide that additional nudge required to eliminate those paths from r_e. Best wishes, Peter On Mon, 17 Feb 2020 at 00:50, Tymofii Nikolaienko tim_mail]_[ukr.net < owner-chemistry+*+ccl.net> wrote: > Dear Tobias, > > although this is not a direct answer, I'd still like to highlight the > following publication related to QTAIM methodology in general, > and discussing whether or not this analysis does(not) reveal bonding: > > Z. A. Keyvani, S. Shahbazian, M. Zahedi, Chem. Eur. J. 2016, 22, 5003, > https://onlinelibrary.wiley.com/doi/abs/10.1002/chem.201504862 > > Roughly speaking, they show that by applying QTAIM to the sum of densitie= s > of isolated atoms, one gets almost the same > graph of bond paths as if the true molecular density was analyzed. > However, the former 'model' density has no information about > anyt bonding... > > Many more similar indications can be found in the papers citing the above > one (see, e.g., > https://scholar.google.com.ua/scholar?cites=3D2642471166107455109 ) > > > Best regards, > Tymofii Nikolaienko > --- > Tymofii Nikolaienko, Ph.D., > Faculty of Physics, Taras Shevchenko National University of Kyiv > > > 14.02.2020 13:56, Tobias Kraemer tobias.kraemer]~[mu.ie =D0=BF=D0=B8=D1= =88=D0=B5: > > Sent to CCL by: "Tobias Kraemer" [tobias.kraemer*mu.ie] > Dear all, > > I have a question for those of you with experience in QTAIM analysis, in > particular the Laplacian topology. I have seen a number of of publication= s > that showed isosurface representations of the Valence-Shell Charge > Concentration (VSCC) regions around a specific atom (in a molecule), nice= ly > highlighting bonding (bcc) and lonepair (nbcc) regions. One such example > can be found in Stalke's paper Organometallics, 2008, 27, 2306. I have be= en > playing around with some model systems and the AIMALL software, and whils= t > I was able to figure out how to perform a topological analysis of the > Laplacian itself, it is not clear to me how to visualise these VSCC regio= ns > as envelope surfaces. As far as I understand this is not simply a 3D plot > of the Laplacian (or L(rho) function), but I might be wrong. > > Could anybody give me some advise which programs can do this and how it i= s > done? I'd be curious to learn this and appreciate your help. > > Kind regards, > > TobiasE-mail to subscribers: CHEMISTRY|a|ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST|a|ccl.net or usehttp://www.ccl.net/c= hemistry/sub_unsub.shtml > > --=20 Sent from your iPhone. No, really. --00000000000086da6e059ee7f0fb Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Tymofii,
thank you for the article. I = have to admit, that I have never used QTAIM, despite finding the theory rat= her elegant ever since Prof. Farrugia mentioned it in my undergrad...
<= /div>

My take away message from the paper you mentioned = is rather different, however: rather than sticking to Bader's original = intention of doing away with the hazy concept of "chemical bond" = altogether, it might be easier to rename the (3, -1) critical points (and a= ssociated paths) as "line critical points" (or paths).
=
The idea that the MG's of a structure derived from the o= ptimized density and from the "promolecule" density are rather si= milar is not surprising to anyone who looked at how accurate the superposit= ion of atomic densities is as a guess for QM calculations!

As a final point, if we assume the H=C2=B7=C2=B7=C2=B7H line paths= to be "artefacts" due to distorted structure, I wonder whether s= imply re-optimizing the structures with dispersion corrections (the authors= used plain B3LYP) would provide that additional nudge required to eliminat= e those paths from r_e.

Best wishes,
Pet= er


On Mon, 17 Feb 2020 at 00:50, Tymofii Nikolaienk= o tim_mail]_[ukr.net <owner-chemistry+*+ccl.net> wrote:
=20 =20 =20

Dear Tobias,

although this is not a direct answer, I'd still like to highligh= t the following publication related to QTAIM methodology in general, and discussing whether or not this analysis does(not) reveal bonding:

Z. A. Keyvani, S. Shahbazian, M. Zahedi, Chem. Eur. J. 2016, 22, 5003, https://onlinelibrary.wiley.com/doi/abs/10.1002/che= m.201504862

Roughly speaking, they show that by applying QTAIM to the sum of densities of isolated atoms, one gets almost the same
graph of bond paths as if the true molecular density was analyzed. However, the former 'model' density has no information about<= br> anyt bonding...

Many more similar indications can be found in the papers citing the above one (see, e.g., https://scholar.google.com.ua/scholar?cites=3D26= 42471166107455109 )


Best regards,
Tymofii Nikolaienko

---
Tymofii Nikolaienko, Ph.D.,
Faculty of Physics, Taras Shevchenko National University of Kyiv


14.02.2020 13:56, Tobias Kraemer tobias.kraemer]~[mu.ie= =D0=BF=D0=B8=D1=88=D0=B5:
Sent to CCL by: "Tobias  Kraemer" [tobias.kraemer*mu.ie]
Dear all,

I have a question for those of you with experience in QTAIM analysis, in=20
particular the Laplacian topology. I have seen a number of of publications=
=20
that showed isosurface representations of the Valence-Shell Charge=20
Concentration (VSCC) regions around a specific atom (in a molecule), nicely=
=20
highlighting bonding (bcc) and lonepair (nbcc) regions. One such example=20
can be found in Stalke's paper Organometallics, 2008, 27, 2306. I have =
been=20
playing around with some model systems and the AIMALL software, and whilst=
=20
I was able to figure out how to perform a topological analysis of the=20
Laplacian itself, it is not clear to me how to visualise these VSCC regions=
=20
as envelope surfaces. As far as I understand this is not simply a 3D plot=
=20
of the Laplacian (or L(rho) function), but I might be wrong.=20

Could anybody give me some advise which programs can do this and how it is=
=20
done? I'd be curious to learn this and appreciate your help.=20

Kind regards,

TobiasE-mail to subscribers: CHEMISTRY|a|ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST|a|ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.c=
cl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n=
et/jobs=20
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nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/


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Sent from your iPhone. No, really.
--00000000000086da6e059ee7f0fb-- From owner-chemistry@ccl.net Wed Feb 19 03:05:01 2020 From: "Alessandro Erba alessandro.erba{}unito.it" To: CCL Subject: CCL: MSSC2020 Summer School, 6-11 Sept. 2020, Torino (Italy) Message-Id: <-53982-200219030050-23881-Q2tcrz3pCUY/eKyiHjIwVw-#-server.ccl.net> X-Original-From: "Alessandro Erba" Date: Wed, 19 Feb 2020 03:00:49 -0500 Sent to CCL by: "Alessandro Erba" [alessandro.erba*|*unito.it] Dear friends of the CCL community, I am pleased to announce a new edition of the established series of MSSC Summer Schools on the Ab initio Modeling in Solid State Chemistry, to be held in the beautiful city of Torino (Italy), 6-11 September 2020: http://www.crystal.unito.it/mssc2020/ This week-long Summer School with lectures in the morning and hands-on sessions in the afternoon aims at introducing advanced functionalities of modern quantum-mechanical codes in the context of computational materials science. In particular, the CRYSTAL program will be used in the afternoon sessions and some of its new features, to be released in a next version, will be presented. Lectures from CRYSTAL developers will be complemented by lectures from CRYSTAL experienced users presenting their research activity in different fields: computational crystallography, mineralogy, vibrational spectroscopy, electronics, thermal transport, biology. See you in Torino! Alessandro Erba, on behalf of the Organizing Committee. From owner-chemistry@ccl.net Wed Feb 19 16:02:01 2020 From: "Benoit Gearald ablux13 .. gmail.com" To: CCL Subject: CCL: Radical optimisation Message-Id: <-53983-200219160001-7011-t3IGrCKg+XynCBZxeaGyeQ a server.ccl.net> X-Original-From: "Benoit Gearald" Date: Wed, 19 Feb 2020 15:59:59 -0500 Sent to CCL by: "Benoit Gearald" [ablux13:-:gmail.com] Dear CCLers, I lauched a radical optimisation at G3 level. The radical corresponds to butadiene without a hydrogen atom at carbone 2. but in the output file I don't get this structure. I get two succesive double bond and the alternance is lost. I don't know whether there is a keyword to restrict the strucure or something in this way. Any help is appreciated Bonoit From owner-chemistry@ccl.net Wed Feb 19 16:55:01 2020 From: "Dr.N Sukumar n.sukumar- -snu.edu.in" To: CCL Subject: CCL: Isosurface representation of VSCC Message-Id: <-53984-200219042956-11478-M+QHpu3UeeRZ1Ad2PFtVVg---server.ccl.net> X-Original-From: "Dr.N Sukumar" Content-Type: multipart/alternative; boundary="000000000000ec227f059eea6d0f" Date: Wed, 19 Feb 2020 14:59:35 +0530 MIME-Version: 1.0 Sent to CCL by: "Dr.N Sukumar" [n.sukumar+*+snu.edu.in] --000000000000ec227f059eea6d0f Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable I would also add that the optimized bond lengths show a very strong correlation with the electron density (and Laplacian) at the (3, -1) critical point, for a given pair of atoms, which is a simple consequence of the fact that the electron density or wavefunction determines the molecular structure or external potential, and the molecular structure in turn determines the ground state density uniquely (first Hohenberg-Kohn theorem)= . *N. SukumarProfessor of ChemistryDirector, Center for Informatics**Shiv Nadar University, India* https://chemistry.snu.edu.in/people/faculty/n-sukumar =E2=80=9CYou generally cannot design success; rather you nurture it when it (rarely) happens.=E2=80=9D - Peter Murray-Rust On Wed, Feb 19, 2020 at 12:58 PM Peter Kraus peter.kraus##geeksonbikes.net = < owner-chemistry _ ccl.net> wrote: > Dear Tymofii, > thank you for the article. I have to admit, that I have never used QTAIM, > despite finding the theory rather elegant ever since Prof. Farrugia > mentioned it in my undergrad... > > My take away message from the paper you mentioned is rather different, > however: rather than sticking to Bader's original intention of doing away > with the hazy concept of "chemical bond" altogether, it might be easier t= o > rename the (3, -1) critical points (and associated paths) as "line critic= al > points" (or paths). > > The idea that the MG's of a structure derived from the optimized density > and from the "promolecule" density are rather similar is not surprising t= o > anyone who looked at how accurate the superposition of atomic densities i= s > as a guess for QM calculations! > > As a final point, if we assume the H=C2=B7=C2=B7=C2=B7H line paths to be = "artefacts" due > to distorted structure, I wonder whether simply re-optimizing the > structures with dispersion corrections (the authors used plain B3LYP) wou= ld > provide that additional nudge required to eliminate those paths from r_e. > > Best wishes, > Peter > > > On Mon, 17 Feb 2020 at 00:50, Tymofii Nikolaienko tim_mail]_[ukr.net ~~ ccl.net> wrote: > >> Dear Tobias, >> >> although this is not a direct answer, I'd still like to highlight the >> following publication related to QTAIM methodology in general, >> and discussing whether or not this analysis does(not) reveal bonding: >> >> Z. A. Keyvani, S. Shahbazian, M. Zahedi, Chem. Eur. J. 2016, 22, 5003, >> https://onlinelibrary.wiley.com/doi/abs/10.1002/chem.201504862 >> >> Roughly speaking, they show that by applying QTAIM to the sum of >> densities of isolated atoms, one gets almost the same >> graph of bond paths as if the true molecular density was analyzed. >> However, the former 'model' density has no information about >> anyt bonding... >> >> Many more similar indications can be found in the papers citing the abov= e >> one (see, e.g., >> https://scholar.google.com.ua/scholar?cites=3D2642471166107455109 ) >> >> >> Best regards, >> Tymofii Nikolaienko >> --- >> Tymofii Nikolaienko, Ph.D., >> Faculty of Physics, Taras Shevchenko National University of Kyiv >> >> >> 14.02.2020 13:56, Tobias Kraemer tobias.kraemer]~[mu.ie =D0=BF=D0=B8=D1= =88=D0=B5: >> >> Sent to CCL by: "Tobias Kraemer" [tobias.kraemer*mu.ie] >> Dear all, >> >> I have a question for those of you with experience in QTAIM analysis, in >> particular the Laplacian topology. I have seen a number of of publicatio= ns >> that showed isosurface representations of the Valence-Shell Charge >> Concentration (VSCC) regions around a specific atom (in a molecule), nic= ely >> highlighting bonding (bcc) and lonepair (nbcc) regions. One such example >> can be found in Stalke's paper Organometallics, 2008, 27, 2306. I have b= een >> playing around with some model systems and the AIMALL software, and whil= st >> I was able to figure out how to perform a topological analysis of the >> Laplacian itself, it is not clear to me how to visualise these VSCC regi= ons >> as envelope surfaces. As far as I understand this is not simply a 3D plo= t >> of the Laplacian (or L(rho) function), but I might be wrong. >> >> Could anybody give me some advise which programs can do this and how it = is >> done? I'd be curious to learn this and appreciate your help. >> >> Kind regards, >> >> TobiasE-mail to subscribers: CHEMISTRY|a|ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST|a|ccl.net or usehttp://www.ccl.net/= chemistry/sub_unsub.shtml > >> >> > > -- > Sent from your iPhone. No, really. > --000000000000ec227f059eea6d0f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I would also add that the optimized bond lengths show a ve= ry strong correlation with the electron density (and Laplacian) at the (3, -1) critical point, for a given pair of atoms, which is a simple c= onsequence of the fact that the electron density or wavefunction determines= the molecular structure or external potential, and=20 the molecular structure in turn determines the ground state density uniquel= y (first Hohenberg-Kohn theorem).
N. Sukumar
Profess= or of Chemistry
Director, Center for Informatics
Shiv Nadar Un= iversity, India
https://chemistry.snu.edu.in/people/faculty/n-sukumar
<= span>=E2=80=9CYou generally cannot design success; rather you = nurture it when it (rarely) happens.=E2=80=9D - <= span>Peter Murray-Rust
=


On Wed, Feb 19, 2020 at= 12:58 PM Peter Kraus peter.kraus##geek= sonbikes.net <owner-chemi= stry _ ccl.net> wrote:
Dear Tymofii,
thank you for the= article. I have to admit, that I have never used QTAIM, despite finding th= e theory rather elegant ever since Prof. Farrugia mentioned it in my underg= rad...

My take away message from the paper yo= u mentioned is rather different, however: rather than sticking to Bader'= ;s original intention of doing away with the hazy concept of "chemical= bond" altogether, it might be easier to rename the (3, -1) critical p= oints (and associated paths) as "line critical points" (or paths)= .

The idea that the MG's of a structure derive= d from the optimized density and from the "promolecule" density a= re rather similar is not surprising to anyone who looked at how accurate th= e superposition of atomic densities is as a guess for QM calculations!

As a final point, if we assume the H=C2=B7=C2=B7=C2=B7= H line paths to be "artefacts" due to distorted structure, I wond= er whether simply re-optimizing the structures with dispersion corrections = (the authors used plain B3LYP) would provide that additional nudge required= to eliminate those paths from r_e.

Best wishes,
Peter


On Mon, 17 Feb 2020 at 00:50, Tymofi= i Nikolaienko tim_mail]_[ukr.n= et <= owner-chemistry ~~ ccl.net> wrote:
=20 =20 =20

Dear Tobias,

although this is not a direct answer, I'd still like to highligh= t the following publication related to QTAIM methodology in general, and discussing whether or not this analysis does(not) reveal bonding:

Z. A. Keyvani, S. Shahbazian, M. Zahedi, Chem. Eur. J. 2016, 22, 5003, https://onlinelibrary.wiley.com/doi/abs/10.1002/che= m.201504862

Roughly speaking, they show that by applying QTAIM to the sum of densities of isolated atoms, one gets almost the same
graph of bond paths as if the true molecular density was analyzed. However, the former 'model' density has no information about<= br> anyt bonding...

Many more similar indications can be found in the papers citing the above one (see, e.g., https://scholar.google.com.ua/scholar?cites=3D26= 42471166107455109 )


Best regards,
Tymofii Nikolaienko

---
Tymofii Nikolaienko, Ph.D.,
Faculty of Physics, Taras Shevchenko National University of Kyiv


14.02.2020 13:56, Tobias Kraemer tobias.kraemer]~[mu.ie= =D0=BF=D0=B8=D1=88=D0=B5:
Sent to CCL by: "Tobias  Kraemer" [tobias.kraemer*mu.ie]
Dear all,

I have a question for those of you with experience in QTAIM analysis, in=20
particular the Laplacian topology. I have seen a number of of publications=
=20
that showed isosurface representations of the Valence-Shell Charge=20
Concentration (VSCC) regions around a specific atom (in a molecule), nicely=
=20
highlighting bonding (bcc) and lonepair (nbcc) regions. One such example=20
can be found in Stalke's paper Organometallics, 2008, 27, 2306. I have =
been=20
playing around with some model systems and the AIMALL software, and whilst=
=20
I was able to figure out how to perform a topological analysis of the=20
Laplacian itself, it is not clear to me how to visualise these VSCC regions=
=20
as envelope surfaces. As far as I understand this is not simply a 3D plot=
=20
of the Laplacian (or L(rho) function), but I might be wrong.=20

Could anybody give me some advise which programs can do this and how it is=
=20
done? I'd be curious to learn this and appreciate your help.=20

Kind regards,

TobiasE-mail to subscribers: CHEMISTRY|a|ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST|a|ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.c=
cl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n=
et/jobs=20
Conferences: http://server.ccl.net/chemistry/announcements/co=
nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/


--
Sent from your iPhone. No, really.
--000000000000ec227f059eea6d0f-- From owner-chemistry@ccl.net Wed Feb 19 21:44:01 2020 From: "Nandini Gattadahalli nandipranav1234!=!gmail.com" To: CCL Subject: CCL: Radical optimisation Message-Id: <-53985-200219212643-9216-H2tDo0J4uG/vD7Wq03cdew[-]server.ccl.net> X-Original-From: Nandini Gattadahalli Content-Type: multipart/alternative; boundary="0000000000005f6f0e059ef8a2ec" Date: Thu, 20 Feb 2020 07:56:21 +0530 MIME-Version: 1.0 Sent to CCL by: Nandini Gattadahalli [nandipranav1234() gmail.com] --0000000000005f6f0e059ef8a2ec Content-Type: text/plain; charset="UTF-8" i think running calculations for radical in gas phase, use HF theory with basis sets like 6-311g or 6-31+g++ same in solvent medium. we get structure of the radical. i run for diglycine zwitterrion 20years back same.way. Dr.Nandini .G > from IISc On Thu, Feb 20, 2020, 04:17 Benoit Gearald ablux13 .. gmail.com < owner-chemistry.:.ccl.net> wrote: > > Sent to CCL by: "Benoit Gearald" [ablux13:-:gmail.com] > Dear CCLers, > > I lauched a radical optimisation at G3 level. The radical corresponds to > butadiene without a hydrogen atom at carbone 2. but in the output file I > don't get this structure. I get two succesive double bond and the > alternance is lost. I don't know whether there is a keyword to restrict > the > strucure or something in this way. > > Any help is appreciated > > Bonoit> > > --0000000000005f6f0e059ef8a2ec Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
i think running calculations for radical in gas phase, us= e HF theory with basis sets like 6-311g or 6-31+g++ same in solvent medium.= we get structure of the radical. i run for diglycine zwitterrion 20years b= ack same.way.

Dr.Nandini .G
from IISc

On Thu, Feb 20, 2020, 04:17 Benoit Gear= ald ablux13 .. gmail.com <owner-chemistry.:.ccl.net> wrote:

Sent to CCL by: "Benoit=C2=A0 Gearald" [ablux13:-:gmail.com= ]
Dear CCLers,

I lauched a radical optimisation at G3 level. The radical corresponds to butadiene without a hydrogen atom at carbone 2. but in the output file I don't get this structure. I get two succesive double bond and the
alternance is lost. I don't know whether there is a keyword to restrict= the
strucure or something in this way.

Any help is appreciated

Bonoit



-=3D This is automatically added to each message by the mailing script =3D-=
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--0000000000005f6f0e059ef8a2ec--