From owner-chemistry@ccl.net Sun Aug 2 17:21:00 2020 From: "Nike Dattani ndattani]=[gmail.com" To: CCL Subject: CCL: bond order calculation method Message-Id: <-54153-200802151011-22578-QWHL10HoQo8UwvwpZqkp9Q*_*server.ccl.net> X-Original-From: Nike Dattani Content-Type: multipart/alternative; boundary="0000000000000afb9f05abe9c50b" Date: Sun, 2 Aug 2020 15:09:54 -0400 MIME-Version: 1.0 Sent to CCL by: Nike Dattani [ndattani .. gmail.com] --0000000000000afb9f05abe9c50b Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Very interesting indeed! We also have a bond-order resource here: https://mattermodeling.stackexchange.com/q/901/5 And if there's any you or the grad student thinks we missed, we would like to include them. With my very best wishes! Nike On Thu, Jul 30, 2020 at 11:22 PM Thomas Manz thomasamanz : gmail.com < owner-chemistry+*+ccl.net> wrote: > Dear colleagues, > > One of my graduate students is in the process of preparing a YouTube vide= o > on the topic of computing bond orders using the method introduced in the > following paper: > > T. A. Manz, "Introducing DDEC6 atomic population analysis: part 3. > Comprehensive method to compute bond orders," RSC Advances, 7 (2017) > 45552-45581 (open access) DOI: 10.1039/c7ra07400j > > The video will be a less technical presentation, emphasizing chemical > concepts with less focus on mathematics. > > Were any of the concepts presented in the above paper unclear to you? If > so, could you please explain which of those concepts you did not > understand? If there is a pattern of some aspects being unclear, then I > would like to know so that it can be explained in a more understandable w= ay. > > If any of you have not taken the time to carefully read that paper, I > believe it would be worth your while to do so. Bond order is a foundation= al > chemical concept that has wide-ranging impacts and numerous applications > throughout the chemical sciences. The above paper presents the first > comprehensive and computationally efficient method to compute accurate bo= nd > orders across an extremely wide range of material types. > > This method to compute bond orders enabled the first study of > quantum-mechanically computed bond orders for a large number of diatomic > molecules: > > T. Chen and T. A. Manz, "Bond orders of the diatomic molecules," RSC > Advances, 9 (2019) 17072-17092 (open access) DOI: 10.1039/c9ra00974d > > In this work, bond orders were quantum-mechanically computed for 288 > diatomic molecules and ions, which is >10 times the number of diatomics f= or > which bond orders were quantum-mechanically computed in each prior work. > > Because diatomic molecules are the smallest molecules containing a > chemical bond, they are natural textbook examples for studying bond order= . > Therefore, I view the accurate bond orders for diatomic molecules as > foundational to chemical theory. Even among the diatomic molecules, there > are many interesting effects that you may not be familiar with yet. These > can often provide insights that are helpful to understand larger material= s > with more atoms. > > In two recent papers, the above bond order method was applied to identify > misbonded atoms in the experimentally-derived crystal structures of > metal-organic frameworks: > > T. Chen and T. A. Manz, "Identifying misbonded atoms in the 2019 CoRE > metal=E2=80=93organic framework database," RSC Advances, 10 (2020) 26944-= 26951 > (open access) DOI: 10.1039/d0ra02498h > > T. Chen and T. A. Manz, "A collection of forcefield precursors for > metal-organic frameworks," RSC Advances, 9 (2019) 36492-36507 (open acces= s) > DOI: 10.1039/c9ra07327b > > For example, carbon atoms in organic compounds often have a sum of bond > orders (SBOs) of approximately 4, because they have four electrons to sha= re > in covalent bonding. Therefore, in the above two studies, carbon atoms > having abnormally low or abnormally high SBOs were flagged as misbonded. = (A > low carbon SBO might be caused by a missing hydrogen atom that was not > reported in the crystal structure.) This kind of screening would have bee= n > much harder or perhaps infeasible without the above method to compute bon= d > orders. > > Another important application of these bond orders is to understand > changes that occur during chemical reactions. For example, several studie= s > reported changes in these bond orders during catalytic reactions. > > Finally, last year an interesting paper explored correlations between > these bond orders and crystal orbital Hamilton populations (a bond energy > projection method): > > R.Y. Rohling, I.C. Tranca, E.J.M. Henen, and E.A. Pidko, "Correlations > between density-based bond orders and orbital-based bond energies for > chemical bonding analysis," J. Phys. Chem. C, 123 (2019) 2843-2854 DOI: > 10.1021/acs.jpcc.8b08934 > > Within the same material class, the bond order between two specific > chemical elements was shown to be proportional to the COHP. The bond orde= r > is easier to interpret than the COHP. > > An encouraging sign is this bond order method is starting to gain some > traction in VASP and CP2K calculations (using the Chargemol code for > post-processing), which going back >3 years bond order calculations using > those codes were nearly unheard of. > > I believe the impact could be even much larger, which is why I'm reaching > out to try to highlight some of the use cases for this method as well as = to > give you an opportunity to explain to me what aspects of the method you a= re > having trouble understanding. > > Sincerely, > > Tom Manz > --0000000000000afb9f05abe9c50b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Very interesting indeed!
We also have a bon= d-order resource here:=C2=A0https://mattermodeling.stackexchange.com/q/901/5
And if there's any you or the grad student thinks we missed, we would= like to include them.
With my very best wishes!
Nike
On Thu, J= ul 30, 2020 at 11:22 PM Thomas Manz thomasamanz : gmail.com <owner-chem= istry+*+ccl.net> wrote:
Dear colleagues,

One of my graduate st= udents is in the process of preparing a YouTube video on the topic of compu= ting bond orders using the method introduced in the following paper:
T. A. Manz, "Introducing DDEC6 atomic population analysis: part 3. Co= mprehensive method to compute bond orders," RSC Advances, 7 (2017) 455= 52-45581 (open access) DOI: 10.1039/c7ra07400j

The video will be a l= ess technical presentation, emphasizing chemical concepts with less focus o= n mathematics.

Were any of the concepts presented in the above paper= unclear to you? If so, could you please explain which of those concepts yo= u did not understand? If there is a pattern of some aspects being unclear, = then I would like to know so that it can be explained in a more understanda= ble way.

If any of you have not taken the time to carefully read tha= t paper, I believe it would be worth your while to do so. Bond order is a f= oundational chemical concept that has wide-ranging impacts and numerous app= lications throughout the chemical sciences. The above paper presents the fi= rst comprehensive and computationally efficient method to compute accurate = bond orders across an extremely wide range of material types.

This m= ethod to compute bond orders enabled the first study of quantum-mechanicall= y computed bond orders for a large number of diatomic molecules:

T. = Chen and T. A. Manz, "Bond orders of the diatomic molecules," RSC= Advances, 9 (2019) 17072-17092 (open access) DOI: 10.1039/c9ra00974d
In this work, bond orders were quantum-mechanically computed for 288 diat= omic molecules and ions, which is >10 times the number of diatomics for = which bond orders were quantum-mechanically computed in each prior work.
Because diatomic molecules are the smallest molecules containing a che= mical bond, they are natural textbook examples for studying bond order. The= refore, I view the accurate bond orders for diatomic molecules as foundatio= nal to chemical theory. Even among the diatomic molecules, there are many i= nteresting effects that you may not be familiar with yet. These can often p= rovide insights that are helpful to understand larger materials with more a= toms.

In two recent papers, the above bond order method was applied = to identify misbonded atoms in the experimentally-derived crystal structure= s of metal-organic frameworks:

T. Chen and T. A. Manz, "Identif= ying misbonded atoms in the 2019 CoRE metal=E2=80=93organic framework datab= ase," RSC Advances, 10 (2020) 26944-26951 (open access) DOI: 10.1039/d= 0ra02498h =C2=A0

T. Chen and T. A. Manz, "A collection of force= field precursors for metal-organic frameworks," RSC Advances, 9 (2019)= 36492-36507 (open access) DOI: 10.1039/c9ra07327b

For example, carb= on atoms in organic compounds often have a sum of bond orders (SBOs) of app= roximately 4, because they have four electrons to share in covalent bonding= . Therefore, in the above two studies, carbon atoms having abnormally low o= r abnormally high SBOs were flagged as misbonded. (A low carbon SBO might b= e caused by a missing hydrogen atom that was not reported in the crystal st= ructure.) This kind of screening would have been much harder or perhaps inf= easible without the above method to compute bond orders.

Another imp= ortant application of these bond orders is to understand changes that occur= during chemical reactions. For example, several studies reported changes i= n these bond orders during catalytic reactions.

Finally, last year a= n interesting paper explored correlations between these bond orders and cry= stal orbital Hamilton populations (a bond energy projection method):
R.Y. Rohling, I.C. Tranca, E.J.M. Henen, and E.A. Pidko, "Correlation= s between density-based bond orders and orbital-based bond energies for che= mical bonding analysis," J. Phys. Chem. C, 123 (2019) 2843-2854 DOI: 1= 0.1021/acs.jpcc.8b08934

Within the same material class, the bond ord= er between two specific chemical elements was shown to be proportional to t= he COHP. The bond order is easier to interpret than the COHP.

An enc= ouraging sign is this bond order method is starting to gain some traction i= n VASP and CP2K calculations (using the Chargemol code for post-processing)= , which going back >3 years bond order calculations using those codes we= re nearly unheard of.

I believe the impact could be even much larger= , which is why I'm reaching out to try to highlight some of the use cas= es for this method as well as to give you an opportunity to explain to me w= hat aspects of the method you are having trouble understanding.

Sinc= erely,

Tom Manz
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