CCL: bond order calculation method
- From: Thomas Manz <thomasamanz++gmail.com>
- Subject: CCL: bond order calculation method
- Date: Thu, 30 Jul 2020 19:41:46 -0600
Dear colleagues,
One of my graduate students is in the
process of preparing a YouTube video 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 way.
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 foundational 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 bond 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 for 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 materials 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–organic 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 access) 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 share 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 been much harder or perhaps
infeasible without the above method to compute bond orders.
Another
important application of these bond orders is to understand changes that occur
during chemical reactions. For example, several studies 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 order 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
are having trouble understanding.
Sincerely,
Tom Manz