Hello everyone,
Recently I‘m thinking about the a suitable way to describe the π-π interaction in benzene-rich system, such as liquid phenol, liquid benzene, etc.
The scripts written by Dr. Reinier Akkermans, Reinier and jian-jie.liang give me a tip that a statistics of angle and distance between benzene planes maybe helpful.
“How to measure angle between atomic Planes”
“Script to measure angle(s) between best-fit plane monitors”
However, the π-π interaction could be found in many kinds of stacking style, such as “T” shape and parallel-displaced, etc. The scripts written by Reinier, etc cannot distinguish them in detail.
I think a 3-D surface of probability distribution (Z) towards ring angle (X) and ring distance (Y) would be straightforward to understand the above π-π interaction. That is, a scan job of ring angle (X) and ring distance (Y) may need to be done.
It is worth noting that the calculation should be done only between benzene rings that was close enough. Therefore, there are Cn2 steps are needed, not n! steps.
Unfortunately, as a fresh hand in programming, especially in Perl, I found it is very hard for me to modify the above script and achieve my target, at least for the moment.
Can someone help me to achieve the above calculation? I think the above thoughts would also inspire other researchers.
Thanks a lot!
Bian,
Jun. 12, 2015
Recently I‘m thinking about the a suitable way to describe the π-π interaction in benzene-rich system, such as liquid phenol, liquid benzene, etc.
The scripts written by Dr. Reinier Akkermans, Reinier and jian-jie.liang give me a tip that a statistics of angle and distance between benzene planes maybe helpful.
“How to measure angle between atomic Planes”
“Script to measure angle(s) between best-fit plane monitors”
However, the π-π interaction could be found in many kinds of stacking style, such as “T” shape and parallel-displaced, etc. The scripts written by Reinier, etc cannot distinguish them in detail.
I think a 3-D surface of probability distribution (Z) towards ring angle (X) and ring distance (Y) would be straightforward to understand the above π-π interaction. That is, a scan job of ring angle (X) and ring distance (Y) may need to be done.
It is worth noting that the calculation should be done only between benzene rings that was close enough. Therefore, there are Cn2 steps are needed, not n! steps.
Unfortunately, as a fresh hand in programming, especially in Perl, I found it is very hard for me to modify the above script and achieve my target, at least for the moment.
Can someone help me to achieve the above calculation? I think the above thoughts would also inspire other researchers.
Thanks a lot!
Bian,
Jun. 12, 2015
