Multicenter Bond Index for aromatic macrocycles

mkedwards · Yesterday 00:18:24

Thank you for Multiwfn! It's amazing!

I observe that there is an implementation of the Multicenter Bond Index, but it is limited to 10 atoms. Is there any way around this? I have an 18-atom macrocycle for which I would like to calculate MBI to verify aromaticity (in comparison to a related non-aromatic molecule).

sobereva · Yesterday 21:40:39

Please do not use very old version. Due to my special algorithm for Multicenter Bond Index (see "Appendix: The extremely efficient implementation of MCBO in Multiwfn" in Section 3.11.2 of latest Multiwfn manual), current version of Multiwfn is able to calculate Multicenter Bond Index for arbitrarily large rings (even more than 100 atoms!)

mkedwards · Yesterday 23:03:38

I'm on the current dev version, I think; I installed it on MacOS through Homebrew (which builds from source using cmake). Is there a way to check the date on the source code?

mkedwards · Yesterday 23:05:12

(base) MKE-Air:orca medwards$ multiwfn
Warning: "settings.ini" was found neither in current folder nor in the path defined by "Multiwfnpath" environment variable. Now using default settings instead

Multiwfn -- A Multifunctional Wavefunction Analyzer
Version 3.8(dev), update date: 2024-Nov-13

mkedwards · Yesterday 23:11:27

Maybe the command line version applies an artificial constraint? Or maybe I'm using the wrong option?

I can calculate a multi-center bond order:

================ Bond order analysis ===============
-1 Define fragment 1 and 2 for options 1,3,4,7,8,10 (to be defined)
0 Return
1 Mayer bond order analysis
2 Multicenter bond order analysis
-2 Multicenter bond order analysis in NAO basis
3 Wiberg bond order analysis in Lowdin orthogonalized basis
4 Mulliken bond order (Mulliken overlap population) analysis
5 Decompose Mulliken bond order between two atoms to orbital contributions
6 Orbital occupancy-perturbed Mayer bond order
7 Fuzzy bond order analysis (FBO)
8 Laplacian bond order (LBO)
9 Decompose Wiberg bond order in NAO basis as atomic orbital pair contribution
10 Intrinsic bond strength index (IBSI)
11 AV1245 index (approximate multicenter bond order for large rings) and AVmin
20 Bond order density (BOD) and natural adaptive orbital (NAdO) analyses
2
Calculating PS matrix, please wait...
Note: Because the PS matrix may be not symmetric, the result may be dependent of inputting order of atomic indices. Settings the iMCBOtype in settings.ini to 1 is recommended, in this case the results corresponding to forward and reverse inputting orders will be automatically averaged

Input atom indices, e.g. 3,4,7,8,10 (number of centers is arbitrary)
Note: The input order must be in consistency with atomic connectivity. You can also input e.g. 4-10 if the indices are contiguous
Input -3/-4/-5/-6 will search all possible three/four/five/six-center bonds
Input 0 can return to upper level menu
1,2,3,4,5,6,22,9,10,11,12,13,14,15,16,24,19,20
The multicenter bond order: 0.1980697050
The normalized multicenter bond order: 0.9139750416

But I can't calculate a multi-center delocalization index:

======== Fuzzy atomic space analysis ========
-10 Set X,Y,Z of reference point, current: 0.00000 0.00000 0.00000 Bohr
-6 Choose type of integration grid for AOM, current: Atomic grid
-5 Define the atoms to be considered in options 1, 2, 13, current: all atoms
-4 Adjust reference parameter for FLU
-3 Set the number of iterations for Becke partition, current: 3
-2 Select radius definition for Becke partition, current: Modified CSD
-1 Select method for partitioning atomic spaces, current: Becke
0 Return
1 Perform integration in fuzzy atomic spaces for a real space function
2 Calculate atomic and molecular multipole moments and <r^2>
3 Calculate and output atomic overlap matrix (AOM) in current folder
33 Calculate and output fragment overlap matrix (FOM) in current folder
4 Calculate localization (LI) and delocalization index (DI)
44 Calculate fragment LI (FLI) and interfragment DI (IFDI)
5 Calculate PDI (Para-delocalization index)
6 Calculate FLU (Aromatic fluctuation index)
7 Calculate FLU-pi
8 Perform integration in fuzzy overlap region for a real space functions
9 Calculate condensed linear response kernel (CLRK)
10 Calculate PLR (Para linear response index)
11 Calculate multi-center delocalization index
12 Calculate information-theoretic aromaticity index (ACS Omega, 3, 18370)
13 Calculate atomic effective volume, free volume, polarizability and C6 coefficient
11
Note: The highest 2565 virtual orbitals will not be taken into account
Allocating memory...
Radial points: 45 Angular points: 170 Total: 7650 per center
Please wait...

Progress: [##################################################] 100.0 % -
Calculation took up 99 seconds wall clock time
Error of AOM is 0.00280439
Maximum diagonal deviation to 1: 0.000345 at orbital 95
Maximum nondiagonal deviation to 0: 0.000149 between orbitals 70 112

Warning: The integration is not very accurate
To improve accuracy, please try one or some of following treatments:
(1) Enlarge "radpot" and "sphpot" in settings.ini
(2) Set "radcut" in settings.ini to 0
(3) Choose option -6 to change to much more expensive molecular grid
(4) If diffuse functions were heavily employed, remove them

Input atom indices, e.g. 3,4,7,8,10 (Up to 10 atoms)
Input q can return to upper level menu
1,2,3,4,5,6,22,9,10,11,12,13,14,15,16,24,19,20
Please wait...
Multicenter DI: 0.0000000

Multicenter DI in normalized form: 0.0000000

sobereva · Today 00:30:30

For a large ring, please only use multi-center bond order (alternatively, use AV1245), do not use multicenter DI (only supports up to 10 atoms). Your Multiwfn version is new enough.

mkedwards · Today 01:51:12

AV1245 is a great suggestion. Thank you!

mkedwards · Today 07:28:44

I don't really understand the numbers I'm getting out of AV1245, though.

1,2,3,4,5,6,22,9,10,11,12,13,14,15,16,24,19,20
Number of selected atoms: 18
Atomic sequence:
1 2 3 4 5 6 22 9 10 11 12 13
14 15 16 24 19 20

4-center electron sharing index of 1 2 4 5: 0.17676882
4-center electron sharing index of 2 3 5 6: -0.50162138
4-center electron sharing index of 3 4 6 22: 0.36387824
4-center electron sharing index of 4 5 22 9: -0.16439330
4-center electron sharing index of 5 6 9 10: -0.49054669
4-center electron sharing index of 6 22 10 11: -0.81549232
4-center electron sharing index of 22 9 11 12: -0.14739340
4-center electron sharing index of 9 10 12 13: -0.45451047
4-center electron sharing index of 10 11 13 14: -0.39040796
4-center electron sharing index of 11 12 14 15: 0.12690133
4-center electron sharing index of 12 13 15 16: 0.45539971
4-center electron sharing index of 13 14 16 24: -0.25926207
4-center electron sharing index of 14 15 24 19: 0.14457754
4-center electron sharing index of 15 16 19 20: 0.11225174
4-center electron sharing index of 16 24 20 1: 0.17069799
4-center electron sharing index of 24 19 1 2: -0.06304604
4-center electron sharing index of 19 20 2 3: -0.17882162
4-center electron sharing index of 20 1 3 4: 0.20749270

AV1245 times 1000 for the selected atoms is -94.86262021
AVmin times 1000 for the selected atoms is 63.046041 ( 24 19 1 2)

sobereva · Today 11:14:28

Please read Section 3.11.10 of Multiwfn manual, the theoretical background has been carefully introduced.

Multiwfn forum

#1 Yesterday 00:18:24

Multicenter Bond Index for aromatic macrocycles

#2 Yesterday 21:40:39

Re: Multicenter Bond Index for aromatic macrocycles

#3 Yesterday 23:03:38

Re: Multicenter Bond Index for aromatic macrocycles

#4 Yesterday 23:05:12

Re: Multicenter Bond Index for aromatic macrocycles

#5 Yesterday 23:11:27

Re: Multicenter Bond Index for aromatic macrocycles

#6 Today 00:30:30

Re: Multicenter Bond Index for aromatic macrocycles

#7 Today 01:51:12

Re: Multicenter Bond Index for aromatic macrocycles

#8 Today 07:28:44

Re: Multicenter Bond Index for aromatic macrocycles

#9 Today 11:14:28

Re: Multicenter Bond Index for aromatic macrocycles

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