Hi all,
Im trying to calculate the strength of intramolecular hydrogen bond.
which software do i need to use?
and basic examples please?
I appreciate if you can help me.
Thank you in advance.
Strength of bond, including intramolecular hydrogen, can be estimated based on the Mayer bond order.
In many packages of computational chemistry, this parameter is calculated by default. For example, in an ORCA, section:
Mayer bond orders larger than 0.100000
B( 0-S , 1-O ) : 1.5881 B( 0-S , 2-O ) : 1.6306 B( 0-S , 3-O ) : 0.9483
B( 1-O , 2-O ) : 0.1976 B( 1-O , 3-O ) : 0.1396 B( 2-O , 3-O ) : 0.1453
B( 3-O , 4-H ) : 0.5753 B( 4-H , 6-O ) : 0.2700 B( 5-S , 6-O ) : 1.0879
B( 5-S , 7-O ) : 1.5463 B( 5-S , 8-O ) : 1.5957 B( 6-O , 7-O ) : 0.1559
B( 6-O , 8-O ) : 0.1462 B( 7-O , 8-O ) : 0.1865
4-H , 6-O is hydrogen bond.
The hydrogen bond Mayer order is usually between 0.1 and 0.3.
software: ORCA, Gamess, Firefly etc.
Look into our groups (CATCO group) work (which would directly answer your question):
Decoding chemical information from vibrational spectroscopy data: Local vibrational mode theory, DOI:10.1002/wcms.1480
The local mode program enables users to gather information on intrinsic bond strength for all types of bonds including hydrogen bonds through the use a local vibrational force constants - providing the most adequate measure of bond strength. In the article above the software is introduced - I believe our group has released the software or is near to releasing the software for public use.
There are articles are group has published based upon determining the strength of hydrogen bonds in various systems - I have listed a few below:
- A Comprehensive Analysis of Hydrogen Bond Interactions Based on Local Vibrational Modes DOI: 10.1002/qua.24118
- Different Ways of Hydrogen Bonding in Water - Why Does Warm Water Freeze Faster than Cold Water? DOI: 10.1021/acs.jctc.6b00735
-
Article Strengthening of hydrogen bonding with the push-pull effect
You can find more related articles from our groups and download copies of the publications for free here:
https://sites.smu.edu/dedman/catco/publications/2009-present.html
Dear Alexis Antoinette Ann Delgado ,
It sounds really interesting.
I will have a look. Thank you!
Dear Woojin,
It may be useful for you to check our latest article (DOI:10.1039/D0RA05802E), in which we estimate intramolecular H-bond strength with different methods using Gaussian and Multiwfn packages.
Dear Leandro Mena ,
Actually this is exactly what i'm trying to test now.
If you don't mind, could we share the Gaussian input file without your data? :) (i'm new to Gaussian.. I usually use GAMESS and molpro)
Thank you for your answer!
A reliable and very easy way of evaluating H-bond energy is using the relationship based on AIM theory proposed in my recent work J. Comput. Chem., 40, 2868–2881 (2019) DOI: 10.1002/jcc.26068. This analysis can be easily and very quickly realized using Multiwfn (http://sobereva.com/multiwfn). For Gaussian user, one only need to generate .wfn or .wfx or .fch first (see beginning of Chapter 4 of Multiwfn manual on how to generate them), then load the file into Multiwfn, enter topology analysis module, search critical point, then read electron density corresponding to the H-bond you are interested, and finally substitute this value into the formula proposed in the J. Comput. Chem. paper to predict H-bond energy. Please carefully check Section 4.2.1 of Multiwfn manual, this is a very detailed example showing how to use this method to predict H-bond energy between 2-pyridoxine and 2-aminopyridine in their dimer.
By the way, Multiwfn is also able to perform this analysis based on output file of GAMESS-US (you need to change the suffix to .gms), and based on .molden file generated by Molpro, see beginning of Chapter 4 of Multiwfn manual for detail.
Dear Tian Lu ,
I tried your program and i was awesome!
I think this is very useful.
Thank you for your answer.
Hi, you can try the IGMPlot software package. An Intrinsic Bond Strength Index is available. You can download it :
http://igmplot.univ-reims.fr/download.php
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