What is Hydrogen Bond Auto-correlation function?

In summary, Hydrogen Bond Auto-correlation function is a tool used in molecular dynamics simulations to analyze the dynamics and strength of hydrogen bonds between molecules. It calculates the correlation between the hydrogen bond lengths and angles over time, providing insight into the stability and fluctuations of these bonds. This function is critical in understanding the behavior of molecules and their interactions in various systems, such as proteins and liquids.
  • #1
DHN
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Can somebody explain the Hydrogen bond Auto-correlation function in Computational Chemistry (Molecular Dynamics and Simulations) and what does Intermittent and Continuous Hydrogen bond means? Why the graph decays over time? and it's applications?
 
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  • #2
I think this page: https://www.mdanalysis.org/docs/documentation_pages/analysis/hbond_autocorrel.html
explains the difference between continuous and intermittent bonding. The autocorrelation is correlation over time of the population of hydrogen bonds at distinct times.

Understanding the decays over time would enable one to appreciate, say, reaction rates that depend on a hydrogen bond breaking, or not breaking, also on bulk properties like viscosity. (Is that 10W-40 or WD-40?)
 
  • #3
@jambaugh, Thank you for the link. But i am unable to understand what is "10W-40 or WD-40"..?? Can u kindly tell me what is it?
 
  • #4
DHN said:
@jambaugh, Thank you for the link. But i am unable to understand what is "10W-40 or WD-40"..?? Can u kindly tell me what is it?
That was a reference to viscosity of oils, 10W-40 motor oil vs WD-40 penetrating oil. I was attempting to be cute.
 
  • #5
@jambaugh i want to know with respect to pure water and in presence of ions like KCl, LiCl. What would be the Hydrogen bonding autocorrelation (tau value) for pure water and in the presence of ions like KCl, LiCl.
 
  • #6
DHN said:
@jambaugh i want to know with respect to pure water and in presence of ions like KCl, LiCl. What would be the Hydrogen bonding autocorrelation (tau value) for pure water and in the presence of ions like KCl, LiCl.

I understand what it represents in principle but I haven't a clue as to its values. You'll have to search that on your own or ask if anyone else on the forum can be of assistance.
 

1. What is a hydrogen bond auto-correlation function?

A hydrogen bond auto-correlation function is a mathematical tool used to measure the strength and duration of hydrogen bonds between molecules. It calculates the probability that a hydrogen bond formed at a specific time will still be present after a certain amount of time has passed.

2. How is a hydrogen bond auto-correlation function calculated?

The hydrogen bond auto-correlation function is typically calculated using molecular dynamics simulations or experimental techniques such as nuclear magnetic resonance (NMR) spectroscopy. It involves analyzing the position and orientation of hydrogen bonds over time to determine their stability.

3. What is the significance of studying hydrogen bond auto-correlation functions?

Studying hydrogen bond auto-correlation functions can provide valuable insights into the dynamics and stability of biological systems, such as protein folding and DNA replication. It can also help in understanding the properties of materials and their interactions with water.

4. How does temperature affect hydrogen bond auto-correlation functions?

The strength and duration of hydrogen bonds are highly dependent on temperature. As temperature increases, the auto-correlation function decreases, indicating weaker and shorter-lived hydrogen bonds.

5. Can hydrogen bond auto-correlation functions be used to predict the properties of a molecule?

While hydrogen bond auto-correlation functions can provide important information about the dynamics of a system, they cannot be used to accurately predict the properties of a molecule. Other factors, such as molecular structure and intermolecular forces, also play a significant role in determining a molecule's properties.

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