Re: [ccp4bb] Hydrophobic/ vander waal forces

[Brian Shoichet]

Hi Amit,

They are related but different.  van der Waals
(dispersion-attraction/repulsion, London) forces are real forces arising
from instantaneous-induced dipoles.  Whereas in most quantitative
treatments in biophysics they have an arbitrary component (e.g., the exact
way to represent the repulsive term in a classic function is open to
debate), they do represent real forces and interactions, as classically
understood.

Hydrophobic "interactions" are not formally interactions at all, they are
preferential associations reflecting a less favorable energy in the
solvated state.  Thus there is no hydrophobic interaction between groups
and atoms, there is rather the higher free energy of the solvated state
that drives them together, reducing the free energy of the system.

Hydrophobicity is one step more complicated still, in that it reflects
changes in the heat capacity of the system (moving from a solvated -->
buried hydrophobic interface reduces the heat capacity at room temperature,
in an aqueous environment).  Indeed, the formal way to measure a
hydrophobic effect is to show that there is a substantial DCp in the
process.  This, and the behavior of water, makes the hydrophobic effect
highly temperature dependent.  A hydrophobic "driving force" at one
temperature can disappear at another temperature.

The reason hydrophobic effects and van der Waals interactions are often
conflated is that the same sort of non-polar atoms lead to both.  But of
course polar atoms also interact through van der Waals interactions.

Hope this helps.

brian

On Fri, Jul 2, 2021 at 10:50 AM amit gaur  wrote:

> Hi everyone,
>  I hope everything is going well with all of you. I want to
> know that, Are hydrophobic and vander waal forces are similar? and what is
> criteria for formation of these and interatomic distances needed to form
> these interactions between amino acids? What kinds of atoms have propensity
> to form these interactions?
>
> Thank you,
> --
> *Dr. Amit Gaur*
>
> *Research AssociateThomas Jefferson University*
> *Department of Translational medicine*
> *1020, Locust Street, Jefferson Alumni Hall*
> *Philadelphia, PA 19107*
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>


-- 
Brian Shoichet, Professor, UCSF
latest science from the lab:  *http://www.bkslab.org/
*



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Hydrophobic/ vander waal forces

[amit gaur]

Hi everyone,
 I hope everything is going well with all of you. I want to
know that, Are hydrophobic and vander waal forces are similar? and what is
criteria for formation of these and interatomic distances needed to form
these interactions between amino acids? What kinds of atoms have propensity
to form these interactions?

Thank you,
-- 
*Dr. Amit Gaur*

*Research AssociateThomas Jefferson University*
*Department of Translational medicine*
*1020, Locust Street, Jefferson Alumni Hall*
*Philadelphia, PA 19107*



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/