JISCMail - CCP4BB Archives

Stefano is correct that hydrophobic interactions are chiefly entropically driven. Thank you for your

input, Stefano. I disagree with Matthew, however. It is true that van der Waals forces are always

present and therefore form a small contribution to even hydrogen bonds. However, since the major contributions

to hydrogen bonds are various types of electronic components, it is proper

to group hydrogen bonds with electrostatic interactions. When using computational

software, one must look under the hood (or read the user manual) to see how different

force components are being grouped for calculations.

I would say to Sheila that, when you write up your analysis, just be sure to define how you are

using terms such as "electrostatic" or else specifically list the individual types of interatomic

attractive forces that you are surveying (which I know you prefer to avoid).

If any computational chemists are following this discussion, perhaps you can pipe in and

share your perspective and expertise.

-Daniel

On Wed, Sep 19, 2018 at 3:51 PM Sheila Boreiko <[log in to unmask]> wrote:

Interesting discussion is coming out of this question. I thank all that have provided input.

Let me go a bit further concerning Daniel's considerations. What other dipole interaction might be distinctively ascribed by programs out of hydrogen bonds (and of course, they use to describe salt bridges in addition, as an ionic interaction)? Possibly difficult for programs that use only atom positions, distances and angles (excluding the question of pH dependence, let us suppose neutral pH)?

I might here be specific with program PISA, which lists Hydrogen Bonds and Salt Bridges. They seem to use these bonds to estimate a Gibbs energy for the formation of the interface.

Sheila

De: Daniel M. Himmel, Ph. D. <[log in to unmask]>
Enviado: terça-feira, 18 de setembro de 2018 15:10
Para: [log in to unmask]
Cc: [log in to unmask]
Assunto: Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

Sorry. I may have been unclear. H-bonds are actually a subset of dipole interactions.

On Tue, Sep 18, 2018 at 1:57 PM Daniel M. Himmel, Ph. D. <[log in to unmask]> wrote:

By the way, distinguishing between dipole and ionic (salt bridge) interactions could

be a slippery slope, because which one you have sometimes depends on the protonation

state of the protein(s), which is pH dependent.

-Daniel

On Tue, Sep 18, 2018 at 1:31 PM Daniel M. Himmel, Ph. D. <[log in to unmask]> wrote:

Sheila,

Hydrogen bonds, ionic (i.e. salt bridge), and polar (dipole) interactions are often collectively called

electrostatic interactions. Note that dipole interactions involve partial charges. If you want to exclude

dipole interactions, you have say so specifically in your manuscript. Non-bonded interactions include

both electrostatic and van der Waals contacts (where hydrophobic interactions result from van der Waals

forces in an aqueous environment). Water can also interact with dipoles (partial charges), so it would

NOT be correct to use the term "hydrophilic" if you were excluding dipolar interactions.

-Daniel

On Mon, Sep 17, 2018 at 4:17 PM Sheila Boreiko <[log in to unmask]> wrote:

Dear all,

I had some literature search, but could not find clearly. Would there be an appropriate term to call the sum of hydrogen bonds (HB) and salt bridges (SB)? What about "hydrophilic interactions" or "polar interactions"? I am analyzing the different number of theses interactions in different monomers of my protein, as a totality I wanted to cite (compare) the number of HB + SB, yet I think to specify them separately could take out some focus of the discussion.

Thank you,

Sheila

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