Just to put a finer point on some of this, the Lennard-Jones (6-12)
potential is short-range, containing an attractive component arising from
London dispersion forces (quantum mechanical induced dipole-induced dipole
interactions) that decay as 1/r^6 and a repulsive component arising from
the Pauli exclusion principle that rises as 1/r^12. The minimum of this
potential for a given homoatomic interaction vs. interatomic distance
corresponds to the van der Waals radius for that atom. Also, while
hydrogen bonds are predominantly electrostatic, it is worth noting that
there are some unresolved issues with the exact physical nature of these
interactions, particularly at short donor-acceptor distances.
Best regards,
Mark
Mark A. Wilson
Associate Professor
Department of Biochemistry/Redox Biology Center
University of Nebraska
N118 Beadle Center
1901 Vine Street
Lincoln, NE 68588
(402) 472-3626
[log in to unmask]
On 9/20/18, 10:13 AM, "CCP4 bulletin board on behalf of Daniel M. Himmel,
Ph. D." <[log in to unmask] on behalf of [log in to unmask]> wrote:
>Hello again. I just want to add that hydrogen bonds by convention are
>usually
>considered to be a type of electrostatic interaction (please see the
>review by
>E. N. Baker in the International Tables of Crystallography Volume F,
>second edition,
>p. 721) and are generally grouped with other "short range" electrostatic
>interactions
>along with dipole-dipole, dipole-ionic, and ionic-ionic interactions.
>This is by
>contrast to long term interactions that are approximated by the Lennard
>Jones potential,
>which includes van der Waals forces. My understanding is that van der
>Waals forces
>result from weak overall attractions between the protons in the nucleus
>of one atom
>and the electron cloud of another atom and therefore increase as the
>atomic number
>of the atoms increase.
>
>
>-Daniel
>
>
>
>
>On Thu, Sep 20, 2018 at 10:04 AM Daniel M. Himmel, Ph. D.
><[log in to unmask]> wrote:
>
>
>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
>
>
>
>
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