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. < danielmhim...@gmail.com> 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 <sheila_bore...@hotmail.com> > 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. <danielmhim...@gmail.com> >> *Enviado:* terça-feira, 18 de setembro de 2018 15:10 >> *Para:* sheila_bore...@hotmail.com >> *Cc:* CCP4BB@jiscmail.ac.uk >> *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. < >> danielmhim...@gmail.com> 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. < >> danielmhim...@gmail.com> 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 < >> sheila_bore...@hotmail.com> 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 >> >> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
