We should also be aware that there is a formal IUPAC definition of hydrogen bonds as well, although its not really optimized for protein crystallography.
https://www.iupac.org/publications/pac/pdf/2011/pdf/8308x1637.pdf Matthew Merski Univ. of Warsaw On Thu, Sep 20, 2018 at 5:28 PM Mark Wilson <mwilso...@unl.edu> wrote: > 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 > mwilso...@unl.edu > > > > > > On 9/20/18, 10:13 AM, "CCP4 bulletin board on behalf of Daniel M. Himmel, > Ph. D." <CCP4BB@JISCMAIL.AC.UK on behalf of danielmhim...@gmail.com> > 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. > ><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 > >< > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_c > >gi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNs > >YHeFX_rg6kWhlkLF8Eft-wwo&r=pWFylCwRYnT2UZGAgJCqKaJCAAfFi00TZEWmZXJvhsA&m=X > >xsP22281ki64gRRtFipETeAesjfv6LxkN_UKBsCtP4&s=vjq9SG_X6T-qmrW4lfDLB42hDw_iZ > >hxvSx0jQvJS4bY&e=> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >________________________________________ > >To unsubscribe from the CCP4BB list, click the following link: > >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > >< > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_c > >gi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNs > >YHeFX_rg6kWhlkLF8Eft-wwo&r=pWFylCwRYnT2UZGAgJCqKaJCAAfFi00TZEWmZXJvhsA&m=X > >xsP22281ki64gRRtFipETeAesjfv6LxkN_UKBsCtP4&s=vjq9SG_X6T-qmrW4lfDLB42hDw_iZ > >hxvSx0jQvJS4bY&e=> > > > ######################################################################## > > 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
