Hi Before people get carried away, it may be useful to mention that we are discussing Lewis acids & bases here, not Brønsted (or Brønsted-Lowry) acids and bases.
Simply put, Brønsted acids are electron pair acceptors whereas Lewis acids are proton donors. Some (not all) Lewis acids are also Brønsted acids. On the other hand, Lewis bases (proton acceptor) are all Brønsted bases (electron pair donor). On 24 Feb 2011, at 23:28, Michael Thompson wrote: > Jacob, > > Roger is correct, this concept does refer to the Pearson HSAB theory. To > summarize: This theory is applicable outside of inorganic chemistry as well, > but it is extremely useful for explaining coordination chemistry of > metal-ligand complexes. The theory states that "hard" acids interact with > "hard" bases and "soft" acids interact with "soft" bases to form a bond that > is covalent-like in nature. "Hardness" vs. "softness" is based on the > energetic properties of the HOMO and LUMO of the acid and base. Generally > hard acids/bases have small atomic/ionic radii, low polarizability, and high > electronegativity whereas "soft" acids/bases tend to have larger radii, high > polarizability, and low electronegativity. > > Hard bases are things like carboxylates, whereas soft bases are things like > thiolates. Ligands with nitrogen (imidazole) are often in the middle > somewhere. > > Hard acids are ions like Na+, K+, Mg2+, etc., while soft acids are metals > like mercury, silver, etc. Again, many biologically relevant things lie in > the middle of the spectrum somewhere (Fe, Co, Zn). > > It is possible to calculate the "chemical hardness" of a species, but that's > where my knowledge stops. > > Hope this is helpful, > > Mike > > > > > ----- Original Message ----- > From: "Jacob Keller" <j-kell...@fsm.northwestern.edu> > To: CCP4BB@JISCMAIL.AC.UK > Sent: Thursday, February 24, 2011 10:39:09 AM GMT -08:00 US/Canada Pacific > Subject: Re: [ccp4bb] strange density > > I have heard "hard" and "soft" many times now about O's and N's--to > what property of those ligands does this metaphor refer? > > JPK > > On Thu, Feb 24, 2011 at 12:47 PM, Jeffrey D Brodin <jbro...@ucsd.edu> wrote: >> Alex, >> >> I modeled in the bis-tris with the tertiary amine and and his imidazole >> coordinating axially and the four oxygens coordinating in the equatorial >> plane. However, it's hard for me to tell from your images if there are two >> His coordinating? Either way, that crescent shape could easily be explained >> by a bis-tris molecule, you'll just have to figure out how exactly to model >> it in. It's also possible that the metal is a Mg, but as people have already >> mentioned, nitrogens probably wouldn't coordinate very tightly to a hard >> metal. Lastly, I'm also not sure off the top of my head how tightly bis-tris >> binds metals, but it should be an easy number to look up. Hope this helps, >> >> Jeff >> On Feb 24, 2011, at 9:02 AM, Alex Singer wrote: >> >>> Hi -- thank you for all your help. The majority opinion seems to be a >>> metal for the sphere (Ni from the Ni-affinity column, which (Joe >>> Patel, correct) was used during purification, but Zn and Fe were also >>> mentioned), and either water molecules, bis-tris or some other small >>> molecule forming the crescent. Just looking at the density, the >>> occupancy would seem to be quite high, so I'm surprised that a Ni ion >>> (or a contaminating metal ion) could have gone through the >>> purification and still remained at high enough concentration to be >>> clearly visible in the crystals. However, I'll still try this but >>> first some points of clarification and questions which you can either >>> email me seperately or post to the the group. >>> >>> a. it was collected at beamline 19-BM at Argonne, so radiation damage >>> is an issue. Thierry Fishmann -- for the gln residue, there was >>> difference density for the gamma carbon after the first conformation >>> was modeled in, thus the addition of the second conformation, which I >>> agree is suspect. What does the radiation damage do chemically and >>> would that make the gamma carbon more mobile? >>> >>> b. Jeffrey D Brodin -- how did you model in the bis-tris? Looking at >>> the bis-tris molecule from Hic-up, was the N at the centre of the >>> crescent and the O6 and O8 at the edges? >>> >>> c. JR Helliwell -- there are 4 molecules in the AU, but two H138's >>> are pointing into the solvent. Thus the molar ratio of protein >>> molecules to "thing 1" is 4:1. Also looking at the images, I see no >>> ice rings -- the images look pretty good. Can you tell me more about >>> the series termination effects? >>> >>> Again thank you for your help and I'll let the group know how it worked >>> out. >>> >>> Alex >>> >>> -- >>> Dr. Alex Singer >>> C.H. Best Institute >>> 112 College St. Room 70 >>> University of Toronto >>> Toronto, Canada, M5G 1L6 >>> 416-978-4033 >> > > > > -- > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > cel: 773.608.9185 > email: j-kell...@northwestern.edu > ******************************************* > > -- > Michael C. Thompson > > Graduate Student > > Biochemistry & Molecular Biology Division > > Department of Chemistry & Biochemistry > > University of California, Los Angeles > > mi...@chem.ucla.edu Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
