If I recall correctly this refers to the Pearson (?) hard/soft acid base theory. It's been a long time since inorganic chemistry.
Cheers, Roger Rowlett On Feb 24, 2011 1:39 PM, "Jacob Keller" <[email protected]> wrote: > 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 <[email protected]> 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: [email protected] > *******************************************
