Hi folks Whoops, brain not engaged before hitting "send".
Lewis acid/bases are to do with electron-pair donor/acceptance, Brønsted acid/bases with protons. So my second two paragraphs define things the wrong way round. I need a coffee... On 25 Feb 2011, at 10:49, Harry Powell wrote: > 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" <[email protected]> >> To: [email protected] >> 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 <[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] >> ******************************************* >> >> -- >> Michael C. Thompson >> >> Graduate Student >> >> Biochemistry & Molecular Biology Division >> >> Department of Chemistry & Biochemistry >> >> University of California, Los Angeles >> >> [email protected] > > Harry > -- > Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, > Cambridge, CB2 0QH Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
