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" <[log in to unmask]>
>> To: [log in to unmask]
>> 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 <[log in to unmask]> 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: [log in to unmask]
>> *******************************************
>> 
>> -- 
>> Michael C. Thompson
>> 
>> Graduate Student
>> 
>> Biochemistry & Molecular Biology Division
>> 
>> Department of Chemistry & Biochemistry
>> 
>> University of California, Los Angeles
>> 
>> [log in to unmask]
> 
> 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