Nine questions for the cognoscenti

        If you’re really secure, you can admit when you don’t know something, so this post proves I’m reasonably secure.  What follows are a series of questions I’ve not been able to find the answers to easily.  Please enlighten me if you’re able to help.

        #1. In NMR, how long does it take a hydrogen nucleus to absorb a quantum of radiation in a 500/42.5 Tesla field? (e.g. at 500 megaHertz).  

            a. Is this even a reasonable question?

        #2. Rotation about the carbon carbon bond attaching a methyl group is ‘fast’, so fast that all 3 hydrogens of the methyl group appear equivalent on NMR.  How fast is this?    How slow would it have to be in CClBrI-CH3 for us to see distinct signals from each of the 3 hydrogens of the methyl group?

         #3. How many kiloCalories high must a transition state be at room temperature (300 K) between conformations A and B of a single molecule to isolate each conformation?  How many kT is this?

          #4. What is the velocity in meters/second of a calcium ion at room temperature 

              a. In the gas state

             b.  What is the effective velocity of a calcium ion in water — e.g. does the Ca++ drag water molecules along with it slowing it down?  

          #5.  How far on average does a a calcium ion move in water at room temperature in 1 milliSecond (I have an ulterior motive for knowing this).

           #6. Chemists are always dealing in concentrations (molar, milliMolar, microMolar, nanoMolar, picoMolar, godzillaMolar etc. etc.).  At what volume does the notion of concentration cease to make sense?   Another ulterior motive here.  Clearly it doesn’t at the cubic Angstrom level, and it does at the cubic milliLiter.  

           #7.  Grignard reagents use magnesium.  Has anyone ever tried using calcium to make one?  If not, why not? 

           #8.  Can the lone pairs of electrons on oxygen in a ketone be considered in any sense a MOLECULAR orbital? 

           #9.  Does anyone really believe a molecular orbital exists for the X chromosome with its 155,000,000 nucleotides all linked together in one long chain?

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  • Wavefunction  On February 23, 2010 at 11:14 am

    Great questions. More later but recall for #3 that the magic number is 3 kcal/mol. This is the energy difference between two conformers required to reduce the higher energy one to essentially non-existence; that’s when the lower energy conformer exists to the extent of 99.96%. Also note that practically speaking it is virtually impossible to detect conformers less than 1-2% by NMR. That is where our methodology of NAMFIS (published in J. Med. Chem. last month with another paper due next month) comes in handy.

  • Yggdrasil  On February 23, 2010 at 8:53 pm

    #1 – I’d have to recheck my spectroscopy notes to give you a full explanation, but look up the concept of Rabi oscillations.

    #2 – If you have a nuclei converting between two or more chemical environments, you will see distinct NMR signals for each state if the rates of exchange between the state are shorter than the timescale of the NMR signal (i.e. the differences in Larmor frequency between the states). IIRC, for typical NMR field strengths, this corresponds to lifetimes of ~ms timescale.

    #5 – If you’re thinking of applying this to biological systems (i.e. neurons) recall that there are many protein in the cell that strongly bind and sequester calcium, so calcium diffusion is severely hindered within biological environments (for example, see work looking at calcium diffusion inside neurons by Karel Svoboda).

    #6 – Likely once the number of molecules inside your volume stop behaving statistically (i.e. the central limits theorem stops applying), the idea of concentration would stop applying. If I had to put a number on this, I’d say its on the order of hundreds of molecules.

  • Wavefunction  On February 23, 2010 at 10:47 pm

    A pointless take on #9: Does a wavefunction exist for the chromosome? How is it collapsed?! An orbital after all is a single electron wavefunction.

    #8: Yes, it’s a non-bonding MO.

  • luysii  On February 24, 2010 at 9:48 pm

    Wavefunction #1 comment — question #3 is not about equilibria freely arrived at, but about high the free energy barrier has to be at room temperature to prevent it from being reached. An answer with how many multiples of kT this takes would be nice

    Second comment — people are pretty glib about orbitals — but the rubber meets the road with large molecules like chromosomes. “An orbital is a single electron wavefunction” — do you mean an atomic or molecular wavefunction?

  • luysii  On February 24, 2010 at 10:05 pm

    Yggdrasil — thanks. Like all good answersl yours raise a lot of questions. #1 What does IIRC stand for? #2 How about a citation (or a link) to Svoboda’s papers. What’s going on inside neurons is exactly where I’m going with #5 and #6. Some of the claims made about calcium levels and kinetics in neurons are chemically outrageous.

    I’ve come up with a 10th question, but I’ll save it for later.

  • Wavefunction  On February 25, 2010 at 10:05 am

    Sorry, kinetics vs thermodynamics. I think that number would be more than 20 kcal/mol. A past post could be helpful.

    #5 Would Debye-Huckel theory give you the answer you are looking for?

  • J-bone  On February 25, 2010 at 11:55 am

    Drive-by posting: IIRC = If I remember correctly

  • Yggdrasil  On March 4, 2010 at 4:29 pm

    As J-bone said, IIRC is internetspeak for “if I remember correctly”. As my previous comment about calcium diffusion, despite hearing similar assertions many times in neurobio talks, I can’t find any good papers that actually say this (note that neurobio is not my field so I am not so embarrassed about this). In fact, it seems to be an active field of research and interestingly, older reviews seem to make stronger claims about restricted calcium diffusion than newer reviews.

    Anyway, if you’re interested, here’s a review on calcium signaling in neurons from a former postdoc in the Svoboda lab:

    Bloodgood and Sabatini. (2007) “Ca(2+) signaling in dendritic spines.” Curr Opin Neurobiol. 17(3):345-5. doi:10.1016/j.conb.2007.04.003

  • Michelle  On March 9, 2010 at 12:03 am

    Lots of good questions!

    As to the barrier – it’s somewhat more complicated than simple classical rotation — it’s a hop, not a continuous motion, and you get interesting results for nominal high barriers in X-ray structures.

    Molecular orbitals aren’t real entities…they are mathematical constructions used in an approach to approximating solutons to the Schrodinger equation.

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