Have you had your molybdenum today?
Chemists don’t usually think of the products of a chemical reaction barreling off and penetrating another structure. Because of the equipartition of energy, the energy of a given exothermic chemical reaction quickly gets redistributed into electronic, vibration and rotational energy and some translational energy. It’s exactly why blasting a particular bond with exactly the right energy to break it, isn’t widely used in synthetic organic chemistry — the energy redistributes over the whole molecule too rapidly. But that’s exactly what is thought to happen in the molybdenum storage protein according to Proc. Natl. Acad. Sci. vol. 116 pp. 26497 – 26504 ’19.
Back off a bit. Without molybdenum we’d all be dead, as it is a critical component of the plant enzyme breaking the triple nitrogen to nitrogen (aka nitrogenase), so it can be fixed into biologic material of the plant (and ultimately us). It takes 225 kiloCalories/mole to break N2 apart (compared to 90 kiloCalories/mole for the carbon carbon bond in ethane).
The paper concerned discusses the molybdenum storage protein of a bacterium (Azotobacter vinelandii). The protein is a heterohexamer of 3 alpha and 3 beta subunits with a total molecular mass of 180 kiloDaltons.
The mechanism if cleverness itself — here’s a direct quote from the abstract of the paper. “First, we show that molybdate, ATP, and Mg2+ consecutively bind into the open ATP-binding groove of the β-subunit, which thereafter becomes tightly locked by fixing the previously disordered N-terminal arm of the α-subunit over the β-ATP. Next, we propose a nucleophilic attack of molybdate onto the γ-phosphate of β-ATP, analogous to the similar reaction of the structurally related UMP kinase. The formed instable phosphoric-molybdic anhydride becomes immediately hydrolyzed and, according to the current data, the released and accelerated molybdate is pressed through the cage wall, presumably by turning aside the Metβ149 side chain. A structural comparison between MoSto and UMP kinase provides valuable insight into how an enzyme is converted into a molecular machine during evolution. The postulated direct conversion of chemical energy into kinetic energy via an activating molybdate kinase and an exothermic pyrophosphatase reaction to overcome a proteinous barrier represents a novelty in ATP-fueled biochemistry, because normally, ATP hydrolysis initiates large-scale conformational changes to drive a distant process.”
What drives the MO4 away from the ADP ? Probably electrostatic repulsion between two negative charges in the very low dielectric constant environment of the storage protein (said to be around 7 with water at 80) which does relatively little to shield the charges from each other.
Of course the SN2 reaction is like two billiard balls hitting each other with the leaving group barreling off at about the same velocity as the attacking group. How fast is that?
Pretty fast. To figure out how fast any chemical entity is moving at 300 K (80 F) just divide 2735 by the square root of the molecular mass. So when Iodine barrels in to methyl bromide at 243 meters second, the bromine leaves at 307 meters second.
Well the C – Br bond length is 1.9 Angstroms, the atomic radii of Br and C are 1.8 and .7 Angstroms — So methyl bromide is 4.5 Angstroms long or 4.5 x 10^-10 meters. So 307 meters/ second means that the bromine ion takes roughly 10^-3 seconds to go a meter, and 10^-3 * ( 1/4.5) * 10^-10 ) seconds to go the diameter of the methyl bromide molecule. (Of course this ignores the solvent that’s in the way impeding the Bromine anion’s progress — but that’s another story). I put this numerology in because chemists (including me) usually don’t think about reactions this way and it’s rather humbling to do so.