The p97 AAA (ATPase associated with diverse cellular activities), also called VCP (valosin-containing protein), is an important therapeutic target for cancer and neurodegenerative diseases. p97 forms a hexamer composed of two AAA domains (D1 and D2) that form two stacked rings, and an N-terminal domain that binds numerous cofactor proteins. The interplay between the three domains in p97 is complex, and a deeper biochemical understanding is needed in order to design selective p97 inhibitors as therapeutic agents. It is clear that the D2 ATPase domain hydrolyzes ATP in vitro, but whether D1 contributes to ATPase activity is controversial. Here, we use Walker A and B mutants to demonstrate that D1 is capable of hydrolyzing ATP, and show for the first time that nucleotide binding in the D2 domain increases the catalytic efficiency (kcat/Km) of D1 ATP hydrolysis 280-fold, by increasing kcat 7-fold and decreasing Km about 40-fold. We further show that an ND1 construct lacking D2 but including the linker between D1 and D2 is catalytically active, resolving a conflict in the literature. Applying enzymatic observations to small-molecule inhibitors, we show that four p97 inhibitors (DBeQ, ML240, ML241, and NMS-873) have differential responses to Walker A and B mutations, to disease-causing IBMPFD mutations, and to the presence of the N-domain binding cofactor protein p47. These differential effects provide the first evidence that p97 cofactors and disease mutations can alter p97 inhibitor potency and suggest the possibility of developing context-dependent inhibitors of p97.

Both C-H bond dissociation energies for cyclobutene were measured in the gas phase (BDE = 91.2 +/- 2.3 (allyl) and 112.5 +/- 2.5 (vinyl) kcal mol-1) via a thermodynamic cycle by carrying out proton affinity and electron-binding energy measurements on 1- and 3-cyclobutenyl anions. The results were compared to those for an acyclic model compound, cis-2-butene, and provide the needed information to experimentally establish the heat of formation of cyclobutadiene. Chemically accurate G3 and W1 calculations also were carried out on cycloalkanes, cycloalkenes, and selected reference compounds. It appears that commonly cited bond energies for cyclopropane, cyclobutane, and cyclohexane are 3 to 4 kcal mol-1 too small and their pi bond strengths, as given by BDE1 - BDE2, are in error by up to 8 kcal mol-1.

Hydrogen bonds are the dominant motif for organizing the three-dimensional structures of biomolecules such as carbohydrates, nucleic acids, and proteins, and serve as templates for proton transfer reactions. Computations, gas-phase acidity measurements, and pK(a) determinations in dimethyl sulfoxide on a series of polyols indicate that multiple hydrogen bonds to a single charged center lead to greatly enhanced acidities. A new class of Brønsted acids, consequently, is proposed.

Cyclobutadiene (1) and its derivatives have beckoned to chemists ever since Kekules deduction of the structure of benzene and his attempt to synthesize 1 in 1872.[1] Pioneering efforts by Willstätter and Finkelstein were followed by a century of studies which produced many remarkable findings. Room temperature stable derivatives such as tri-tert-butylcyclobutadiene [2] and tetra-tert-butylcyclobutadiene [3] were successfully prepared and spectroscopically characterized, whereas the parent compound was found to be more elusive. It dimerizes in solid matrices at ! 35 K, is a transient reactive intermediate in solution, and has a lifetime of only 2 ms at 0.1 Torr in the gas phase.[1a] Nevertheless, trapping [4] and spectroscopic results have revealed that cyclobutadiene has a ground-state singlet configuration and adopts a rectangular D 2h structure which rapidly undergoes automerization. An isolable and room temperature stable complex consisting of 1 in the cavity of a spherical crown ether (that is, a hemicarceplex) has even been prepared, [5] but the thermodynamic stability of cyclobutadiene remains experimentally unknown.Conventional calorimetric methods are precluded when it comes to cyclobutadiene and its simple derivatives because of their high reactivity. Electrochemical, [6] pK a , [7] and kinetic [8] measurements of model compounds have been carried out and interpreted as indicating that 1 has a negative resonance energy of at least 50-67 kJ mol À1 . This conclusion is in accord with many of the early computational findings and a