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Tubulin nucleation, microtubule assembly, stability, and dynamics depend on fluxes of chemical energy, controlled by hydrolysis of guanosine triphosphate (GTP) to guanosine diphosphate (GDP), and nucleotide exchange reactions. In this paper, we determined how tubulin self-association in glycerol-free assembly buffers affects the rate of GTP hydrolysis and the thermodynamics of nucleotide exchange. In the absence of tubulin, GTP hydrolysis was negligible. In the presence of tubulin, below the critical conditions for microtubule assembly, no GTP hydrolysis was observed, even though tubulin 1D curved oligomers and single rings were formed, suggesting that GTP hydrolysis was not involved in their formation. Under conditions permitting spontaneous tubulin nucleation and microtubule assembly, GTP hydrolysis was detected and followed pseudo-first-order kinetics, limited by the rate of tubulin nucleation and microtubule assembly. By simultaneously determining the concentrations of tubulin-free and tubulin-bound GTP and GDP at steady-state, we investigated the nucleotide exchange reaction under conditions where GTP hydrolysis was negligible. The exchange reaction strongly depended on the molar ratio between tubulin-free GDP and GTP and the total tubulin concentration. To analyze these data, we used a thermodynamic model of isodesmic tubulin self-association, terminated by the formation of tubulin single-rings, to calculate the distribution of tubulin single rings, 1D oligomers, and free dimers, and thereby the molar fractions of tubulin dimers with exposed and buried nucleotide exchangeable sites (E-sites). Our data suggest that the exchange reaction occurred to a different extent on tubulin dimers with buried E-sites than on dimers with exposed E-sites.

A comprehensive study on the isomerization, decomposition and ring-closure reaction kinetics, as well as thermodynamic properties of methyl pentanoate radicals were carried out in this work. The M06–2X/cc-pVTZ level of theory was employed to optimize geometries and analyze frequencies for all the stationary points on the potential energy surfaces. The CCSD(T) method with two basis sets, cc-pVDZ and cc-pVTZ, was used to calculate single point energies, which were further extrapolated to the complete basis set (CBS) limit to construct the potential energy surfaces. The energy calculation results indicated that isomerization of δ-R to α-R, decomposition of γ-R to CH2C(=O)OCH3 and propene, and ring-closure reaction of δ-R to 1-methoxycyclopentanoxyl radical are the most energetically favored reactions among the studied isomerization, decomposition and ring-closure reaction channels, respectively. High pressure limit, and temperature and pressure dependent rate coefficients were determined by solving the one-dimensional energy-dependent master equations with Tsinghua University Minnesota Master Equation program (TUMME). The rate coefficients and branching ratios were found to be significantly affected by temperature and pressure. The decomposition reactions yielding small unsaturated esters or small ester radicals dominate at high temperatures, while the isomerization reactions proceeding via five- and six-membered ring saddle points, as well as the ring-closure reactions play more important roles at low temperatures. Significant discrepancies are observed between the theoretically calculated rate coefficients and estimated results. The thermochemical properties of methyl pentanoate radicals were calculated using isodesmic reaction method and atomization method together with the multistructural torsional anharmonicity partition functions. This study provides accurate kinetic and thermodynamic data on methyl pentanoate radicals, which are expected to advance our understanding of combustion chemistry of methyl pentanoate and larger methyl esters.

The electronic structures of sumanene and several heterasumanenes have been calculated using high-level ab initio method: Green’s function method (OVGF). The vertical, valence ionization energies were calculated and gas phase photoelectron spectra simulated on the basis of those ionization energies. The Franck-Condon analysis of vibronic effects has also been performed and changes between molecular geometries in neutral and ionic state have been discussed Standard formation enthalpies for some sumanenes were calculated using isodesmic reaction scheme. The results help in the understanding of how is the electronic structure affected when molecule deviates from planar geometry and what is the influence of substituents in benzylic positions. We have demonstrated that the substituent effects affect not only geometry, but also the electronic structure (reflected in ionization energies). This can be used in preparing new functional materials for various applications.