Atomistic Mechanisms of The Tautomerization of The G·C Base Pairs Through The Proton Transfer: Quantum-Chemical Survey

This study is devoted to the investigation of the G·C*tO2(WC)↔G*NH3·C*t(WC), G·C*O2(WC)↔G*NH3·C*(WC) and G*·C*O2(WC)↔G*NH3·C(wWC)↓ tautomerization reactions occurring through the proton transfer, obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory in gas phase under normal conditions (T=298.15 K). These reactions lead to the formation of the G*NH3·C*t(WC), G*NH3·C*(WC) and G*NH3·C(wWC)↓ base pairs by the participation of the G*NH3 base with NH3 group. Gibbs free energies of activation for these reactions are 6.43, 11.00 and 1.63 kcal·mol-1, respectively. All of these tautomerization reactions are dipole active. Finally, we believe that these non-dissociative processes, which are tightly connected with the tautomeric transformations of the G·C base pairs, play outstanding role in the supporting of the spatial structure of the DNA and RNA molecules with various functional purposes.

Electron-impact ionization and ionic fragmentation of O2 from threshold to 120 eV energy range

We study the electron-impact induced ionization of O2 from threshold to 120 eV using the electron spectroscopy method. Our approach is simple in concept and embodies the ion source with a collision chamber and a mass spectrometer with a quadruple filter as a selector for the product ions. The combination of these two devices makes it possible to unequivocally collect all energetic fragment ions formed in ionization and dissociative processes and to detect them with known efficiency. The ion source allows varying and tuning the electron-impact ionization energy and the target-gas pressure. We demonstrate that for obtaining reliable results of cross-sections for inelastic processes and determining mechanisms for the formation of O[Formula: see text]([Formula: see text]) ions, it is crucial to control the electron-impact energy for production of ion and the pressure in the ion source. A comparison of our results with other experimental and theoretical data shows good agreement and proves the validity of our approach.

CO2 or SO2: Should It Stay or Should It Go?

<div><div><div><p>A broad computational analysis of carbon-centered radical formation via the loss of either CO2 or SO2 from the respective RXO2 radical precursors (X = C or S) reveals dramatic differences between these two types of dissociative processes. Whereas the C-C scission with the loss of CO2 is usually exothermic, the C-S scission with the loss of SO2 is generally endothermic. However, two factors can make the C-S scissions thermodynamically favorable: increased entropy, characteristic for the dissociative processes, and stereoelectronic influences of substituents. The threshold between endergonic and exergonic C-S fragmentations depends on subtle structural effects. In particular, the degree of fluorination in a radical precursor has a notable impact on the reaction outcome. This study aims to demystify the intricacies in reactivity regarding the generation of radicals from sulfinates and carboxylates, as related to their role in radical cross-coupling.</p></div></div></div>

CO2 or SO2: Should It Stay or Should It Go?

<div><div><div><p>A broad computational analysis of carbon-centered radical formation via the loss of either CO2 or SO2 from the respective RXO2 radical precursors (X = C or S) reveals dramatic differences between these two types of dissociative processes. Whereas the C-C scission with the loss of CO2 is usually exothermic, the C-S scission with the loss of SO2 is generally endothermic. However, two factors can make the C-S scissions thermodynamically favorable: increased entropy, characteristic for the dissociative processes, and stereoelectronic influences of substituents. The threshold between endergonic and exergonic C-S fragmentations depends on subtle structural effects. In particular, the degree of fluorination in a radical precursor has a notable impact on the reaction outcome. This study aims to demystify the intricacies in reactivity regarding the generation of radicals from sulfinates and carboxylates, as related to their role in radical cross-coupling.</p></div></div></div>

Accelerating Dissociative Events in Molecular Dynamics Simulations by Selective Potential Scaling

ABSTRACTMolecular dynamics (or MD) simulations can be a powerful tool for modeling complex dissociative processes such as ligand unbinding. However, many biologically relevant dissociative processes occur on timescales that far exceed the timescales of typical MD simulations. Here, we implement and apply an enhanced sampling method in which specific energy terms in the potential energy function are selectively “scaled” to accelerate dissociative events during simulations. Using ligand unbinding as an example of a complex dissociative process, we selectively scaled-up ligand-water interactions in an attempt to increase the rate of ligand unbinding. By applying our selectively scaled MD (or ssMD) approach to three cyclin-dependent kinase 2 (CDK2)-inhibitor complexes, we were able to significantly accelerate ligand unbinding thereby allowing, in some cases, unbinding events to occur within as little as 2 ns. Moreover, we found that we could make realistic estimates of the unbinding as well as the binding free energies (∆Gsim) of the three inhibitors from our ssMD simulation data. To accomplish this, we employed a previously described Kramers’-based rate extrapolation (KRE) method and a newly described free energy extrapolation (FEE) method. Because our ssMD approach is general, it should find utility as an easy-to-deploy, enhanced sampling method for modeling other dissociative processes.