Balancing kinetic and thermodynamic control: the mechanism of carbocation cyclization by squalene cyclase

Molecular dynamics simulations with a combined quantum mechanical and molecular mechanical (QM/MM) potential have been carried out to investigate the squalene-to-hopene carbocation cyclization mechanism in squalene-hopene cyclase (SHC). The present study is based on free energy simulations by constructing the free energy surface for the cyclization steps along the reaction pathway. The picture that emerges for the carbocation cyclization cascade is a delicate balance of thermodynamic and kinetic control that ultimately favors the formation of the final hopanoids carbon skeleton. A key finding is that the five- to six-membered ring expansion process is not a viable reaction pathway for either C- or D-ring formation in the cyclization reaction. The only significant intermediate is the A/B-bicyclic cyclohexyl cation (III), from which two asynchronous concerted reaction pathways lead to, respectively, the 6,6,6,5-tetracyclic carbon skeleton and the 6,6,6,6,5-pentacyclic hopanoids. Experimentally, these two products are observed to have 1% and 99% yields, respectively, in the wild-type enzyme. We conclude that the product distribution in the wild-type enzyme is dictated by kinetic control of these two reaction pathways.     

Expanded Organic Building Units for the Construction of Highly Porous Metal–Organic Frameworks

Two new organic building units that contain dicarboxylate sites for their self‐assembly with paddlewheel [Cu₂(CO₂)₄] units have been successfully developed to construct two isoreticular porous metal–organic frameworks (MOFs), ZJU‐35 and ZJU‐36, which have the same tbo topologies (Reticular Chemistry Structure Resource (RCSR) symbol) as HKUST‐1. Because the organic linkers in ZJU‐35 and ZJU‐36 are systematically enlarged, the pores in these two new porous MOFs vary from 10.8 Å in HKUST‐1 to 14.4 Å in ZJU‐35 and 16.5 Å in ZJU‐36, thus leading to their higher porosities with Brunauer–Emmett–Teller (BET) surface areas of 2899 and 4014 m² g^?1 for ZJU‐35 and ZJU‐36, respectively. High‐pressure gas‐sorption isotherms indicate that both ZJU‐35 and ZJU‐36 can take up large amounts of CH₄ and CO₂, and are among the few porous MOFs with the highest volumetric storage of CH₄ under 60 bar and CO₂ under 30 bar at room temperature. Their potential for high‐pressure swing adsorption (PSA) hydrogen purification was also preliminarily examined and compared with several reported MOFs, thus indicating the potential of ZJU‐35 and ZJU‐36 for this important application. Studies show that most of the highly porous MOFs that can volumetrically take up the greatest amount of CH₄ under 60 bar and CO₂ under 30 bar at room temperature are those self‐assembled from organic tetra‐ and hexacarboxylates that contain m‐benzenedicarboxylate units with the [Cu₂(CO₂)₄] units, because this series of MOFs can have balanced porosities, suitable pores, and framework densities to optimize their volumetric gas storage. The realization of the two new organic building units for their construction of highly porous MOFs through their self‐assembly with [Cu₂(CO₂)₄] units has provided great promise for the exploration of a large number of new tetra‐ and hexacarboxylate organic linkers based on these new organic building units in which different aromatic backbones can be readily incorporated into the frameworks to tune their porosities, pore structures, and framework densities, thus targeting some even better performing MOFs for very high gas storage and efficient gas separation under high pressure and at room temperature in the near future.     

Rational Design of Microporous MOFs with Anionic Boron Cluster Functionality and Cooperative Dihydrogen Binding Sites for Highly Selective Capture of Acetylene

Separation of acetylene (C₂H₂) from carbon dioxide (CO₂) or ethylene (C₂H₄) is important in industry but limited by the low capacity and selectivity owing to their similar molecular sizes and physical properties. Herein, we report two novel dodecaborate‐hybrid metal–organic frameworks, MB₁₂H₁₂(dpb)₂ (termed as BSF‐3 and BSF‐3‐Co for M=Cu and Co), for highly selective capture of C₂H₂. The high C₂H₂ capacity and remarkable C₂H₂/CO₂ selectivity resulted from the unique anionic boron cluster functionality as well as the suitable pore size with cooperative proton‐hydride dihydrogen bonding sites (B?H^δ????H^δ+?C≡C?H^δ+???H^δ??B). This new type of C₂H₂‐specific functional sites represents a fresh paradigm distinct from those in previous leading materials based on open metal sites, strong electrostatics, or hydrogen bonding.     

Rifampicin inhibits alpha-synuclein fibrillation and disaggregates fibrils

The aggregation of alpha-synuclein in dopaminergic neurons of the substantia nigra is a critical step in the pathogenesis of Parkinson's disease. We show that the antibiotic rifampicin inhibited alpha-synuclein fibrillation and disaggregated existing fibrils in a concentration-dependent manner. Size-exclusion chromatography data indicated that rifampicin stabilized alpha-synuclein as both a monomer and soluble oligomers comprised of partially folded alpha-synuclein. Experiments using aged samples of rifampicin indicated that the most active species in inhibiting fibrillation and disaggregating fibrils is an oxidation product of rifampicin, which was confirmed in experiments under anaerobic conditions. These results indicate that rifampicin-mediated inhibition of alpha-synuclein fibrillation and disaggregation of fibrils involves preferential stabilization of monomeric and soluble oligomeric forms, and that rifampicin potentially may have therapeutic application for Parkinson's disease.     

Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution

We describe the implementation of an adaptive umbrella sampling method, making use of the weighted histogram analysis method, for computing multidimensional potential of mean force for chemical reaction in solution. The approach is illustrated by investigating the effect of aqueous solution on the free energy surface for the proton transfer reaction of [H(3)N-H-NH(3)](+) using a combined quantum mechanical and molecular mechanical AM1/TIP3P potential.     

Two‐Dimensional Covalent Organic Frameworks for Carbon Dioxide Capture through Channel‐Wall Functionalization

Ordered open channels found in two‐dimensional covalent organic frameworks (2D COFs) could enable them to adsorb carbon dioxide. However, the frameworks’ dense layer architecture results in low porosity that has thus far restricted their potential for carbon dioxide adsorption. Here we report a strategy for converting a conventional 2D COF into an outstanding platform for carbon dioxide capture through channel‐wall functionalization. The dense layer structure enables the dense integration of functional groups on the channel walls, creating a new version of COFs with high capacity, reusability, selectivity, and separation productivity for flue gas. These results suggest that channel‐wall functional engineering could be a facile and powerful strategy to develop 2D COFs for high‐performance gas storage and separation.