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.     

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.     

Cationic Poly([R]‐3‐hydroxybutyrate) Copolymers as Antimicrobial Agents

Poly([R]‐3‐hydroxybutyrate) (PHB), a natural biodegradable polyester, has attracted much attention as a new biomaterial because of its sustainability and good biocompatibility. In this study, it is discovered that PHB can be conveniently functionalized to obtain a number of platform chain architectures that may provide a wide range of functional copolymers. In a transesterification reaction, linear (di‐hydroxylated) and star shaped (tri‐ and tetra‐hydroxylated) PHB oligomers are synthesized, followed by copolymerization with 2‐(dimethylamino)ethyl methacrylate and quaternization with benzyl bromide to afford antimicrobial properties. The antimicrobial activities of the quaternary salts against clinically relevant pathogens on the interactions with outer and cytoplasmic membranes, lethal mechanisms, multipassage resistance, and synergy effect with antibiotics are investigated. Cationic PHB copolymers show effectiveness as antimicrobial agents, with minimum inhibitory concentration values 0.24–0.65 µm (or µmol dm^?3) (or 32–128 µg mL^?1) against Gram‐positive and Gram‐negative bacteria. Modifying the copolymer architectures into star shapes results in enhanced effectiveness to disrupt the membrane integrity. Synergistic effects are attained for all the quaternized PHB derivatives when they are used together with tobramycin. Multipassage resistance does not occur in both the linear and star derivatives against Gram‐negative bacteria after 20 passages.     

18‐Crown‐6 Catalyzed Microwave‐mediated Synthesis of Symmetric Bis‐Heterocyclic Compounds under Solvent‐free Condition

An efficient, solvent‐free and 18‐crown‐6 catalyzed method for the synthesis of N‐alkyl‐4‐(4‐(5‐(2‐(alkyl‐amino)thiazol‐4‐yl)pyridin‐3‐yl)phenyl)thiazol‐2‐amine, N‐alkyl‐4‐(5‐(2‐alkyamino)thiazol‐4‐yl)pyridine‐3‐yl)thiazol‐2‐amine, and 4,4′‐bis‐{2‐[amino]‐4‐thiazolyl}biphenyl bis‐heterocyclic derivatives via microwave accelerated cyclization is presented.