Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions

Proper balance between protein-protein and protein-water interactions is vital for atomistic molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered proteins (IDPs). The overestimation of protein-protein interactions tends to make IDPs more compact than those in experiments. Likewise, multiple proteins in crowded solutions are aggregated with each other too strongly. To optimize the balance, Lennard-Jones (LJ) interactions between protein and water are often increased about 10% (with a scaling parameter, λ = 1.1) from the existing force fields. Here, we explore the optimal scaling parameter of protein-water LJ interactions for CHARMM36m in conjunction with the modified TIP3P water model, by performing enhanced sampling MD simulations of several peptides in dilute solutions and conventional MD simulations of globular proteins in dilute and crowded solutions. In our simulations, 10% increase of protein-water LJ interaction for the CHARMM36m cannot maintain stability of a small helical peptide, (AAQAA)₃ in a dilute solution and only a small modification of protein-water LJ interaction up to the 3% increase (λ = 1.03) is allowed. The modified protein-water interactions are applicable to other peptides and globular proteins in dilute solutions without changing thermodynamic properties from the original CHARMM36m. However, it has a great impact on the diffusive properties of proteins in crowded solutions, avoiding the formation of too sticky protein-protein interactions.     

The Conversion of Superoxide to Hydroperoxide on Cobalt(III) Depends on the Structural and Electronic Properties of Azole-Based Chelating Ligands

Conversion from superoxide (O₂⁻) to hydroperoxide (OOH⁻) on the metal center of oxygenases and oxidases is recognized to be a key step to generating an active species for substrate oxidation. In this study, reactivity of cobalt(III)-superoxido complexes supported by facially-capping tridentate tris(3,5-dimethyl-4-X-pyrazolyl)hydroborate ([HB(pz^Me2,X)₃]⁻; Tp^Me2,X) and bidentate bis(1-methyl-imidazolyl)methylborate ([B(Im^N-Me)₂Me(Y)]⁻; L^Y) ligands toward H-atom donating reagent (2-hydroxy-2-azaadamantane; AZADOL) has been explored. The oxygenation of the cobalt(II) precursors give the corresponding cobalt(III)-superoxido complexes, and the following reaction with AZADOL yield the hydroperoxido species as has been characterized by spectroscopy (UV-vis, resonance Raman, EPR). The reaction of the cobalt(III)-superoxido species and a reducing reagent ([Co^II(C₅H₅)₂]; cobaltocene) with proton (trifluoroacetic acid; TFA) also yields the corresponding cobalt(III)-hydroperoxido species. Kinetic analyses of the formation rates of the cobalt(III)-hydroperoxido complexes reveal that second-order rate constants depend on the structural and electronic properties of the cobalt-supporting chelating ligands. An electron-withdrawing ligand opposite to the superoxide accelerates the hydrogen atom transfer (HAT) reaction from AZADOL due to an increase in the electrophilicity of the superoxide ligand. Shielding the cobalt center by the alkyl group on the boron center of bis(imidazolyl)borate ligands hinders the approaching of AZADOL to the superoxide, although the steric effect is insignificant.     

Molecular orientation of paramagnetic metal complex by melt-drawing thermotropic liquid crystalline polymers

New liquid-crystalline polyesters and paramagnetic vanadyl complex were prepared as host polymer and guest complex. Melt-drawn fibers were made from the blend of host polymer and guest complex at the mesophase temperature. ESR spectra of the melt-drawn fibers indicated that the base of pyramidal vanadyl complex is completely oriented parallel to the fiber axis.     

Beyond Reduction Cocatalysts: Critical Role of Metal Cocatalysts in Photocatalytic Oxidation of Methane with Water**

Environmentally sustainable and selective conversion of methane to valuable chemicals under ambient conditions is pivotal for the development of next-generation photocatalytic technology. However, due to the lack of microscopic knowledge about non-thermal methane conversion, controlling and modulating photocatalytic oxidation processes driven by photogenerated holes remain a challenge. Here, we report novel function of metal cocatalysts to accept photogenerated holes and dominate selectivity of methane oxidation, which is clearly beyond the conventional concept in photocatalysis that the metal cocatalysts loaded on the surfaces of semiconductor photocatalysts mostly capture photogenerated electrons and dominate reduction reactions exclusively. The novel photocatalytic role of metal cocatalysts was verified by operando molecular spectroscopy combined with real-time mass spectrometry for metal-loaded Ga₂O₃ model photocatalysts under methane and water vapor at ambient temperature and pressure. Our concept of metal cocatalysts that work as active sites for both photocatalytic oxidation and reduction provides a new understanding of photocatalysis and a solid basis for controlling non-thermal redox reactions by metal-cocatalyst engineering.     

Pnictogen-Bridged Diphenyl Sulfones as Photoinduced Pnictogen Bond Forming Emission Motifs

In this study, pnictogen (Pn)-bridged diphenyl sulfones were synthesized as motifs for photoinduced dynamic rearrangement. The newly synthesized sulfones exhibited dual fluorescence at 298 K. Density functional theory calculations revealed that the longer-wavelength fluorescence was derived from the geometries after structural relaxation through photo-driven pnictogen bond formation between the O atom lone pair of the sulfonyl moiety and the antibonding orbital of the Pn−C bond. This is the first report on emission dynamics driven by pnictogen bond formation upon photoexcitation.     

Reductive dimerization and reduction of imines using lanthanum metal

The treatment of N‐benzylideneaniline ( 1a ) with a half‐equivalent of lanthanum metal and a catalytic amount of iodine gave the reductive dimerization product of 1a , a vic‐diamine, in good yield. Various vic‐diamines were synthesized from aldimines in this manner in moderate to good yields. Our findings suggest that electrons of a zero‐valent lanthanum metal were efficiently utilized in this reductive dimerization. In the reaction of ketimines, however, a similar reductive dimerization did not take place, and the corresponding amines were formed as the sole products. © 2002 Wiley Periodicals, Inc. Heteroatom Chem 13:131–135, 2002; Published online in Wiley Interscience (www.interscience.wiley.com). DOI 10.1002/hc.10007