Mediating Order and Modulating Porosity by Controlled Hydrolysis in a Phosphonate Monoester Metal–Organic Framework

A crystalline and permanently porous copper phosphonate monoester framework has been synthesized from a tetraaryl trigonal phosphonate monoester linker. This material has a surface area over 1000 m² g^?1, as measured by N₂ sorption, the highest reported for a phosphonate‐based metal–organic framework (MOF). The monoesters result in hydrophobic pore surfaces that give a low heat of adsorption for CO₂ and low calculated selectivity for CO₂ over N₂ and CH₄ in binary mixtures. By careful manipulation of synthetic conditions, it is possible to selectively remove some of the monoesters lining the pore to form a hydrogen phosphonate while giving an isomorphous structure. This increases the affinity of the framework for CO₂ giving higher ambient uptake, higher heat of adsorption, and much higher calculated selectivity for CO₂ over both N₂ and CH₄. Formation of the acid groups is noteworthy as complexation with the parent acid gives a different structure.     

Ambient temperature ring-opening polymerisation (ROP) of cyclic chlorophosphazene trimer [N(3)P(3)Cl(6)] catalyzed by silylium ions

The temperature required for ring-opening polymerisation of cyclo-N(3)P(3)Cl(6) can be dramatically lowered by employing trialkylsilylium carboranes [R(3)Si(CHB(11)X(11)] as catalysts.     

Kinetics of the hydrogen abstraction CHO + Alkane → HCHO + Alkyl reaction class: an application of the reaction class transition state theory

The kinetics of the hydrogen abstraction at alkanes by formyl radicals is investigated using the reaction class transition state theory (RC-TST) approach combined with the linear energy relationship (LER) or the barrier height grouping (BHG). The rate constants of a reaction in this class can be estimated through those of the reference reaction, CHO + C₂H₆, which are obtained from rate constants of the reaction that involves the smallest species, namely CHO + CH₄, using the explicit RC-TST scaling. The thermal rate constants of this smallest reaction are evaluated at the canonical variational transition state theory (CVT) with the corrections from the small-curvature tunneling (SCT) and hindered rotation (HR) treatments. Our analyses indicate that less than 40% systematic errors, on the average, exist in the predicted rate constants using both the LER approach, where only reaction energy is needed, and the BHG approach, where no additional information is needed; while comparing to explicit rate calculations the differences are less than 60%. Contribution to Mark S. Gordon 65th Birthday Festschrift Issue.     

Calculating protein–ligand binding affinities with MMPBSA: Method and error analysis

Molecular Mechanics Poisson–Boltzmann Surface Area (MMPBSA) methods have become widely adopted in estimating protein–ligand binding affinities due to their efficiency and high correlation with experiment. Here different computational alternatives were investigated to assess their impact to the agreement of MMPBSA calculations with experiment. Seven receptor families with both high‐quality crystal structures and binding affinities were selected. First the performance of nonpolar solvation models was studied and it was found that the modern approach that separately models hydrophobic and dispersion interactions dramatically reduces RMSD's of computed relative binding affinities. The numerical setup of the Poisson–Boltzmann methods was analyzed next. The data shows that the impact of grid spacing to the quality of MMPBSA calculations is small: the numerical error at the grid spacing of 0.5 Å is already small enough to be negligible. The impact of different atomic radius sets and different molecular surface definitions was further analyzed and weak influences were found on the agreement with experiment. The influence of solute dielectric constant was also analyzed: a higher dielectric constant generally improves the overall agreement with experiment, especially for highly charged binding pockets. The data also showed that the converged simulations caused slight reduction in the agreement with experiment. Finally the direction of estimating absolute binding free energies was briefly explored. Upon correction of the binding‐induced rearrangement free energy and the binding entropy lost, the errors in absolute binding affinities were also reduced dramatically when the modern nonpolar solvent model was used, although further developments were apparently necessary to further improve the MMPBSA methods. © 2016 Wiley Periodicals, Inc.     

Synthesis, structures, and stability of N-donor-stabilized N-silylphosphoranimine cations

A series of DMAP-stabilized (DMAP=4-dimethylaminopyridine) N-silylphosphoranimine cations [DMAPPR(2)==NSiMe(3)](+), bearing R=Cl ([8](+)), Me ([10 a](+)), Me/Ph ([10 b](+)), Ph ([10 c](+)), and OCH(2)CF(3) ([10 d](+)) substituents, have been synthesized from the reactions of the parent phosphoranimines Cl(3)P==NSiMe(3) (3) and XR(2)P==NSiMe(3) (X=Cl (9), Br (11); R=Me (9 a and 11 a), Me/Ph (9 b and 11 b), Ph (9 c and 11 c), and OCH(2)CF(3) (9 d and 11 d)) with DMAP and silver salts as halide abstractors. Reactions in the absence of silver salts yield the corresponding cations, with halide counterions. The stability of the salts is highly dependent on the phosphoranimine substituent and the nature of the counteranion, such that electron-withdrawing substituents and non-coordinating anions yield the most stable salts. X-ray structural determination of the cations reveal extremely short phosphoranimine P--N bond lengths for the cations [8](+) and [10 d](+) (1.47-1.49 A) in which electron-withdrawing substituents are present and a longer phosphoranimine P--N length for the cation [10 a](+) (1.53 A) in which electron-donating substituents are present. Very wide bond angles at nitrogen are observed for the salts containing the cation [10 d](+) (158-166 degrees ) and indicate significant sp hybridization at the nitrogen centre.     

A molecular docking simulation study on potent inhibitors against Rhizoctonia solani and Magnaporthe oryzae in rice: silver-tetrylene and bis-silver-tetrylene complexes vs. validamycin and tricyclazole pesticides

Structural Chemistry - Rice, well known as the most important staple food source worldwide, is highly susceptible to many infectious diseases, especially rice sheath blight caused by fungus...     

Structure-Based Discovery of ABCG2 Inhibitors: A Homology Protein-Based Pharmacophore Modeling and Molecular Docking Approach

ABCG2 is an ABC membrane protein reverse transport pump, which removes toxic substances such as medicines out of cells. As a result, drug bioavailability is an unexpected change and negatively influences the ADMET (absorption, distribution, metabolism, excretion, and toxicity), leading to multi-drug resistance (MDR). Currently, in spite of promising studies, screening for ABCG2 inhibitors showed modest results. The aim of this study was to search for small molecules that could inhibit the ABCG2 pump. We first used the WISS MODEL automatic server to build up ABCG2 homology protein from 655 amino acids. Pharmacophore models, which were con-structed based on strong ABCG2 inhibitors (IC₅₀ < 1 μM), consist of two hydrophobic (Hyd) groups, two hydrogen bonding acceptors (Acc2), and an aromatic or conjugated ring (Aro|PiR). Using molecular docking method, 714 substances from the DrugBank and 837 substances from the TCM with potential to inhibit the ABCG2 were obtained. These chemicals maybe favor synthesized or extracted and bioactivity testing.     

Synthesis and α-Glucosidase Inhibitory Activity of Ursolic Acid,Lupeol, and Betulinic Acid Derivatives

Chemistry of Natural Compounds - Seven synthetic derivatives of ursolic acid, lupeol, and betulinic acid (1a–1b, 2a–2b, and 3a–3c) were synthesized to study their...