Effect of Water Microsolvation on the Excited-State Proton Transfer of 3-Hydroxyflavone Enclosed in γ-Cyclodextrin.

The effect of microsolvation on excited-state proton transfer (ESPT) reaction of 3-hydroxyflavone (3HF) and its inclusion complex with γ-cyclodextrin (γ-CD) was studied using computational approaches. From molecular dynamics simulations, two possible inclusion complexes formed by the chromone ring (C-ring, Form I) and the phenyl ring (P-ring, Form II) of 3HF insertion to γ-CD were observed. Form II is likely more stable because of lower fluctuation of 3HF inside the hydrophobic cavity and lower water accessibility to the encapsulated 3HF. Next, the conformation analysis of these models in the ground (S0) and the first excited (S1) states was carried out by density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations, respectively, to reveal the photophysical properties of 3HF influenced by the γ-CD. The results show that the intermolecular hydrogen bonding (interHB) between 3HF and γ-CD, and intramolecular hydrogen bonding (intraHB) within 3HF are strengthened in the S1 state confirmed by the shorter interHB and intraHB distances and the red-shift of O-H vibrational modes involving in the ESPT process. The simulated absorption and emission spectra are in good agreement with the experimental data. Significantly, in the S1 state, the keto form of 3HF is stabilized by γ-CD, explaining the increased quantum yield of keto emission of 3HF when complexing with γ-CD in the experiment. In the other word, ESPT of 3HF is more favorable in the γ-CD hydrophobic cavity than in aqueous solution.

Selective adsorption mechanisms of pharmaceuticals on benzene-1,4-dicarboxylic acid-based MOFs: Effects of a flexible framework, adsorptive interactions and the DFT study.

The synergetic effects of benzene-1,4-dicarboxylic acid (BDC) linker structure and the metal cluster of MOFs on adsorption mechanisms of carbamazepine, ciprofloxacin and mefenamic acid were investigated in single and mixed solutions. A 1D flexible framework MIL-53(Al), 3D rigid framework UiO-66(Zr) and 3D flexible framework MIL-88B(Fe) were applied as adsorbents. The breathing effect of MIL-53(Al) caused by its flexible structure can enhance intraparticle diffusion for all pharmaceuticals and perform a critical role in excellent adsorption performances. The 3D rigid BDC structure of UiO-66(Zr) caused a steric effect that reflected low or negligible adsorption. Unless concerning accessibility through the internal structure of the MOFs, the binding strengths calculated by the DFT study were in the following order: MIL-88B(Fe) > MIL-53(Al) > UiO-66(Zr). The Fe cluster in MIL-88B(Fe) seems to have the highest affinity for the carboxylic group of pharmaceuticals compared with Al and Zr; however, the lower porosity of MIL-88B(Fe) might limit the adsorption capacity. Moreover, in mixed solutions, the higher acidity of mefenamic acid can enhance competitive performance in interactions with the metal cation cluster of each MOF. Together with the breathing effect, H-bonding and π-π interaction were shown to be the alternative interactions of synergetic adsorption mechanisms.

A DFT study of the unusual substrate-assisted mechanism of Serratia marcescens chitinase B reveals the role of solvent and mutational effect on catalysis.

Serratia marcescens chitinase B (SmChiB) catalyzes the hydrolysis of ß-1,4-glycosidic bond, via an unusual substrate-assisted mechanism, in which the substrate itself acts as an intramolecular nucleophile. In this paper, the catalytic mechanism of SmChiB has been investigated by using density functional theory. The details of two consecutive steps (glycosylation and deglycosylation), the structures and energetics along the whole catalytic reaction, and the roles of solvent molecules as well as some conserved SmChiB residues (Asp142, Tyr214, Asp215, and Arg294) during catalysis are highlighted. Our calculations show that the formation of the oxazolinium cation intermediate in the glycosylation step was found to be a rate-determining step (with a barrier of 23 kcal/mol), in line with our previous computational studies (Jitonnom et al., 2011, 2014). The solvent water molecules have a significant effect on a catalytic efficiency in the degycosylation step: the catalytic water is essentially placed in a perfect position for nucleophic attack by hydrogen bond network, lowering the barrier height of this step from 11.3 kcal/mol to 2.9 kcal/mol when more water molecules were introduced. Upon the in silico mutations of the four conserved residues, their mutational effects on the relative stability of the reaction intermediates and the computed energetics can be obtained by comparing with the wild-type results. Mutations of Tyr214 to Phe or Ala have shown a profound effect on the relative stability of the oxazolinium intermediate, emphasizing a direct role of this residue in destabilizing the intermediate. In line with the experiment that the D142A mutation leads to almost complete loss of SmChiB activity, this mutation greatly decreases the stability of the intermediate, resulting in a very large increase in the activation barrier up to 50 kcal/mol. The salt-bridges residues (Asp215 and Arg294) were also found to play a role in stabilizing the oxazolinium intermediate.

Theoretical investigation on the mechanism and kinetics of the ring-opening polymerization of ε-caprolactone initiated by tin(II) alkoxides.

A theoretical investigation of the ring-opening polymerization (ROP) mechanism of ε-caprolactone (CL) with tin(II) alkoxide, Sn(OR)2 initiators (R = n-C4H9, i-C4H9, t-C4H9, n-C6H13, n-C8H17) was studied. The density functional theory at B3LYP level was used to perform the modeled reactions. A coordination-insertion mechanism was found to occur via two transition states. Starting with a coordination of CL onto tin center led to a nucleophilic addition of the carbonyl group of CL, followed by the exchange of alkoxide ligand. The CL ring opening was completed through classical acyl-oxygen bond cleavage. The reaction barrier heights of ε-caprolactone with different initiators were calculated using potential energy profiles. The reaction of ε-caprolactone with Sn(OR)2 having R = n-C4H9 has the least value of barrier height compared to other reactions. The rate constants for each reaction were calculated using the transition state theory with TheRATE program. The rate constants are in good agreement with available experimental data.