Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints

Chain-of-state methods are becoming important tools in studying the chemical reaction mechanisms, especially for biomacromolecules. In this article, three chain-of-state methods, the nudged elastic band (NEB) method and the replica path method with restraints or constraints, were tested and compared using three model systems with various sizes and at different levels of theory: alanine dipeptide isomerization, β-alanine intramolecular condensation, and the matrix metalloproteinase 2 inhibition mechanism. The levels of theory used to describe the three model systems include molecular mechanics (MM), quantum mechanics (QM), and combined quantum mechanics and molecular mechanics (QM/MM). All three methods could correctly determine a reaction path with reasonable estimation of reaction barriers in most cases. The RMSD measurement with additional weighting schemes provides practically infinite choices of reaction coordinates to describe the reaction progress. These findings demonstrate that the chain-of-state methods are powerful tools when being used carefully to generate a plausible reaction mechanism with full pathway for complex systems at an affordable computational cost

Disaggregation is a Mechanism for Emission Turn-On of <i>ortho</i>-Aminomethylphenylboronic Acid-Based Saccharide Sensors

<i>ortho</i>-Aminomethylphenylboronic acid-based receptors with appended fluorophores are commonly used as molecular sensors for saccharides in aqueous media. The mechanism for fluorescence modulation in these sensors has been attributed to some form of photoinduced electron transfer (PET) quenching, which is diminished in the presence of saccharides. Using a well-known boronic acid-based saccharide sensor (<b>3</b>), this work reveals a new mechanism for fluorescence turn-on in these types of sensors. Compound <b>3</b> exhibits an excimer, and the associated ground-state aggregation is responsible for fluorescence modulation under certain conditions. When fructose was titrated into a solution of <b>3</b> in 2:1 water/methanol with NaCl, the fluorescence intensity increased. Yet, when the same titration was repeated in pure methanol, a solvent in which the sensor does not aggregate, no fluorescence response to fructose was observed. This reveals that the fluorescence increase is not fully associated with fructose binding, but instead disaggregation of the sensor in the presence of fructose. Further, an analogue of the sensor that does not contain a boronic acid (<b>4</b>) responded nearly identically to <b>3</b> in the presence of fructose, despite having no functional group with which to bind the saccharide. This further supports the claim that fluorescence modulation is not primarily a result of binding, but of disaggregation. Using an indicator displacement assay and isothermal titration calorimetry, it was confirmed that fructose does indeed bind to the sensor. Thus, our evidence reveals that while binding occurs with fructose in the aqueous solvent system used, it is not related to the majority of the fluorescence modulation. Instead, disaggregation dominates the signal turn-on, and is thus a mechanism that should be investigated in other <i>ortho</i>-aminomethylphenylboronic acid-based sensors