Lipids are key factors in regulating membrane fusion. Lipids are not only structural components to form membranes but also active catalysts for vesicle fusion and neurotransmitter release, which are driven by soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. SNARE proteins seem to be partially assembled before fusion, but the mechanisms that arrest vesicle fusion before Ca2+ influx are still not clear. Here, we show that phosphatidylinositol 4,5-bisphosphate (PIP2) electrostatically triggers vesicle fusion as an electrostatic catalyst by lowering the hydration energy and that a myristoylated alanine-rich C-kinase substrate (MARCKS), a PIP2-binding protein, arrests vesicle fusion in a vesicle docking state where the SNARE complex is partially assembled. Vesicle-mimicking liposomes fail to reproduce vesicle fusion arrest by masking PIP2, indicating that native vesicles are essential for the reconstitution of physiological vesicle fusion. PIP2 attracts cations to repel water molecules from membranes, thus lowering the hydration energy barrier.

The adsorption capacity of synthetic NaX zeolite for Pb2+, Cd2+, Cu2+ and Zn2+ in single and multi-component systems were investigated. The effects of electronegativity and hydration energy on the selective adsorption, as well as potential selective adsorption mechanism of the NaX zeolite for Pb2+, Cd2+, Cu2+ and Zn2+ were also discussed. The maximum adsorption capacity order of the heavy metals in the single system was Pb2+ > Cd2+ > Cu2+ > Zn2+, and this could be related to their hydration energy and electronegativity. The values of the separation factors (α) and affinity constant (KEL) in different binary systems indicated that Pb2+ was preferentially adsorbed, and Zn2+ presented the lowest affinity for NaX zeolite. The selective adsorption capacities of the metals were in the order, Pb2+ > Cd2+ ≈ Cu2+ > Zn2+. The trend for the selective adsorption of NaX zeolite in ternary and quaternary systems was consistent with that in the binary systems. Pb2+ and Cu2+ reduced the stability of the Si-O-Al bonds and the double six-membered rings in the NaX framework, due to the high electronegativity of Pb2+ and Cu2+ than that of Al3+. The selective adsorption mechanism of NaX zeolite for the high electronegative metal ions could mainly result from the negatively charged O in the Si-O-Al structure of the NaX zeolite, hence heavy metal ions with high electronegativity display a strong affinity for the electron cloud of the oxygen atoms in the Si-O-Al. This study could evaluate the application and efficiency of zeolite in separating and recovering certain metal ions from industrial wastewater.

The interaction between sugars and water molecules plays a crucial role in exploring the complex metabolic reactions of living systems. The fully random conformational search is employed to investigate the first hydration shell structure of glucose. The circumference of glucose is divided into three hydrate sites according to the location of water molecules. Especially, four water molecules can saturate hydrate site AI and while more water molecules will be required to saturate hydrate sites AIII and AII. Moreover, the hydration energies of water molecules at different hydration region indicate that the competition of the three hydrate sites for water molecules changes dynamically with the increase of water molecules. In addition, we calculate the Raman spectra of the hydrated glucose, which are in good agreement with the experimental and theoretical Raman spectra of the glucose solution.

Thermodynamic integration (TI), a powerful formalism for computing Gibbs free energy, has been implemented for many biophysical processes with alchemical schemes that require delicate human efforts to choose/design biasing potentials for sampling the desired biophysical events and to remove their artifactitious consequences afterwards. Theoretically, an alchemical scheme is exact but practically, an unsophisticated implementation of this exact formula can cause error amplifications. Small relative errors in the input parameters can be amplified many times in their propagation into the computed free energy [due to subtraction of similar numbers such as (105 ± 5)‒(100 ± 5) = 5 ± 7]. In this paper, we present an unsophisticated implementation of TI in 3n dimensions (3nD) (n=1,2,3…) for the potential of mean force along a 3nD path connecting one state in the bound state ensemble to one state in the unbound state ensemble. Fluctuations in these 3nD are integrated in the bound and unbound state ensembles but not along the 3nD path. Using TI3nD, we computed the standard binding free energies of three protein complexes: trometamol in Salmonella effector SpvD (n=1), biotin-avidin (n=2), and Colicin E9 endonuclease with cognate immunity protein Im9 (n=3). We employed three different protocols in three independent computations of E9-Im9 to show TI3nD\'s robustness. We also computed the hydration energies of ten biologically relevant compounds (n=1 for water, acetamide, urea, glycerol, trometamol, ammonium and n=2 for erythritol, 1,3-propanediol, xylitol, biotin). Each of the 15 computations is accomplishable within one (for hydration) to ten (for E9-Im9) days on an inexpensive GPU workstation. The computed results all agree with the available experimental data.

Here we review a new method for calculating a hydration free energy (HFE) of a solute and discuss its physical implication for biomolecular functions in aqueous environments. The solute hydration is decomposed into processes 1 and 2. A cavity matching the geometric characteristics of the solute at the atomic level is created in process 1. Solute-water van der Waals and electrostatic interaction potentials are incorporated in process 2. The angle-dependent integral equation theory combined with our morphometric approach is applied to process 1, and the three-dimensional reference interaction site model theory is employed for process 2. Molecular models are adopted for water. The new method is characterized by the following. Solutes with various sizes including proteins can be treated in the same manner. It is almost as accurate as the molecular dynamics simulation despite its far smaller computational burden. It enables us to handle a solute possessing a significantly large total charge without difficulty. The HFE can be decomposed into a variety of physically insightful, energetic, and entropic components. It is best suited to the elucidation of mechanisms of protein folding, pressure and cold denaturation of a protein, and different types of molecular recognition.

Due to their use in various domestic and industrial formulations, benzalkonium compounds have been isolated in many environmental matrices. Sorption to soil components has been shown to play a key role in their environmental fate. Whereas sorption of benzalkonium compounds to soils is attributed to cation exchange and van der Waals forces, the relative contributions of these two mechanisms at environmental levels have not been clearly defined. In this study a previously reported algal toxicity assay-based method was employed to determine the distribution coefficients (Kd) of benzalkonium compounds between water and soil components, at environmental concentrations. Cation exchange capacity corrected Kd values for organic matter and clays were all within one order of magnitude. This implies that ion exchange is the dominant mechanism of sorption for benzalkonium compounds. When the sorption data were used to compute sorption energies for four homologues of benzalkonium ions, the magnitude of the free energy change of sorption increased with size of the molecule. The increase in sorption energy could be partly explained by increased energy of hydration with addition of methylene groups to the alkyl chain. A model that predicts sorption coefficients of benzalkonium compounds to soils using organic carbon content and cation exchange capacity was also defined. When tested using an artificial soil, the model estimates were all within one order of magnitude of the experimental values.

We have predicted the free energy of hydration for 40 monovalent and multivalent cations and anions using density functional theory and the implicit solvent model COnductor like Screening MOdel for Real Solvents (COSMO-RS) at the Becke-Perdew (BP)/Triple zeta valence with polarization functions (TZVP) level. Agreement with experimental data for monovalent and divalent ions is good and shows no significant systematic errors. Predictions are noticeably better than with standard COSMO. The agreement with experimental data for trivalent and tetravalent ions is slightly worse and shows systematic errors. Our results indicate that quantum chemical calculations combined with COSMO-RS solvent treatment is a reliable method for treating multivalent ions in solution, provided one hydration shell of explicit water molecules is included for metal cations. The accuracy is not high enough to allow absolute predictions of hydration energies but could be used to investigate trends for several ions, thanks to the low computational cost, in particular for ligand exchange reactions.