Structural Characteristics of Homogeneous Hydrophobic Ionic Liquid-HNO3-H2O Ternary System: Experimental Studies and Molecular Dynamics Simulations.

The solubility of water in the hydrophobic ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C2mim][NTf2]) increases significantly in the presence of HNO3. [C2mim][NTf2] is completely miscible with HNO3 but immiscible with water. The triangular phase diagram of the ternary system [C2mim][NTf2]-HNO3-H2O was determined at 300.1 K. The homogeneous [C2mim][NTf2]-HNO3-H2O phase is thermodynamically stable, while it can be separated into two phases with an increase of water content. Experiments (electrospray ionization mass spectrometry, Fourier transform infrared spectrometry, and (1)H-nuclear magnetic resonance spectrometry) and molecular dynamics simulations were carried out to investigate the interaction between [C2mim][NTf2], HNO3, and water in the homogeneous phase. It was found that NO3(-) ions interact with both C2mim(+) and water via H-bonding and act as a "bridge" to induce a large amount of water to be dissolved in the hydrophobic IL phase. This confirms that the complexes [C2mim-NTf2-C2mim](+) and [NTf2-C2mim-NTf2](-) exist in the homogeneous [C2mim][NTf2]-HNO3-H2O system at the concentration of HNO3 up to 27.01 wt % and of water as high as 20.74 wt %.

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling.

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ - ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C-H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.

Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories.

High potential energy barriers and engagement of solvent coordinates set challenges for in silico studies of chemical reactions, and one is quite commonly limited to study reactions along predefined reaction coordinate(s). A systematic protocol, QM/MM MD simulations using enhanced sampling of reactive trajectories (ESoRT), is established to quantitatively study chemical transitions in complex systems. A number of trajectories for Claisen rearrangement in water and toluene were collected and analyzed, respectively. Evidence was found that the bond making and breaking during this reaction are concerted processes in solutions, preferentially through a chairlike configuration. Water plays an important dynamic role that helps stabilize the transition sate, and the dipole-dipole interaction between water and the solute also lowers the transition barrier. The calculated rate coefficient is consistent with the experimental measurement. Compared with water, the reaction pathway in toluene is "narrower" and the reaction rate is slower by almost three orders of magnitude due to the absence of proper interactions to stabilize the transition state. This study suggests that the "in-water" nature of the Claisen rearrangement in aqueous solution influences its thermodynamics, kinetics, as well as dynamics.

DNA Structural Correlation in Short and Long Ranges.

Recent single-molecule measurements have revealed the DNA allostery in protein/DNA binding. MD simulations showed that this allosteric effect is associated with the deformation properties of DNA. In this study, we used MD simulations to further investigate the mechanism of DNA structural correlation, its dependence on DNA sequence, and the chemical modification of the bases. Besides a random sequence, poly d(AT) and poly d(GC) are also used as simpler model systems, which show the different bending and twisting flexibilities. The base-stacking interactions and the methyl group on the 5-carbon site of thymine causes local structures and flexibility to be very different for the two model systems, which further lead to obviously different tendencies of the conformational deformations, including the long-range allosteric effects.

Computer simulation studies of Aß37-42 aggregation thermodynamics and kinetics in water and salt solution.

In vivo self-assembly of proteins into aggregates known as amyloids is related to many diseases. Although a large number of studies have been performed on the formation of amyloid, the molecular mechanism of polypeptide aggregation remains largely unclear. In this paper, we studied the aggregation of amyloid-forming peptide Aß37-42 using all-atom molecular dynamics simulations. Using the integrated temperature sampling (ITS) simulation method, we observed the reversible formation of Aß37-42 oligomers. The free-energy landscape for the polypeptide association was calculated, and aggregated states were then defined based on the landscape. To explore the kinetics and especially salt effects on the process of polypeptide aggregation, normal MD simulations were performed in pure water and NaCl solution, respectively. We then used the transition path theory (TPT) to analyze the transition network of polypeptide aggregation in solution. The dominant pathways of Aß37-42 aggregation were found to differ significantly in pure water and the salt solution, indicating the change of molecular mechanism of polypeptide aggregation with the solution conditions.