Hybrid Solvation Model with First Solvation Shell for Calculation of Solvation Free Energy

Role of Explicit Solvation in Computational Modeling of Chemical Reactions: Mechanism of Cu(I) Transfer Between Thiolate-Based Chelators in Water

Solvation plays important roles in controlling the thermodynamic and kinetic aspects of chemical reactions. The conventional approaches to treat solvation via electronic structure methods are likely to become inadequate, when the reacting solutes have strong electrostatic and hydrogen bonding interactions with the solvent and undergo significant structural changes during the course of the reaction. In this article, we present evidence of such solvent and structural effects in the computational study of the Cu(I) transfer reaction between thiolate-based chelators dithiobutylamine (DTBA) and dithiotheritol (DTT) in water, inspired from biological copper trafficking phenomena. We propose a general solution to the problem by combining classical molecular dynamics (MD) simulations of the bulk system and static quantum chemistry calculations. The fluctuating solvation shell was estimated from MD, and energetics was assessed by averaging QM energies of a series of molecular clusters constructed from the MD snapshots. Applying this approach, we propose a reaction pathway with estimates of relative intermediate stabilities and barriers, which suggest the overall reaction to be reversible in nature and likely to go through both two and three coordinated intermediates, confirming previous studies of similar protein analogues. An interesting fact that emerged from our study was the strong indication that the rate-determining step is the deprotonation of initial thiol bound Cu(I) complex, without involving any Cu(I)-S bonds. The proposed method will lead to a better treatment of solvations, and these mechanistic insights will aid our understanding of biological copper(I) trafficking.

Virtual Screening-Based Study of Novel Anti-Cancer Drugs Targeting G-Quadruplex

In order to develop new anti-cancer drugs more efficiently and reduce side effects based on active drug targets, the virtual drug screening was carried out through the target of G-quadruplexes and 23 hit compounds were, thus, screened out as potential anticancer drugs. Six classical G-quadruplex complexes were introduced as query molecules, and the three-dimensional similarity of molecules was calculated by shape feature similarity (SHAFTS) method so as to reduce the range of potential compounds. Afterwards, the molecular docking technology was utilized to perform the final screening followed by the exploration of the binding between each compound and four different structures of G-quadruplex. In order to verify the anticancer activity of the selected compounds, compounds 1, 6 and 7 were chosen to treat A549 cells in vitro, the lung cancer epithelial cells, for further exploring their anticancer activity. These three compounds were found to be of good characteristics in the treatment of cancer, which revealed the great application prospect of the virtual screening method in developing new drugs.

Atomic-Level Mechanism, Solvent Effect, and Potential of the Mean Force of the F- + CH3CH2Cl SN2 Reaction in Aqueous Solution

We investigate the bimolecular nucleophilic substitution (S_N2) reaction of F^- with CH₃CH₂Cl in aqueous solution using combined multilevel quantum mechanism (ML-QM) theories with molecular mechanics (MM). The synchronized, atomic-level structural and charge evolutions are analyzed along the reaction path. The potential mean force along the reaction path in water is calculated at high-accuracy CCSD(T)/aug-cc-pVTZ/MM level of theory with a free energy barrier of 16.8 kcal/mol and a free energy of reaction of -9.7 kcal/mol. The water solvent hinders the reactivity by raising its reaction barrier by 15.1 kcal/mol, of which 13.6 kcal/mol comes from solvent energy contribution and 1.5 kcal/mol comes from the polarization effect. This indicates that the water solvent plays an essential role on this reaction in aqueous solution. We also predict the potential mean force profile based on the gas-phase reaction path and the solvation free energies of the stationary points; the comparison between our calculated result at CCSD(T)/MM level shows an excellent agreement with the predicted one with the free energy barrier at 16.2 kcal/mol and the free energy of reaction at -8.3 kcal/mol.

Theoretical investigation of the cooperative effect of solvent: a case study

The effect of solvent was investigated at the DFT level, M06-2X/6-31++G(d,p), for the implicit, namely the universal solvent model based on solute electron density (SMD), and hybrid solvation models, and...

Single-ion solvation free energy: A new cluster-continuum approach based on the cluster expansion method

Accurate calculation of the solvation free energy of single ions remains an important goal, involving development in the dielectric continuum solvation models, and statistical mechanics with explicit solvent and hybrid discrete-continuum methods. In the last case, many of the research studies involve a quasi-chemical approach using the monomer cycle or the cluster cycle to calculate the solvation free energy of single ions. In this work, a different cluster-continuum approach based on the cluster expansion method was tested for solvation of 16 cations and 32 anions in aqueous solution. The SMD model was used for the dielectric continuum part and three explicit water molecules were introduced in the region of the solute with the highest interaction energy. Harmonic frequency calculations and molecular dynamics sampling of configurations are not required. An empirical γ_N parameter for cations and another for anions is introduced. The method produces a substantial improvement of the SMD model with a mean absolute deviation of 2.3 kcal mol^-1 for cations and 2.9 kcal mol^-1 for anions. The analysis of the correlation between theoretical and experimental data produces a linear regression line with a slope of 1.09 for cations and 1.01 for anions. The good results of this approximated cluster expansion approach suggest that the method could be further improved by including more solvent molecules and sampling the configurations.