This paper describes a hybrid ab initio quantum mechanical/molecular mechanics (QM/MM) method for calculating activation free energies of chemical reactions in solution, using molecular mechanics force fields for the solvent and an ab initio technique that incorporates the potential from the solvent in its Hamiltonian for the solute. The empirical valence bond (EVB) method is used as a referenc...

Fluorescent semiconductor nanoparticles, or quantum dots, have potential uses as an optical material, in which the optoelectronic properties can be tuned precisely by particle size. Advances in chemical synthesis have led to improvements in size and shape control, cost, and safety. A limiting step in large-scale production is identified to be the raw materials cost, in which a common synthesis ...

We have studied the solvent effect on structures and potential energy surfaces along proton transfer in the ground and the excited states of 7-hydroxyquinoline interacting with an ethanol dimer using ab initio calculations. The proton transfer is forbidden in the ground state not only in vacuum but also in solvents of n-heptane, ethanol, and dimethyl sulfoxide. In the excited state, although th...

In the aftermath of the tragic events of 9/11, I became responsible for research and development (R&D) on infrastructure security at the Electric Power Research Institute (EPRI). At first, I was faced with many reports and files claiming either that “we were bullet proof” or that “the sky was falling.” It turned out that neither extreme was true of the entire electric-power sector. The truth de...

The effect of solvent polarity on the quality of self-assembled n-octadecanethiol (C18SH) on Cu surfaces was systematically analyzed using first-principles calculations. The results indicate that the adsorption energy for C18SH on a Cu surface is -3.37 eV, which is higher than the adsorption energies of the solvent molecules. The higher adsorption energy of dissociated C18SH makes the monolayer...

The interaction between nanoparticles and biomolecules such as protein andDNA is one of the major instructions of nanobiotechnology research. In this study,we have explored the interaction of adenine nucleic base with a representativegolden cluster (Au13) by using dispersion corrected density functional theory(DFT-D3) within GGA-PBE model of theory. Various active sites ...

We employ molecular dynamics simulations to study the solubility and molecular conformations of n-alkane chains in water. We find nearly exponential decrease in solubility with carbon number up to n-eicosane (C(20)), and excellent agreement with experiment up to n-dodecane (C(12)). We detect no sharp break in the dependence of the solubility upon carbon number. A free energy landscape analysis ...

In N-(2,5-di-tert-butylphenyl)-9-pyrrolidinoperylene-3,4-dicarboximide (5PI) the absorption and emission spectra display large solvatochromic shifts, but, remarkably, the Stokes shift is practically independent of solvent polarity. This unique behavior is caused by the extraordinarily large ground state dipole moment of 5PI, which further increases upon increasing solvent polarity, while the ex...

The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions, and protein–ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibra...

A hypothesis is proposed on a potential role of protein dielectricity as an unfolding factor in protein-protein interactions. It is suggested that large protein complexes and aggregation seeds can unfold target proteins by virtue of their effect on the dielectric properties of water at the protein-solvent interface. Here, similar to the effect of membrane surfaces, protein surface can cause dec...