The thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H(+)) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H(3)O(+)). Using the computed solvation free energy of H(+) as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pK(a) and normal hydrogen electrode (NHE) potentials. This conversion requires certain thermochemical corrections which were first presented in a similar study of the oxidation of hydrobenzoquinone [J. Cheng, M. Sulpizi, and M. Sprik, J. Chem. Phys. 131, 154504 (2009)]. Taking a different view of the thermodynamic status of the hydronium ion, these thermochemical corrections are revised in the present work. The key difference with the previous scheme is that the hydronium is now treated as an intermediate in the transfer of the proton from solution to the gas-phase. The accuracy of the method is assessed by a detailed comparison of the computed pK(a), NHE potentials and dehydrogenation free energies to experiment. As a further application of the technique, we have analyzed the role of the solvent in the oxidation of tyrosine by the tryptophan radical. The free energy change computed for this hydrogen atom transfer reaction is very similar to the gas-phase value, in agreement with experiment. The molecular dynamics results however, show that the minimal solvent effect on the reaction free energy is accompanied by a significant reorganization of the solvent.

Absolute pKa values of the amino acid side chains of arginine, aspartate, cysteine, histidine, and tyrosine; the C- and N-terminal group of tyrosine; and the tryptophan radical cation are calculated using a revised density functional based molecular dynamics simulation technique introduced previously [ Cheng , J. ; Sulpizi , M. ; Sprik , M. J. Chem. Phys. 2009 , 131 , 154504 ]. In the revised scheme, acid deprotonation is considered as a dissociation rather than a proton transfer reaction, and a correction term for treating the proton as a hydronium ion is suggested. The acidity constants of the amino acids are obtained from the vertical energy gaps for removal or insertion of the acidic proton and the computed solvation free energy of the proton. The unsigned mean error relative to experimental results is 2.1 pKa units with a maximum error of 4.0 pKa units. The estimated mean statistical uncertainty due to the finite length of the trajectories is ±1.1 pKa units. The solvation structures of the protonated and deprotonated amino acids are analyzed in terms of radial distribution functions, which can serve as reference data for future force field developments.

We investigate the interaction of the H2 molecule with a graphene layer and with a small-radius carbon nanotube using ab initio density functional methods. H2 can interact with carbon materials like graphene, graphite, and nanotubes either through physisorption or chemisorption. The physisorption mechanism involves the binding of the hydrogen molecule on the material as a result of weak van der Waals forces, while the chemisorption mechanism involves the dissociation of the hydrogen molecule and the ensuing reaction of both hydrogen atoms with the unsatured C-C bonds to form C-H bonds. In our calculations, we take into account van der Waals interactions using a recently developed method based on the concept of maximally localized Wannier functions. We explore several adsorption sites and orientations of the hydrogen molecule relative to the carbon surface and compute the associated binding energies and adsorption potentials. The most stable physisorbed state on graphene is found to be the hollow site in the center of a carbon hexagon, with a binding energy of -48 meV, in good agreement with experimental results. The analysis of diffusion pathways between different physisorbed states on graphene shows that molecular hydrogen can easily diffuse at room temperature from one configuration to another, which are separated by energy barriers as small as 10 meV. We also compute the potential energy surfaces for the dissociative chemisorption of H2 on highly symmetric sites of graphene, the lowest activation barrier found being 2.67 eV. Much weaker adsorption characterizes instead the physisorption interaction of the H2 molecule with the small radius (2,2) CNT. The barriers for H2 dissociation on the nanotube external surface are significantly lowered with respect to the graphene case, showing the remarkable effect of the substrate curvature in promoting hydrogen dissociation.

Accurately modeling the chemisorption dynamics of N 2 on metal surfaces is of both practical and fundamental interest. The factors that may have hampered this achievement so far are the lack of an accurate density functional and the use of approximate methods to deal with surface phonons and non-adiabatic effects. In the current work, the dissociation of molecular nitrogen on W(110) has been studied using ab initio molecular dynamics (AIMD) calculations, simulating both surface temperature effects, such as lattice distortion, and surface motion effects, like recoil. The forces were calculated using density functional theory, and two density functionals were tested, namely the PBE and the RPBE functionals. The computed dissociation probability considerably differs from earlier static surface results, with AIMD predicting a much larger contribution of the indirect reaction channel, in which molecules dissociate after being temporally trapped in the proximity of the surface. Calculations suggest that the surface motion effects play a role here, since the energy transfer to the lattice does not allow molecules that have been trapped into potential wells close to the surface to find their way back to the gas ⇤ Email: f.nattino@chem.leidenuniv.nl 1 phase. In comparison to experimental data, AIMD results overestimate the dissociation probability at the lowest energies investigated, where trapping dominates, suggesting a failure of both tested exchange-correlation functionals in describing the potential energy surface in the area sampled by trapped molecules.

Since the recent achievement of Kurotobi and Murata to capture a water molecule in a C(60) fullerene (Science 2011, 333, 613), there has been a debate about the properties of this H(2)O@C(60) complex. In particular, the polarity of the complex, which is thought to be underlying the easy separation of H(2)O@C(60) from the empty fullerene by HPLC, was calculated and found to be almost equal to that of an isolated water molecule. Here we present our detailed analysis of the charge distribution of the water-encapsulated C(60) complex, which shows that the polarity of the complex is, with 0.5 ± 0.1 D, indeed substantial, but significantly smaller than that of H(2)O. This may have important implications for the aim to design water-soluble and biocompatible fullerenes.