Crystalline structures of L-cysteine and L-cystine: a combined theoretical and experimental characterization.

It is assumed that genetic diseases affecting the metabolism of cysteine and the kidney function lead to two different kinds of pathologies, namely cystinuria and cystinosis whereby generate L-cystine crystals. Recently, the presence of L-cysteine crystal has been underlined in the case of cystinosis. Interestingly, it can be strikingly seen that cystine ([-S-CH2-CH-(NH2)-COOH]2) consists of two cysteine (C3H7NO2S) molecules connected by a disulfide (S-S) bond. Therefore, the study of cystine and cysteine is important for providing a better understanding of cystinuria and cystinosis. In this paper, we elucidate the discrepancy between L-cystine and L-cysteine by investigating the theoretical and experimental infrared spectra (IR), X-ray diffraction (XRD) as well as Raman spectra aiming to obtain a better characterization of abnormal deposits related to these two genetic pathologies.

A model for the effect of ion pairing on an outer sphere electron transfer.

Ion pairing can strongly affect the rates of electron transfer reactions. To explain this effect, we propose a model Hamiltonian that describes the interactions between the pairing ion and the reactant, solvent and inner sphere reorganization, and bond breaking. Explicit expressions for the energies of the initial and final states, and for the energy of activation are derived in the weak adiabatic limit. The model is applied to the reduction of Cu(ii) in the presence of chloride ions. For this purpose, the pertinent system parameters are obtained from density functional theory. Our model explains why the chloride ion enhances the rate of the first electron transfer in copper deposition.

Interactions of ions across carbon nanotubes.

The interactions between a pair of Li+ ions across a semiconducting (8,0)CNT and a conducting (5,5)CNT has been investigated by density functional theory. The direct Coulomb interaction between the ions is almost completely screened. The band structure of the CNTs is not affected by the Li+ ions, but the Fermi level is raised to accommodate the extra electrons. Because of the unique band structure of CNTs this results in an effective attraction between the ions, which is greater for the (8,0)CNT. In contrast, a Cl- ion inside a CNT forms a chemical bond which modifies the band structure. Again, the electrostatic field of the ion is almost completely screened outside of the tube. Nevertheless, the adsorption of a Li+ ion outside is favored by a Cl- ion inside. This apparent attraction is mainly caused by a lowering of the work function of the CNT by the presence of the Cl-.

Quantified Binding Scale of Competing Ligands at the Surface of Gold Nanoparticles: The Role of Entropy and Intermolecular Forces.

A basic understanding of the driving forces for the formation of multiligand coronas or self-assembled monolayers over metal nanoparticles is mandatory to control and predict the properties of ligand-protected nanoparticles. Herein, 1 H nuclear magnetic resonance experiments and advanced density functional theory (DFT) modeling are combined to highlight the key parameters defining the efficiency of ligand exchange on dispersed gold nanoparticles. The compositions of the surface and of the liquid reaction medium are quantitatively correlated for bifunctional gold nanoparticles protected by a range of competing thiols, including an alkylthiol, arylthiols of varying chain length, thiols functionalized by ethyleneglycol units, and amide groups. These partitions are used to build scales that quantify the ability of a ligand to exchange dodecanethiol. Such scales can be used to target a specific surface composition by choosing the right exchange conditions (ligand ratio, concentrations, and particle size). In the specific case of arylthiols, the exchange ability scale is exploited with the help of DFT modeling to unveil the roles of intermolecular forces and entropic effects in driving ligand exchange. It is finally suggested that similar considerations may apply to other ligands and to direct biligand synthesis.

Unravelling the hydrogen absorption process in Pd overlayers on a Au(111) surface.

The hydrogen absorption into overlayers of Pd deposited on Au(111) has been investigated by density functional theory (DFT). Hydrogen concentrations, absorption environments, and geometrical and electronic effects have been analyzed, seeking for a better understanding of the general principles governing the process and the effect of foreign supports. The results show that the absorption is more favored than in pure Pd leading to lower absorption energies and less repulsive interactions due to the surface expansion induced by the gold larger lattice constant. Our findings also suggest that the hydrogen absorption process is more favorable for a less number of Pd overlayers. This situation changes gradually until the substrate influence is no longer detected and the pure palladium nature appears. An entangled combination of repulsive forces, strain effect, structural ordering and chemical affinity has been found. The kinetics of hydrogen absorption has been studied as well. Two cases were explored: (1) the absorption of an adsorbed hydrogen atom and (2) the bond-breaking and penetration of a H2 molecule.

On the Energetics of Ions in Carbon and Gold Nanotubes.

We investigate the insertion of halide and alkali atoms into narrow single-walled carbon nanotubes with diameters <9 Šby density functional theory; both chiral and non-chiral tubes are considered. The atoms are stored in the form of ions; the concomitant charge transfer affects the band structure and makes originally semiconducting tubes conducting. The electrostatic interaction between a charge and the walls of the tube is explicitly calculated. The insertion energies and the positions of the ions are determined by a competition between electrostatic energy and Pauli repulsion. For comparison, we consider ions in gold nanotubes. Alkali ions follow the same principles in gold as in carbon tubes, but chloride is specifically adsorbed inside gold tubes.

Volcano plots in hydrogen electrocatalysis - uses and abuses.

Sabatier's principle suggests, that for hydrogen evolution a plot of the rate constant versus the hydrogen adsorption energy should result in a volcano, and several such plots have been presented in the literature. A thorough examination of the data shows, that there is no volcano once the oxide-covered metals are left out. We examine the factors that govern the reaction rate in the light of our own theory and conclude, that Sabatier's principle is only one of several factors that determine the rate. With the exception of nickel and cobalt, the reaction rate does not decrease for highly exothermic hydrogen adsorption as predicted, because the reaction passes through more suitable intermediate states. The case of nickel is given special attention; since it is a 3d metal, its orbitals are compact and the overlap with hydrogen is too low to make it a good catalyst.

Electrochemical adsorption of OH on Pt(111) in alkaline solutions: combining DFT and molecular dynamics.

The adsorption of OH on Pt(111) in alkaline solution has been investigated by a method that combines density functional theory, molecular dynamics, and quantum statistical mechanics. In particular, we have calculated the free energy surface for the reaction. A physisorbed hydroxide ion in a metastable state and a stable adsorbed uncharged OH group are observed. The energy of activation at equilibrium is comparatively low, so that the reaction is fast.

On the electrochemical deposition and dissolution of divalent metal ions.

The deposition of Cu(2+) and Zn(2+) from aqueous solution has been investigated by a combination of classical molecular dynamics, density functional theory, and a theory developed by the authors. For both cases, the reaction proceeds through two one-electron steps. The monovalent ions can get close to the electrode surface without losing hydration energy, while the divalent ions, which have a stronger solvation sheath, cannot. The 4s orbital of Cu interacts strongly with the sp band and more weakly with the d band of the copper surface, while the Zn 4s orbital couples only to the sp band of Zn. At the equilibrium potential for the overall reaction, the energy of the intermediate Cu(+) ion is only a little higher than that of the divalent ion, so that the first electron transfer can occur in an outer-sphere mode. In contrast, the energy of the Zn(+) ion lies too high for a simple outer-sphere reaction to be favorable; in accord with experimental data this suggests that this step is affected by anions.

Why silver deposition is so fast: solving the enigma of metal deposition.

A perfect match: Silver deposition is one of the fastest electrochemical reactions, even though the Ag(+) ion loses more than 5 eV solvation energy in the process. This phenomenon, an example of the enigma of metal deposition, was investigated by a combination of MD simulations, DFT, and specially developed theory. At the surface, the Ag(+) ion experiences a strong interaction with the sp band of silver, which catalyzes the reaction.

Hydrogen electrocatalysis on single crystals and on nanostructured electrodes.

We investigate hydrogen evolution on plain and nanostructured electrodes with a theory developed by us. On electrodes involving transition metals the most strongly adsorbed hydrogen is often only a spectator, while the reaction proceeds via a weakly adsorbed species. For Pt(111) the isotherms for both species are calculated. We explain why a nanostructure consisting of a monolayer of Pd on Au(111) is a good catalysts, and predict that Rh/Au(111) should be even better. Our calculations for a fair number of metals are in good agreement with experiment.

Stability of gold and platinum nanowires on graphite edges.

The stability of coinage and noble metal nanowires supported on graphite steps is examined by density functional theory. In particular, we study the stability of supported gold and platinum wires and compare their chemical properties with those of surfaces and bare wires. A substantially stronger bond with graphite was found for platinum wires due to unfilled antibonding states, which are occupied in the case of gold. This difference has direct consequences for the adsorption of hydrogen. This reaction can occur either on the wire or directly on graphite steps. In the case of gold, the reaction is favoured on steps, while on platinum wires, it has no thermodynamical preferences. Our results suggest that, in early stages of wire formation, hydrogen could desorb gold from graphite, but not platinum.

Hydrogen evolution on single-crystal copper and silver: a theoretical study.

Hydrogen evolution on single-crystal copper and silver is investigated by a combination of density functional theory and a theory developed in our own group. At short times, the reaction rate is determined by the transfer of the first proton to the electrode surface. In accord with experiment, we find for both metals that this reaction proceeds faster on the (111) surfaces than on the (100) ones. The main cause is the lower, that is, more favourable, adsorption energy on the former surfaces. On both silver surfaces, the second step is electrochemical desorption. The same mechanism is likely to operate on copper.