Mechanistic understanding of N2 activation: a comparison of unsupported and supported Ru catalysts.

N2 dissociative adsorption is commonly the rate-determining step in thermal ammonia synthesis. Herein, we performed density functional theory (DFT) calculations to understand the N2 dissociation mechanism on models of unsupported Ru(0001) terraces, Ru B5 sites, and polar MgO(111)-supported Ru8 cluster mimicking a B5 site geometry, denoted (Ru8(B5-like)/MgO(111)). The activation energy of N2 dissociative adsorption on the Ru8(B5-like)/MgO(111) model (Ea = 0.33 eV) is much lower than that on the unsupported Ru(0001) terrace (Ea = 1.74 eV) and Ru B5 (Ea = 0.62 eV) models. The lower N2 dissociation barrier on Ru B5 sites is facilitated by the enhanced σ donation and π* back-donation between N2(σ, π*) and Ru(d) orbitals resulting in the stronger activation of the molecular side-on N2* dissociation precursor. The Ru8(B5-like)/MgO(111) also exhibits enhanced σ donation because of the B5-like cluster geometry. Furthermore, the Ru cluster of the bare Ru8(B5-like)/MgO(111) model is positively charged. This induced an unusual π donation from N2(π) to Ru(d) orbitals as revealed by analyses of the density of states and partial charge densities. The combined σ and π donation resulted in an increased synergistic π* back-donation. The total interactions between N2(σ, π, π*) and Ru(d) resulted in an overall electron transfer to the adsorbed N2 from the Ru atoms in the B5-like site with no direct involvement of the MgO(111) substrate. Analyses of bond stretching vibrations and bond lengths show that the N2(σ, π, π*) and Ru(d) interactions lead to a weaker N-N bond and stronger Ru-N bonds. These correspond to a lower barrier of N2 dissociation on the Ru8(B5-like)/MgO(111) model, where the highest red-shift of N-N vibration and the longest N-N bond length were observed after side-on N2* adsorption. These results demonstrate that an electron-deficient Ru catalyst are not always inhibited from donating electrons to adsorbed N2. Rather, this study shows that the electron deficiency of Ru can promote π* back-donation and N2 activation. These new insights may therefore open new avenues to design supported Ru catalysts for nitrogen activation.

Functionalization of Polyethyleneimine with Hollow Cyclotriveratrylene and Its Subsequent Supramolecular Interaction with Doxorubicin.

In this paper, a modified Cyclotriveratrylene was synthesized and linked to a branched Polyethylenimine, and this unique polymeric material was subsequently examined as a potential supramolecular carrier for Doxorubicin. Spectroscopic analysis in different solvents had shown that Doxorubicin was coordinated within the hollow-shaped unit of the armed Cyclotriveratrylene, and the nature of the host-guest complex revealed intrinsic Van der Waals interactions and hydrogen bonding between the host and guest. The strongest interaction was detected in water because of the hydrophobic effect shared between the aromatic groups of the Doxorubicin and Cyclotriveratrylene unit. Density functional theory calculations had also confirmed that in the most stable coordination of Doxorubicin with the cross-linked polymer, the aromatic rings of the Doxorubicin were localized toward the Cyclotriveratrylene core, while its aliphatic chains aligned closer with amino groups, thus forming a compact supramolecular assembly that may confer a shielding effect on Doxorubicin. These observations had emphasized the importance of supramolecular considerations when designing a novel drug delivery platform.

DFT study on the effect of proximal residues on the Mycobacterium tuberculosis catalase-peroxidase (katG) heme compound I intermediate and its bonding interaction with isoniazid.

Isoniazid (INH) is converted into isonicotinyl radical through its interaction with the catalase-peroxidase (katG) enzyme present in the cells of Mycobacterium tuberculosis (M. tb.), the bacteria that causes the tuberculosis disease. This process is important because resistance of M. tb. cells to INH treatment has been associated with the failure of completion of this process. However, this process is poorly understood and there are a variety of conflicting theories about the details of the mechanism of this process. One theory suggests that INH binds to katG and transfers a single electron to the heme while the heme is in its two electron oxidized state, compound I [Fe(iv)Por˙+] (CpdI). In this study, DFT calculations at the UB3LYP/6-31g(d)-LANL2DZ level of theory are used to study the M. tb. katG CpdI molecule. Different models of the M. tb. CpdI molecule were prepared and the calculations revealed the impact of Trp321 on the electronic properties of the heme. Without Trp321 the heme assumed a triradical state with single electrons on the πxy and πyz orbitals of Fe and another on the a2u orbital of the porphyrin ring that can either be coupled with the first two, to assume a quartet state, or decoupled to form a doublet state. With Trp321, however, a transfer of an electron from the πTrp orbital to a2u porphyrin orbital leads to loss of radical character of the porphyrin and leaves the Trp321 group with a radical character. INH was observed to have strong interaction with CpdI and the absence of Trp321 significantly decreased the binding energy by 2 kcal mol-1 explaining the importance of Trp321 in the binding of INH. The results in this study show the importance of Trp321 in the binding of INH and its effect on its electronic properties, which is consistent with previous experimental findings that mutation of Trp321 results in an increase in drug resistance.

Dispersed surface Ru ensembles on MgO(111) for catalytic ammonia decomposition.

Ammonia is regarded as an energy vector for hydrogen storage, transport and utilization, which links to usage of renewable energies. However, efficient catalysts for ammonia decomposition and their underlying mechanism yet remain obscure. Here we report that atomically-dispersed Ru atoms on MgO support on its polar (111) facets {denoted as MgO(111)} show the highest rate of ammonia decomposition, as far as we are aware, than all catalysts reported in literature due to the strong metal-support interaction and efficient surface coupling reaction. We have carefully investigated the loading effect of Ru from atomic form to cluster/nanoparticle on MgO(111). Progressive increase of surface Ru concentration, correlated with increase in specific activity per metal site, clearly indicates synergistic metal sites in close proximity, akin to those bimetallic N2 complexes in solution are required for the stepwise dehydrogenation of ammonia to N2/H2, as also supported by DFT modelling. Whereas, beyond surface doping, the specific activity drops substantially upon the formation of Ru cluster/nanoparticle, which challenges the classical view of allegorically higher activity of coordinated Ru atoms in cluster form (B5 sites) than isolated sites.

Electrochemical and quantum mechanical investigation of various small molecule organic compounds as corrosion inhibitors in mild steel.

The corrosion inhibition property of selected small organic compounds was investigated using electrochemical measurements, including potentiodynamic polarization (PDP), linear polarization resistance (LPR), electrochemical impedance spectroscopy (EIS), and density functional theory (DFT) calculations. The inhibition efficiency (IE %) of the inhibitor on mild steel (MS) in 1 M HCl was then determined. Results show that the presence of the inhibitors resulted in decreased corrosion current density (I corr) values and increased polarization resistance (R p). Furthermore, the use of higher concentrations of inhibitors led to an increased inhibition efficiency. Tafel slopes and shifts in the E corr values suggested that the inhibitors tested are mixed-type inhibitors that form a protective layer on the surface of the substrate. Of the organic compound inhibitors tested, the inhibitor 4-ethylpyridine (EP) exhibited the highest R p values and inhibition efficiency values from the PDP, LPR, and EIS analyses, respectively. DFT calculations showed negative adsorption energies and confirmed the chemisorption of the inhibitors allowing for the formation of a hydrophobic protective film against corrosion and correlations between the quantum chemical values and electrochemical data were demonstrated. The results show the influence of the presence of electronegative O, S, and N atoms, as well as the role of aromatic rings in the promotion of surface protection by preventing aggressive ionic species from binding onto MS.

Theoretical insights on the binding of isoniazid to the active site residues of Mycobacterium tuberculosis catalase-peroxidase.

Isoniazid (INH) is known to cause the exclusive lethal action to Mycobacterium tuberculosis (M. tb.) cells because of the pathogen's own catalase-peroxidase (katG) enzyme that converts INH to a very reactive radical. Thus, in order to gain insights on the interaction of INH with the individual active site residues (Res) of katG, this study presents a computational approach via molecular docking and density functional theory (DFT) using augmented models to study the individual INH-Res interactions. Seven amino acid residues directly interacts with INH: Arg104, Asp137, His108, Ile228, Trp107, Tyr229, and Val230. The residues with the highest interaction energies are Arg104 (-39.64 kcal/mol) and Asp137 (-32.85 kcal/mol) mainly due to strong ion-dipole and H-bonding interactions present in the complexes, while the weakest interaction was observed for Ile228 (-13.78 kcal/mol). Molecular electrostatic potential surface revealed complementary regions for dipole interactions and charge distribution analysis further shows that INH generally donates electrons to the residues. The results in this study agrees with the previous experimental findings and provides new insights into the catalase dependent activation of INH and the methods presented may be valuable in the study of biological metabolism of molecules.