Adhitya G. Saputro

Adsorption of O2 on Cobalt-(n)Pyrrole Molecules from First-Principles Calculations

In order to clarify the adsorption mechanism of the O 2 molecule on Co–polypyrrole composite metallo-organic catalyst, we have investigated the interaction between the molecule and Co–( n )pyrrole model clusters ( n =4,6) using the density functional theory. The stable adsorption site of the O 2 molecule on Co–(4)pyrrole is found to be at the O–O center of mass located on top of the Co atom in side-on configuration, while for the case of Co–(6)pyrrole cluster, the O 2 molecule is slightly deviated from the side-on configuration. The O–O bonds of the O 2 /Co–(4)pyrrole and the O 2 /Co–(6)pyrrole systems have elongated by 10.84 and 9.86%, respectively. The elongation mechanism of O 2 on Co–( n )pyrrole is induced by the interaction between the cobalt d -orbitals and the O 2 anti-bonding π * orbital, which results in a charge transfer from the cobalt atom toward the O 2 molecule. This effect seems important in the adsorption of the O 2 molecule on Co–( n )pyrrole. It is likely that the extra charge in the O ...

Density Functional Theory Study on the Interaction of O2 Molecule with Cobalt–(6)Pyrrole Clusters

We have investigated the interaction between cobalt?(6)pyrrole [Co?(6)Ppy] clusters and O2 molecule, including the adsorption and dissociation of O2 molecule using the density functional theory (DFT) calculations. We found that O2 molecule is adsorbed on Co?(6)Ppy clusters with side-on configuration and the O?O bond length elongated around 10%. The elongation of the O?O bond when O2 is adsorbed on the clusters will weaken the O?O bond and increase the reactivity of the molecule. The calculated dissociation energies of O2 molecule on Co?(6)Ppy clusters span from 0.89 to 1.23 eV. The order of the dissociation energy is affected by the amount of the charge transferred from Co?(6)Ppy clusters to the O2 molecule in the transition state.

Comparative Study on the Catalytic Activity of the TM–N2 Active Sites (TM = Mn, Fe, Co, Ni) in the Oxygen Reduction Reaction: Density Functional Theory Study

We investigate the interaction of transition metal–nitrogen (TM–N2; TM = Mn, Fe, Co, and Ni) active sites with oxygen reduction reaction (ORR) related molecules using the density functional theory (DFT) calculations. Generally, the trend of molecular adsorption energy in TM–N2 systems is Mn–N2 > Fe–N2 > Co–N2 > NiN2. In the case of O2 adsorption, the O2 molecule is adsorbed with a symmetric side-on configuration on the TM–N2 systems, regardless the type of TM atom. We also find that when the reaction of the adsorbed HO2 molecule and an H atom takes place, instead of forming H2O2 molecule the reaction produces two OH radicals. From the evaluation of the potential energy surface profiles of the oxygen reduction reaction (ORR), we find that a direct four-electron reduction pathway could be facilitated on the TM–N2 active sites. However, all of the TM–N2 systems share the same main rate-limiting reaction, which is the OH reduction step. Generally, the edge-like TM–N2 active site has stronger molecular adsorpt...

First principles calculation on the adsorption of water on lithium?montmorillonite (Li?MMT)

The interaction of water molecules and lithium-montmorillonite (Li-MMT) is theoretically investigated using density functional theory (DFT) based first principles calculation. The mechanism of water adsorption at two different water concentrations on Li-MMT as well as their structural and electronic properties are investigated. It is found that the adsorption stability in Li-MMT is higher in higher water concentration. It is also found that an adsorbed water molecule on Li-MMT causes the Li to protrude from the MMT surface, so it is expected that Li may be mobile on H(2)O/Li-MMT.

Mechanism of dopachrome tautomerization into 5,6-dihydroxyindole-2-carboxylic acid catalyzed by Cu(II) based on quantum chemical calculations

BACKGROUND Tautomerization of dopachrome to 5,6-dihydroxyindole-2-carboxylic acid (DHICA) is a biologically crucial reaction relevant to melanin synthesis, cellular antioxidation, and cross-talk among epidermal cells. Since dopachrome spontaneously converts into 5,6-dihydroxyindole (DHI) via decarboxylation without any enzymes at physiologically usual pH, the mechanism of how tautomerization to DHICA occurs in physiological system is a subject of intense debate. A previous work has found that Cu(II) is an important factor to catalyze the tautomerization of dopachrome to DHICA. However, the effect of Cu(II) on the tautomerization has not been clarified at the atomic level. METHODS We propose the reaction mechanism of the tautomerization to DHICA by Cu(II) from density functional theory-based calculation. RESULTS We clarified that the activation barriers of α-deprotonation, β-deprotonation, and decarboxylation from dopachrome are significantly reduced by coordination of Cu(II) to quinonoid oxygens (5,6-oxygens) of dopachrome, with the lowest activation barrier of β-deprotonation among them. In contrast to our previous work, in which β-deprotonation and quinonoid protonation (O5/O6-protonation) were shown to be important to form DHI, our results show that the Cu(II) coordination to quinonoid oxygens inhibits the quinonoid protonation, leading to the preference of proton rearrangement from β-carbon to carboxylate group but not to the quinonoid oxygens. CONCLUSION Integrating these results, we conclude that dopachrome tautomerization first proceeds via proton rearrangement from β-carbon to carboxylate group and subsequently undergoes α-deprotonation to form DHICA. GENERAL SIGNIFICANCE This study would provide the biochemical basis of DHICA metabolism and the generalized view of dopachrome conversion which is important to understand melanogenesis.

Effect of pH on elementary steps of dopachrome conversion from first-principles calculation.

Dopachrome conversion, in which dopachrome is converted into 5,6‐dihydroxyindole (DHI) or 5,6‐dihydroxyindole‐2‐carboxylic acid (DHICA) upstream of eumelanogenesis, is a key step in determining the DHI/DHICA monomer ratio in eumelanin, which affects the antioxidant activity. Although the ratio of DHI/DHICA formed and the conversion rate can be regulated depending on pH, the mechanism is still unclear. To clarify the mechanism, we carried out first‐principles calculations. The results showed the kinetic preference of proton rearrangement to form quinone methide intermediate via β‐deprotonation. We also identified possible pathways to DHI/DHICA from the quinone methide. The DHI formation can be achieved by spontaneous decarboxylation after proton rearrangement from carboxyl group to 6‐oxygen. α‐Deprotonation, which leads to DHICA formation, can also proceed with a significantly reduced activation barrier compared with that of the initial dopachrome. Considering the rate of the proton rearrangements in a given pH, we conclude that the conversion is suppressed at acidic pH.

Density Functional Theory Study on the Interaction of O2 and H2O2 Molecules with the Active Sites of Cobalt–Polypyrrole Catalyst

We investigate the interaction of O2 and H2O2 molecules with the active sites of cobalt–polypyrrole (Co–Ppy) catalyst using the density functional theory (DFT) calculations. Several configurations of Co–Nx clusters (x = 2, 3) are used to mimic the active sites structures of pyrolized Co–Ppy catalyst. The highest O–O bond elongation of the adsorbed O2 molecule on Co–Nx clusters is of about 17.14%. The O2 side-on adsorption configuration could be realized in the Co–N2 active sites that have bent N–Co–N angles and strong dxz/yz-orbitals characters in their frontier molecular orbitals (FMOs) and in the Co–N3–pyridinic–trimer active site that has no occupied dz2-like-orbital in its FMOs. Depending on the configuration of O2 adsorption on Co–Nx clusters and the amount of extra charges in anti-bonding orbitals (π*) of the adsorbed O2 molecule, the formed H2O2 molecule on Co–Nx clusters will be spontaneously dissociated into OH* molecules; otherwise it will be adsorbed in its molecular form.

Oxygen Reduction Reaction on Cobalt-(6)Pyrrole Cluster: Density Functional Theory Study

We investigate the potential energy surface profile for various water formation reaction schemes on an unsupported cobalt–(6)pyrrole [Co–(6)Ppy] cluster in the vacuum state by density functional theory (DFT) calculations. We find that in the Co–(6)Ppy cluster, the formation of H 2 O 2 is energetically not favorable. Instead of forming H 2 O 2ad , the HO 2ad + H reaction forms 2OH ad or O ad + H 2 O immediately. The adsorption of H 2 O 2 on the Co–(6)Ppy cluster is possible only if the H 2 O 2 molecule comes from or forms outside of the cluster. The formation of two OH molecules instead of H 2 O 2 on the Co–(6)Ppy cluster suggests that the oxygen reduction reaction (ORR) mechanism on the unsupported Co–(6)Ppy cluster in the vacuum state prefers the direct four-electron reduction to water.

Density functional study of adsorptions of CO2, NO2 and SO2 molecules on Zn(0002) surfaces

We report on a theoretical study of adsorptions of CO2, NO2 and SO2 molecules on ZnO(0002) surfaces using density functional theory-based (DFT-based) calculations. These adsorptions are done on perfect and defective ZnO(0002) surfaces. We find that all of these molecules are chemically adsorbed on the perfect ZnO(0002) surface. In the presence of Zn vacancy, we find that the surface is only active toward SO2 molecule. On the hydroxylated ZnO(0002) surfaces, CO2 and SO2 molecules can react with the preadsorbed OH molecule to form various adsorbates such as: carboxyl (COOH), bicarbonate (CO3H), sulfonyl hydroxide (SO3H), SO3 and water. However, NO2 molecule cannot react with the pre-adsorbed OH molecule and only physically adsorbed on the surface.

DFT study of adsorption of CO2 on palladium cluster doped by transition metal

We report on a theoretical study of CO2 adsorption on Pd6-M (M: Ni, Cu, Pt, Rh) cluster using first-principles density functional theory (DFT) calculations. We find that CO2 molecule is adsorbed with a bidendate configuration on Pd7 and on most of Pd6M clusters. The bidendate adsorption configuration is formed due to the filling of the unoccupied n* orbital of CO2 molecule upon its interaction with d-orbitals of the cluster. We find that transition metal doping could modify the adsorption energy, adsorption site and adsorption configuration of CO2 molecule on Pd7 cluster. We also predict that the usage of Pd6M clusters as CO2 hydrogenation catalysts might facilitate the formations of HCOO/COOH.