Febdian Rusydi

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.

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.

Dipole Strength Calculation Based on Two-Level System Approximation to Study Q/B-Band Intensity Ratio of ZnTBP in Solvent

We study the Q/B-band dipole strength of zinc tetrabenzoporphyrin (ZnTBP) using density functional theory (DFT) in various solvents. The solvents are modeled using the polarized continuum model (PC...

A Density-Functional Study on the Change of Q/B-Band Intensity Ratio of Zinc Tetraphenylporphyrin in Solvents

We study the Q/B-band intensity ratio (IQ/B) of zinc tetraphenylporphyrin (ZnTPP) in various solvents from its electronic structure by utilizing the polarizable continuum model and density functional theory (DFT). The selected solvents are benzene, chloroform, dichloromethane, pyridine and methanol. The Q/B-band intensity ratio is simplified by dipole strength of HOMO → LUMO and HOMO−1 → LUMO from a two-level system, or fQ/B. The results show the linear correlation between the calculated fQ/B and the experimental IQ/B. This suggests that IQ/B of ZnTPP in solvents can be studied from dipole strength ratio from a two-level system, where the orbitals are determined by DFT. The change of fQ/B is due to the change of frontier molecular orbital shape of ZnTPP which are dominantly constructed by pz-orbital. In the core part of ZnTPP, the change of pz-orbital shape is inversely proportional to the solvent dielectric constant, ϵ.

Frontier Orbitals of Dehydrogenated Tetrahydrocurcumin in Water Solvent: A Theoretical Study

We studied two frontier orbitals - the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO)- of tetrahydrocurumin (THC) using density-functional theory (DFT) in water solvent. These orbitals were observed in THC molecule without one hydrogen atom (dehydrogenated THC). The loss of hydrogen atom is due to the transfer of the atom from THC molecule toward reactive oxygen species (ROS) (Hydrogen atom transfer –HAT- mechanism). We began our investigation by optimizing dehydrogenated THC at three X-H sites. Then, water solvent was added by using polarized continuum model (PCM) method. This study observed that dehydrogenated THC at two O-H sites has wider gap of HOMO-LUMO compare to C-H site.

The first-principle study on the stability of trans-HCOH in various solvents

We attempt to study about the solvent effects of the stability of trans-HCOH molecules using the density-functional theory. Experimentally, trans-HCOH rearranges to H2CO with half-life of two hours [1] which we theoretically proved that it occurs through quantum tunneling. [2] In this work, we calculate the rearrangement rate of the molecules in various solvents. The solvents are selected based on their dielectric constant values, from lower to higher ones; they are benzene, dichloroethane, benzaldehyde, acetone, methanol, ethanediol, dimethylsulfoxide, formic acid, water, and formamide. We use polarizable continuum to model the solvents (PCM). We begin from determining the reaction path from trans-HCOH to H2CO and its corresponding energy barrier using intrinsic reaction coordinate calculation with PCM. Then, we use Wentzel-Kramers-Brillouin (WKB) approximation to calculate the rearrangement rates. The calculation results showed a general trend in which there were arrangement rate was decreasing inversely proportional to dielectric constant value.

Implementation of density functional theory method on object-oriented programming (C++) to calculate energy band structure using the projector augmented wave (PAW)

This study implemented DFT method into the C++ programming language with object-oriented programming rules (expressive software). The use of expressive software results in getting a simple programming structure, which is similar to mathematical formula. This will facilitate the scientific community to develop the software. We validate our software by calculating the energy band structure of Silica, Carbon, and Germanium with FCC structure using the Projector Augmented Wave (PAW) method then compare the results to Quantum Espresso calculations results. This study shows that the accuracy of the software is 85% compared to Quantum Espresso.

DFT study of the formate formation on Ni(111) surface doped by transition metals [Ni(111)-M; M=Cu, Pd, Pt, Rh]

We report on a theoretical study of the formation of formate (HCOO) from the reaction of CO2 gas and a pre- adsorbed H atom (CO2 (g) + *H → *HCOO) on Ni(111) surface doped by transition-metals [Ni(111)-M; M= Cu, Pd, Pt, Rh] by means of density functional theory (DFT) calculations. This *HCOO formation reaction is one of the most important rate- limiting steps in the methanol synthesis process. We find that the presence of transition metal doping on the first-layer of Ni(111) surface could reduce the activation barrier of this reaction [up to ~38.4%, compared to clean Ni(111) surface].

A first principle study on the interaction between acetylcholinesterase and acetylcholine, and also rivastigmine in alzheimer's disease case

The catalytic activity of acetylcholinesterase enzyme (AChE) relates to the symptom progress in Alzheimers disease. Interaction of AChE with rivastigmine (from the medicine) can reduce its catalytic activity toward acetylcholine to decelerate the progression of Alzheimers disease. This research attempts to study the interaction between AChE and rivastigmine, and also acetylcholine (without the presence of rivastigmine) using density functional theory by simplifying the reaction occurs in the active site, which is assumed to be C2H5OH, C3N2H3(Ch3), and CH3COO-. The results suggest that AChE interacts easier with acetylcholine than with rivastigmine, which implies that the medicine does not effectively reduce the catalytic activity of AChE. At this stage, no experimental data is available to be compared with the calculation results. Nonetheless, this study has shown a good prospect to understand the AChE-substrate interaction using a first-principles calculation.

Progress on ligands effects in porphyrin-based molecules in benzene solvent for photodynamic therapy applications

Density Functional Theory (DFT) calculations are carried out to investigate the ligands effects on porphyrin-based molecule in benzene solvent environment. Benzene solvent is modeled by PCM Tomasi. We are motivated to study the alternation of electronic and geometric structure of porphyrin-based molecule in the presence of ligands for achieving theoretical explanation about ligand porphyrin-based behaviours. We aim to investigate the ligands effect on the groundstate electronic structure of porphyrin-based molecules. This investigation will lead us in better understanding on characteristic of porphyrin-based molecule as photosensitizer in benzene solvent environment. We perform the electronic structure calculation of ZnP, ZnTPP, ZnTBP, H2TPP and H2TBP in the ground state. The results show that ligands distortion induces the point group symmetry of ZnTBP, ZnTPP, H2TBP and H2TPP belong to the trivial point group (C1) in benzene environment. Tetrabenzo ligand distortions significantly change the Zn-N bond of ZnP. The energy difference between HOMO and HOMO-1 is increasing in the present of ligand. We also report that benzene solvent has only significant contribution to the alternation of EΔ of porphyrin-based molecules.