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DFT Study of Leuco-Indigo and Indigo as Active Material in Dye-Sensitized Solar Cell Maahury, Mirella Fonda; Male, Yusthinus Thobias; Martoprawiro, Muhamad Abdulkadir
Molekul Vol 15, No 2 (2020)
Publisher : Universitas Jenderal Soedirman

Computational study of natural indigo has been carried out to get the optimized structure and electronic properties of two indigo at different pH.Â It has been found that indigo has the potential to be applied asÂ active material in the dye-sensitized solar cell. Computational calculations are performed using Density Functional Theory (DFT) with B3LYP functional and 6-31G(d,p) for ground state geometry optimization and Time Dependent-Density Functional Theory (TD-DFT) for excited states single point calculation. All calculations are carried out in the gas phase. Geometry optimization results show that Indigo has a planar structure, whereas leuco-indigo structure is not planar. Leuco-indigo absorption wavelength is shorter than indigo. The density of HOMO and LUMO is spreading throughout the molecule. The density of electrons at LUMO extends to the anchoring group. Based on excitation energy, absorption wavelength, excitation composition, and HOMO-LUMO density, it can be concluded that indigoÂ has the potential to be applied inÂ dye-sensitized solar cell (DSSC)

Graphite as A Hydrogen Storage in Fuel Cell System: Computational Material Study for Renewable Energy Gunawan, Rahmat; Radiman, Cynthia Linaya; Martoprawiro, Muhamad Abdulkadir; Dipojono, Hermawan K.
Jurnal ILMU DASAR Vol 17 No 2 (2016)
Publisher : Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Jember

The Hydrogen storage based-graphite materials have been investigated theoretically via Density Functional Theory (DFT) approach. The native graphite was compared to the modified graphite, namely the intercalation graphite (GICs, graphite intercalated compounds). Here the GICs was intercalated by alkali metals (Li, Na and K). The electronic structures, energetics and atomic orbital contributions of hydrogen-graphite system, GICs, and hydrogen-GICs were studied by calculation approach of gradient corrected PBE (Perdew-Burke-Ernzerhof) for recovery of exchange-correlation energy. The calculation was supported by using basis set of the plane waves whereas the computation of electron-core by using Ultrasoft Vanderbilt pseudopotential. The computational calculation provides four main studies i.e. molecular geometry relaxation, determination of electronic bands structure of energy, energy state density (DOS) and atomic orbital contribution by charge density differences.Keywords: Density Functional Theory, hydrogen gas, graphite intercalated material

Computational Study of The Effect of Structure on Antioxidant Activity and Drug Score of Coumarin Derivatives Bakti, Andi Budi; Martoprawiro, Muhamad Abdulkadir
Walisongo Journal of Chemistry Vol. 7 No. 2 (2024): Walisongo Journal of Chemistry
Publisher : Department of Chemistry Faculty of Science and Technology Walisongo

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21580/wjc.v7i2.23327

The presence of reactive oxygen species in the body must be maintained at low concentrations, as an excess can lead to oxidative stress. Coumarin, a secondary metabolite found in plants, exhibits potential as an antioxidant agent. However, the development of synthetic antioxidants based on coumarin remains limited. Computational studies enable the manipulation of coumarin structures to predict antioxidant activity. Correspondingly, this research aimed to investigate the effect of the type, number, and position of substituents on the antioxidant activity and drug score of coumarin derivatives utilizing computational methods, specifically ORCA and OSIRIS Property Explorer software. The results revealed that electron-donating substituents (e.g., OCH₃) could enhance antioxidant activity, while electron-withdrawing substituents (e.g., CHO) tended to reduce it. Substitution on the benzene ring of coumarin exerted a more significant effect on antioxidant activity compared to substitution on the pyrone ring. Compounds such as Umbelliferone, Scoparone, and 3-Bromoscoparone exhibited potential as new antioxidants due to their structural similarity to ascorbic acid or TBHQ. However, further studies are necessary to confirm their development as safe and effective antioxidants free from side effects.

Computational Study of The Effect of Structure on Antioxidant Activity and Drug Score of Coumarin Derivatives Bakti, Andi Budi; Martoprawiro, Muhamad Abdulkadir
Walisongo Journal of Chemistry Vol. 7 No. 2 (2024): Walisongo Journal of Chemistry
Publisher : Department of Chemistry Faculty of Science and Technology UIN Walisongo

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21580/wjc.v7i2.23327

The presence of reactive oxygen species in the body must be maintained at low concentrations, as an excess can lead to oxidative stress. Coumarin, a secondary metabolite found in plants, exhibits potential as an antioxidant agent. However, the development of synthetic antioxidants based on coumarin remains limited. Computational studies enable the manipulation of coumarin structures to predict antioxidant activity. Correspondingly, this research aimed to investigate the effect of the type, number, and position of substituents on the antioxidant activity and drug score of coumarin derivatives utilizing computational methods, specifically ORCA and OSIRIS Property Explorer software. The results revealed that electron-donating substituents (e.g., OCH₃) could enhance antioxidant activity, while electron-withdrawing substituents (e.g., CHO) tended to reduce it. Substitution on the benzene ring of coumarin exerted a more significant effect on antioxidant activity compared to substitution on the pyrone ring. Compounds such as Umbelliferone, Scoparone, and 3-Bromoscoparone exhibited potential as new antioxidants due to their structural similarity to ascorbic acid or TBHQ. However, further studies are necessary to confirm their development as safe and effective antioxidants free from side effects.

Computational Study of the Influence of Structure on Antioxidant Activity and Drug Score of Coumarin Derivatives Bakti, Andi Budi; Martoprawiro, Muhamad Abdulkadir
Jambura Journal of Chemistry Vol 7, No 2 (2025): August
Publisher : Universitas Negeri Gorontalo

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.37905/jambchem.v7i2.27350

The presence of reactive oxygen species (ROS) in the body must be maintained at low concentrations, excessive ROS and an inability to neutralize them can lead to oxidative stress. Coumarin, a secondary metabolite in plants, is used in pharmacology as an antioxidant agent. This study aims to identify the effects of the type, number, and position of substituents on coumarin derivatives's antioxidant activity and drug score using DFT methods. Computational tools, including ORCA software and OSIRIS Property Explorer, were employed. The results indicate that the number and position of electron-donating substituents, such as OCH3, enhance antioxidant activity, while electron-withdrawing substituents, like CHO, decrease it. Additionally, the presence of conjugated double bonds in the pyrone ring causes electron delocalization, complicating electron transfer. The compound 6,7-dimethoxyhydrocoumarin (hydroscoparone) shows potential as a new antioxidant due to its energy gap similar to commercial antioxidants like ascorbic acid and TBHQ, and a drug score of 0.5 with very low toxicity risk. However, further research is needed to confirm that this compound can be used as an effective antioxidant without side effects.

Computational Study on Apoptosis-Inducing Factor (AIF)-Mediated Modulation of Menadione using Molecular Docking and Parametrized Quantum Methods Listyawati, Muklisatum; Hildayani, Suci Zulaikha; Ledyastuti, Mia; Warganegara, Fida Madayanti; Martoprawiro, Muhamad Abdulkadir
Molekul Vol 20 No 3 (2025)
Publisher : Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jm.2025.20.3.12428

ABSTRACT. Apoptosis-inducing factor (AIF) is a protein that is crucial for apoptosis which its dysregulation has been connected to the emergence of cancer. Mitochondria are organelles that in healthy cells function as energy factories that are important for maintaining cell life. AIF is located in the mitochondrial intermembrane space with active sites, namely FAD and NADH. Meanwhile in the recent studies, quinone compounds have shown potential as anti-cancer agents by targeting mitochondrial function, but the mechanism is still unclear. In this study, we used computational methods, including molecular docking and the Divide-and-Conquer Density Functional Tight-Binding Molecular Dynamics (DCDFTBMD) method, a type of parametrized quantum calculation, to investigate the interaction between mitochondrial AIF and menadione, as a quinone compound with anticancer potential. From the calculation result, AIF interaction with menadione was stronger in the FAD domain than in NADH. The partial charges of the ligands before and after the interactions were calculated using the DCDFTBMD technique, and the results show that the charge in the bonding area becomes more negative. This indicates the strengthening of electrostatic interactions through polarization effects in the bonding molecule. Additionally, it was discovered through this study's data that all ligands interacted with the ser-175 residue in the AIF protein. These residues are modulated by the involvement of AIF in the cell death process. From this study, it can be concluded that menadione has the potential as an anticancer agent through the AIF modulation mechanism. Keywords: AIF, enzyme-catalyzed modulation, docking, quantum parametrization, menadione

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