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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

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (408.899 KB) | DOI: 10.20884/1.jm.2020.15.2.592

Abstract

Computational study of natural indigo has been carried out to get the optimized structure and electronic properties of two indigo at different pH. It has been found that indigo has the potential to be applied as 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 indigo has the potential to be applied in dye-sensitized solar cell (DSSC)
Video Demonstrations of a Benzene Derivative Reaction from Its Optimized Intermediate Structure Awal, Jumaidil; Martoprawiro, Muhamad Abdulkadir
J-PEK (Jurnal Pembelajaran Kimia) Vol 8, No 1 (2023): J-PEK (JURNAL PEMBELAJARAN KIMIA)
Publisher : Universitas Negeri Malang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17977/um026v8i12023p20-26

Abstract

A number of researchers have performed studies on the application of chemical reaction visualization by means of computational chemistry techniques for the purpose of teaching and learning chemistry at secondary and higher education levels. However, on practical grounds, the presented approach thus far was generally unattainable for teachers due to the time-consuming process of finding the transition states. This research offers a less time-consuming computational chemistry technique for producing organic reaction-modelling videos upon which the students may sufficiently build their understanding of fundamental concepts of chemical reactions. The technique being proposed here consists of (1) intermediate structure modelling, (2) reactant-wise and product-wise optimizations of the intermediate structures without the search for transition states, and (3) visualizations of the optimized results. The application of this technique has managed to produce a video demonstration of an organic reaction of benzene derivatives that may serve as modelling videos in chemistry lessons at secondary education or undergraduate degree levels.REFERENCESBode, B. M., & Gordon, M. S. (1998). Macmolplt: A graphical user interface for GAMESS. Journal of Molecular Graphics and Modelling, 16(3), 133–138. https://doi.org/10.1016/S1093-3263(99)00002-9Carey, F. A. (2000). Organic chemistry (4th ed). McGraw-Hill.Cohlberg, J. A. (2021). Exploring Proteins and Nucleic Acids with Jmol. W. H. Freeman and Company. https://home.csulb.edu/~cohlberg/Jmolmanual.pdfCramer, C. J. (2004). Essentials of computational chemistry: Theories and models (2nd ed). Wiley.Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. 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African Journal of Chemical Education, 4(3), 22–33.Ikuo, A., Saito, K., Yoshinaga, Y., & Ogawa, H. (2013). Development of Teaching Material in Tablet PC for Experiment of Nitration of Benzene Based on Computer Graphics by Quantum Chemical Calculation. Work-in-Progress Poster of the International Conference on Computers in Education: ICCE 2013, 21–23.Koreeda, M. (2011). Chem 216 S11 Notes [Lab work notes].  http://websites.umich.edu/~chem216/216% 20S11-Expt%201.pdfLevine, I. N. (2009). Physical chemistry (6th ed). McGraw-Hill.Lewars, E. G. (2016). Computational Chemistry: Introduction to the Theory and Applications of Molecular and Quantum Mechanics. Springer.Mendera, I. G. (2020). Kimia: Benzena dan Turunannya. Direktorat SMA Ditjen PAUD, Dikdas, dan Dikmen Kemendikbud.Neese, F., Wennmohs, F., Becker, U., & Riplinger, C. (2020). The ORCA quantum chemistry program package. The Journal of Chemical Physics, 152(22), 224108. https://doi.org/10.1063/5.0004608Nursanti, Y. I. (2020). Modul Tema 15: Berpadu dan Bersenyawa. Direktorat Dikmas dan Diksus Ditjen PAUD, Dikdas, dan Dikmen Kemendikbud.Omer, R., Koparir, P., Ahmed, L., & Koparir, M. (2020). Computational determination the reactivity of salbutamol and propranolol drugs. Turkish Computational and Theoretical Chemistry, 4(2), 67–75. https://doi.org/10.33435/tcandtc.768758Polik, W. F., & Schmidt, J. R. (2022). WebMO: Web‐Based Computational Chemistry Calculations in Education and Research. WIREs Computational Molecular Science, 12(1), e1554.Putri, P. (2016). Tata Nama Senyawa dan Perhitungan Kimia—Karakteristik Peserta Didik. P4TK Bisnis dan Pariwisata Ditjen GTK Kemendikbud.Rahayu, I. (2009). Praktis Belajar Kimia untuk Kelas XII SMA/MA Program IPA. Pusat Perbukuan Depdiknas.S. Fernandes, H., Ramos, M. J., & M. F. S. A. Cerqueira, N. (2018). molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software: A VMD Plugin to Handle QM and ONIOM Calculations. Journal of Computational Chemistry, 39(19), 1344–1353. https://doi.org/10.1002/jcc.25189Schaftenaar, G., Vlieg, E., & Vriend, G. (2017). Molden 2.0: Quantum chemistry meets proteins. Journal of Computer-Aided Molecular Design, 31(9), 789–800. https://doi.org/10.1007/s10822-017-0042-5Wardiyah. (2016). Kimia Organik. BPPSDMK Pusdik SDM Kesehatan Kemenkes.                  
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

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (376.871 KB) | DOI: 10.19184/jid.v17i2.3499

Abstract

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

Abstract

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

Abstract

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

Abstract

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.
- Implementasi Reaksi Metanogenesis sebagai Materi Pembelajaran Kimia pada Pelajaran Kimia SMA dengan Pendekatan Chemistry, Life, Universe, and Everything (CLUE) Oktavianti, Nur Azlina; Martoprawiro, Muhamad Abdulkadir; Rattyananda, Badra Sanditya
Jurnal Penelitian Pendidikan IPA Vol 10 No 1 (2024): January
Publisher : Postgraduate, University of Mataram

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/jppipa.v10i1.4889

Abstract

Palm Oil Mill Effluent (POME) is the biggest waste from palm oil production. This liquid waste contain much methane gas (CH4) which has potential as renewable energy, namely biogas. The last stage of processing biogas called methanogenesis reaction, the process of synthesis methane and carbon dioxide. The methanogenesis reaction can be studied by computational studies as learning media source for SeniorHigh School Chemistry with the Chemistry, Life, Universe, and Everything (CLUE) approach. According to learning outcomes of Merdeka Curriculum, the methanogenesis reaction can be used as a learning source forthree chapters in F phase. The chapters areChemical Bonding, Rate of Reaction,and Thermochemistry. The chapter of Chemical Bonding describe hydrogen bonding in acetic acid intermediate species and its effect on the molecular characteristics. The chapter Rate of Reactiondiscuss the result of computational calculation to determine the activation energy (AE). Methanogenesis reaction have two transition states (TS), with AE of each TS are 228.56 kJ.mol-1 and 281.31 kJ.mol-1, while the second stage act as the rate-determining step. The last, for Thermochemistry chapter, the content material is define the quantity of thermodynamic variables on methanogenesis reaction.The value of∆S = 50.14 kJ.mol-1T, ∆G = 139.7 kJ.mol-1, and ∆H =168.84 kJ.mol-1.
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

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