Computational Study of Photosynthetic Pigments: Toward Synthetic Photosynthesis Engineering
Chlorophyll is a widely known photosynthetic pigment in plants, algae, and cyanobacteria, along with bacteriochlorophyll in some photosynthetic bacteria. The pigments consist of tetrapyrrole structures that carry a single magnesium atom at the center. They play important parts in the light-harvestin...
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| Format: | Article |
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Department of Chemistry, Universitas Gadjah Mada
2025-07-01
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| Series: | Indonesian Journal of Chemistry |
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| Online Access: | https://jurnal.ugm.ac.id/ijc/article/view/105059 |
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| author | Adhityo Wicaksono Muhammad Ja'far Prakoso Afif Maulana Yusuf Ridarto Arli Aditya Parikesit |
| author_facet | Adhityo Wicaksono Muhammad Ja'far Prakoso Afif Maulana Yusuf Ridarto Arli Aditya Parikesit |
| author_sort | Adhityo Wicaksono |
| collection | DOAJ |
| description | Chlorophyll is a widely known photosynthetic pigment in plants, algae, and cyanobacteria, along with bacteriochlorophyll in some photosynthetic bacteria. The pigments consist of tetrapyrrole structures that carry a single magnesium atom at the center. They play important parts in the light-harvesting process in photosynthesis. This study aimed to characterize and compare the electronic profiles of chlorophyll and bacteriochlorophyll pigments by using in silico computational approaches, such as density functional theory (DFT), electronic transfer property analysis, and protein-pigment interaction studies via molecular docking. The results showed that chlorophylls a, b, and c have the highest energy gaps at the ground state DFT. For bacteriochlorophylls, bacteriochlorophylls g and b have the highest energy gaps. The time-dependent DFT and the follow-up calculations, including extinction coefficient, tunneling rate, and coherence time, indicated bacteriochlorophyll g as a highly promising and efficient pigment. Additionally, chlorophyll c and bacteriochlorophylls c and d showed the strongest binding affinities with the chlorophyll-binding protein of plant photosystem II. This study provides a comprehensive and replicable computational pipeline for pigment profiling, advancing future synthetic photosynthesis designs through combined quantum and synthetic biology insights. |
| format | Article |
| id | doaj-art-950abb04e19c46f1b2c0d7f71b89f170 |
| institution | Kabale University |
| issn | 1411-9420 2460-1578 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Department of Chemistry, Universitas Gadjah Mada |
| record_format | Article |
| series | Indonesian Journal of Chemistry |
| spelling | doaj-art-950abb04e19c46f1b2c0d7f71b89f1702025-08-20T03:57:39ZengDepartment of Chemistry, Universitas Gadjah MadaIndonesian Journal of Chemistry1411-94202460-15782025-07-012541209122510.22146/ijc.10505937759Computational Study of Photosynthetic Pigments: Toward Synthetic Photosynthesis EngineeringAdhityo Wicaksono0Muhammad Ja'far Prakoso1Afif Maulana Yusuf Ridarto2Arli Aditya Parikesit3Scientific Department, Genomik Solidaritas Indonesia Lab (GSI Lab), Jl. Sultan Agung No. 29, Setiabudi, Jakarta 12980, Indonesia; Biosciences and Biotechnology Research Center, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 40132, IndonesiaTheoretical and Computational Condensed Matter Physics Group, Department of Physics, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, IndonesiaDepartment of Materials and Metallurgical Engineering, Faculty of Industrial Technology and System Engineering, Institut Teknologi Sepuluh Nopember, ITS Sukolilo Campus, Surabaya 60111, IndonesiaDepartment of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat No. Kav. 88, RT. 4/RW. 9, Kayu Putih, Pulo Gadung, Jakarta 13210, IndonesiaChlorophyll is a widely known photosynthetic pigment in plants, algae, and cyanobacteria, along with bacteriochlorophyll in some photosynthetic bacteria. The pigments consist of tetrapyrrole structures that carry a single magnesium atom at the center. They play important parts in the light-harvesting process in photosynthesis. This study aimed to characterize and compare the electronic profiles of chlorophyll and bacteriochlorophyll pigments by using in silico computational approaches, such as density functional theory (DFT), electronic transfer property analysis, and protein-pigment interaction studies via molecular docking. The results showed that chlorophylls a, b, and c have the highest energy gaps at the ground state DFT. For bacteriochlorophylls, bacteriochlorophylls g and b have the highest energy gaps. The time-dependent DFT and the follow-up calculations, including extinction coefficient, tunneling rate, and coherence time, indicated bacteriochlorophyll g as a highly promising and efficient pigment. Additionally, chlorophyll c and bacteriochlorophylls c and d showed the strongest binding affinities with the chlorophyll-binding protein of plant photosystem II. This study provides a comprehensive and replicable computational pipeline for pigment profiling, advancing future synthetic photosynthesis designs through combined quantum and synthetic biology insights.https://jurnal.ugm.ac.id/ijc/article/view/105059excitonphotosystemphotosynthesisquantum tunnelingquantum biology |
| spellingShingle | Adhityo Wicaksono Muhammad Ja'far Prakoso Afif Maulana Yusuf Ridarto Arli Aditya Parikesit Computational Study of Photosynthetic Pigments: Toward Synthetic Photosynthesis Engineering Indonesian Journal of Chemistry exciton photosystem photosynthesis quantum tunneling quantum biology |
| title | Computational Study of Photosynthetic Pigments: Toward Synthetic Photosynthesis Engineering |
| title_full | Computational Study of Photosynthetic Pigments: Toward Synthetic Photosynthesis Engineering |
| title_fullStr | Computational Study of Photosynthetic Pigments: Toward Synthetic Photosynthesis Engineering |
| title_full_unstemmed | Computational Study of Photosynthetic Pigments: Toward Synthetic Photosynthesis Engineering |
| title_short | Computational Study of Photosynthetic Pigments: Toward Synthetic Photosynthesis Engineering |
| title_sort | computational study of photosynthetic pigments toward synthetic photosynthesis engineering |
| topic | exciton photosystem photosynthesis quantum tunneling quantum biology |
| url | https://jurnal.ugm.ac.id/ijc/article/view/105059 |
| work_keys_str_mv | AT adhityowicaksono computationalstudyofphotosyntheticpigmentstowardsyntheticphotosynthesisengineering AT muhammadjafarprakoso computationalstudyofphotosyntheticpigmentstowardsyntheticphotosynthesisengineering AT afifmaulanayusufridarto computationalstudyofphotosyntheticpigmentstowardsyntheticphotosynthesisengineering AT arliadityaparikesit computationalstudyofphotosyntheticpigmentstowardsyntheticphotosynthesisengineering |