* Corresponding Author
Computational Study of Photosynthetic Pigments: Toward Synthetic Photosynthesis Engineering
https://doi.org/10.22146/ijc.105059 Adhityo Wicaksono(1*), Muhammad Ja'far Prakoso(2), Afif Maulana Yusuf Ridarto(3), Arli Aditya Parikesit(4)
(1) Scientific 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, Indonesia
(2) Theoretical and Computational Condensed Matter Physics Group, Department of Physics, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
(3) Department of Materials and Metallurgical Engineering, Faculty of Industrial Technology and System Engineering, Institut Teknologi Sepuluh Nopember, ITS Sukolilo Campus, Surabaya 60111, Indonesia
(4) Department 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, Indonesia
(*) Corresponding Author
Abstract
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.
Keywords
References
[1] Baroch, M., and Dian, J., 2024, Electrochemical behavior of chlorophylls, bacteriochlorophylls, and related macrostructures—A review, Monatsh. Chem., 155 (8), 771–782.
[2] Buscemi, G., Vona, D., Trotta, M., Milano, F., and Farinola, G.M., 2022, Chlorophylls as molecular semiconductors: Introduction and state of art, Adv. Mater. Technol., 7 (2), 2100245.
[3] Shevela, D., Kern, J.F., Govindjee, G., and Messinger, J., 2023, Solar energy conversion by photosystem II: principles and structures, Photosynth. Res., 156 (3), 279–307.
[4] Myśliwa-Kurdziel, B., Latowski, D., Strzałka, K., 2019, “Chlorophylls c—Occurrence, synthesis, properties, photosynthetic and evolutionary significance” in Advances in Botanical Research, vol. 90, Eds. Grimm, B., Academic Press, Cambridge, MA, US, 91–119.
[5] Tsuzuki, Y., Tsukatani, Y., Yamakawa, H., Itoh, S., Fujita, Y., and Yamamoto, H., 2022, effects of light and oxygen on chlorophyll d biosynthesis in a marine cyanobacterium Acaryochloris marina, Plants, 11 (7), 915.
[6] Mendili, M., and Khadhri, A., 2025, “Chlorophylls: The Verdant World of Photosynthetic Pigments” in Microbial Colorants: Chemistry, Biosynthesis and Applications, Eds. Rather, L.J., Shahid, M., and Jameel, S., Scrivener Publishing, Beverly, MA, US, 223–239.
[7] Allakhverdiev, S.I., Kreslavski, V.D., Zharmukhamedov, S.K., Voloshin, R.A., Korol’kova, D.V., Tomo, T., and Shen, J.R., 2016, Chlorophylls d and f and their role in primary photosynthetic processes of cyanobacteria, Biochemistry (Moscow), 81 (3), 201–212.
[8] Chen, M., 2019, “Chlorophylls d and f: Synthesis, occurrence, light-harvesting, and pigment organization in chlorophyll-binding protein complexes” in Advances in Botanical Research, vol. 90, Eds. Grimm, B., Academic Press, Cambridge, MA, US, 121–139.
[9] Pareek, S., Sagar, N.A., Sharma, S., Kumar, V., Agarwal, T., González‐Aguilar, G.A., and Yahia, E.M., 2017, “Chlorophylls: Chemistry and biological functions” in Fruit and Vegetable Phytochemicals: Chemistry and Human Health, 2nd Ed., Wiley-Blackwell, Hoboken, NJ, US, 269–284.
[10] Guberman-Pfeffer, M.J., 2019, Mechanisms of Porphyrinoid and Carotenoid Spectral Tuning Revealed with Quantum Chemistry, Dissertations, University of Connecticut, US.
[11] Govindjee, G., Stirbet, A., Lindsey, J.S., and Scheer, H., 2024, On the Pelletier and Caventou (1817, 1818) papers on chlorophyll and beyond, Photosynth. Res., 160 (1), 55–60.
[12] da Silva, J.C., and Lombardi, A.T., 2020. “Chlorophylls in Microalgae: Occurrence, Distribution, and Biosynthesis” in Pigments from Microalgae Handbook, Eds. Jacob-Lopes, E., Queiroz, M., and Zepka, L., Springer International Publishing, Cham, Switzerland, 1–18.
[13] Wang, P., and Grimm, B., 2015, Organization of chlorophyll biosynthesis and insertion of chlorophyll into the chlorophyll-binding proteins in chloroplasts, Photosynth. Res., 126 (2), 189–202.
[14] Tanaka, K., and Chujo, Y., 2021, New idea for narrowing an energy gap by selective perturbation of one frontier molecular orbital, Chem. Lett., 50 (2), 269–279.
[15] Zhu, Z., Higashi, M., and Saito, S., 2022, Excited states of chlorophyll a and b in solution by time-dependent density functional theory, J. Chem. Phys., 156 (12), 124111.
[16] Sokolov, M., and Cui, Q., 2025, Impact of fluctuations in the peridinin-chlorophyll a-protein on the energy transfer: Insights from classical and QM/MM molecular dynamics simulations, Biochemistry, 64 (4), 879–894.
[17] Saito, K., Suzuki, T., and Ishikita, H., 2018, Absorption-energy calculations of chlorophyll a and b with an explicit solvent model, J. Photochem. Photobiol., A, 358, 422–431.
[18] Poddubnyy, V.V., Kozlov, M.I., and Glebov, I.O., 2021, The origin of the red shift of Qy band of chlorophylls d and f, Chem. Phys. Lett., 778, 138792.
[19] Takabayashi, Y., Sato, H., and Higashi, M., 2023, Theoretical analysis of the coordination-state dependency of the excited-state properties and ultrafast relaxation dynamics of bacteriochlorophyll a, Chem. Phys. Lett., 826, 140669.
[20] Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J.A., Jr., Peralta, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J.C., Iyengar, S.S., Tomasi, J., Cossi, M., Rega, N., Millam, J.M., Klene, M., Knox, J.E., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Martin, R.L., Morokuma, K., Zakrzewski, V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, Ö., Foresman, J.B., Ortiz, J.V., Cioslowski, J., and Fox, D.J., 2013, Gaussian-09 Revision D.01, Gaussian, Inc., Wallingford, CT.
[21] O'Boyle, N.M., Banck, M., James, C.A., Morley, C., Vandermeersch, T., and Hutchison, G.R., 2011, Open Babel: An open chemical toolbox, J. Cheminf., 3 (1), 33.
[22] Trott, O., and Olson, A.J., 2010, AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J. Comput. Chem., 31 (2), 455–461.
[23] Schrödinger, LLC, 2015, The PyMOL Molecular Graphics System, Version 3.1.3.
[24] Tatsumi, Y., and Saito, R., 2018, Interplay of valley selection and helicity exchange of light in Raman scattering for graphene and MoS2, Phys. Rev. B, 97 (11), 115407.
[25] Becke, A.D., 1988, Density-functional exchange-energy approximation with correct asymptotic behavior, Phys Rev A, 38 (6), 3098–3100.
[26] Lee, C., Yang, W., and Parr, R.G., 1988, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B, 37 (2), 785–789.
[27] Yanai, T., Tew, D.P., and Handy, N.C., 2004, A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP), Chem. Phys. Lett., 393 (1), 51–57.
[28] Marenich, A.V., Cramer, C.J., and Truhlar, D.G., 2009, Performance of SM6, SM8, and SMD on the SAMPL1 test set for the prediction of small-molecule solvation free energies, J. Phys. Chem. B, 113 (14), 4538–4543.
[29] Yan, J., Rodríguez-Martínez, X., Pearce, D., Douglas, H., Bili, D., Azzouzi, M., Eisner, F., Virbule, A., Rezasoltani, E., Belova, V., Dörling, B., Few, S., Szumska, A.A., Hou, X., Zhang, G., Yip, H.L., Campoy-Quiles, M., and Nelson, J., 2022, Identifying structure–absorption relationships and predicting absorption strength of non-fullerene acceptors for organic photovoltaics, Energy Environ. Sci., 15 (7), 2958–2973.
[30] Zeng, L., Wang, Y., and Zhou, J., 2016, Spectral analysis on origination of the bands at 437 nm and 475.5 nm of chlorophyll fluorescence excitation spectrum in Arabidopsis chloroplasts, Luminescence, 31 (3), 769–774.
[31] Kume, A., Akitsu, T., and Nasahara, K.N., 2018, Why is chlorophyll b only used in light-harvesting systems?, J. Plant Res., 131 (6), 961–972.
[32] Heidenreich, K.M., and Richardson, T.L., 2020, Photopigment, absorption, and growth responses of marine cryptophytes to varying spectral irradiance, J. Phycol., 56 (2), 507–520.
[33] Hintz, N.H., Zeising, M., and Striebel, M., 2021, Changes in spectral quality of underwater light alter phytoplankton community composition, Limnol. Oceanogr., 66 (9), 3327–3337.
[34] Kaucikas, M., Nürnberg, D., Dorlhiac, G., Rutherford, A.W., and van Thor, J.J., 2017, Femtosecond visible transient absorption spectroscopy of chlorophyll f-containing photosystem I, Biophys. J., 112 (2), 234–249.
[35] Emeliantsev, P.S., Zhiltsova, A.A., Krasnova, E.D., Voronov, D.A., Rymar, V.V., and Patsaeva, S.V., 2020, Quantification of chlorosomal bacteriochlorophylls using absorption spectra of green sulfur bacteria in natural water, Moscow Univ. Phys. Bull., 75 (2), 137–142.
[36] Borah, K.D., and Bhuyan, J., 2017, Magnesium porphyrins with relevance to chlorophylls, Dalton Trans., 46 (20), 6497–6509.
[37] Simkin, A.J., Kapoor, L., Doss, C.G.P., Hofmann, T.A., Lawson, T., and Ramamoorthy, S., 2022, The role of photosynthesis related pigments in light harvesting, photoprotection and enhancement of photosynthetic yield in planta, Photosynth. Res., 152 (1), 23–42.
[38] Vaz, B., and Pérez-Lorenzo, M., 2023, Unraveling structure–performance relationships in porphyrin-sensitized TiO2 photocatalysts, Nanomaterials, 13 (6), 1097.
[39] Tros, M., Mascoli, V., Shen, G., Ho, M.Y., Bersanini, L., Gisriel, C.J., Bryant, D.A., and Croce, R., 2021, Breaking the red limit: Efficient trapping of long-wavelength excitations in chlorophyll-f-containing photosystem I, Chem, 7 (1), 155–173.
[40] Shahab, S., Sheikhi, M., Filippovich, L., Khaleghian, M., Dikusar, E., Yahyaei, H., and Borzehandani, M.Y., 2018, Spectroscopic studies (geometry optimization, E→Z isomerization, UV/Vis, excited states, FT-IR, HOMO-LUMO, FMO, MEP, NBO, polarization) and anisotropy of thermal and electrical conductivity of new azomethine dyes in stretched polymer matrix, Silicon, 10 (5), 2361–2385.
[41] Mumit, M.A., Pal, T.K., Alam, M.A., Islam, M.A.A.A.A., Paul, S., and Sheikh, M.C., 2020, DFT studies on vibrational and electronic spectra, HOMO–LUMO, MEP, HOMA, NBO and molecular docking analysis of benzyl-3-N-(2,4,5-trimethoxyphenylmethylene)hydrazinecarbodithioate, J. Mol. Struct., 1220, 128715.
[42] Janani, S., Rajagopal, H., Muthu, S., Aayisha, S., and Raja, M., 2021, Molecular structure, spectroscopic (FT-IR, FT-Raman, NMR), HOMO-LUMO, chemical reactivity, AIM, ELF, LOL and molecular docking studies on 1-benzyl-4-(N-Boc-amino)piperidine, J. Mol. Struct., 1230, 129657.
[43] Giannozzi, P., Baseggio, O., Bonfà, P., Brunato, D., Car, R., Carnimeo, I., Cavazzoni, C., de Gironcoli, S., Delugas, P., Ferrari Ruffino, F., Ferretti, A., Marzari, N., Timrov, I., Urru, A., and Baroni, S., 2020, Quantum ESPRESSO toward the exascale, J. Chem. Phys., 152 (15), 154105.
[44] Erb, T.J., 2024, Photosynthesis 2.0: Realizing new-to-nature CO2-fixation to overcome the limits of natural metabolism, Cold Spring Harbor Perspect. Biol.,16 (2), a041669.
[45] Batista-Silva, W., da Fonseca-Pereira, P., Martins, A.O., Zsögön, A., Nunes-Nesi, A., and Araújo, W.L., 2020, Engineering improved photosynthesis in the era of synthetic biology, Plant Commun., 1 (2), 100032.
[46] Leister, D., 2019, Genetic engineering, synthetic biology and the light reactions of photosynthesis, Plant Physiol., 179 (3), 778–793.
DOI: https://doi.org/10.22146/ijc.105059
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