Raman properties of chlorophyll d, the major pigment of Acaryochloris marina: studies using both Raman spectroscopy and density functional theory
Abstract
The Raman spectroscopy of purified chlorophyll (Chl) d extracted from Acaryochloris marina has been measured over the wide region of 250-3200 cm(-1) at 77 K following excitation of its Soret band at 488 nm and analyzed with the aid of hybrid density-functional vibrational analyses. A Raman peak specific to Chl d, which arises from the formyl group 3(1) C=O stretching, was clearly observed at 1659 cm(-1) with medium intensity. Peaks due to other C=O stretching vibrations of the 13(1) keto-, 13(3) ester- and 17(3) groups were also observed. Four very strong peaks were observed in the range of 1000-1600 cm(-1), assigned to the CC stretching and mixtures of the CH3 bend and CN stretching. CCC and NCC bending contribute to medium intensity peaks at 986 and 915 cm(-1). Out-of-plane CH bending at Chl d methine sites 10, 5 and 20 contribute to observed peaks at 885, 864 and 853 cm(-1), respectively. A few modes involving the MgN stretching and MgNC bending motions were observed in the very low frequency range. Density functional theory (DFT) calculations have been used to make assignments on the observed Raman spectrum and the DFT results have been found to be in good agreement with the experimental results.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
When detecting Raman scattered light, Rayleigh and Tyndall scattering must first be eliminated, elucidating faint characteristic spectra comprising astaxanthin, chlorophyll a, chlorophyll b, chlorophyll c, lipids, fatty acids, proteins, carbohydrates, nucleic acids.
“When detecting Raman scattered light, Rayleigh and Tyndall scattering must first be eliminated, elucidating faint characteristic spectra comprising astaxanthin, chlorophyll a, chlorophyll b, chlorophyll c, lipids, fatty acids, proteins, carbohydrates, nucleic acids, [18,38-44] (Fig. 2 & Fig. 3).”
From Microalgal process-monitoring based on high-selectivity spectroscopy tools: status and future perspectives (2018) · cites this paper as [38]
Cites
Density-functional thermochemistry. III. The role of exact exchange
Becke, A. D. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464913 · Cited by 103,767 · see citing works
Lee, C., Yang, W., & Parr, R. G. (1988) · Physical Review B · doi:10.1103/physrevb.37.785 · Cited by 100,874 · see citing works
The influence of polarization functions on molecular orbital hydrogenation energies
Hariharan, P. C., & Pople, J. A. (1973) · Theoretical Chemistry Accounts · doi:10.1007/bf00533485 · Cited by 15,848 · see citing works
Francl, M. M., Pietro, W. J., Hehre, W. J., Binkley, J. S., Gordon, M. S., DeFrees, D. J., & Pople, J. A. (1982) · The Journal of Chemical Physics · doi:10.1063/1.444267 · Cited by 8,202 · see citing works
Molecular Mechanisms of Photosynthesis
Blankenship, R. E. (2002) · Wiley eBooks · doi:10.1002/9780470758472 · Cited by 2,394 · see citing works
Chlorophyll d as a major pigment
Miyashita, H., Ikemoto, H., Kurano, N., Adachi, K., Chihara, M., & Miyachi, S. (1996) · Nature · doi:10.1038/383402a0 · Cited by 515 · see citing works
Cai, Z.-L., Sendt, K., & Reimers, J. R. (2002) · The Journal of Chemical Physics · doi:10.1063/1.1501131 · Cited by 331 · see citing works
Self-citationA DFT/TDDFT interpretation of the ground and excited states of porphyrin and porphyrazine complexes
Baerends, E. J., Ricciardi, G., Rosa, A., & van Gisbergen, S. J. A. (2002) · Coordination Chemistry Reviews · doi:10.1016/s0010-8545(02)00093-0 · Cited by 314 · see citing works
Golbeck, J. H., & Bryant, D. A. (1991) · Elsevier eBooks · doi:10.1016/b978-0-12-152516-3.50006-1 · Cited by 235 · see citing works
A photosystem I reaction center driven by chlorophyll d in oxygenic photosynthesis
Hu, Q., Miyashita, H., Iwasaki, I., Kurano, N., Miyachi, S., Iwaki, M., & Itoh, S. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.22.13319 · Cited by 214 · see citing works
Miyashita, H., Adachi, K., Kurano, N., Ikemot, H., Chihara, M., & Miyach, S. (1997) · Plant and Cell Physiology · doi:10.1093/oxfordjournals.pcp.a029163 · Cited by 193 · see citing works
CHLOROPHYLL D, A GREEN PIGMENT OF RED ALGAE
Manning, W. M., & Strain, H. H. (1943) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)72109-1 · Cited by 191 · see citing works
Density functional theory calculations of the visible spectrum of chlorophyll a
Sundholm, D. (1999) · Chemical Physics Letters · doi:10.1016/s0009-2614(99)00194-3 · Cited by 176 · see citing works
Florián, J., Baumruk, V., & Leszczyński, J. (1996) · The Journal of Physical Chemistry · doi:10.1021/jp953284w · Cited by 132 · see citing works
The role of chlorophyll b in photosynthesis: Hypothesis
Eggink, L. L., Park, H., & Hoober, J. K. (2001) · BMC Plant Biology · doi:10.1186/1471-2229-1-2 · Cited by 127 · see citing works
MARQUARDT, J., Senger, H., Miyashita, H., Miyachi, S., & Mörschel, E. (1997) · FEBS Letters · doi:10.1016/s0014-5793(97)00631-5 · Cited by 126 · see citing works
Resonance Raman spectra of chlorophyll in solution
Lutz, M. (1974) · Journal of Raman Spectroscopy · doi:10.1002/jrs.1250020506 · Cited by 123 · see citing works
Sendt, K., Johnston, L. A., Hough, W. A., Crossley, M. J., Hush, N. S., & Reimers, J. R. (2002) · Journal of the American Chemical Society · doi:10.1021/ja020081u · Cited by 114 · see citing works
Sundholm, D. (2000) · Chemical Physics Letters · doi:10.1016/s0009-2614(99)01428-1 · Cited by 88 · see citing works
The major light‐harvesting pigment protein of Acaryochloris marina
Chen, M., Quinnell, R. G., & Larkum, A. W. D. (2002) · FEBS Letters · doi:10.1016/s0014-5793(02)02315-3 · Cited by 85 · see citing works
Self-citationAkiyama, M., Miyashita, H., Kise, H., Watanabe, T., Miyachi, S., & Kobayashi, M. (2001) · Analytical Sciences · doi:10.2116/analsci.17.205 · Cited by 82 · see citing works
Mimuro, M., Akimoto, S., Yamazaki, I., Miyashita, H., & Miyachi, S. (1999) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/s0005-2728(99)00048-1 · Cited by 76 · see citing works
A PROPOSED STRUCTURE FOR CHLOROPHYLL d
Holt, A. S., & Morley, H. V. (1959) · Canadian Journal of Chemistry · doi:10.1139/v59-069 · Cited by 73 · see citing works
Schiller, H., Senger, H., Miyashita, H., Miyachi, S., & Dau, H. (1997) · FEBS Letters · doi:10.1016/s0014-5793(97)00620-0 · Cited by 61 · see citing works
Mimuro, M., Hirayama, K., Uezono, K., Miyashita, H., & Miyachi, S. (2000) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/s0005-2728(99)00095-x · Cited by 51 · see citing works
Diers, J. R., Zhu, Y., Blankenship, R. E., & Bocian, D. F. (1996) · The Journal of Physical Chemistry · doi:10.1021/jp953544+ · Cited by 50 · see citing works
Ultrastructure of Acaryochloris marina , an oxyphotobacterium containing mainly chlorophyll d
MARQUARDT, J., Mörschel, E., Rhiel, E., & Westermann, M. (2000) · Archives of Microbiology · doi:10.1007/s002030000194 · Cited by 41 · see citing works
Molecular Aspects of Light-harvesting Processes in Algae
Larkum, T., & HOWE, C. (1997) · Advances in botanical research · doi:10.1016/s0065-2296(08)60283-9 · Cited by 38 · see citing works
Raman spectroscopy of chlorophyll d from Acaryochloris marina
Cai, Z.-L., Zeng, H., Chen, M., & Larkum, A. W. D. (2002) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/s0005-2728(02)00357-2 · Cited by 38 · see citing works
Self-citationNieuwenburg, P., Clarke, R. J., Cai, Z.-L., Chen, M., Larkum, A. W. D., Cabral, N. M., Ghiggino, K. P., & Reimers, J. R. (2003) · Photochemistry and Photobiology · doi:10.1562/0031-8655(2003)0770628eotppo2.0.co2 · Cited by 31 · see citing works
Self-citationHastings, G. (2001) · Applied Spectroscopy · doi:10.1366/0003702011952695 · Cited by 31 · see citing works
A Density Functional Normal Mode Calculation of a Bacteriochlorophyll a Derivative
Ceccarelli, M., Lutz, M., & Marchi, M. (2000) · Journal of the American Chemical Society · doi:10.1021/ja993849s · Cited by 29 · see citing works
Structure and Interactions of the Chlorophyll a Molecules in the Higher Plant Lhcb4 Antenna Protein
Pascal, A. A., Peterman, E. J. G., Gradinaru, C. C., van Amerongen, H., van Grondelle, R., & Robert, B. (2000) · The Journal of Physical Chemistry B · doi:10.1021/jp001504m · Cited by 27 · see citing works
Chlorophyll d as the major photopigment in Acaryochloris marina
Chen, M., Quinnell, R. G., & Larkum, A. W. D. (2002) · Journal of Porphyrins and Phthalocyanines · doi:10.1142/s1088424602000889 · Cited by 23 · see citing works
Self-citationGall, A., Robert, B., Cogdell, R. J., Bellissent‐Funel, M., & Fraser, N. J. (2001) · FEBS Letters · doi:10.1016/s0014-5793(01)02161-5 · Cited by 18 · see citing works
Frolov, D., Gall, A., Lutz, M., & Robert, B. (2002) · The Journal of Physical Chemistry A · doi:10.1021/jp0133586 · Cited by 17 · see citing works
Picorel, R., Chumanov, G. D., Torrado, E., Cotton, T. M., & Seibert, M. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp980188x · Cited by 17 · see citing works
Schlücker, S., Koster, J., Nissum, M., Popp, J., & Kiefer, W. (2001) · The Journal of Physical Chemistry A · doi:10.1021/jp012350t · Cited by 13 · see citing works
Pająk, J., Ramaekers, R., Rospenk, M., Alexandrov, V., Stepanian, S. G., Adamowicz, L., & Maes, G. (2003) · Chemical Physics · doi:10.1016/s0301-0104(02)00922-9 · Cited by 13 · see citing works
Sashima, T., Abe, M., Kurano, N., Miyachi, S., & Koyama, Y. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp981118t · Cited by 11 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Micro‐Raman spectroscopy of algae: Composition analysis and fluorescence background behavior
Huang, Y. Y., Beal, C. M., Cai, W. W., Ruoff, R. S., & Terentjev, E. M. (2010) · Biotechnology and Bioengineering · doi:10.1002/bit.22617 · Cited by 145 · see citing works
Identification of the special pair of photosystem II in a chlorophyll d -dominated cyanobacterium
Tomo, T., Okubo, T., Akimoto, S., Yokono, M., Miyashita, H., Tsuchiya, T., Noguchi, T., & Mimuro, M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701847104 · Cited by 128 · see citing works
Song, Y., Yin, H., & Huang, W. E. (2016) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2016.04.002 · Cited by 108 · see citing works
Raman Spectroscopy and Its Modifications Applied to Biological and Medical Research
Allakhverdiev, E. S., Khabatova, V. V., Kossalbayev, B. D., Zadneprovskaya, E. V., Rodnenkov, O. V., Martynyuk, T. V., Maksimov, G. V., Alwasel, S., Tomo, T., & Allakhverdiev, S. I. (2022) · Cells · doi:10.3390/cells11030386 · Cited by 88 · see citing works
Weiss, T. L., Chun, H. J., Okada, S., Vitha, S., Holzenburg, A., Laane, J., & Devarenne, T. P. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.157230 · Cited by 83 · see citing works
Gamsjaeger, S., Barańśka, M., Schulz, H., Heiselmayer, P., & Musso, M. E. (2011) · Journal of Raman Spectroscopy · doi:10.1002/jrs.2860 · Cited by 65 · see citing works
Bhopate, D. P., Mahajan, P. G., Garadkar, K. M., Kolekar, G. B., & Patil, S. R. (2015) · New Journal of Chemistry · doi:10.1039/c5nj01228g · Cited by 55 · see citing works
Raman Spectroscopy of Algae: A Review
Tomar, V. (2012) · Journal of Nanomedicine & Nanotechnology · doi:10.4172/2157-7439.1000131 · Cited by 56 · see citing works
Multimodal vibrational imaging of cells
Pérez-Guaita, D., Kochan, K., Martin, M., Andrew, D. W., Heraud, P., Richards, J. S., & Wood, B. R. (2016) · Vibrational Spectroscopy · doi:10.1016/j.vibspec.2016.07.017 · Cited by 56 · see citing works
Daneshkhah, A., Shrestha, S., Siegel, A. P., Varahramyan, K., & Agarwal, M. (2017) · Sensors · doi:10.3390/s17030595 · Cited by 37 · see citing works
Podevin, M., Fotidis, I. A., & Angelidaki, I. (2018) · Critical Reviews in Biotechnology · doi:10.1080/07388551.2017.1398132 · Cited by 34 · see citing works
Vallejo-Pérez, M. R., Sosa-Herrera, J. A., Navarro-Contreras, H. R., Álvarez-Preciado, L. G., Rodríguez, Á. G., & Lara-Ávila, J. P. (2021) · Plants · doi:10.3390/plants10081542 · Cited by 31 · see citing works
Generalova, A. N., Олейников, В. А., Zarifullina, M. M., В., Л. Е., Sizova, S. V., Artemyev, M. V., & Zubov, V. P. (2011) · Journal of Colloid and Interface Science · doi:10.1016/j.jcis.2011.02.002 · Cited by 25 · see citing works
Hastings, G., & Wang, R. (2007) · Photosynthesis Research · doi:10.1007/s11120-007-9228-3 · Cited by 18 · see citing works
Reconstitution of Chlorophyll d into the Bacterial Photosynthetic Light-harvesting Protein LH2
Saga, Y., Yamashita, M., Imanishi, M., & Kimura, Y. (2018) · Chemistry Letters · doi:10.1246/cl.180483 · Cited by 15 · see citing works
Neverov, K. V., Santabarbara, S., & Krasnovsky, А. А. (2011) · Photosynthesis Research · doi:10.1007/s11120-011-9657-x · Cited by 15 · see citing works
Fluorescence Line Narrowing Studies on Isolated Chlorophyll Molecules
Telfer, A., Pascal, A. A., Bordes, L., Barber, J. P., & Robert, B. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp907537a · Cited by 14 · see citing works
Krishnan, N., Singh, P. K., Sakthivelu, M., Velusamy, P., Gopinath, S. C. B., & Pachaiappan, R. (2022) · Biomass Conversion and Biorefinery · doi:10.1007/s13399-022-03415-y · Cited by 13 · see citing works
Zamzam, N., & van Thor, J. J. (2019) · Molecules · doi:10.3390/molecules24071326 · Cited by 13 · see citing works
Good vibrations: Raman spectroscopy enables insights into plant biochemical composition†
Zavafer, A., & Ball, M. C. (2022) · Functional Plant Biology · doi:10.1071/fp21335 · Cited by 10 · see citing works
Generalova, A. N., & Zubov, V. P. (2016) · Polymer Science Series B · doi:10.1134/s1560090416040023 · Cited by 10 · see citing works
Jehlička, J., Culka, A., & Mareš, J. (2019) · Journal of Raman Spectroscopy · doi:10.1002/jrs.5671 · Cited by 10 · see citing works
Sytina, O. A., Alexandre, M. T. A., Heyes, D. J., Hunter, C. N., Robert, B., van Grondelle, R., & Groot, M. L. (2010) · Physical Chemistry Chemical Physics · doi:10.1039/c0cp01686a · Cited by 10 · see citing works
Bhattacharyya, K., Bhattacharjee, N., Sen, D., Lai, T. K., Ghosh, A. K., Pal, R. R., & Ganguly, S. (2024) · Scientific Reports · doi:10.1038/s41598-024-66336-y · Cited by 8 · see citing works
Xu, S., Huang, P., Zhong, W., Luo, Y., Yan, Z., Liu, L., & Xiao, Z. (2023) · Applied Physics A · doi:10.1007/s00339-023-06958-7 · Cited by 7 · see citing works
Bhat, M., Saha, P., Narasimhan, M., Shelar, A., Hole, A. R., Krishna, C. M., & Govekar, R. B. (2025) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2025.130771 · Cited by 6 · see citing works
Ghosh, T., Kandpal, S., Rani, C., Pathak, D. K., Tanwar, M., Chaudhary, A., Jha, H. C., & Kumar, R. (2021) · ACS Applied Bio Materials · doi:10.1021/acsabm.1c00650 · Cited by 4 · see citing works
Williams, I., Matthews, H., Holtkamp, H. U., Nieuwoudt, M. K., Sewell, M. A., Simpson, M. C., Broderick, N. G. R., & Novikova, N. I. (2023) · Chemometrics and Intelligent Laboratory Systems · doi:10.1016/j.chemolab.2023.104985 · Cited by 3 · see citing works
Spectroscopic Experiments: A Review of Raman Spectroscopy of Biological Systems
Tomar, V., Qu, T., Dubey, D. K., Verma, D. K., & Zhang, Y. (2015) · Springer eBooks · doi:10.1007/978-1-4939-3453-9_2 · Cited by 3 · see citing works
Wet chemical synthesis of quantum dots for medical applications
Cepeda‐Pérez, E., López–Luke, T., Perez‐Mayen, L., Hidalgo, A., la Rosa, E. D., Torres-Castro, A., Ceja‐Fdez, A., Vivero-Escoto, J. L., & González-Yebra, A. L. (2015) · doi:10.1364/ecbo.2015.95371h · Cited by 1 · see citing works
Mokrani, M. A., Sayah, Z. B. D., Chabane, H., Mekki, A., Cherif, Y. B., Nedjar, L., Kaufa, M., Slimani, Z. Y., Manseri, A., Livi, S., et al. (2026) · Journal of Electronic Materials · doi:10.1007/s11664-026-12764-7 · Cited by 1 · see citing works
Senge, M. O. (2009) · Heterocycles · doi:10.3987/com-09-11674 · Cited by 1 · see citing works
Sadaoka, K., & Saga, Y. (2014) · Journal of Porphyrins and Phthalocyanines · doi:10.1142/s1088424614500242 · Cited by 1 · see citing works
Mesure en ligne par spectroscopie Raman appliquée à un photobioréacteur de microalgues
Lieutaud, C. (2019) · theses.fr (ABES) · doi:10.70675/b149f935zc54az4f46z877az5412eeee4d12 · Cited by 1 · see citing works
Estudo teórico da espectroscopia da clorofila d
Nuñez, A. N. S. (2017) · doi:10.11606/d.43.2017.tde-19112017-173908
Current Awareness in Phytochemical Analysis
(2004) · Phytochemical Analysis · doi:10.1002/pca.751
Xu, S., Huang, P., Zhang, L., Luo, Y., Wang, Y., Liu, Y., Fu, K., Fu, H., & Huang, Y. (2025) · Journal of Electronic Materials · doi:10.1007/s11664-025-12054-8
Ching, C. P., Wang, W., LAU, H. C., Lai, H. Y., Chen, Y., & Lau, C. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.6910758
Bacterial capture and lysis on diatom spines reveal a suspension-feeding strategyPreprint
Forget, M., Wollweber, F., Case, E., Henshaw, R. J., Blitvic, N., Słomka, J., Pilhofer, M., Hehemann, J., & Stocker, R. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.07.749814
Raman a banana: mapping banana peel composition and ripening process by Raman spectroscopy
Pilát, Z., Modlitbová, P., Benešová, M., Šiler, M., Bernatová, S., Ježek, J., Plešinger, F., Doskocil, O., Samek, O., & Zemánek, P. (2026) · Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy · doi:10.1016/j.saa.2026.128898
Wet chemical synthesis of quantum dots for medical applications
Cepeda‐Pérez, E., López–Luke, T., Perez‐Mayen, L., Hidalgo, A., la Rosa, E. D., Torres-Castro, A., Ceja‐Fdez, A., Vivero-Escoto, J. L., & González-Yebra, A. L. (2015) · Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · doi:10.1117/12.2183183
- Authors
- Chen, M., Zeng, H., Larkum, A. W. D., & Cai, Z.-L.
- Affiliations
- The University of Sydney (AU)
- Corresponding author
- Cai, Zheng-Li
- Venue
- Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
- Publisher
- Elsevier BV
- Published
- 2004-02
- Volume
- 60
- Issue
- 3
- Pages
- 527-534
- ISSN
- 1386-1425 (ISSN-L)
- OpenAlex
- W1979610127
- Cited by
- 41
- References
- 40
- Citations by year
- 2026: 4 · 2025: 2 · 2024: 1 · 2023: 2 · 2022: 3 · 2021: 2 · 2019: 3 · 2018: 1 · 2017: 3 · 2016: 3 · 2015: 4 · 2014: 1 · 2012: 1
- FWCI
- 0.21
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy (publishedVersion)
- PubMed (publishedVersion)
- Funders
- East China Normal University
- Topics
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Spectroscopy and Quantum Chemical Studies
- Physical Sciences › Materials Science › Materials Chemistry › Porphyrin and Phthalocyanine Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Spectroscopy Techniques in Biomedical and Chemical Research
- Keywords
- chlorophyll d, Acaryochloris marina, Raman spectra, vibrational assignment, C=O stretching, formyl group, low-frequency vibrational modes, DFT calculations
- MeSH terms
- Bacteria, Chlorophyll, Spectrum Analysis, Raman
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
