Literature

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A complete list of journal articles that document PhotochemCAD 3, accompanying databases, development, and related papers.

PhotochemCAD™ – a program and spectral databases to advance the photosciences – was conceived in the late 1980s by Jonathan S. Lindsey, and has been developed chiefly with his colleagues Masahiko Taniguchi and Hai Du. The programs Cyclaplex™ and PorphyrinViLiGe™ also have been developed by this team in the Department of Chemistry at North Carolina State University.

For more about this group and their work, visit the Lindsey Lab

PhotochemCAD Program

• "PhotochemCAD 3: Diverse Modules for Photophysical Calculations with Access to Multiple Spectral Databases,"
  Taniguchi, M.; Du, H.; Lindsey, J. S. Photochem. Photobiol. 2018, 94, 277–289.
  Provides a complete description of all 8 calculational modules (including the formulas in each) for the most recent version of the program.

PhotochemCAD Databases

• "Aqueous-Membrane Partitioning of β-Substituted Porphyrins Encompassing Diverse Polarity,"
  Soares, A. R. M.; Thanaiah, Y.; Taniguchi, M.; Lindsey, J. S. New J. Chem. 2013, 37, 1087–1097.
  12 spectra of uroporphyrins, derivatives thereof, or synthetic analogues.
• "Database of Absorption and Fluorescence Spectra of >300 Common Compounds for Use in PhotochemCAD,"
  Taniguchi, M.; Lindsey, J. S. Photochem. Photobiol. 2018, 94, 290–327.
  552 spectra accompanied by 720 references to the original scholarly literature.
• "Absorption and Fluorescence Spectral Database of Chlorophylls and Analogues,"
  Taniguchi, M.; Lindsey, J. S. Photochem. Photobiol. 2021, 97, 136–165.
  305 Absorption spectra and 72 fluorescence for 150 native chlorophylls and derivatives, with 146 references tying the spectra to the original scholarly literature.
• "Tolyporphins A–R, unusual tetrapyrrole macrocycles in a cyanobacterium from Micronesia, assessed quantitatively from the culture HT-58-2,"
  O'Donnell, T. J.; Gurr, J. R.; Dai, J.; Taniguchi, M.; Williams, P. G.; Lindsey, J. S.  New J. Chem. 2021, 45, 11481–11494.
  Absorption spectra for 14 available tolyporphins.
• "Beyond green with synthetic chlorophylls – Connecting structural features with spectral properties,"
  Taniguchi, M.; Bocian, D. F.; Holten, D.; Lindsey, J. S.J. Photochem. Photobiol. 2022, 52, 100513.
  324 Absorption spectra and 247 fluorescence spectra enable an Aufbau approach for understanding the spectral properties of native chlorophylls and analogues (190 references).
• "Phyllobilins – Bioactive Natural Products Derived from Chlorophyll ­– Plant Origins, Structures, Absorption Spectra, and Biomedical Properties,"
  Karg, C. A.; Taniguchi, M.; Lindsey, J. S.; Moser, S.Planta Medica 2023, 6, 637-662.
  Absorption and fluorescence spectra of 73 phyllobilins – open-chain tetrapyrroles equipped with the isocyclic ring E – to facilitate identification in phytochemical analyses.
• "Digital Database of Absorption Spectra of Diverse Flavonoids Enables Structural Comparisons and Quantitative Evaluations,"
  Taniguchi, M.; LaRocca, C.; Bernat, J. D.; Lindsey, J. S. J. Nat. Prod. 2023, 86, 1087–1119.
  Absorption and fluorescence spectra of 177 flavonoids (12 distinct types), diverse small molecules from plants (560 references).
• "Absorption and Fluorescence Spectra of Open-chain Tetrapyrrole Pigments – Bilirubins, Biliverdins, Phycobilins, and Synthetic Analogues,"
  Taniguchi, M.; Lindsey, J. S. J. Photochem. Photobiol. C: Photochem. Rev. 2023, 55, 100585.

PhotochemCAD Development

• "PhotochemCAD. A Computer-Aided Design and Research Tool in Photochemistry and Photobiology,"
  Du, H.; Fuh, R.-C. A.; Li, J.; Corkan, L. A.; Lindsey, J. S. Photochem. Photobiol. 1998, 68, 141–142.
  The first publication concerning PhotochemCAD (after more than a decade of development and internal testing) including a database of absorption and fluorescence spectra for 125 common compounds.
• "PhotochemCAD 2. A Refined Program with Accompanying Spectral Databases for Photochemical Calculations,"
  Dixon, J. M.; Taniguchi, M.; Lindsey, J. S. Photochem. Photobiol. 2005, 81, 212–213.
  The second publication concerning PhotochemCAD, including a Windows interface, more extensive calculational modules, and expansion of the spectral database for 150 common compounds.
• "Developing a User Community in the Photosciences. A Website for Spectral Data and PhotochemCAD,"
  Guo, Y.; Xu, Z.; Norcross, A. E.; Taniguchi, M.; Lindsey, J. S. Proc. SPIE 2019, 10893, 108930O.
  This paper surveys >45,000 scholarly papers in considering how to connect with the very broad community of photoscientists – whose interests range from art to zoochromy – and for whom available spectral data have comprised an inverse “tragedy of the commons.”
• "Absorption and Fluorescence Spectra of Organic Compounds from 40 Sources – Archives, Repositories, Databases, and Literature Search Engines,"
  Taniguchi, M.; Lindsey, J. S. Proc. SPIE 2020, 11256, 112560J.
  This paper explains why spectral traces are superior to mere tabulations of spectral data, and where spectra can be found (86 references).
• "PhotochemCAD Spectra Viewer for Web-based Visualization of Absorption and Fluorescence Spectra,"
  Wu, Z.; Kittinger, A.; Norcross, A. E.; Taniguchi, M.; Lindsey, J. S. Proc. SPIE 2021, 11660, 116600I-19.
  Evaluation of 11 spectra viewers and then making PhotochemCAD spectral databases viewable on the web.
• "Digitization of Print-based Absorption and Fluorescence Spectra - Extracting Clarity from Clutter,"
  Taniguchi, M.; Wu, Z.; Sterling, C. D.; Lindsey, J. S. Proc. SPIE 2023, 12398, 1239806.
  Two spreadsheet-based tools for accurate rendition of print spectra into digital form: (i) conversion of xy-coordinate data from uneven to uniform x-axis intervals, and (ii) calibration of the digitized spectrum with appropriate wavelength values.

PhotochemCAD Related Papers

• "Red and Near-Infrared Fluorophores Inspired by Chlorophylls. Consideration of Practical Brightness in Multicolor Flow Cytometry and Biomedical Sciences,"
  Taniguchi, M.; Hu, G.; Liu, R.; Du, H.; Lindsey, J. S. Proc. SPIE 2018, 10508, 1050806.
  In-depth discussion of how spectral parameters alter brightness in practical situations and how brightness can be altered (67 references).
• "Heuristics from Modeling of Spectral Overlap in Förster Resonance Energy Transfer (FRET),"
  Qi, Q.; Taniguchi, M.; Lindsey, J. S. J. Chem. Inf. Model. 2019, 59, 652–667.
  An in-depth exploration of the meaning of the J (spectral overlap) term, with consideration of the values for perfect spectral overlap of diverse chromophores (94 references).
• "Analysis of Wikipedia Pageviews to Identify Popular Chemicals,"
  Cao, Y.; Mehta, H.; Norcross, A. E.; Taniguchi, M.; Lindsey, J. S. Proc. SPIE 2020, 11256, 112560I.
  An illustrative dry run for identifying what compounds should be considered for inclusion in a broadly valuable spectral database (58 references).
• "Comprehensive Review of Photophysical Parameters of Tetraphenylporphyrin (H2TPP) and Zinc Tetraphenylporphyrin (ZnTPP) – Critical Benchmark Molecules in Photochemistry and Photosynthesis,"
  Taniguchi, M.; Lindsey, J. S.; Bocian, D. F.; Holten, D. J. Photochem. Photobiol. C: Photochem. Rev. 2021, 46, 100401.
  Widely used but often mangled – here consensus values are arrived at for the molar absorption coefficient, fluorescence quantum yield, and singlet excited-state lifetime for two central benchmarks in the photosciences (914 references).
• "The Fluorescence Quantum Yield Parameter in Förster Resonance Energy Transfer (FRET) – Meaning, Misperception, and Molecular Design,"
  Lindsey, J. S.; Taniguchi, M.; Bocian, D. F.; Holten, D. Chem. Phys. Rev. 2021, 2, 011302.
  A concise tutorial encompassing 10 examples shows that a donor can exhibit an extremely low (< 0.01) fluorescence quantum yield and still afford nearly quantitative energy transfer to an acceptor (56 references).