PyFREC 2.0: Software for excitation energy transfer modeling.
BODIPY
Exciton
FRET
Förster
bioorthogonal chemistry
Journal
Journal of computational chemistry
ISSN: 1096-987X
Titre abrégé: J Comput Chem
Pays: United States
ID NLM: 9878362
Informations de publication
Date de publication:
15 07 2022
15 07 2022
Historique:
revised:
21
04
2022
received:
08
03
2022
accepted:
28
04
2022
pubmed:
25
5
2022
medline:
15
6
2022
entrez:
24
5
2022
Statut:
ppublish
Résumé
Excitation energy transfer is a ubiquitous process of fundamental importance for understanding natural phenomena, such as photosynthesis, as well as advancing technologies ranging from photovoltaics to development of photosensitizers and fluorescent probes used to explore molecular interactions inside living cells. The current version of PyFREC 2.0 is an advancement of the previously reported software (D. Kosenkov, J. Comput. Chem. 2016, 37, 1847-1854). The current update is primarily focused on providing a computational tool based on Förster theory for bridging a gap between theoretically calculated molecular properties (e.g., electronic couplings, orientation factors, etc.) and experimentally measured emission and absorption spectra of molecules. The software is aimed to facilitate deeper understanding of photochemical mechanisms of fluorescence resonance energy transfer (FRET) in donor-acceptor pairs. Specific updates of the software include implementations of overlap integrals between donor emission and acceptor absorption spectra of FRET pairs, estimation of Strickler-Berg fluorescence lifetimes, calculation of Förster radii, energy transfer efficiency, and radiation zones that, in particular, determine applicability of the Förster theory.
Substances chimiques
Fluorescent Dyes
0
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1320-1328Subventions
Organisme : American Chemical Society Petroleum Research Fund
ID : #58019-UR6
Organisme : National Science Foundation
ID : CHE-1955649 RUI-D3SC
Informations de copyright
© 2022 Wiley Periodicals LLC.
Références
D. Kosenkov, J. Comput. Chem. 2016, 37, 1847.
Y. Kholod, M. DeFilippo, B. Reed, D. Valdez, G. Gillan, D. Kosenkov, J. Comput. Chem. 2018, 39, 438.
Y. K. Kosenkov, D. Kosenkov, J. Chem. Phys. 2019, 151, 144101.
G. Linden, L. Zhang, F. Pieck, U. Linne, D. Kosenkov, R. Tonner, O. Vazquez, Angew. Chem. Int. Ed. 2019, 58, 12868.
Q. Qi, M. Taniguchi, J. S. Lindsey, J. Chem. Inf. Model. 2019, 59, 652.
B. W. van der Meer, in FRET−Förster Resonance Energy Transfer (FRET)−From Theory to Applications (Eds: I. Medintz, N. Hildebrandt), Wiley VCH, Weinheim 2014; Chapter 3, p. 23.
S. J. Strickler, R. A. Berg, J. Chem. Phys. 1962, 37, 814.
M. Taniguchi, H. Du, J. S. Lindsey, Photochem. Photobiol. 2018, 94, 277.
M. Taniguchi, J. S. Lindsey, Photochem. Photobiol. 2018, 94, 290.
J. C. T. Carlson, L. G. Meimetis, S. A. Hilderbrand, R. Weissleder, Angew. Chem. Int. Ed. 2013, 52, 6917.
F. Schweighöfer, L. Dworak, C. A. Hammer, H. Gustmann, M. Zastrow, K. Rück-Braun, J. Wachtveitl, Sci. Rep. 2016, 6, 28638.
T. Förster, Naturwissenschaften 1946, 33, 166.
T. Förster, Faraday Discuss. 1959, 27, 7.
T. Förster, Delocalized Excitation and Excitation Transfer, Florida State University, Tallahassee, FL 1965.
C. Curutchet, B. Mennucci, Chem. Rev. 2017, 117, 294.
V. May, O. Kühn, Charge and Energy Transfer Dynamics in Molecular Systems, 3rd ed., Wiley VCH, Weinheim 2011.
T. Renger, Photosynth. Res. 2009, 102, 471.
C. Curutchet, G. D. Scholes, B. Mennucci, R. Cammi, J. Phys. Chem. B 2007, 111, 13253.
B. Cohen, C. E. Crespo-Hernandez, B. Kohler, Faraday Discuss. 2004, 127, 137.
B. W. van der Meer, D. M. van der Meer, S. S. Vogel, FRET−Förster Resonance Energy Transfer (FRET)−From Theory to Applications. in (Eds: I. Medintz, N. Hildebrandt), Wiley VCH, Weinheim 2014; Chapter 4, p. 63.
J. S. Lindsey, M. Taniguchi, D. F. Bocian, D. Holten, Chem. Phys. Rev. 2021, 2, 011302.
The Python Standard Library Accessed March 2, 2022. https://docs.python.org/2.7/library/
NumPy Accessed March 2, 2022. https://numpy.org/
SciPy Accessed March 2, 2022. https://www.scipy.org/
D. Magde, R. Wong, P. G. Seybold, Photochem. Photobiol. 2002, 75, 327.
A. S. Kristoffersen, S. R. Erga, B. Hamre, Ø. Frette, J. Fluoresc. 2014, 24, 1015.
N. Boens, W. Qin, N. Basarić, J. Hofkens, M. Ameloot, J. Pouget, J.-P. Lefèvre, B. Valeur, E. Gratton, M. V. Ven, N. D. Silva, Y. Engelborghs, K. Willaert, A. Sillen, G. Rumbles, D. Phillips, A. J. W. G. Visser, A. van Hoek, J. R. Lakowicz, H. Malak, I. Gryczynski, A. G. Szabo, D. T. Krajcarski, N. Tamai, A. Miura, Anal. Chem. 2007, 79, 2137.
Y. Kubota, in Progress in the Science of Functional Dyes (Eds: Y. Ooyama, S. Yagi), Springer, Singapore 2021, p. 119.
R. M. Hochstrasser, D. S. King, A. B. Smith III, J. Am. Chem. Soc. 1977, 99, 3923.
D. Cao, L. Zhu, Z. Liu, W. Lin, J Photochem Photobiol C: Photochem Rev 2020, 44, 100371.