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Title: Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3

Abstract

Accurate modeling of optical spectra requires careful treatment of the molecular structures and vibronic, environmental, and thermal contributions. The accuracy of the computational methods used to simulate absorption spectra is limited by their ability to account for all the factors that affect the spectral shapes and energetics. The ensemble-based approaches are widely used to model the absorption spectra of molecules in the condensed-phase, and their performance is system dependent. The Franck–Condon approach is suitable for simulating high resolution spectra of rigid systems, and its accuracy is limited mainly by the harmonic approximation. In this work, the absorption spectrum of the widely used cyanine Cy3 is simulated using the ensemble approach via classical and quantum sampling, as well as, the Franck–Condon approach. The factors limiting the ensemble approaches, including the sampling and force field effects, are tested, while the vertical and adiabatic harmonic approximations of the Franck–Condon approach are also systematically examined. Our results show that all the vertical methods, including the ensemble approach, are not suitable to model the absorption spectrum of Cy3, and recommend the adiabatic methods as suitable approaches for the modeling of spectra with strong vibronic contributions. We find that the thermal effects, the low frequency modes,more » and the simultaneous vibrational excitations have prominent contributions to the Cy3 spectrum. The inclusion of the solvent stabilizes the energetics significantly, while its negligible effect on the spectral shapes aligns well with the experimental observations.« less

Authors:
ORCiD logo; ; ORCiD logo
Publication Date:
Research Org.:
Princeton Univ., NJ (United States); Temple Univ., Philadelphia, PA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); National Science Foundation (NSF); US Army Research Laboratory (USARL)
OSTI Identifier:
1873912
Alternate Identifier(s):
OSTI ID: 1904336; OSTI ID: 1994528
Grant/Contract Number:  
SC0019394; GM-15792; 1625061; W911NF-16-2-0189; ACI-1548562
Resource Type:
Published Article
Journal Name:
Molecules
Additional Journal Information:
Journal Name: Molecules Journal Volume: 27 Journal Issue: 13; Journal ID: ISSN 1420-3049
Publisher:
MDPI AG
Country of Publication:
Switzerland
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; cyanines; Cy3; optical spectra; ensemble approaches; QM/MM; molecular dynamics; Wigner distribution; Franck–Condon; FC; ab initio; adiabatic Hessian FC; 74 ATOMIC AND MOLECULAR PHYSICS

Citation Formats

Sorour, Mohammed I., Marcus, Andrew H., and Matsika, Spiridoula. Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3. Switzerland: N. p., 2022. Web. doi:10.3390/molecules27134062.
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Sorour, Mohammed I., Marcus, Andrew H., & Matsika, Spiridoula. Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3. Switzerland. https://doi.org/10.3390/molecules27134062
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Sorour, Mohammed I., Marcus, Andrew H., and Matsika, Spiridoula. Fri . "Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3". Switzerland. https://doi.org/10.3390/molecules27134062.
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@article{osti_1873912,
title = {Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3},
author = {Sorour, Mohammed I. and Marcus, Andrew H. and Matsika, Spiridoula},
abstractNote = {Accurate modeling of optical spectra requires careful treatment of the molecular structures and vibronic, environmental, and thermal contributions. The accuracy of the computational methods used to simulate absorption spectra is limited by their ability to account for all the factors that affect the spectral shapes and energetics. The ensemble-based approaches are widely used to model the absorption spectra of molecules in the condensed-phase, and their performance is system dependent. The Franck–Condon approach is suitable for simulating high resolution spectra of rigid systems, and its accuracy is limited mainly by the harmonic approximation. In this work, the absorption spectrum of the widely used cyanine Cy3 is simulated using the ensemble approach via classical and quantum sampling, as well as, the Franck–Condon approach. The factors limiting the ensemble approaches, including the sampling and force field effects, are tested, while the vertical and adiabatic harmonic approximations of the Franck–Condon approach are also systematically examined. Our results show that all the vertical methods, including the ensemble approach, are not suitable to model the absorption spectrum of Cy3, and recommend the adiabatic methods as suitable approaches for the modeling of spectra with strong vibronic contributions. We find that the thermal effects, the low frequency modes, and the simultaneous vibrational excitations have prominent contributions to the Cy3 spectrum. The inclusion of the solvent stabilizes the energetics significantly, while its negligible effect on the spectral shapes aligns well with the experimental observations.},
doi = {10.3390/molecules27134062},
journal = {Molecules},
number = 13,
volume = 27,
place = {Switzerland},
year = {Fri Jun 24 00:00:00 EDT 2022},
month = {Fri Jun 24 00:00:00 EDT 2022}
}
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