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, 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.

Using transition density models to interpret experimental optical spectra of exciton-coupled cyanine (iCy3)2dimer probes of local DNA conformations at or near functional protein binding sites

“…However, the theory generally fails to predict the exact spectral line shapes, as it overestimates the intensities of the blue-edge shoulder of the 0-0 feature and the vibrationally excited 1-0 and 2-0 features. This is likely due to inaccuracies of the vibronic Hamiltonian used to describe the iCy3 monomer, which assumes a single effective harmonic mode [21]. Nevertheless, the H-F model predicts that the essential features of the absorbance and CD spectra of the +15 (iCy3) 2 dimer-labeled ss-dsDNA construct are consistent with experimental results over a broad range of environmental parameters [13-15].…”

“…Nevertheless, the homogeneous spectral lineshape of the Cy3 monomer in solution is broadened due to rapid electronic dephasing and thermal occupation of low energy vibrational levels. The lowest energy electronic transition from ground state | g ⟩ to excited state | e ⟩ is predominantly coupled to one low-frequency (∼30 cm −1 ) symmetric bending vibration along the trimethine bridge, which couples anharmonically to a cluster of relatively high-frequency modes in the vicinity of ∼1,300 cm -1 [21]. The spectrum of the Cy3 monomer in solution – and that of the iCy3 monomer in the DNA sugar-phosphate backbone – can be simulated using a relatively simple quantum mechanical Hamiltonian, , where the | g ⟩ → | e ⟩ transition (with energy ε eg = ∼18,250 cm -1 ) is coupled to a single ‘effective’ harmonic mode (with energy ℏω 0 = ∼1,100 cm -1 ) [13-15].…”

“…1 A ) [6]. The linear absorbance spectrum of free Cy3 monomer in polar solvent, as well as when it is attached internally as an iCy3 monomer in a nucleic acid framework, is relatively insensitive to the local environment of the chromophore and exhibits a pronounced vibronic progression [13, 20, 21]. By annealing two complementary strands of DNA with opposed iCy3 labeling positions, an exciton-coupled (iCy3) 2 dimer probe (with monomers labeled A and B ) can be formed at a predetermined position within a model DNA fork construct (see Fig.…”

Multiscale QM/MM modelling of catalytic systems with ChemShell

“…149 QM/MM simulations of biomolecules are not limited to proteins, and several recent ChemShell studies have focussed on DNA, RNA, and their components. [150][151][152][153][154][155][156][157] Biocatalysis applications involving DNA repair enzymes are an active topic in this area. [158][159][160][161] Naydenova et al used ChemShell to investigate the catalytic mechanism of uracil DNA glycosylase, which initiates excision of uracil DNA lesions.…”

Unravelling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 Dimer

“…Since this model usually accounts for one effective vibrational mode, contributions from other modes, especially low-frequency modes, are not taken into account. 34 The Franck−Condon (FC) method 35−40 is widely used to simulate the spectra of molecules, especially those with strong vibrational contributions, as it uses the vibrational wave functions of the ground and excited states to calculate FC overlaps. 40−43 The FC approximation accounts for the dipoleallowed transitions while it is necessary to use the Franck− Condon/Herzberg−Teller approach 44,45 to account for the contributions from weak transitions.…”