A UV/VIS spectra investigation of pH‐sensitive dyes using time‐dependent density functional theory

Preat, Julien; Jacquemin, Denis; Perpète, Éric A.

doi:10.1002/qua.22558

Cited by 13 publications

(22 citation statements)

References 28 publications

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“…One is the "ensemble" based approach, where the many environment-molecule configurations are explicitly sampled and then used as geometries for excitation energy calculations. [19][20][21][22][23] These configurations are often sampled along a molecular dynamics (MD) simulation, and excitation energies are computed with QM/MM multiscale methods. 2,24,25 Given the necessity of an extended sampling, time-dependent density functional theory (TDDFT) is usually the method of choice to compute the excitations, thanks to its good accuracy/efficiency ratio.With the ensemble approach, temperature effects are naturally included in the sampling, as is the anharmonicity of the potential energy surface (PES), which is thoroughly sampled along the classical trajectory.…”

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confidence: 99%

Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review

Loco

Cupellini

2018

Int J of Quantum Chemistry

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In this tutorial review, we focus on a multiscale method to compute the electronic absorption line shape of molecular dyes embedded in a biological environment. To treat the coupling of the electronic excitations with the nuclear degrees of freedom of the system, we use the spectral density (SD) of the exciton-phonon coupling computed from a Born-Oppenheimer molecular dynamics, which takes into account the effect of the biological environment on the dye's nuclear and electronic degrees of freedom. The theoretical basis of the approach is given, as well as a comprehensive description of the computational protocol for the extraction of the energy gap autocorrelation function evaluating the electronic excitation along the classical trajectory. Furthermore a benchmark application from a recently published study is presented as an example of how the derived SD can be used in computational spectroscopy to accurately simulate the absorption lineshape, including both vibronic and temperature effects. K E Y W O R D S absorption lineshape, spectral density, QM/MM molecular dynamics 1 | INTRODUCTIONThe accurate modeling of electronic absorption spectra is a fundamental tool to understand and complement experimental data. Experimental and computational techniques are widely used to identify molecular species and to predict environment effects on the molecular response and photochemistry.From a computational point of view, many different approaches have been exploited in theoretical spectroscopy. [1][2][3][4] The most basic one applied to the simulation of absorption spectra, is based on the computation of the excitation energies of a dye in the ground-state equilibrium geometry, including, if necessary, the solvent effects with an implicit model 5-8 or within an atomistic approach. 9-16 These vertical excitation energies are then compared to the maxima of the corresponding experimental absorption bands. This approach is commonly used, even to benchmark the level of theory for excited-state simulations against experiments. 17 However, comparison of vertical excitation energies can easily become inadequate when accurate estimations of the absorption spectrum are needed. 1 The coupling of electronic transitions to nuclear degrees of freedom (DOFs), for example, generates a characteristic vibronic progression, and can result in an asymmetrical lineshape even when the vibronic structure is hidden in homogeneous and inhomogeneous broadening. 18 Other factors, such as the configurations sampled by the chromophore and the finite lifetime of the excited state, contribute to the spectral shape.For molecules in condensed phase, peaks positions and intensities in the absorption spectra are also affected by the interactions with the inhomogeneous environment, owing to the many different configurations that the solvent adopts around the molecule. The resulting spectra are thus broadened by the many possible solvatochromic shifts.A method able to reproduce both peak positions and line shapes would be of crucial importance to the computatio...

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confidence: 99%

Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review

Loco

Cupellini

2018

Int J of Quantum Chemistry

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“…It is a powerful tool with low computational cost. Jacquemin, Preat, Perpéte and Adamo have published a series of works on various organic dyes concerning the weakness and strength of TDDFT as well as the efficiency, and reliability of DFT functionals for spectroscopic calculations [31][32][33][34][35][36][37][38][39][40]. The calculated transition energies of many organic dyes including cyanines with TDDFT are in good agreement with experiment although some limitations of TDDFT such as extended p systems [41,42], Rydberg states [43,44], double excitations [45][46][47], and charge transfer [48][49][50] …”

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confidence: 63%

A computational study on the excited state properties of a cationic cyanine dye: TTBC

Karaca

Elmaci

2011

Computational and Theoretical Chemistry

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a b s t r a c tThe ground and excited state behaviors of a biologically important mitochondria selective dye, 5,5 0 ,6,6 0 -tetrachloro-1,1 0 ,3,3 0 -tetraethyl-benzimidazolo carbocyanine (TTBC), were investigated in order to give useful information related to the enhancement of its electronic and optical properties. DFT and TDDFT levels of theory with different functionals and basis sets were used. The results obtained by using PBEPBE/6-31+G(d,p)/C-PCM are in good agreement with the experiments. The potential energy surface sections of TTBC were explored and the geometry optimized in the first excited state, S 1 , to analyze the fluorescence spectrum of the dye. There are two distinct minima on the S 1 surface, one located near the ground state geometry and an energetically favorable twisted geometry, having a charge transfer character. The observation of similar ground and excited state dipoles as well as solvent-independent fluorescence and absorption wavelengths reveals that there is no competition between the two minima; the emission is dominantly coming from the more planar configuration.

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“…[43] The molecular ground state geometries of all the investigated compounds (Scheme 2) were optimized using the 6-31G** basis set [44][45] starting from the X-ray geometry of CPT. [46] The calculated residual mean square forces were always less than 1 10 À5 a.u.…”

Section: Computational Methodologymentioning

confidence: 99%

Camptothecin and Thiocamptothecin: the Role of Sulfur in Shifting the Hydrolysis Equilibrium towards the Closed Lactone Form

et al. 2011

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Adverse effects have limited the clinical potential of 20-(S)-camptothecin (CPT) and led to a growing interest in the development of CPT analogues that exhibit less severe drawbacks, while maintaining their therapeutic activity. Recently, a thiopyridone isostere of CPT, 20-(S)-thiocamptothecin (TCPT), was developed that resulted more potent than the parent compound in H460, HT29 and IGROV-1 cell lines. The improved activity of TCPT over CPT might be due to the greater stability of the lactone ring. Here, reversible hydrolysis to the ring-open carboxylate forms of CPT and TCPT was studied by HPLC, both in the presence and absence of human serum albumin (HSA). The amount of TCPT that exists in the lactone form at equilibrium in buffer solution (24 h) was found to be significantly higher than CPT, and the same trend was observed in the presence of HSA. Specifically, HSA caused a shift in the hydrolysis equilibrium of TCPT towards the carboxylate form, but the proportion of lactone form remained higher than that observed for CPT under the same conditions, and also in the presence of a higher excess of the protein. The role of the sulfur atom in the stability of the open and closed lactone derivatives was investigated by theoretical calculations using stabilization energies and comparison between experimental and calculated absorption spectra. Our results suggest that, in aqueous solution, more ionic species (anionic and enolic forms) are present for TCPT. This study provides further insights into the effects of oxygen/sulfur replacement in the CPT pyridone ring.

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A UV/VIS spectra investigation of pH‐sensitive dyes using time‐dependent density functional theory

Cited by 13 publications

References 28 publications

Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review

Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review

A computational study on the excited state properties of a cationic cyanine dye: TTBC

Camptothecin and Thiocamptothecin: the Role of Sulfur in Shifting the Hydrolysis Equilibrium towards the Closed Lactone Form

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