Polarizable dielectric model of solvation with inclusion of charge penetration effects

Cossi, Maurizio; Rega, Nadia; Scalmani, Giovanni; Barone, Vincenzo

doi:10.1063/1.1354187

Cited by 336 publications

(219 citation statements)

References 39 publications

Supporting

Mentioning

213

Contrasting

Unclassified

Order By: Relevance

“…[41][42][43][44][45][46] Calculations on the n = π* transition energies of diazines performed by Mennucci 42 and Cossi and Barone 44 have shown results which are in very good agreement with the experiments. However, calculations with TDDFT are still not straightforward in the optimization of gemetries on the excited state surfaces.…”

Section: Absorption Spectrasupporting

confidence: 72%

Experimental and DFT Studies: Novel Structural Modifications Greatly Enhance the Solvent Sensitivity of Live Cell Imaging Dyes

et al. 2007

View full text Add to dashboard Cite

Structural modifications of previously reported merocyanine dyes (J. Am. Chem. Soc. 2003, 125, 4132-4145) were found to greatly enhance the solvent dependence of their absorbance and fluorescence emission maxima. Density functional theory (DFT) calculations have been performed to understand the differences in optical properties between the new and previously synthesized dyes. Absorption and emission energies were calculated for several new dyes using DFT vertical self-consistent reaction field methods (VSCRF). Geometries of ground and excited states were optimized with a Conductor-like screening model (COSMO) and self-consistent-field (SCF) methods. The new dyes have enhanced zwitterionic character in the ground state, and much lower polarity in the excited state, as shown by the DFT-VSCRF calculations. Consistently, the position of the absorption bands are strongly blue-shifted in more polar solvent (methanol compared to benzene) as predicted by the DFT spectral calculations. Inclusion of explicit H-bonding solvent molecules within the quantum model further enhances the predicted shifts, and is consistent with the observed spectral broadening. Smaller, but significant spectral shifts in polar versus nonpolar solvent are predicted and observed for emission bands. The new dyes show large fluorescence quantum yields in polar hydrogen bonding solvents; qualitatively, the longest bonds along the conjugated chain at the excited S 1 state minimum are shorter in the more polar solvent, inhibiting photoisomerization. The loss of photostability of the dyes is a consequence of the reaction with and electron transfer to singlet oxygen, starting oxidative dye cleavage. The calculated vertical ionization potentials of three dyes I-SO, AI-SO(4), and AI-BA(4) in benzene and methanol are consistent with their relative photobleaching rates; the charge distributions along the conjugated chains for the three dyes are similarly predictive of higher reaction rates for AI-SO(4) and AI-* Corresponding authors. khahn@med.unc.edu, lou@scripps.edu. 2 These authors contributed equally to this work. Supporting InformationThe Cartesian coordinates of the S 0 and S 1 state COSMO optimized dye structures, and more detailed atomic ESP charges of the S 0 state dye molecules in MeOH are given in the Supporting Information. BA(4) than for I-SO. Time dependent DFT (TDDFT) calculations were also performed on AI-BA(4); these were less accurate than the VSCRF method in predicting the absorption energy shift from benzene (C 6 H 6 ) to methanol (MeOH). NIH Public Access

show abstract

Section: Absorption Spectrasupporting

confidence: 72%

Experimental and DFT Studies: Novel Structural Modifications Greatly Enhance the Solvent Sensitivity of Live Cell Imaging Dyes

et al. 2007

View full text Add to dashboard Cite

show abstract

“…Aqueous solvation was described with the conductor-like polarizaable continuum model (C-PCM) technique [27,28], which describes the solvent as a polarizable dielectric continuum. The solute, which occupies a cavity defined as the envelope of spheres centered at non-hydrogen atoms, polarizes the dielectric medium and creates an electric field which, in turn, disturbs the solute.…”

Section: Methodsmentioning

confidence: 99%

Bidimensional electronic spectroscopy on indole in gas phase and in water from first principles

Nenov

Rivalta

Mukamel

et al. 2014

Computational and Theoretical Chemistry

View full text Add to dashboard Cite

a b s t r a c tThe electronic transitions of indole, the aromatic UV chromophore of the amino acid tryptophan, are characterized by using state-of-the-art multiconfigurational methods in gas-phase and aqueous solution, revealing the electronic spectrum up to 10 eV. Bidimensional near-ultraviolet (2D-NUV) electronic spectra of indole are simulated using the sum-over-states approach, based on ab initio calculations, accounting for different experimental set-ups, including rephasing ðKI ¼ Àk 1 þ k 2 þ k 3 ), quasi-absorptive (PP) and double quantum coherence ðKIII ¼ k 1 þ k 2 À k 3 ) signals, and both one-color (2D-NUV) and two-colors (2D-NUV/Vis) regimes. In order to obtain accurate energies of high lying excited states and reliable 2DES spectra, extravalence virtual orbitals have been included using the restricted active space technique. The 2D-NUV spectrum of indole shows off-diagonal signals due to the correlation of the GS ? L b and GS ? L a transitions, an indole ''fingerprint'' in the NUV region that differentiate it from other aromatic chromophores in proteins. Further indole-specific transitions are resolved in the whole Vis-NUV range. A background-free region bellow the ionization potential, which shows no absorption signals in the monomer, can be used to resolve charge transfer states in coupled chromophore aggregates with a two-color 2D-NUV/Vis experimental set-up. Fundamental information for design of the 2DES experiments of indole is provided, including possible experimental pulse configurations that improve spectral resolution, revealing anharmonicities and selecting transitions. The proposed 2DES experiments could provide unprecedented level of detail for tracking indole electronic transitions in proteins, laying the groundwork for the use of nonlinear ultrafast optical spectroscopy for the study of protein structure and dynamics in solution.

show abstract

“…Next, their energies were recalculated in the 6-31?G(3df,2p) basis. Solvent effects were modeled by performing analogous calculation with PCM model [63,64] in a series of solvents with dielectric constants (e) varying from 1.88 (n-hexane) to 78.36 (water). All the calculations were performed with Gaussian09 program [65].…”

Section: Computational Detailsmentioning

confidence: 99%

Nucleophilic properties of purine bases: inherent reactivity versus reaction conditions

Stachowicz‐Kuśnierz

Korchowiec

2015

Struct Chem

View full text Add to dashboard Cite

In the present study, nucleophilic properties of adenine and guanine are examined by means of density functional theory. H? is used as a model electrophile. Two modes of H ? attack on the bases are considered: on the neutral molecule and on the anion. Solvent effects are modeled by means of polarizable continuum model. Regioselectivity of attack is studied by analyzing two contributions. The first one is the energetic ordering of the tautomers. The second is the relative inherent reactivity of nucleophilic sites in the bases. Atomic softnesses calculated by means of charge sensitivity analysis are employed for this purpose. The most reactive sites in various tautomers are identified on the ground of Li-Evans model. For adenine, it is demonstrated that both in basic and in neutral pH N7 atom possesses the most nucleophilic character. In polar solvents, N7 substitution is also most favored energetically. In basic pH and nonpolar solvents as well as in the gas phase, N9 substitution is slightly more probable. For guanine, a mixture of N7-and N9-substituted products can be expected in basic pH. In neutral pH, inherent reactivity and energy trends are opposite to each other; therefore, the substitution does not occur. Experimentally observed products of reactions with various electrophiles and in various conditions confirm the results obtained in this study.

show abstract

Polarizable dielectric model of solvation with inclusion of charge penetration effects

Cited by 336 publications

References 39 publications

Experimental and DFT Studies: Novel Structural Modifications Greatly Enhance the Solvent Sensitivity of Live Cell Imaging Dyes

Experimental and DFT Studies: Novel Structural Modifications Greatly Enhance the Solvent Sensitivity of Live Cell Imaging Dyes

Bidimensional electronic spectroscopy on indole in gas phase and in water from first principles

Nucleophilic properties of purine bases: inherent reactivity versus reaction conditions

Contact Info

Product

Resources

About