Binding of cationic conjugated polymers to DNA: atomistic simulations of adducts involving the Dickerson's dodecamer.

We here describe the investigation at the atomistic level of the structure, stability, and dynamics of several complexes resulting from the interaction of oxidized poly(3,4-ethylenedioxythiophene) with the well-known Dickerson's dodecamer sequence. Four specific arrangements have been selected as referential structures for molecular dynamics simulations, and the resulting independent trajectories tend to converge in two distinguishable models with the strongest interactions. The first one presents a coiled DNA strand enveloping the oligomer chain, whereas in the second model, the conducting polymer chain and the disorganized DNA strand are facing side-by-side. Analysis of the intermolecular interactions indicates that the electrostatic interactions involving the negatively charged DNA phosphates and the positively charged units of the oligomer are much more frequent in the first model. In addition, aside from these electrostatic interactions, specific O · · · H and S · · · H hydrogen bonds, π-π stacking, and N-H · · · π interactions have been detected. Among all of these four specific interactions, we show that the π-π stacking is the most abundant and shows the best stability, whereas O · · · H hydrogen bonds are also frequent with long lifetimes. At the end, we have to underline that these specific interactions are predominant for the thymine and the guanine, which is in perfect agreement with previous experimental observations.

Specific interactions in complexes formed by DNA and conducting polymer building blocks: guanine and 3,4-(ethylenedioxy)thiophene.

In the present paper we report direct experimental evidence of the existence of hydrogen bonds between poly(3,4-(ethylenedioxy)thiophene) (PEDOT) and DNA complexes and bring deeper knowledge about how such interactions can take place in such species. To this end, we used both experimental and theoretical methodologies to examine the interactions between the building blocks composing these two macromolecules. The specific interaction natures between 3,4-(ethylenedioxy)thiophene (EDOT, E) and doubly protonated guanine (GH(2)(2+)) monomers have been investigated using UV-vis spectroscopy. Quantum mechanical calculations in the density functional theory (DFT) and time-dependent density functional theory (TDDFT) frameworks have been used to identify the structures of the possible complexes. These differ in the interaction pattern, and it was possible to interpret the absorption spectra in terms of intermolecular interactions. Our results allow verification of the previous hypothesis about the formation of specific N-H···O interactions between G-containing nucleotide sequences and PEDOT. Clearly, DFT calculations indicate that E:GH(2)(2+) complexes are stabilized by N-H···O interactions, which involve an E oxygen and the -NH and -NH(2) moieties of GH(2)(2+). Furthermore, TDDFT calculations are able to reproduce the absorption spectra (both energy gaps and relative oscillator strength magnitudes) of E and GH(2)(2+), as well as the complex.

Parameterization of the torsional potential for calix[4]arene-substituted poly(thiophene)s.

Three different strategies have been followed to develop the torsional force-field parameters of the inter-ring dihedral angles for calix[4]arene-substituted poly(thiophene)s, a family of highly sensitive ion receptors. These procedures, which are based on the rotational profiles calculated using quantum mechanical methods, differ in the complexity of the model compounds and the processing applied to the quantum mechanical energies before the fitting. The performance of the three sets of developed parameters, which are essentially compatible with the General Amber Force Field, has been evaluated by computing the potential of mean forces for the inter-ring rotation of 2,2'-bithiophene, and its substituted analog bearing a calix[4]arene group in different environments. Finally, the ability of the new sets of torsional parameters to describe a calix[4]arene-substituted poly(thiophene) in tetrahydrofuran solution has been checked using Molecular Dynamics simulations. Specifically, the molecular shape, the polymer conformation, and the effects of the Na(+) ions trapped in the cavity of the receptor have been examined. Although the potential derived from unsubstituted 2,2'-bithiophene is able to reproduce the experimental free energies of the minima, the overall results indicate that the parameters derived from the analog bearing a calix[4]arene group provide the best description of the systems under study. This should be attributed to the strong constraints found in complex substituted poly(thiophene)s, which require parameterization strategies able to capture all the interactions and phenomena involved in their inter-ring rotations.

Sensing abilities of crown ether functionalized polythiophenes.

Tuning sensing abilities! The affinity of three different [15]crown-5 ether functionalized polythiophenes for alkali ions has been explored (see figure). Ab initio and DFT quantum mechanical calculations show that the binding energy between neutral conducting polymers and metallic ions, which interact attractively, decreases as the size of the ion increases. Oxidation of these polythiophene derivatives significantly reduces their affinity towards alkali ions, becoming low or even nonexistent.This work reports a theoretical study of the affinity of three different [15]crown-5 ether functionalized polythiophenes for alkali ions. Ab initio and DFT quantum mechanical calculations have evidenced that the binding energy between neutral conducting polymers and metallic ions, which interact attractively, decreases as the size of the ion increases. However, the preferences of these polythiophene derivatives have been found to be influenced by the entropic contribution, which favors binding with Na(+) in preference to Li(+). Molecular dynamics simulations have shown that this behavior can be accounted for on the basis of the large fluctuations that Li(+) undergoes when it is contained in the cavity of the [15]crown-5 ether macrocycle. In contrast, the fluctuations detected for complexes with Na(+) and K(+) were particularly low, even though only the former ion fits into the center of the macrocyclic cavity. Oxidation of these polythiophene derivatives produces a drastic change in their sensing abilities, their affinities towards alkali ions becoming low or even nonexistent. Moreover, calculations indicate that the presence of unsubstituted thiophene rings directly attached to a functionalized thiophene modulates the strength of the binding in the oxidized state by reducing the repulsive interaction between the metallic cation and the pi-conjugated system. On the other hand, the influence of alkali ions on the electronic properties, in particular, on the ionization potentials and the lowest pi-pi* transitions, of both the neutral and oxidized polythiophenes is discussed.

Sensing mechanism of calix[4]arene-substituted poly(thiophene) ion receptor: effects of the selectivity on the molecular rigidity.

The sensing response of poly(thiophene)s functionalized with calix[4]arene to Li+, Na+, and K+ has been investigated at the microscopic level using quantum mechanical calculations and molecular dynamics simulations. Results indicate that Na+ interacts electrostatically with the oxygen-rich site of the receptor reducing the conformational flexibility of the polymer backbone. In contrast, Li+ and K+ interact with the tert-butyl groups of the macrocycle enhancing such conformational flexibility. These features are consistent with available experimental data explaining the selectivity of this material for Na+ over Li+ and K+.

Ab initio tools for the accurate prediction of the visible spectra of anthraquinones.

The UV/vis absorption spectra of 101 anthraquinones solvated in two protic solvents (methanol and ethanol) has been theoretically predicted using the time-dependent density functional theory (TD-DFT) for the excited state calculations and the polarizable continuum model (PCM) for evaluating bulk solvent effects. Two functionals (B3LYP and PBE0) have been used and they provide similar mean absolute deviations (approximately 0.09 eV) but mean signed errors presenting opposite signs. The errors can be minimized by using simple or multiple linear regression, the latter combining the results of both functionals to reach an optimal estimation of the lambda(max) (mean absolute error 0.06 eV). Specific fittings for the two media have been performed and it turned out that our approach is even more efficient for anthraquinones solvated in ethanol.

Ab initio studies of the lambda(max) of naphthoquinones dyes.

Using a state-of-the-art time-dependent density functional (TD-DFT) approach that includes the explicit consideration of bulk medium effects on both the ground-state geometry and the electronic spectrum, we have determined the lambda(max) of 86 naphthoquinones (NQ) dyes in various solvents for a total of 151 cases. In most cases, TD-DFT provides the correct ordering of transitions for substituted NQ dyes. Comparisons with experimental values lead to a mean signed error of -7.2 nm (0.039 eV) and a mean absolute error of 20.1 nm (0.113 eV). It turns out that the average errors are smaller for the hydroxy and methoxy derivatives, than for amino substituted dyes. It is also demonstrated that the statistical treatment of the data does not significantly improve the agreement between the experimental and the theoretical values. We also discuss average basis set effects and solvatochromism.

Response of crown ether functionalized polythiophenes to alkaline ions.

The sensing response of 15-crown-5-ether functionalized polythiophene to Li+, Na+, and K+ has been investigated at the atomistic level using molecular dynamics simulations. The stability associated with all the identified binding sites has been corroborated by quantum mechanical calculations. Although the cavity of the macrocycle is not the most visited binding site, such receptor is responsible of the selective sensing response of this polythiophene derivative. PF6(-) counterions reduce the mobility of the alkaline cations, which do not occupy the crown ether cavity of consecutive repeating units due to electrostatic repulsions. Furthermore, the relative entropy for the "free state → bound state" has been estimated using a procedure based on the covariance matrix atom-positional fluctuations. Evaluation of the entropic contributions allow us to complete the thermodynamics scenario of binding process, which was recently initiated by calculating the enthalpies at quantum mechanical level [ Chem. Eur. J. 2009, 15, 4676]. Results indicate an entropycally driven binding preference.

Design of new triphenylamine-sensitized solar cells: a theoretical approach.

This work reports a theoretical study of the photovoltaic properties of a series of original conjugated metal-free organic dyes containing the triphenylamine (TPA) moiety. These compounds have recently been develop for dye sensitized solar cells (DSSCs). Our (TD)DFT-based procedure made it possible to get insights into the geometrical and electronic structures of the dyes and to unravel the structural modifications optimizing the properties of TPA-based DSSCs. In particular, we aimed at improving the electron injection process as well as the light harvesting efficiency of the dyes. On the other hand, molecular dynamic (MD) investigations of the kinetics of the regeneration step have been performed for both "classical" (CHCl(3)/I(3)(-)/I(-)/Li(+)) and iodide imidazolium-based solvent-free electrolytes (DMII(+)/I(-)). The MD simulations helped to understand the regeneration mechanism for the solvent-free electrolyte: it combines the DMII(+)/DMII(0) couple to the I(3)(-)/I(-) redox system which acts as a "mediator".

Theoretical Investigation of the Geometries and UV-vis Spectra of Poly(l-glutamic acid) Featuring a Photochromic Azobenzene Side Chain.

The geometries and UV-vis spectra of azobenzene dyes grafted as a side chain on poly(l-glutamic acid) have been investigated using a combination of quantum mechanics/molecular mechanics (QM/MM) and time-dependent density functional theory (TD-DFT) methods at the TD-PBE0/6-311+G(d,p)//B3LYP/6-311G(d,p):Amber ff99 level of theory. The influence of the secondary structure of the polypeptide on the electronic properties of both the trans and cis conformations of azobenzene dyes has been studied. It turns out that the grafted dyes exhibit a red-shift of the π → π* absorption energies mainly due to the auxochromic shift induced by the peptidic group used to link the chromophoric unit to the polypeptide and that specific interactions between the glutamic side chain and the azobenzene moiety lead to a large blue-shift of the n → π* transition.

Substitution and chemical environment effects on the absorption spectrum of indigo.

The UV/visible spectra of a series of indigo derivatives have been evaluated by using ab initio methods. The combination of the Polarizable continuum model for estimating bulk solvent effects with the TD-B3LYP6-311 + G(2d,p)B3LYP6-311G(d,p) level of approximation, leads to an accurate description of the wavelength of maximum absorption of indigoids compounds. Using this procedure, we have assessed the effects of both the surroundings (solvent and solid state) and the substitution pattern. For the latter, we obtained a mean absolute deviation of only 7 nm (0.02 eV) compared to experiment, for a set of 86 molecules/solvents.

An ab initio study of the absorption spectra of indirubin, isoindigo, and related derivatives.

The UV/visible spectra of a series of indirubin, isoindigo, and other indigo/thioindigo related dyes have been evaluated in various solvent environments by using the time-dependent density functional theory in conjunction with the polarizable continuum model. Even for molecules of the same family, significant differences in the excitation processes have been noted. Two hybrid functionals have been selected: B3LYP and PBE0. For a set of the 50 selected molecular cases, both functionals provide accurate lambda(max), with mean absolute deviations limited to 0.1 eV. Actually, isoindigo is the main challenging series, with systematically underestimated excitation energies, due to the different nature of the excitation process. In most cases, we found that PBE0 is more efficient in reproducing the experimental values than B3LYP for sulfur-containing dyes not featuring internal hydrogen bonds, the reverse assertion being also true. In addition, the spectra of a series of unknown dyes have been predicted.

TD-DFT investigation of the UV spectra of pyranone derivatives.

The UV absorption spectra of more than 80 substituted coumarins and chromones have been investigated with the PCM-TD-DFT theoretical scheme using three hybrid functionals (O3LYP, B3LYP, and PBE0) and taking into account methanol or ethanol solvation effects. For most of the studied derivatives, there are at least two allowed excited states presenting a strong oscillator strength in the UV region. The first allowed excitation is associated to a HOMO-LUMO transition whereas the second corresponds to a transition from the HOMO-1 to the LUMO. Both involve a charge transfer from the benzenic cycle to the pyranone moiety. Statistically treating the PBE0 results allows a prediction of the lambda(max) with small standard deviations: in methanol, 6 nm (0.07 eV) for the first excitation (lambda(max)(1)) and 5 nm (0.08 eV) for the second one (lambda(max)(2)), whereas in ethanol 6 nm (0.08 eV) for (lambda(max)(1)) and 6 nm (0.13 eV) for (lambda(max)(2)).

Thioindigo dyes: highly accurate visible spectra with TD-DFT.

The structure and visible spectra of a large panel of thioindigo dyes and derivatives have been evaluated using a TD-PBE0/6-311+G(2d,p)//PBE0/6-311G(d,p) approach explicitly taking bulk solvent effects into account by means of the polarizable continuum model. The influence of the solvent characteristics, the trans-cis isomerization, and the chemical substitution on the benzene rings have been investigated. In addition, hemi-thioindigo dyes, thiazine-indigo, chromophore-like molecules, and selenoindigo have been considered. Though the relative oscillator strengths of the two allowed visible transitions in the nonplanar cis isomers are not always correctly reproduced by theory, the agreement between theoretical and experimental results is far above expectations. For the 170 cases studied, we obtained a mean unsigned error on the predicted lambda(max) limited to 6.9 nm or 0.03 eV, with only 6 (4) cases for which the difference exceeds 20 nm (0.10 eV). These errors are 1 order of magnitude smaller than what has previously been reported for indigoids. A linear correlation between the central double bond length and the lambda(max) has been established, while the bond length and vibrational frequency of the carbonyl groups do not correlate with the thioindigo color. The higher excitation energies of the cis conformers, compared to the trans structures, result from a less stabilized LUMO in the former case. Indeed, for cis thioindigo, the two electron-rich (in the excited state) carbonyl units lie close to each other.

Toward a Theoretical Quantitative Estimation of the λmax of Anthraquinones-Based Dyes.

We have computed the absorption spectra of a large series of anthraquinone dyes by using the time-dependent density functional theory (TD-DFT) for the excited-state calculations and the polarizable continuum model (PCM) for evaluating bulk solvent effects. On one hand, we compare the results obtained with the B3LYP and the PBE0 hybrid functionals, combined with different atomic basis sets. On the other hand, using multiple linear regression, we take advantage of the λmax predicted by these two functionals in order to reach the best agreement between theoretical estimates and experimental measurements. It turns out that 1. PBE0 provides more accurate results than B3LYP; in addition the average errors provided by the former are less basis set dependent. 2. Multiple linear regression provides excited state spectra in better agreement with experiment than any simple linear fit that could be performed. 3. Using our best fitting procedure, we obtained a mean absolute error of 6 nm for a set of 66 anthraquinones, with no deviations exceeding 25 nm. The related standard deviation, useful for predictions, is only 8 nm, i.e.,[Formula: see text] =[Formula: see text] ± 8 nm (or ±0.05 eV) for unknown anthraquinone compounds.

Theoretical investigation of substituted anthraquinone dyes.

We have investigated with computational chemistry techniques the visible spectra of substituted anthraquinones. A wide panel of theoretical methods has been used, with various basis sets and density functional theory (DFT) functionals, in order to assess a level of theory that would lead to converged excitation energies. It turns out that the hybrid Becke-Lee-Yang-Parr and Perdew-Burke-Erzenrhof functionals with the 6-31G (d,p) atomic basis set provide reliable lambda(max) when the solvent effects are included in the model. Combining the results of both DFT schemes allows the prediction of lambda(max) with a standard deviation limited to 13 nm.