Biomedical subjects

Denis Jacquemin

Publications and source records attributed to Denis Jacquemin.

16 recordsLinked to original sources

PubMed2006

Time-dependent density functional theory investigation of the absorption, fluorescence, and phosphorescence spectra of solvated coumarins.

Using time-dependent density functional theory (TD-DFT) and the polarizable continuum model, we have computed the electronic transitions of a large panel of coumarin dyes in their enol, keto, cationic, and anionic forms. Several processes have been studied: absorption, fluorescence, 0-0 phosphorescence, and triplet-triplet excitations. For each process, detailed comparison with experimental data has been carried out. Using the PBE06-31+G(d) scheme, it turns out that for a given electronic transition the experimental shifts resulting from the substitution of the coumarin core are nicely reproduced. Indeed, once a simple statistical correction is applied, the mean absolute errors on the absorption and fluorescence wavelengths are limited to 8 nm (0.09 eV) and 9 nm (0.07 eV), respectively. A valuable correlation between the experimental and theoretical phosphorescence auxochromic displacements has also been unravelled. The differences between the wavelengths of the various electronic processes of a given dye tend to be fairly predicted, especially for the fluorescence-phosphoresence shifts that are strongly overestimated by TD-DFT.

Journal Article↗

PubMed2006

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.

Anthraquinones↗

PubMed2006

Ab initio investigation of the n --> pi* transitions in thiocarbonyl dyes.

The n --> pi* transitions in more than 100 thiocarbonyl dyes have been calculated with an ab initio procedure relying on the combination of time-dependent density functional theory (TD-DFT) for evaluating excited states and the polarizable continuum model (PCM) for modeling the bulk solvent effects on both the geometrical and electronic structures. Two hybrid functionals (B3LYP and PBE0) and several basis sets, some including f polarization functions, have been used. B3LYP provides the most accurate raw estimates, but once simple linear regression is performed, both functionals give similar results with a small advantage for PBE0. By use of the latter, the mean absolute deviation with respect to experiment is limited to 0.06 eV whereas less than 20% of the estimates differ from absorption data by more than 0.10 eV. To assess the validity limits of our model, compounds containing multiple C=S chromophores have also been considered.

Journal Article↗

PubMed2006

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)).

Journal Article↗

PubMed2006

Excitation spectra of nitro-diphenylaniline: accurate time-dependent density functional theory predictions for charge-transfer dyes.

Using time-dependent density functional theory (TD-DFT) and the polarizable continuum model (PCM), we have computed the absorption spectra of nitro-diphenylamine dyes. It turns out that the 6-311+G(2d,p) and 6-311G(d,p) basis sets provide, respectively, almost perfectly converged excitation spectra and geometries. Using the PBE0 hybrid functional, we obtain a valuable correlation between PCM-TD-DFT and experimental lambdamax with mean signed/absolute deviations of -4 nm (0.03 eV)8 nm (0.06 eV) and relatively small extreme discrepancies, although the excitations responsible for the color of this class of dyes present a charge-transfer character. The changes in the electron density upon absorption are analyzed through an orbital picture. In addition, a relationship between the light fastness and a well-identified vibrational frequency is proposed.

Journal Article↗

PubMed2006

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.

Computer Simulation↗

PubMed2006

Assessment of several hybrid DFT functionals for the evaluation of bond length alternation of increasingly long oligomers.

We have optimized the ground-state geometry of nine series of increasingly long oligomers, using six hybrid density functionals (O3LYP, B3LYP, B97-1, B98, PBE0, and BHHLYP) combined with three different atomic basis sets. In each case, the obtained bond length alternation (BLA) is compared to the corresponding MP2 values. Three phenomenological categories have been set up. In the first, the BLA exponentially decreases, in which case all the tested functionals give results in very good agreement with MP2. In the second category fall the symmetric oligomers that, due to the Peierls theorem, show large BLA. For these chains, BHHLYP tends to give too large and quickly converging BLA wrt chain length, while O3LYP often leads to the opposite misjudgments, and the remaining hybrids provide valuable results. In the third category, one finds asymmetric compounds presenting significantly unequal bond lengths, for which the divergence between DFT and wave function approaches can be dramatic. Indeed, all hybrids yield too small BLA values, especially for long chain lengths. We also study the effect of chain conformation on the BLA.

Journal Article↗

PubMed2006

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.

Journal Article↗

PubMed2006

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.

Coloring Agents↗

PubMed2005

Ab initio assessment of the first hyperpolarizability of saturated and unsaturated polyaminoborane/polyphosphinoborane copolymers.

The linear and nonlinear optical properties of trans-cisoïd saturated and unsaturated polyaminoborane/polyphosphinoborane alternating copolymers are studied at the MP2/6-311G(2d)//PBE0/6-31G(2d) level of approximation, by using the increasingly large oligomer series methodology. We report the evolution with chain length of geometry parameters, partial atomic charges, electric dipole moments, polarizabilities and first hyperpolarizabilities of both phosphorus- and nitrogen-terminated chains. It turns out that for the saturated copolymer, linear and nonlinear optics properties of the saturated copolymer correspond to an average of the response of polyaminoborane and polyphosphinoborane. For the conjugated copolymer, the response is guided by the least delocalizable component.

Journal Article↗

PubMed2005

Second-order Møller-Plesset evaluation of the bond length alternation of several series of linear oligomers.

We investigate, at the second-order Møller-Plesset level, the bond length alternation of 30 series of increasingly long linear oligomers for a total of more than 250 compounds, polyacetylene, polymethineimine, polyphosphinoborane, polyaminoborane, polyphosphazene, etc., for which, often for the first time, an accurate estimate of the polymeric bond length alternation is given. The variations induced either by chemical substitution of the backbone atoms or conformational modifications are discussed. Only three polymers present a large bond length alternation (>0.03 A). Systematic basis set effects have been unravelled, i.e., MP2/6-311G(2d) always overshoots the bond length alternation. Best estimates of the bond length alternation are provided for more than a dozen of polymers.

Journal Article↗

PubMed2004

Geometry, dipole moment, polarizability and first hyperpolarizability of polymethineimine: an assessment of electron correlation contributions.

We have investigated the geometries as well as the longitudinal dipole moment (micro), polarizability (alpha), and first hyperpolarizability (beta) of polymethineimine oligomers using different approaches [Hartree-Fock (HF), second-order Møller-Plesset (MP2), and hybrid density functional theory (DFT) methods (B3LYP and PBE0)] for evaluating the geometries and the nonlinear optical properties. It turns out that (i) HF and the selected DFT methods provide the incorrect sign for beta of short and medium size oligomers. (ii) The B3LYP and PBE0 electron correlation correction are too small for micro, too large for alpha, and for some oligomer lengths, they are in the wrong direction for beta. (iii) On the contrary to polyacetylene, the hybrid-DFT geometries are in poor agreement with MP2 geometries; the former showing much smaller bond length alternations.

Journal Article↗

PubMed2004

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.

Journal Article↗

PubMed2004

Theoretical study of the longitudinal first hyperpolarizability of polysilaacetylene.

With the help of ab initio tools taking into account dynamic electron correlation effects, we study the longitudinal electronic first hyperpolarizability of carbon-silicon analogues to polyacetylene. It turns out that the MP2/6-31G(d)//HF/6-31G(d) scheme is suitable to obtain a semiquantitative accuracy for the first hyperpolarizability of long polysilaacetylene oligomers. The conformation of the chain has a crucial impact on its second-order nonlinear optical properties. We also show that, for some chain lengths, the frequency dispersion effects may have a huge impact, even when far away from resonance. These phenomena are rationalized in terms of delocalization and asymmetry.

Journal Article↗

PubMed2004

Second-order nonlinear optical coefficient of polyphosphazene-based materials: a theoretical study.

The second-order nonlinear optical coefficient of polyphosphazene oligomers of increasing size has been determined by using ab initio methods taking into account electron correlation and frequency dispersion effects. The calculated first hyperpolarizability per unit cell converges rapidly with respect to chain length. It attains an amplitude of about one-third of the one of classical push-pull systems. This amplitude can be strongly increased by replacing the nitrogen of the backbone by silicon. The effects of the side groups (H, CH3, F, Cl, Br, and OH) on the first hyperpolarizability have been investigated as well. The different results have been rationalized in terms of alternations of bond lengths and atomic charges.

Journal Article↗

PubMed2002

Integral algorithm and density matrix integration scheme for ab initio band structure calculations on polymeric systems.

A new program for band structure calculations of periodic one-dimensional systems has been constructed. It is distinguishable from other codes by the efficient two-electron integral evaluation and the integration schemes of the density matrix in the first Brillouin zone. The computation of polymeric two-electron integrals is based on the McMurchie Davidson algorithm and builds batches of the different cell indices included in the polymeric system. Consequently it presents efficient scaling with respect to the number of unit cells taken into account. Our algorithm takes into account fully the polymeric symmetry rather than the molecular symmetry. A semidirect procedure where only exchange integrals are computed at each SCF cycle is proposed in order to maintain balance between computation time and disk space. In addition, the integration of the density matrix over a large number of cell indices can be performed by different methods, such as Gauss-Legendre, Clenshaw-Curtis, Filon, and Alaylioglu-Evans-Hyslop. This last scheme is able to obtain an accuracy of 10(-13) a.u. on each individual density matrix element for all cell indices with only 48 k-points.

Journal Article↗