Développement et Application de modèles dépendant et indépendant du temps pour l'étude des propriétés spectroscopiques de composés d'intérêt biologique

Les molécules d intérêt biologique ont pour caractéristique principale de participer aux processus biologiques, que ce soit au sein d un organisme du monde du vivant, ou bien dans l espace (exobiologie). Dans ces deux cas, l eau joue un rôle prépondérant sur les propriétés des systèmes considérés. Les simulations numériques constituant désormais un élément incontournable pour l interprétation des expériences, l objectif de cette thèse sera de tenter de reproduire par des méthodes de chimie quantique les spectres IR expérimentaux relatifs à deux systèmes hydratés : les aérosols de nitrate, présents dans l atmosphère, ainsi que les bases d acides nucléiques microhydratées. Ce travail présente une même démarche afin d obtenir la meilleure adéquation possible entre théorie et expérience. Tout d abord, le modèle géométrique permettant de représenter au mieux nos systèmes a été recherché à partir de l utilisation du code GSAM développé au laboratoire. Puis, nous nous sommes attachés à déterminer la méthode théorique la plus adaptée à l étude de chacun des systèmes. Pour ce faire, différentes méthodes de calcul de structure électronique (dont B3LYP et ses analogues prenant en compte les interactions à moyenne et longue portée B3LYP-D et CAMB3LYP), de traitement vibrationnel (VPT2, VCI-P ou bien DM) ont été testées. L évolution expérimentale observée pour les nombres d onde associés aux cinq modes de vibration de l ion nitrate en fonction du nombre de molécules d eau au sein de l aérosol est ainsi reproductible en utilisant un modèle d agrégats d agrégats du type (NaNO3,nH2O)3 au niveau calculatoire B3LYP/6-311+G(d,p) à 15cm-1 près. En ce qui concerne les bases d acides nucléiques (X=C, T, U, A et G) microhydratées, la meilleure représentation d un environnement aqueux est constitué d un modèle explicite du type X,nH2O avec n=1 à 5 -déterminé à partir de l application du code GSAM-, associé à un modèle implicite tel que PCM. La comparaison des nombres d onde dans la zone de signature vibrationnelle 1000-1800cm-1 pour chaque base et à deux niveaux calculatoires différents B3LYP et B3LYP-D a conduit globalement à favoriser la première. En revanche, les méthodes de traitement vibrationnel dépendantes et indépendantes du temps donnent des résultats voisins dans cette zone, avec un coût calculatoire moins important pour la méthode VPT2.Molecules with biological interest participate to biological processes in living organisms or in space (exobiology). Water plays a predominant part on properties of considered systems.Since computations take an important part in interpretation of experiments, the aim of this phD will be to try to reproduct IR experimental spectra with methods of quantum chemistry for two different hydrated systems : nitrate aerosols and microhydrated nucleic acid bases. This work presents a same approach to obtain the best agreement between experience and theory. First, the geometrical model for representation of hydration was investigated with the GSAM code developed at the laboratory. Then, the most adapted theoretical method was determined for studies of each system. Different methods of determination of electronic structure, especially B3LYP and their analogs considering medium and long range interactions B3LYP-D and CAMB3LYP, and vibrational treatments (VPT2, VCI-P and MD) were tested. The experimental evolution observed for wavenumbers associated to the five vibrational modes of the nitrate ion depending on the number of water molecules within the aerosol is reproducible using a model of aggregates of molecular clusters labeled (NaNO3,nH2O)3 at the B3LYP/6-311+G(d,p) level of theory : the average discrepancy between theory and experience reaches 15cm-1. Concerning microhydrated nucleic acid bases (X=C, T, U, A et G), the best representation of aqueous environment is made of an explicit model labeled X,nH2O with n=1 to 5 -determined from the application of the GSAM code-, with an implicit one like the PCM model. The comparison of wavenumbers calculated at the B3LYP and B3LYP-D levels of theory in the 1000-1800cm-1 spectral region which represents the vibrational signature for each base favoured the first method. But time-dependent and time-independent methods of vibrational treatment provide comparable results in this region, with a computational cost less important for the VPT2 approach.PAU-BU Sciences (644452103) / SudocSudocFranceF

Field and field gradient polarizabilities of BF and CF

The multipole moments and independent components of the α, β, A, C and B polarizability tensors have been calculated for BF and CF+ at three different internuclear distances. These electrical properties and their derivatives were determined by using the SCF wavefunction and large Gaussian basis sets including numerous diffuse orbitals. Most of the results, essentially for CF+, are new. Although the molecular polarizabilities tensors are of different orders of magnitude for BF and CF+ similar trends are observed

An ab initio CI investigation of structure and bonding in LiC2H2 complexes

cited By 10International audienceThe structures and energies of various LiC2H2 complexes have been investigated by means of ab initio molecular orbital calculations. Analytic SCF gradients were employed with a double-ζ basis set to locate and characterize stationary points on the energy surface. Single-point CI calculations using a double-ζ + diffuse and polarization basis set have been carried out at the DZ + P SCF stationary points. With the highest-level theory, the Li-vinylidene complex and the cis bridged adduct are found to be the most favorable arrangements, the former complex being slightly more stable by about 2 kcal mol-1. These molecules are bound respectively by about 5 and 3 kcal mole-1 relative to infinitely separated lithium plus acetylene. Harmonic vibrational frequencies are also reported and confirm the existence of the cis LiC2H2 species recently observed in a solid argon matrix. © 1987

Quantum molecular dynamic approach to modeling the vibrational spectra of propynenitrile and its 1:1 complexes with water

International audienceWe present here a quantum molecular dynamic approach from DFT molecular dynamics (DFT/MD) trajectories around 150 K, 300 K, 450 K and 600 K to compute the IR spectra of the propynenitrile (or cyanoacetylene) molecule HC3N, the simplest linear cyanopolyyne detected in interstellar clouds and circumstellar envelopes of stars. The DFT/MD results in fair agreement with the experimental data for the isolated molecule are close to those obtained, for all the valence modes, from an effective second order treatment (VPT2) at the CCSD(T) level of theory. This DFT/MD simulation is used to predict the IR spectra of the1:1 complexes with water and analyse the shifts expected for the micro-hydrated molecule

Comparative theoretical study of poly[3-(4-octylphenyl)thiophenes] and poly[3-(4-octylphenoxy)thiophenes] as promising photovoltaic cells materials

cited By 0International audienceThe geometric and electronic structure of [3-(4-Octylphenyl)]Thiophenes (POPT) and [3-(4-octylphenoxy)thiophenes] (POPOT) oligomers, ranging in size up to the octamer (240 atoms), have been calculated with density functional theory (B3LYP/6-31G*). The knowledge of the geometries for these polymers is of utmost importance in order to understand their optical properties in different phase (solution and condensed phase). The calculations indicate that, in opposition to the first polymer where the introduction of the pendant phenyl disturb the planarity for the backbone of the conjugated segment, the second polymer has a nice organisation where the conjugated chain still planar even the presence of octylphenyl groups. The optical spectra are calculated with TDDFT and Zindo approaches on the basis of the geometries provided by DFT, and compared to experimental data. © 2007 American Institute of Physics

Vibrational treatment from a variation-perturbation scheme: The VCI-P method. Application to the glycolaldehyde

cited By 0International audienceAn iterative variation-perturbation algorithm allowing a anharmonic vibrational treatment of polyatomic molecules is proposed. This state specific process consists on an iterative construction of small 3N-5 Vibrational Configuration Interation (VCI) matrixes (N being the number of atoms) with the most pertinent couplings and includes a perturbative treatment of the weakest contributions. Thus, this scheme allow to massively reduce the size of the CI matrixes with a minimum loss of correlation energy. Through the example of H2CO, the results stemmed from the VCI-P process are compared to their full VCI counterpart. Moreover, the computations of anharmonic intensities are also implemented. As illustration, the modelization of the medium infrared (MIR) spectrum of the glycolaldehyde is reported. © 2012 American Institute of Physics

Dynamic scalar and tensor polarizabilities of the 2 1P and 2 3P states of He

cited By 22International audienceThe dynamic dipole polarizabilities at real and imaginary frequencies have been determined for the helium atom in its lowest singlet and triplet 2P states, using our time-dependent gauge-invariant method. Contributions of the 2S states to static polarizabilities are strong and negative, particularly in the case of the singlet 2 1P state, for which the static scalar polarizability α0 is negative. The tensor polarizability α2 corresponding to the differential Stark shift between the m Zeeman sublevels was also calculated and compared to previous theoretical and experimental results for the singlet 2 1P state. An evaluation of the C6 dispersion coefficients for the 2 1P-2 1P and 2 3P-2 3P systems is also given, derived from the dynamic polarizabilities at imaginary pulsations ω. © 1994 The American Physical Society

Dipole polarizability and hyperpolarizability of FCN, ClCN, BrCN and ICN

cited By 18International audienceWe have used very large Gaussian-type basis sets to obtain electric dipole polarizabilities and hyperpolarizabilities from finite-field many-body perturbation theory calculations for the cyanogen halides FCN, ClCN, BrCN and ICN. Our best values for the mean dipole polarizability α/e2a02Eh-1 and the anisotropy Δα/e2a02Eh-1 are 18.51 and 10.77 (FCN), 30.80 and 22.21 (ClCN), 36.26 and 24.42 (BrCN), 48.00 and 28.96 (ICN). For the mean second dipole hyperpolarizability 10-3γ/e4a04Eh -3 obtained 1.96 (FCN), 4.29 (ClCN), 6.0 (BrCN) and 11.0 (ICN). Copyright © 1997 Elsevier Science B.V. All rights reserved

The quadrupole moments of Li2, Li2+ and Li3+

cited By 5International audienceBy calculating the static potential energy of the molecule as seen by a distant negative charge, we have determined the total quadrupole moments for Li2, Li2+ and Li3+. In atomic units, the following values were found: 9.0 for Li2, 18.0 for Li2+ and -15.4 for Li3+. © 1983