Quantum mechanical studies of ionization and electron transfer in diatomic systems : O2 and H+ + H-

  The present thesis is based upon two papers concerning the core-valence double onization of molecular oxygen and mutual neutralization of H+ and H- ions at low collision energies. The former of these processes has been studied for the first time using a magnetic bottle time-of-ight electron coincidence spectrometer in combination with ab initio electronic structure calculations. The core-valence photoelectron spectra have been interpreted by comparing with the calculated double ionization energies, as well as the conventional valence band spectrum. Based on this comparison, some general features of the process are discussed and assignments for several of the dicationic states proposed. The latter process has been studied by means of a molecular close coupling approach in which both the nuclei and the electrons have been treated at a quantum mechanical level of theory. Accurate ab initio potential energy curves and non-adiabatic couplings have been used to calculate the neutralization cross section in the collision energy region 0.001 to 100 eV. Special emphasis has been put on the energy region below a few eV from which the low temperature rate coe_cient is evaluated. In this region, the calculated neutralization cross section is in good agreement with several other theoretical studies, but is a factor of two to three lower than the only published experimental data.  QC 2010112

pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena sensory rhodopsin

International audienceA minimal electrostatic model is introduced which aims at reproducing and analyzing the visible- light absorption energy shift of a protein with pH. It relies on the existence of a protein structure, the prediction of titratable amino-acid pKa values and a very limited set of parameters. Applied to the case of the photochromic Anabaena sensory rhodopsin protein, the model succeeds in reproducing qualitatively the reported experimental data, confirming the importance of aspartic acid 217 in the observed blue shift in the lambda(max) of ASR at neutral pH. It also suggests for the first time the role of two other amino acids, glutamic acid 36 at basic pH and aspartic acid 120 at acidic pH

Quantum Scattering with the Driven Schrödinger Approachand Complex Scaling

Quantum scattering calculations of two and three-body systems with Coulomb interaction using thedriven Schrödinger equation combined with exterior complex scaling are discussed. A rigorous formulationfor two-body scattering is reported, and its generalization to three-body scattering is considered

Transient UV pump–IR probe investigation of heterocyclic ring-opening dynamics in the solution phase: the role played by nσ* states in the photoinduced reactions of thiophenone and furanone

The heterocyclic ring-opening dynamics of thiophenone and furanone dissolved in CH3CN have been probed by ultrafast transient infrared spectroscopy. Following irradiation at 267 nm (thiophenone) or 225 nm (furanone), prompt (tau &lt;1 ps) ring-opening is confirmed by the appearance of a characteristic antisymmetric ketene stretching feature around 2150 cm(-1). The ring-opened product molecules are formed highly vibrationally excited, and cool subsequently on a similar to 6.7 ps timescale. By monitoring the recovery of the parent (S-0) bleach, it is found that similar to 60% of the initially photoexcited thiophenone molecules reform the parent molecule, in stark contrast with the case in furanone where there is less than 10% parent bleach recovery. Complementary ab initio calculations of potential energy cuts along the S-C(=O) and O-C(=O) ring-opening coordinate reveals insights into the reaction mechanism, and the important role played by dissociative (n/pi)sigma* states in the UV-induced photochemistry of such heterocyclic systems.</p

Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology

We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their mutants. In the present implementation the information required for the construction of each model is essentially a crystallographic structure or a comparative model complemented with information on the protonation state of ionizable side chains and distributions of external counterions. Starting with such information, a model formed by a fixed environment system, a flexible cavity system, and a chromophore system is automatically generated. The results of the predicted vertical excitation energy for 27 different rhodopsins including vertebrate, invertebrate, and microbial pigments indicate that such basic models could be employed for predicting trends in spectral changes and/or correlate the spectral changes with structural variations in large sets of proteins

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table

In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas–Kroll–Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.status: publishe