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Irmgard Frank

Publications and source records attributed to Irmgard Frank.

10 recordsLinked to original sources
PubMed2006

Modified chemistry of siloxanes under tensile stress: interaction with environment.

We present first principles molecular dynamics simulations of stretched siloxane oligomers in an environment representative of that present in single molecule atomic force microscopy experiments. We determine that the solvent used (hexamethyldisiloxane) does not influence the stretching of the siloxane in the high force regime or the rupture process, but trace amounts of water can induce rupture before the maximum siloxane extension has been attained. This would result in a significantly lower rupture force. The simulations show that the rupture of a covalent bond through a reaction with a molecule from the environment, which would not normally occur between the species when the polymer is not stressed, is possible, opening a route to mechanically induced chemical reactions. The attack of the normally hydrophobic siloxane by water when it is stretched has wider implications for the material failure under tensile stress, where trace amounts of water could induce tearing of the material.

Materials Testing↗
PubMed2006

First-principles simulation of the photoreaction of a capped azobenzene: the rotational pathway is feasible.

We present first-principles molecular dynamics simulations of azobenzene and a sterically hindered derivative in the first excited state. The restricted open-shell Kohn-Sham (ROKS) approach is employed to describe the motion in the lowest excited state. The rotational pathway is observed in the molecular dynamics simulations for both azobenzene and its azacrown ether capped derivative.

Journal Article↗
PubMed2005

Light-driven unidirectional rotation in a molecule: ROKS simulation.

We present a first-principles molecular dynamics study of the excited-state motion in a molecule that has recently been proven to exhibit light-driven unidirectional rotation. The simulations show that the directed motion is due to the complex excited-state dynamics on ultrashort timescales in the chiral system.

Journal Article↗
PubMed2005

Restricted open-shell Kohn-Sham theory for pi-pi* transitions. III. Dynamics of aggregates.

We present molecular-dynamics simulations for 1,3-butadiene, 2,3-dimethyl-1,3-butadiene, and cyclopentadiene at finite temperature using periodic boundary conditions. These systems form weakly bound aggregates in the ground state and exhibit bond formation in the excited state. Monomeric excitation of an ensemble of butadiene molecules leads to a transfer of the excitation between two molecules in the excited state with an intermediate delocalization of the wave function over both moieties.

Journal Article↗
PubMed2004

A molecular spring for vision.

Light absorption by the visual pigment rhodopsin leads to vision via a complex signal transduction pathway that is initiated by the ultrafast and highly efficient photoreaction of its chromophore, the retinal protonated Schiff base (RPSB). Here, we investigate this reaction in real time by means of unrestrained molecular dynamics simulations of the protein in a membrane mimetic environment, treating the chromophore at the density functional theory level. We demonstrate that a highly strained all-trans RPSB is formed starting from the 11-cis configuration (dark state) within approximately 100 fs by a minor rearrangement of the nuclei under preservation of the saltbridge with Glu113 and virtually no deformation of the binding pocket. Hence, the initial step of vision can be understood as the compression of a molecular spring by a minor change of the nuclear coordinates. This spring can then release its strain by altering the protein environment.

Algorithms↗
PubMed2003

QM/MM Car-Parrinello molecular dynamics study of the solvent effects on the ground state and on the first excited singlet state of acetone in water.

We present a hybrid Car-Parrinello quantum mechanical/molecular mechanical (QM/MM) approach that is capable of treating the dynamics of molecular systems in electronically excited states in complex environments. The potential energy surface in the excited state is described either within the restricted open-shell Kohn-Sham (ROKS) formalism or within time-dependent density functional theory (TDDFT). As a test case, we apply this technique to the study of the solvent effects on the ground state and on the first excited singlet state of acetone in water. Our results demonstrate that for this system a purely classical description of the solvent is sufficient, since inclusion of the first solvent shell of 12 water molecules into the quantum system does not show a significant effect on this transition. The excited-state energies calculated with ROKS are red shifted by a constant value compared to the TDDFT results, while the relative variations of the excitation energy for different configurations are in very good agreement. The experimentally observed blue shift of the excitation energy in going from gas phase to condensed phase is well reproduced. Excited-state dynamics carried out with ROKS yield the relaxation of the solute and the rearrangement of the solvent structure on a picosecond timescale. The calculated Stokes shift is in reasonable agreement with experimental data.

Journal Article↗
PubMed2002

Breaking bonds by mechanical stress: when do electrons decide for the other side?

Using first-principles molecular dynamics, we have simulated reactions that can be induced by mechanical stress in a polymer. We have stretched a small piece of poly(ethylene glycol) (PEG) in water at finite temperature. Both the molecule and the solvent were described quantum mechanically on an equal level. The formation of ions was observed, which corresponds to a heterolytic bond cleavage. We were able to monitor the motion of the electrons during the reactions. Our simulations show that the electron transfer and the breaking of the bond occur almost simultaneously and that both processes are initiated by the approach of a solvent molecule toward the destabilized bond.

Journal Article↗
PubMed2001

The Influence of Excess Ammonia on the Mechanism of the Reaction of Boron Trichloride with Ammonia-An Ab Initio Molecular Dynamics Study This work was supported by the Deutsche Forschungsgemeinschaft in the framework of the Sonderforschungsbereich 408 "Anorganische Festkörper ohne Translationssymmetrie". We thank Mauro Boero from the Joint Research Center for Atom Technology, Tsukuba (Japan) for the reoptimization of the Martins-Troullier pseudopotentials for boron and chlorine, as well as the John-von-Neumann-Institut für Computing, Jülich, for making computer time available to us.

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Journal Article↗