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The mechanism for signal transduction from the LOV-domains toward the kinase region of phototropin is still not well understood. We have performed molecular dynamics (MD) simulations and CONCOORD calculations on the LOV2 domain of Adiantum capillus-veneris, with the goal to detect possible differences between the two forms of the LOV domain which may not show up in the static crystal structures. Since no such clear differences are found in the MD simulations also, we suggest that the real, biologically active conformation of the LOV domain within the whole phototropin is different from the crystal structure of the isolated LOV domains. The MD simulations do offer, however, insight into details of the dynamics of the dark and illuminated LOV domains, which are discussed in the light of recent experiments
We investigate femtosecond-laser induced desorption [desorption induced by multiple electronic transitions (DIMET)] of NO molecules from thin Pt(111) films. On the basis of a two-state, open-system density matrix treatment in combination with a two-temperature model, we argue that decreasing the film thickness enhances desorption cross sections by orders of magnitude in comparison to bulk materials. Both the spatial confinement and the laser fluence appear therefore as efficient, nonlinear enhancement factors for nonadiabatic photoreactions of metal surfaces and, possibly, of nanostructered materials in general
Recent experiments using time- and angle-resolved two-photon photoemission (2PPE) spectroscopy at metal/polar adsorbate interfaces succeeded in time-dependent analysis of the process of electron solvation. A fully quantum mechanical, two-dimensional simulation of this process, which explicitly includes laser excitation, is presented here, confirming the origin of characteristic features, such as the experimental observation of an apparently negative dispersion. The inference of the spatial extent of the localized electron states from the angular dependence of the 2PPE spectra has been found to be non-trivial and system-dependent. (C) 2005 American Institute of Physics
In the light of recent intensity-voltage low energy electron diffraction (LEED-IV) experiments [Surf. Sci. 316, 92 (1994); Surf. Rev. Lett. 10, 487 (2003)], the electronic and geometric structure of a water bilayer adsorbed at the Ru(0001) surface are investigated through first-principles total energy calculations, using periodic slab geometries and gradient-corrected density functional theory (DFT). We consider five possible bilayer structures, all roughly consistent with the LEED-IV analysis (three intact structures and two half-dissociated), and a water single layer at Ru(0001). Adsorption energies and substrate-adsorbate geometry parameters are given and discussed in the light of the experiments. We also give a comparative analysis of the electron density redistribution (Delta rho) and of the dipole moment change (Delta mu) induced by water adsorption on the Ru(0001) surface. In agreement with Feibelman [Science 295, 99 (2002)], the half-dissociated structures are found to be more stable than the intact ones, and their adsorption geometries in better agreement with the LEED-IV data. However, the Delta rho analysis shows that a half-dissociated structure induces a Delta mu>0, which would be incompatible with the experimentally measured decrease of the work function following bilayer adsorption; the latter would be consistent, instead, with the Delta mu < 0 induced by the intact structures. It is the aim of this paper to compare various possible adsorption structures, most of them already considered previously, with one and the same method. For this purpose, thick slabs and restrictive computational parameters are chosen to generally address the accuracy and the limits of DFT in reproducing adsorption energies and bond lengths of water-metal interacting systems
In this paper a perturbation-theory study of vibrational lifetimes for the bending and stretching modes of hydrogen adsorbed on a Si(100) surface is presented. The hydrogen-silicon interaction is treated with a semiempirical bond-order potential. Calculations are performed for H-Si clusters of different sizes. The finite lifetime is due to vibration-phonon coupling, which is assumed to be linear or bilinear in the phonon and nonlinear in the H-Si stretching and bending modes. Lifetimes and vibrational transition rates are evaluated with one- and two-phonon processes taken into account. Temperature effects are also discussed. In agreement with the experiment and previous theoretical treatment it is found that the H-Si (upsilon(s)=1) stretching vibration decays on a nanosecond timescale, whereas for the H-Si (upsilon(b)=1) bending mode a picosecond decay is predicted. For higher-excited vibrations, simple scaling laws are found if the excitation energies are not too large. The relaxation mechanisms for the excited H-Si stretching and the H-Si bending modes are analyzed in detail.
The question as to whether state-selective population of molecular vibrational levels by shaped infrared laser pulses is possible in a condensed phase environment is of central importance for such diverse fields as time-resolved spectroscopy, quantum computing, or "vibrationally mediated chemistry." This question is addressed here for a model system, representing carbon monoxide adsorbed on a Cu(100) surface. Three of the six vibrational modes are considered explicitly, namely, the CO stretch vibration, the CO-surface vibration, and a frustrated translation. Optimized infrared pulses for state-selective excitation of "bright" and "dark" vibrational levels are designed by optimal control theory in the framework of a Markovian open-system density matrix approach, with energy flow to substrate electrons and phonons, phase relaxation, and finite temperature accounted for. The pulses are analyzed by their Husimi "quasiprobability" distribution in time-energy space.
Recent progress towards a quantum theory of laser-induced desorption and related phenomena is reviewed, for specific examples. These comprise the photodesorption of NO from Pt(111), the scanning tunnelling microscope and laser- induced desorption and switching of H at Si(100), and the electron stimulated desorption and dissociation of CO at Ru(0001). The theoretical methods used for nuclear dynamics range from open-system density matrix theory over nonadiabatically coupled multi-state models to electron-nuclear wavepackets. Also, aspects of time-dependent spectroscopy to probe ultrafast nonadiabatic processes at surfaces will be considered for the example of two-photon photoemission of solvated electrons in ice layers on Cu(111)
In this work, we present theoretical simulations of laser-driven vibrational control of NO adsorbed on a gold surface. Our goal is to tailor laser pulses to selectively excite specific modes and vibrational eigenstates, as well as to favor photodesorption of the adsorbed molecule. To this end, various control schemes and algorithms are applied. For adsorbates at metallic surfaces, the creation of electron hole pairs in the substrate is known to play a dominant role in the transfer of energy from the system to the surroundings. These nonadiabatic couplings are included perturbatively in our reduced density matrix simulations using a generalization of the state-resolved position-dependent anharmonic rate model we recently introduced. An extension of the reduced density matrix is also proposed to provide a sound model for photodesorption in dissipative systems.
The adsorption of molecules to the surface of carbon nanostructures opens a new field of hybrid systems with distinct and controllable properties. We present a microscopic study of the optical absorption in carbon nanotubes functionalized with molecular spiropyran photoswitches. The switching process induces a change in the dipole moment leading to a significant coupling to the charge carriers in the nanotube. As a result, the absorption spectra of functionalized tubes reveal a considerable redshift of transition energies depending on the switching state of the spiropyran molecule. Our results suggest that carbon nanotubes are excellent substrates for the optical readout of spiropyran-based molecular switches. The gained insights can be applied to other noncovalently functionalized one-dimensional nanostructures in an externally induced dipole field.
The optical switching of molecular ensembles in a dissipative environment is a subject of various fields of chemical physics and physical chemistry. Here we try to switch arrays of molecules from a stable collective ground state to a state in which all molecules have been transferred to another stable higher-energy configuration. In our model switching proceeds through electronically excited intermediates which are coherently coupled to each other through dipolar interactions, and which decay incoherently within a finite lifetime by coupling to a dissipative environment. The model is quite general, but parameters are chosen to roughly resemble the all-trans -> all-cis isomerization of an array of azobenzene molecules on a surface. Using analytical and optimal control pulses and the concept of "laser distillation," we demonstrate that for various aggregates (dimers up to hexamers), controlled and complete switching should be possible.