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Electron transport through molecules treated by LCAO-MO Green's functions with absorbing boundaries
(2004)
In this Letter, we present a method for calculating transport properties of molecular conductors using a time- independent scattering approach based on Green's functions with absorbing boundaries. The method, which has been used before for chemical reaction dynamics in a grid basis [Seideman, Miller, J. Chem. Phys. 96 (1992) 4412], is formulated here in an LCAO-MO form within simple Huckel theory and extended Huckel theory (EHT), respectively. Test calculations are for a quasi-one-dimensional atom chain. As a more realistic application, the organic molecules benzene- 1,4-dithiolate and biphenyl-4,4'-dithiolate between gold electrodes are studied. (C) 2004 Elsevier B.V. All rights reserved
In this contribution, recent advances in the theory of laser and, to a lesser extent, of scanning tunneling microscope (STM) induced cleavage of bonds between an adsorbate and a solid surface, will be reviewed. Special emphasis will be given to the quantum dynamics of electronically non-adiabatic reactions. (c) 2005 Elsevier Ltd. All rights reserved
We report simulations of laser-driven many-electron dynamics by means of the time-dependent configuration interaction singles (doubles) approach. The method accounts for the correlation of ground and excited states, is capable of describing explicitly time-dependent, nonlinear phenomena, and is systematically improvable. Lithium cyanide serves as a molecular test system in which the charge distribution and hence the dipole moment are shown to be switchable, in a controlled fashion, by (a series of) laser pulses which induce selective, state-to-state electronic transitions. One focus of our time-dependent calculations is the question of how fast the transition from the ionic ground state to a specific excited state that is embedded in a multitude of other states can be made, without creating an electronic wave packet. (c) 2005 American Institute of Physics
In this paper we present time-dependent, quantum-dynamical simulations of photoinduced processes at solid surfaces involving nonadiabatic transitions of electrons to and from short-lived intermediate excited states. In particular, two-photon photoemission (2PPE) spectra of naked metal surfaces and free-standing metal films are considered. One major problem in both cases is the presence of electron-electron scattering, which is treated here in various ways. The first way is to adopt an open-system density matrix approach, in which a single electron is weakly coupled to a "bath" of other electrons. The second approach is based on a many-electron Schrodinger equation, which is solved with the help of a time-dependent configuration interactions singles (TD-CIS) method
We apply the multiconfiguration time-dependent Hartree-Fock method to electronic structure calculations and show that quantum chemical information can be obtained with this explicitly time-dependent approach. Different equations of motion are discussed, as well as the numerical cost. The two-electron integrals are calculated using a natural potential expansion, of which we describe the convergence behavior in detail
In this paper we report dynamical simulations of laser-driven, coupled nuclear-electron dynamics for a molecule- surface system. Specifically, the laser desorption of a small molecule (NO) from a metal slab (Pt) in the so-called DIET limit (Desorption Induced by Electronic Transitions), is studied. The excitation of the metal electrons by a laser pulse followed by the formation of a negative ion resonance, its subsequent decay, and the simultaneous desorption of the molecule are all treated within a single quantum mechanical model. This model is based on an earlier theory of Harris and others [S. M. Harris, S. Holloway, and G. R. Darling, J. Chem. Phys. 102, 8235 (1995)], according to which a nuclear degree of freedom is coupled to an electronic one, both propagated on a single non-Born-Oppenheimer potential energy surface. The goals of the present contribution are (i) to make a conceptual connection of this model to the frequently adopted nonadiabatic "multi-state" models of photodesorption, (ii) to understand details of the desorption mechanism, (iii) to explicitly account for the laser pulse, and (iv) to study the photodesorption as a function of the thickness of the metal film, and the laser parameters. As an important methodological aspect we also present a highly efficient numerical scheme to propagate the wave packet in a problem-adapted diabatic basis
A novel quantum method to deal with typical system-bath dynamical problems is introduced. Subsystem discrete variable representation and bath coherent-state sets are used to write down a multiconfigurational expansion of the wave function of the whole system. With the help of the Dirac-Frenkel variational principle, simple equations of motion-a kind of Schrodinger-Langevin equation for the subsystem coupled to (pseudo) classical equations for the bath-are derived. True dissipative dynamics at all times is obtained by coupling the bath to a secondary, classical Ohmic bath, which is modeled by adding a friction coefficient in the derived pseudoclassical bath equations. The resulting equations are then solved for a number of model problems, ranging from tunneling to vibrational relaxation dynamics. Comparison of the results with those of exact, multiconfiguration time-dependent Hartree calculations in systems with up to 80 bath oscillators shows that the proposed method can be very accurate and might be of help in studying realistic problems with very large baths. To this end, its linear scaling behavior with respect to the number of bath degrees of freedom is shown in practice with model calculations using tens of thousands of bath oscillators.
The results of a quantum-mechanical study of vibrational relaxation of hydrogen adsorbed on a Si(100) surface with the multi-configurational time-dependent Hartree (MCTDH) method are presented. A two-dimensional subsystem is coupled non-linearly to a bath of harmonic oscillators (phonons of the Si bulk), and the relaxation of subsystem vibrations proceeds primarily via a two-phonon process. Characteristic times of the system evolution agree well with our previous perturbation theory study. The vibrational population decay is non-exponential, exhibiting pronounced recurrences due to finite bath size. The dependence of the lifetimes of the vibrational levels on the bath size and on the coupling details is investigated.
We report quantum chemical calculations, mostly based on density functional theory, on azobenzene and substituted azobenzenes as neutral molecules or ions, in ground and excited states. Both the cis and trans configurations are computed as well as the activation energies to transform one isomer into the other and the possible reaction paths and reaction surfaces along the torsion and inversion modes. All calculations are done for the isolated species, but results are discussed in light of recent experiments aiming at the switching of surface mounted azobenzenes by scanning tunneling microscopes.
An efficient method for the numerical solution of a non-Markovian, open-system density matrix equation of motion in coordinate representation is developed. We apply the scheme to model simulations of the laser-assisted O+H -> OH association reaction in an environment. The suggested approach is based on the application of the time-evolution operator to the "closed-system" part of the overall Hamiltonian and transformation of the open-system equation of motion to the Heisenberg picture suitable for numerical propagation. A dual role of the system-environment coupling with respect to the infrared (ir) laser-driven association of OH is demonstrated: the association probability is increased due to the coupling at relatively weak laser fields, but decreased at strong laser fields. Moreover, at a certain strength of the ir laser field, the association probability does not depend on the strength of the system-bath coupling at all.
A theoretical model for the selective subsurface absorption of atomic hydrogen in a Pd(111) surface by infrared (IR) laser pulses is presented. The dynamics of the adsorbate is studied within the reduced density matrix approach. Energy and phase relaxation of the hydrogen atom are treated using the semigroup formalism. The vibrational excitation leading to subsurface absorption is performed using rationally designed pulses as well as IR laser pulses optimized on- the-fly. It is shown that dissipation can be used as a tool to transfer population to an otherwise inaccessible state via a mechanism known as "laser distillation." We demonstrate that when the reaction path is generalized from a reduced one-dimensional to full three-dimensional treatment of the system, the laser control strategy can prove very different.
The BLUF (blue-light sensing using flavine) domain of the AppA photoreceptor protein from Rhodobacter sphaeroides was modelled by using quantum chemical chromophore plus amino acid models at the (TD-)B3LYP/6-31G* level of theory. The models were based on NMR structures, and further refined by CHARM force field molecular dynamics simulations. The goal is to explain the total redshift by about 10 nm in the UV/Vis spectra of BLUF domains after illumination, and to relate it to structural changes. For this purpose UV/Vis spectra of the available NMR structures were calculated and related to geometrical features. In particular, the hydrogen network embedding the central chromophore is discussed. Specifically, the position of a conserved glutamine, Q63, is found to be important in agreement with findings from previous works. Additionally, however, we find a systematic dependence also on the geometry of a conserved serine, S41. Based on a series of calculations with known structures and with artificial structural models, we argue that indeed the light-induced switching of both Q63 and S41 is necessary to explain the full similar to 10 nm redshift in the light (signalling) state of serine containing BLUF domains. Following or accompanying the double switching, two structurally highly important residues W104 and M106 exchange places, but do not affect the overall UV/ Vis properties of the chromophore.
Quantum chemical calculations of various azobenzene (AB) derivatives have been carried out with the goal to describe the energetics and kinetics of their thermal cis -> trans isomerization. The effects of substituents, in particular their type, number, and positioning, on activation energies have been systematically studied with the ultimate goal to tailor the switching process. Trends observed for mono- and disubstituted species are discussed. A polarizable continuum model is used to study, in an approximate fashion, the cis -> trans isomerization of azobenzenes in solution. The nature of the transition state(s) and its dependence on substituents and the environment is discussed. In particular for push-pull azobenzenes, the reaction mechanism is found to change from inversion in nonpolar solvents to rotation in polar solvents. Concerning kinetics, calculations based on the Eyring transition state theory give usually reliable activation energies and enthalpies when compared to experimentally determined values. Also, trends in the resulting rate constants are correct. Other computed properties such as activation entropies and thus preexponential rate factors are in only moderate agreement with experiment.
In this paper, we report simulations of laser-driven many-electron dynamics by means of the time-dependent configuration interaction singles (TD-CIS) approach. The method is capable of describing explicitly time-dependent phenomena beyond perturbation theory and is systematically improvable. In contrast to most time-dependent density functional methods it also allows us to treat long-range charge-transfer states properly. As an example, the laser-pulse induced charge transfer between a donor (ethylene) and an acceptor molecule (tetracyanoethylene, TCNE) is studied by means of TD-CIS. Also, larger aggregates consisting of several donors and/or acceptors are considered. It is shown that the charge distribution and hence the dipole moments of the systems under study are switchable by (a series of) laser pulses which induce selective, state-to-state electronic transitions.
We report simulations of laser-pulse driven many-electron dynamics by means of a simple, heuristic extension of the time-dependent configuration interaction singles (TD-CIS) approach. The extension allows for the treatment of ionizing states as nonstationary states with a finite, energy-dependent lifetime to account for above-threshold ionization losses in laser-driven many-electron dynamics. The extended TD-CIS method is applied to the following specific examples: (i) state-to-state transitions in the LiCN molecule which correspond to intramolecular charge transfer, (ii) creation of electronic wave packets in LiCN including wave packet analysis by pump-probe spectroscopy, and, finally, (iii) the effect of ionization on the dynamic polarizability of H-2 when calculated nonperturbatively by TD-CIS.
The biconformational switching of single cyclooctadiene molecules chemisorbed on a Si(001) surface was explored by quantum chemical and quantum dynamical calculations and low-temperature scanning tunneling microscopy experiments. The calculations rationalize the experimentally observed switching driven by inelastic electron tunneling (IET) at 5 K. At higher temperatures, they predict a controllable crossover behavior between IET-driven and thermally activated switching, which is fully confirmed by experiment.
The femtosecond-laser-induced, substrate-mediated associative desorption of molecular hydrogen and deuterium from a Ru(0001) surface in the so-called DIMET limit is studied theoretically. Two widely used models, a "quantum nonadiabatic" approach and a "classical adiabatic" one are employed and compared to each other. The quantum model is realized by the Monte Carlo wave packet (MCWP) method in the framework of open-system density matrix theory: The classical approach is realized with the help of (frictional) Langevin dynamics with stochastic forces. For both models the same ground-state potential energy surface is used and the same two-temperature model adopted to describe the hot- electron-driven desorption dynamics. Apart from these common features both models are different. Still, both account well for the main experimental findings (Wagner et al. Phys. Rev. B 2005, 72, 205404). In particular, an isotope effect in desorption probabilities, the energy content of the desorbing molecules, and the scaling of these observables with laser fluence are reproduced and explained. The similarity of the results obtained with both models is traced back to the fact that, in the present case, the photodynamics takes place dominantly in the ground electronic state because the electronically excited state is rapidly quenched. The short lifetime of the excited state has also the effect that photoreaction cross sections are typically very small. An IR+vis hybrid scheme, by which the adsorbate is vibrationally excited by IR photons prior to the heating of metal electrons with the vis pulse, is shown to successfully promote the reaction even for strongly coupled adsorbate-surface systems.
Near edge X-ray absorption. ne structure and X-ray photoelectron spectroscopy have been employed to follow the reversible trans to cis isomerization of tetra-tert-butyl-azobenzene (TBA) adsorbed on Au(111). For one monolayer the molecules adopt an adsorption geometry characteristic of the trans-TBA isomer. The azo-bridge (N = N) is aligned nearly parallel to the surface and the phenyl rings exhibit a planar orientation with a small tilt angle <= 4 degrees with respect to the surface normal. Illumination of the molecular layer at 455 nm triggers the trans to cis isomerization which is associated with a pronounced change of the geometrical and electronic structure. The N1s to pi* transition of the central azo-bridge shifts by 0.45 +/- 0.05 eV to higher photon energy and the transition dipole moment (TDM) is tilted by 59 +/- 5 degrees with respect to the surface normal. The pi-system of one phenyl ring is tilted by about 30 degrees with respect to the surface normal, while the second ring plane is oriented nearly perpendicular to the surface. This reorientation is supported by a shift and broadening of the C-H resonances associated with the tert-butyl legs of the molecule. These findings support a configuration of the photo-switched TBA molecule on Au(111) which is comparable to the cis-isomer of the free molecule. In the photo-stationary state 53 +/- 5% of the TBA molecules are switched to the cis configuration. Thermal activation induces the back reaction to trans-TBA.
Fluoroionophores of fluorophore-spacer-receptor format were prepared for detection of PdCl2 by fluorescence enhancement. The fluorophore probes 1-13 consist of a fluorophore group, in alkyl spacer and a dithiomaleonitrile PdCl2 receptor. First, varying the length of the alkylene spacer (compounds 1-3) revealed, dominant through-space pathway for oxidative photoinduced electron transfer (PET) in CH2-bridged dithiomaleonitrile fluoroionophores. Second. fluorescent probes 4-9 containing two anthracene or pyrene fragments connected through CH2 bridges to the dithiomaleonitrile unit were synthesized. Modulation of the oxidation potential (E-Ox) through electron-withdrawing or -donating groups on the anthracene moiety regulates file thermodynamic driving force for oxidative PET (Delta G(PET)) in bis(anthrylmethylthio)maleonitriles and therefore the fluorescence quantum yields (Phi(f)), too. The new concept was confirmed and transferred to pyrenyl ligands, and fluorescence enhancements (FE) greater than 3.2 in the presence of PdCl2 were achieved by 7 and 8 (FE=5.4 and 5.2). Finally, for comparison, monofluorophore ligands 10-13 were synthesized.