@phdthesis{Dokić2009, author = {Dokić, Jadranka}, title = {Quantum mechanical study of molecular switches : electronic structure, kinetics and dynamical aspects}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41796}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Molecular photoswitches are attracting much attention lately mostly because of their possible applications in nano technology, and their role in biology. One of the widely studied representatives of photochromic molecules is azobenzene (AB). With light, by a static electric field, or with tunneling electrons this specie can be "switched" from the flat and energetically more stable trans form, into the compact cis form. The back reaction can be induced optically or thermally. Quantum chemical calculations, mostly based on density functional theory, on the AB molecule, AB derivatives and related systems are presented. All the calculations were done for isolated species, however, with implications for latest experimental results aiming at the switching of surface mounted ABs. In some of these experiments, it is assumed that the switching process is substrate mediated, by attaching an electron or a hole to the adsorbate forming short-lived anion or cation resonances. Therefore, we calculated also cationic and anionic ABs in this work. An influence of external electric fields on the potential energy surfaces, was also studied. Further, by the type, number and positioning of various substituent groups, systematic changes on activation energies and rates for the thermal cis-to-trans isomerization can be enforced. The nature of the transition state for ground state isomerization was investigated. Applying Eyring's transition state theory, trends in activation energies and rates were predicted and are, where a comparison was possible, in good agreement with experimental data. Further, thermal isomerization was studied in solution, for which a polarizable continuum model was employed. The influence of substitution and an environment leaves its traces on structural properties of molecules and quantitative appearance of calculated UV/Vis spectra, as well. Finally, an explicit treatment of a solid substrate was demonstrated for the conformational switching, by scanning tunneling microscope, of a 1,5-cyclooctadiene (COD) molecule at a Si(001) surface, treated by a cluster model. At first, we studied energetics and potential energy surfaces along relevant switching coordinates by quantum chemical calculations, followed by the switching dynamics using wave packet methods. We show that, in spite the simplicity of the model, our calculations support the switching of adsorbed COD, by inelastic electron tunneling at low temperatures.}, language = {en} } @article{FuechselKlamrothDokicetal.2006, author = {F{\"u}chsel, Gernot and Klamroth, Tillmann and Dokic, Jadranka and Saalfrank, Peter}, title = {On the electronic structure of neutral and ionic azobenzenes and their possible role as surface mounted molecular switches}, series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, volume = {110}, journal = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, number = {33}, publisher = {Soc.}, address = {Washington}, issn = {1520-6106}, doi = {10.1021/jp060969v}, pages = {16337 -- 16345}, year = {2006}, abstract = {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.}, language = {en} } @article{SchmidtHagenBreteetal.2010, author = {Schmidt, Roland and Hagen, Sebastian and Brete, Daniel and Carley, Robert and Gahl, Cornelius and Dokic, Jadranka and Saalfrank, Peter and Hecht, Stefan and Tegeder, Petra and Weinelt, Martin}, title = {On the electronic and geometrical structure of the trans- and cis-isomer of tetra-tert-butyl-azobenzene on Au(111)}, issn = {1463-9076}, doi = {10.1039/B924409c}, year = {2010}, abstract = {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.}, language = {en} } @article{BlegerDokicPetersetal.2011, author = {Bleger, David and Dokic, Jadranka and Peters, Maike V. and Grubert, Lutz and Saalfrank, Peter and Hecht, Stefan}, title = {Electronic decoupling approach to quantitative photoswitching in linear multiazobenzene architectures}, series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, volume = {115}, journal = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, number = {33}, publisher = {American Chemical Society}, address = {Washington}, issn = {1520-6106}, doi = {10.1021/jp2044114}, pages = {9930 -- 9940}, year = {2011}, abstract = {A strategy to optimize the photoswitching efficiency of rigid, linear multiazobenzene constructs is presented. It consists of introducing large dihedral angles between azobenzene moieties linked via aryl-aryl connections in their para positions. Four bisazobenzenes exhibiting different dihedral angles as well as three single azobenzene reference compounds have been synthesized, and their switching behavior has been studied as well as experimentally and theoretically analyzed. As the dihedral angle between the two azobenzene units increases and consequently the electronic conjugation decreases, the photochromic characteristics improve, finally leading to individual azobenzene switches operating independently in the case of the perpendicular ortho,ortho,ortho',ortho'-tetramethyl biphenyl linker. The electronic decoupling leads to efficient separation of the absorption spectra of the involved switching states and hence by choosing the appropriate irradiation wavelength, an almost quantitative E -> Z photoisomerization up to 97\% overall Z-content can be achieved. In addition, thermal Z -> E isomerization processes become independent of each other with increasing decoupling. The electronic decoupling could furthermore be proven by electrochemistry. The experimental data are supported by theory, and calculations additionally provide mechanistic insight into the preferred pathway for the thermal Z,Z -> Z,E -> E,E isomerization via inversion on the inner N-atoms. Our decoupling approach outlined herein provides the basis for constructing rigid rod architectures composed of multiple azobenzene photochromes, which display practically quantitative photoswitching properties, a necessary prerequisite to achieve highly efficient transduction of light energy directly into motion.}, language = {en} } @article{LuoUtechtDokicetal.2011, author = {Luo, Ying and Utecht, Manuel Martin and Dokic, Jadranka and Korchak, Sergey and Vieth, Hans-Martin and Haag, Rainer and Saalfrank, Peter}, title = {Cis-trans isomerisation of substituted aromatic imines a comparative experimental and theoretical study}, series = {ChemPhysChem : a European journal of chemical physics and physical chemistry}, volume = {12}, journal = {ChemPhysChem : a European journal of chemical physics and physical chemistry}, number = {12}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1439-4235}, doi = {10.1002/cphc.201100179}, pages = {2311 -- 2321}, year = {2011}, abstract = {The cis-trans isomerisation of N-benzylideneaniline (NBA) and derivatives containing a central C=N bond has been investigated experimentally and theoretically. Eight different NBA molecules in three different solvents were irradiated to enforce a photochemical trans (hv) -> cis isomerisation and the kinetics of the thermal backreaction cis (Delta)-> trans were determined by NMR spectroscopy measurements in the temperature range between 193 and 288 K. Theoretical calculations using density functional theory and Eyring transition-state theory were carried out for 12 different NBA species in the gas phase and three different solvents to compute thermal isomerisation rates of the thermal back reaction. While the computed absolute rates are too large, they reveal and explain experimental trends. Time-dependent density functional theory provides optical spectra for vertical transitions and excitation energy differences between trans and cis forms. Together with isomerisation rates, the latter can be used to identify "optimal switches" with good photochromicity and reasonable thermal stability.}, language = {en} } @article{DokicGotheWirthetal.2009, author = {Dokic, Jadranka and Gothe, Marcel and Wirth, Jonas and Peters, Maike V. and Schwarz, Jutta and Hecht, Stefan and Saalfrank, Peter}, title = {Quantum chemical investigation of thermal cis-to-trans isomerization of azobenzene derivatives : substituent effects, solvent effects, and comparison to experimental data}, issn = {1089-5639}, doi = {10.1021/jp9021344}, year = {2009}, abstract = {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.}, language = {en} } @article{NacciFoelschZenichowskietal.2009, author = {Nacci, Christophe and Foelsch, Stefan and Zenichowski, Karl and Dokic, Jadranka and Klamroth, Tillmann and Saalfrank, Peter}, title = {Current versus temperature-induced switching in a single-molecule tunnel junction : 1,5 cyclooctadiene on Si(001)}, issn = {1530-6984}, doi = {10.1021/Nl901419g}, year = {2009}, abstract = {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.}, language = {en} } @article{ZenichowskiDokicKlamrothetal.2012, author = {Zenichowski, Karl and Dokic, Jadranka and Klamroth, Tillmann and Saalfrank, Peter}, title = {Current versus temperature-induced switching of a single molecule - open-system density matrix theory for 1,5-cyclooctadiene on Si(100)}, series = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr}, volume = {136}, journal = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr}, number = {9}, publisher = {American Institute of Physics}, address = {Melville}, issn = {0021-9606}, doi = {10.1063/1.3692229}, pages = {13}, year = {2012}, abstract = {The switching of single cyclooctadiene molecules chemisorbed on a Si(100) surface between two stable conformations, can be achieved with a scanning tunneling microscope [Nacci , Phys. Rev. B 77, 121405(R) (2008)]. Recently, it was shown by quantum chemical and quantum dynamical simulations that major experimental facts can be explained by a single-mode model with switching enforced by inelastic electron tunneling (IET) excitations and perturbed by vibrational relaxation [Nacci , Nano Lett. 9, 2997 (2009)]. In the present paper, we extend the previous theoretical work in several respects: (1) The model is generalized to a two-mode description in which two C2H4 units of COD can move independently; (2) contributions of dipole and, in addition, (cation and anion) resonance-IET rates are considered; (3) the harmonic-linear vibrational relaxation model used previously is generalized to anharmonic vibrations. While the present models highlight generic aspects of IET-switching between two potential minima, they also rationalize specific experimental findings for COD/Si(100): (1) A single-electron excitation mechanism with a linear dependence of the switching rate on tunneling current I, (2) the capability to switch both at negative and positive sample biases, and (3) a crossover temperature around similar to 60 K from an IET-driven, T-independent atom tunneling regime, to classical over-the-barrier isomerization with exponential T-dependence at higher temperatures for a bias voltage of +1.5 V and an average tunneling current of 0.73 nA.}, language = {en} } @article{ZenichowskiNacciFoelschetal.2012, author = {Zenichowski, Karl and Nacci, Ch and F{\"o}lsch, S. and Dokic, Jadranka and Klamroth, Tillmann and Saalfrank, Peter}, title = {STM-switching of organic molecules on semiconductor surfaces: an above threshold density matrix model for 1,5 cyclooctadiene on Si(100)}, series = {Journal of physics : Condensed matter}, volume = {24}, journal = {Journal of physics : Condensed matter}, number = {39}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {0953-8984}, doi = {10.1088/0953-8984/24/39/394009}, pages = {11}, year = {2012}, abstract = {The scanning tunnelling microscope (STM)-induced switching of a single cyclooctadiene molecule between two stable conformations chemisorbed on a Si(100) surface is investigated using an above threshold model including a neutral ground state and an ionic excited state potential. Switching was recently achieved experimentally with an STM operated at cryogenic temperatures (Nacci et al 2008 Phys. Rev. B 77 121405(R)) and rationalized by a below threshold model using just a single potential energy surface (Nacci et al 2009 Nano Lett. 9 2997). In the present paper, we show that experimental key findings on the inelastic electron tunnelling (IET) switching can also be rationalized using an above threshold density matrix model, which includes, in addition to the neutral ground state potential, an anionic or cationic excited potential. We use one and two-dimensional potential energy surfaces. Furthermore, the influence of two key parameters of the density matrix description, namely the electronic lifetime of the ionic resonance and the vibrational lifetimes, on the ground state potential are discussed.}, language = {en} }