TY - JOUR A1 - Klaumünzer, Bastian A1 - Kröner, Dominik A1 - Lischka, Hans A1 - Saalfrank, Peter T1 - Non-adiabatic excited state dynamics of riboflavin after photoexcitation JF - Physical chemistry, chemical physics : a journal of European Chemical Societies N2 - Flavins are chromophores in light-gated enzymes and therefore central in many photobiological processes. To unravel the optical excitation process as the initial, elementary step towards signal transduction, detailed ultrafast (femtosecond) experiments probing the photo-activation of flavins have been carried out recently [Weigel et al., J. Phys. Chem. B, 2011, 115, 3656-3680.]. The present paper contributes to a further understanding and interpretation of these experiments by studying the post-excitation vibrational dynamics of riboflavin (RF) and microsolvated riboflavin, RF center dot 4H(2)O, using first principles non-adiabatic molecular dynamics. By analyzing the characteristic atom motions and calculating time-resolved stimulated emission spectra following pi pi* excitation, it is found that after optical excitation C-N and C-C vibrations in the isoalloxazine rings of riboflavin set in. The Franck-Condon (vertically excited) state decays within about 10 fs, in agreement with experiment. Anharmonic coupling leads to Intramolecular Vibrational energy Redistribution (IVR) on the timescale of about 80-100 fs, first to (other) C-C stretching modes of the isoalloxazine rings, then by energy spread over the whole molecule, including low-frequency in-plane modes. The IVR is accompanied by a red-shift and broadening of the emission spectrum. When RF is microsolvated with four water molecules, an overall redshift of optical spectra by about 20 nm is observed but the relaxation dynamics is only slightly affected. For several trajectories, a tendency for hydrogen transfer from water to flavin-nitrogen (N-5) was found. Y1 - 2012 U6 - https://doi.org/10.1039/c2cp40978j SN - 1463-9076 VL - 14 IS - 24 SP - 8693 EP - 8702 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Zenichowski, Karl A1 - Dokic, Jadranka A1 - Klamroth, Tillmann A1 - Saalfrank, Peter T1 - Current versus temperature-induced switching of a single molecule - open-system density matrix theory for 1,5-cyclooctadiene on Si(100) JF - The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr N2 - 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. Y1 - 2012 U6 - https://doi.org/10.1063/1.3692229 SN - 0021-9606 VL - 136 IS - 9 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Götze, Jan Philipp A1 - Saalfrank, Peter T1 - Quantum chemical modeling of the kinetic isotope effect of the carboxylation step in RuBisCO JF - Journal of molecular modeling N2 - Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the most important enzyme for the assimilation of carbon into biomass, features a well-known isotope effect with regards to the CO2 carbon atom. This kinetic isotope effect alpha = k (12)/k (13) for the carboxylation step of the RuBisCO reaction sequence, and its microscopic origin, was investigated with the help of cluster models and quantum chemical methods [B3LYP/6-31G(d,p)]. We use a recently proposed model for the RuBisCO active site, in which a water molecule remains close to the reaction center during carboxylation of ribulose-1,5-bisphosphate [B. Kannappan, J.E. Gready, J. Am. Chem. Soc. 130 (2008), 15063]. Alternative active-site models and/or computational approaches were also tested. An isotope effect alpha for carboxylation is found, which is reasonably close to the one measured for the overall reaction, and which originates from a simple frequency shift of the bending vibration of (CO2)-C-12 compared to (CO2)-C-13. The latter is the dominant mode for the product formation at the transition state. KW - Cluster model KW - Dark reactions KW - Densityfunctional theory KW - Isotope effect KW - Photosynthesis KW - Quantum chemistry KW - RuBisCO Y1 - 2012 U6 - https://doi.org/10.1007/s00894-011-1207-0 SN - 1610-2940 VL - 18 IS - 5 SP - 1877 EP - 1883 PB - Springer CY - New York ER - TY - JOUR A1 - Füchsel, Gernot A1 - Tremblay, Jean Christophe A1 - Klamroth, Tillmann A1 - Saalfrank, Peter T1 - Selective excitation of molecule-surface vibrations in H2 and D2 dissociatively adsorbed on Ru(0001) JF - Israel journal of chemistry N2 - In this contribution we report about the selective vibrational excitation of H2 and D2 on Ru(0001) as an example for nonadiabatic coupling of an open quantum system to a dissipative environment. We investigate the possibility of achieving state-selective vibrational excitations of H2 and D2 adsorbed on a Ru(0001) surface using picosecond infrared laser pulses. The systems behavior is explored using pulses that are rationally designed and others that are optimized using a time-local variant of Optimal Control Theory. The effects of dissipation on the laser-driven dynamics are studied using the reduced-density matrix formalism. The non-adiabatic couplings between adsorbate and surface are computed perturbatively, for which our recently introduced state-resolved anharmonic rate model is used. It is shown that mode- and state-selective excitation can be achieved in the absence of dissipation when using optimized laser pulses. The inclusion of dissipation in the model reduces the state selectivity and the population transfer yield to highly excited states. In this case, mode activation is most effectively realized by a rational pulse of carefully chosen duration rather than by a locally optimized pulse. KW - dissipative dynamics KW - photochemistry KW - quantum control KW - surface chemistry Y1 - 2012 U6 - https://doi.org/10.1002/ijch.201100097 SN - 0021-2148 VL - 52 IS - 5 SP - 438 EP - 451 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Tremblay, Jean Christophe A1 - Füchsel, Gernot A1 - Saalfrank, Peter T1 - Excitation, relaxation, and quantum diffusion of CO on copper JF - Physical review : B, Condensed matter and materials physics N2 - We investigate the effect of intermode coupling and anharmonicity on the excitation and relaxation dynamics of CO on Cu(100). The nonadiabatic coupling of the adsorbate to the surface is treated perturbatively using a position-dependent state-resolved transition rate model. Using the potential energy surface of Marquardt et al. [J. Chem. Phys. 132, 074108 (2010)], which provides an accurate description of intermode interactions, we propose a four-dimensional model that represents simultaneously the diffusion and the desorption of the adsorbate. The system is driven by both rational and optimized infrared laser pulses to favor either selective mode and state excitations or lateral displacement along the diffusion coordinate. The dissipative dynamics is simulated using the reduced density matrix in its Lindblad form. We show that coupling between the degrees of freedom, mediated by the creation and annihilation of electron-hole pairs in the metal substrate, significantly affects the system excitation and relaxation dynamics. In particular, the angular degrees of freedom appear to play an important role in the energy redistribution among the molecule-surface vibrations. We also show that coherent excitation using simple IR pulses can achieve population transfer to a specific target to some extent but does not allow enforcement of the directionality to the diffusion motion. Y1 - 2012 U6 - https://doi.org/10.1103/PhysRevB.86.045438 SN - 1098-0121 SN - 1550-235X VL - 86 IS - 4 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Bronner, C. A1 - Leyssner, F. A1 - Stremlau, S. A1 - Utecht, Manuel Martin A1 - Saalfrank, Peter A1 - Klamroth, Tillmann A1 - Tegeder, P. T1 - Electronic structure of a subnanometer wide bottom-up fabricated graphene nanoribbon: End states, band gap, and dispersion JF - Physical review : B, Condensed matter and materials physics N2 - Angle-resolved two-photon photoemission and high-resolution electron energy loss spectroscopy are employed to derive the electronic structure of a subnanometer atomically precise quasi-one-dimensional graphene nanoribbon (GNR) on Au(111). We resolved occupied and unoccupied electronic bands including their dispersion and determined the band gap, which possesses an unexpectedly large value of 5.1 eV. Supported by density functional theory calculations for the idealized infinite polymer and finite size oligomers, an unoccupied nondispersive electronic state with an energetic position in the middle of the band gap of the GNR could be identified. This state resides at both ends of the ribbon (end state) and is only found in the finite sized systems, i.e., the oligomers. Y1 - 2012 U6 - https://doi.org/10.1103/PhysRevB.86.085444 SN - 1098-0121 VL - 86 IS - 8 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Zenichowski, Karl A1 - Nacci, Ch A1 - Fölsch, S. A1 - Dokic, Jadranka A1 - Klamroth, Tillmann A1 - Saalfrank, Peter T1 - STM-switching of organic molecules on semiconductor surfaces: an above threshold density matrix model for 1,5 cyclooctadiene on Si(100) JF - Journal of physics : Condensed matter N2 - 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. Y1 - 2012 U6 - https://doi.org/10.1088/0953-8984/24/39/394009 SN - 0953-8984 VL - 24 IS - 39 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Bouakline, Foudhil A1 - Lüder, Franziska A1 - Martinazzo, Rocco A1 - Saalfrank, Peter T1 - Reduced and exact quantum dynamics of the vibrational relaxation of a molecular system interacting with a finite-dimensional bath JF - The journal of physical chemistry : A, Molecules, spectroscopy, kinetics, environment & general theory N2 - We investigate the vibrational relaxation of a Morse oscillator, nonlinearly coupled to a finite-dimensional bath of harmonic oscillators at zero temperature, using two different approaches: Reduced dynamics with the help of the Lindblad formalism of reduced density matrix theory in combination with Fermi's Golden Rule, and exact dynamics (within the chosen model). with the multiconfiguration time-dependent Hartree (MCTDH) method. Two different models have been constructed, the situation where the bath spectrum is exactly resonant with the anharmonic oscillator transition frequencies, and the case for which the subsystem is slightly off-resonant with the environment. At short times, reduced dynamics calculations describe the relaxation process qualitatively well but fail to reproduce recurrences observed with MCTDH for longer times. Lifetimes of all the vibrational levels of the Morse oscillator have been calculated, and both Lindblad and MCTDH. results show the same dependence of the lifetimes on the initial vibrational state quantum number. A prediction, which should be generic for adsorbate systems is a striking, sharp increase of lifetimes of the subsystem vibrational levels close to the dissociation This is contradictory with harmonic/linear extrapolation laws, which predict a monotonic decrease of the lifetime with initial vibrational quantum number. Y1 - 2012 U6 - https://doi.org/10.1021/jp304466u SN - 1089-5639 VL - 116 IS - 46 SP - 11118 EP - 11127 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Floss, Gereon A1 - Granucci, Giovanni A1 - Saalfrank, Peter T1 - Surface hopping dynamics of direct trans -> cis photoswitching of an azobenzene derivative in constrained adsorbate geometries JF - The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr N2 - With ongoing miniaturization of electronic devices, the need for individually addressable, switchable molecules arises. An example are azobenzenes on surfaces which have been shown to be switchable between trans and cis forms. Here, we examine the "direct" (rather than substrate-mediated) channel of the trans -> cis photoisomerization after pi pi* excitation of tetra-tert-butyl-azobenzene physisorbed on surfaces mimicking Au(111) and Bi(111), respectively. In spirit of the direct channel, the electronic structure of the surface is neglected, the latter merely acting as a rigid platform which weakly interacts with the molecule via Van-der-Waals forces. Starting from thermal ensembles which represent the trans-form, sudden excitations promote the molecules to pi pi*-excited states which are non-adiabatically coupled among themselves and to a n pi*-excited and the ground state, respectively. After excitation, relaxation to the ground state by internal conversion takes place, possibly accompanied by isomerization. The process is described here by "on the fly" semiclassical surface hopping dynamics in conjunction with a semiempirical Hamiltonian (AM1) and configuration-interaction type methods. It is found that steric constraints imposed by the substrate lead to reduced but non-vanishing, trans -> cis reaction yields and longer internal conversion times than for the isolated molecule. Implications for recent experiments for azobenzenes on surfaces are discussed. KW - AM1 calculations KW - bismuth KW - configuration interactions KW - excited states KW - gold KW - isomerisation KW - organic compounds KW - photochemistry KW - van der Waals forces Y1 - 2012 U6 - https://doi.org/10.1063/1.4769087 SN - 0021-9606 VL - 137 IS - 23 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Wirth, Jonas A1 - Saalfrank, Peter T1 - The chemistry of water on alpha-alumina kinetics and nuclear quantum effects from first principles JF - The journal of physical chemistry : C, Nanomaterials and interfaces N2 - Water adsorption on an alumina (alpha-Al2O3) surface is studied here from first principles using periodic density functional theory in the generalized gradient approximation. Two different coverage regimes, low and high, are considered. For the low-coverage regime (with a coverage of 1/4 with respect to the number of coordinatively unsaturated Al sites), possible reactions at the surface such as dissociation, rotation, and diffusion of water and its fragments are investigated, using first principles thermodynamics and kinetics. A microkinetic model is set up with rates calculated from Eyring's transition state theory in order to cover a wide range of time scales. Special emphasis of this study is on the magnitude of quantum effects and on anharmonic corrections, particularly for reactions and dynamics. These have often been neglected in the past for water/alumina systems but can influence the system. This is particularly true for processes involving hydrogen atoms, where, for example, tunneling corrections to reaction rates are found to be important even at room temperature. For a higher-coverage regime (with a coverage of 2 ML), hydrogen dynamics becomes even more complex and is characterized, e.g., by concerted atom motion, strong anharmonicity, and delocalization. In this regime, classical molecular dynamics becomes questionable as well as quantum mechanical treatments based on the harmonic approximation. Y1 - 2012 U6 - https://doi.org/10.1021/jp310234h SN - 1932-7447 VL - 116 IS - 51 SP - 26829 EP - 26840 PB - American Chemical Society CY - Washington ER -