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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.
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.
The quantum chemical description of the adsorption, vibrations, and reactions of molecules at periodic solid surfaces is frequently based on a methodological "standard model": density functional theory (DFT) in the generalized gradient approximation (GGA), using plane wave bases and three-dimensional supercells. Although the computationally efficient GGA functionals can be very successful, cases are known where they do not perform so well. Most importantly, activation energies for chemical reactions are typically underestimated, with the consequence of computed reaction rates being too large. In this work, we consider a well-studied model system: water or water fragments adsorbed on an Al-terminated alpha-Al2O3(0001) surface as a test bed for studying the performance of electronic structure methods, both from DFT and wave function theory. On the DFT side, we employ two GGA exchange correlation functionals: PW91 and PBE with and without dispersion corrections, whose results are then compared to those of hybrid functionals B3LYP and HSE06. Further, we follow a periodic wave function approach in the form of local second-order Moller-Plesset perturbation theory, LMP2, on a Hartree-Fock reference. En route, we address issues arising from the choice of the basis set. The key findings of our study are as follows: (i) DFT-GGA adsorption energies are in reasonable agreement with both hybrid-DFT and LMP2 values. In particular, the deviations between the relative energies, corresponding to different adsorption structures, are in the range of the error due to missing dispersion corrections or the basis set error. (ii) Harmonic DFT-GGA vibrational frequencies for oxygen hydrogen stretch modes are by several tens of wavenumbers red-shifted compared to corresponding hybrid-DFT values. The latter are in much better agreement with recent experimental data. (iii) The activation energy for a hydrogen diffusion reaction is grossly underestimated by GGA compared to hybrid-DFT or LMP2, which in turn are quite comparable.
Recent molecular beam experiments have shown that water may adsorb molecularly or dissociatively on an α-Al2O3(0001) surface, with enhanced dissociation probability compared to “pinhole dosing”, i.e., adsorption under thermal equilibrium conditions. However, precise information on the ongoing reactions and their relative probabilities is missing. In order to shed light on molecular beam scattering for this system, we perform ab initio molecular dynamics calculations to simulate water colliding with α-Al2O3(0001). We find that single water molecules hitting a cold, clean surface from the gas phase are either reflected, molecularly adsorbed, or dissociated (so-called 1–2 dissociation only). A certain minimum translational energy (above 0.1 eV) seems to be required to enforce dissociation, which may explain the higher dissociation probability in molecular beam experiments. When the surface is heated and/or when refined surface and beam models are applied (preadsorption with water or water fragments, clustering and internal preexcitation in the beam), additional channels open, among them physisorption, water clustering on the surface, and so-called 1–4 and 1–4′ dissociation.
α-Al2O3 surfaces are common in a wide variety of applications and useful models of more complicated, environmentally abundant, alumino-silicate surfaces. While decades of work have clarified that all properties of these surfaces depend sensitively on the crystal face and the presence of even small amounts of water, quantitative insight into this dependence has proven challenging. Overcoming this challenge requires systematic study of the mechanism by which water interacts with various α-Al2O3 surfaces. Such insight is most easily gained for the interaction of small amounts of water with surfaces in ultra high vacuum. In this study, we continue our combined theoretical and experimental approach to this problem, previously applied to water interaction with the α-Al2O3 (0001) and (11̅02) surfaces, now to water interaction with the third most stable surface, that is, the (112̅0). Because we characterize all three surfaces using similar tools, it is straightforward to conclude that the (112̅0) is most reactive with water. The most important factor explaining its increased reactivity is that the high density of undercoordinated surface Al atoms on the (112̅0) surface allows the bidentate adsorption of OH fragments originating from dissociatively adsorbed water, while only monodentate adsorption is possible on the (0001) and (11̅02) surfaces: the reactivity of α-Al2O3 surfaces with water depends strongly, and nonlinearly, on the density of undercoordinated surface Al atoms.
The oxidation and spin state of a metal-organic molecule determine its chemical reactivity and magnetic properties. Here, we demonstrate the reversible control of the oxidation and spin state in a single Fe porphyrin molecule in the force field of the tip of a scanning electron tunneling microscope. Within the regimes of half-integer and integer spin state, we can further track the evolution of the magnetocrystalline anisotropy. Our experimental results are corroborated by density functional theory and wave function theory. This combined analysis allows us to draw a complete picture of the molecular states over a large range of intramolecular deformations.
The photochemistry as well as electrochemistry of novel donor-acceptor bis(morpholinothiazolyl)maleimides has been investigated. Proper substitution of these diarylethene-type molecular switches leads to the unique situation in which their ring-closure can only be accomplished electrochemically, while ring-opening can only be achieved photochemically. Hence, these switches operate with orthogonal stimuli, i.e. redox potential and light, respectively. The switch system could be optimized by introducing trifluoromethyl groups at the reactive carbon atoms in order to avoid by-product formation during oxidative ring closure. Both photochemical and electrochemical pathways were investigated for methylated, trifluoromethylated, and nonsymmetrical bis(morpholinothiazolyl) maleimides as well as the bis(morpholinothiazolyl) cyclopentene reference compound. With the aid of the nonsymmetrical "mixed" derivative, the mechanism of electrochemically driven ring closure could be elucidated and seems to proceed via a dicationic intermediate generated by two-fold oxidation. All experimental work has been complemented by density functional theory that provides detailed insights into the thermodynamics of the ring-open and closed forms, the nature of their excited states, and the reactivity of their neutral as well as ionized species in different electronic configurations. The particular diarylethene systems described herein could serve in multifunctional (logic) devices operated by different stimuli (inputs) and may pave the way to converting light into electrical energy via photoinduced "pumping" of redox-active meta-stable states.
Combining photochromism and nonlinear optical (NLO) properties of molecular switches-functionalized self-assembled monolayers (SAMs) represents a promising concept toward novel photonic and optoelectronic devices. Using second harmonic generation, density functional theory, and correlated wave function methods, we studied the switching abilities as well as the NLO contrasts between different molecular states of various fulgimide-containing SAMs on Si(111). Controlled variations of the linker systems as well as of the fulgimides enabled us to demonstrate very efficient reversible photoinduced ring-opening/closure reactions between the open and closed forms of the fulgimides. Thus, effective cross sections on the order of 10(-18) cm(-2) are observed. Moreover, the reversible switching is accompanied by pronounced NLO contrasts up to 32%. Further molecular engineering of the photochromic switches and the linker systems may even increase the NLO contrast upon switching.
We perform ab initio molecular dynamics simulations to study the femtosecond laser induced desorption of H-2, D-2, and HD from a H: D-saturated Ru(0001) surface. To this aim we have extended the ab initio molecular dynamics with electronic friction (AIMDEF) scheme to include a random force that is a function of a timedependent electronic temperature. The latter characterizes the action of the ultrashort laser pulse according to a two temperature model. This allows us to perform multidimensional, hot-electron driven reaction dynamics and investigate the dependence of the desorption yields on the relative H: D isotope concentration on the surface. Our AIMDEF simulations show that the desorption process takes place in the presence of a heated adsorbate system that clearly influences the desorption dynamics. The heating of the adsorbate system is more (less) pronounced the larger is the concentration of the lighter (heavier) isotope. As a result, we conclude that the presence of H on the surface favors the desorption of molecules, whereas the presence of D hampers it, in agreement with previous experimental observations in which the phenomenon of "dynamical promotion" of a surface reaction had been postulated.
alpha-Al2O3 surfaces are common in both engineered applications and the environment. Much prior work indicates that their properties, e.g., reactivity, polarity, and charge, change dramatically on interaction with water. Perhaps the simplest question that can be asked of alpha-Al2O3/water interaction is how a single water molecule interacts with the most stable alpha-Al2O3 surface: the alpha-Al2O3(0001). Over the last 15 years, a series of theoretical studies have found that water dissociatively adsorbs on alpha-Al2O3(0001) through two channels. However, to our knowledge no experimental evidence of these dissociation pathways has appeared. By combining sample preparation via supersonic molecular beam dosing, sample characterization via coherent, surface specific vibrational spectroscopy and electronic structure theory, we report the first experimental observation of reaction products of each, theoretically predicted, dissociation channel. These results thus overcome a 15 year old experiment/theory disconnect and make possible a variety of intriguing experiments that promise to provide significant new insights into water/Al2O3 and water/oxide interaction more generally.
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
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.
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.
Improving the photochemical properties of molecular photoswitches is crucial for the development of light-responsive systems in materials and life sciences. ortho-Fluoroazobenzenes are a new class of rationally designed photochromic azo compounds with optimized properties, such as the ability to isomerize with visible light only, high photoconversions, and unprecedented robust bistable character. Introducing sigma-electron-withdrawing F atoms ortho to the N=N unit leads to both an effective separation of the n -> pi* bands of the E and Z isomers, thus offering the possibility of using these two transitions for selectively inducing E/Z iso-merizations, and greatly enhanced thermal stability of the Z isomers. Additional para-electron-withdrawing groups (EWGs) work in concert with ortho-F atoms, giving rise to enhanced separation of the n -> pi* transitions. A comprehensive study of the effect of substitution on the key photochemical properties of ortho-fluoroazobenzenes is reported herein. In particular, the position, number, and nature of the EWGs have been varied, and the visible light photoconversions, quantum yields of isomerization, and thermal stabilities have been measured and rationalized by DFT calculations.
Surface-enhanced Raman scattering is a powerful approach to detect molecules at very low concentrations, even up to the single-molecule level. One important aspect of the materials used in such a technique is how much the signal is intensified, quantified by the enhancement factor (EF). Herein we obtained the EFs for gold nanoparticle dimers of 60 and 80 nm diameter, respectively, self-assembled using DNA origami nanotriangles. Cy5 and TAMRA were used as surface-enhanced Raman scattering (SERS) probes, which enable the observation of individual nanoparticles and dimers. EF distributions are determined at four distinct wavelengths based on the measurements of around 1000 individual dimer structures. The obtained results show that the EFs for the dimeric assemblies follow a log-normal distribution and are in the range of 10(6) at 633 nm and that the contribution of the molecular resonance effect to the EF is around 2, also showing that the plasmonic resonance is the main source of the observed signal. To support our studies, FDTD simulations of the nanoparticle's electromagnetic field enhancement has been carried out, as well as calculations of the resonance Raman spectra of the dyes using DFT. We observe a very close agreement between the experimental EF distribution and the simulated values.
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
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
Ab initio calculations for XPS chemical shifts of poly(vinyl-trifluoroacetate) using trimer models
(2011)
X-ray photoelectron spectra (XPS) of the polymer poly(vinyl-trifluoroacetate) show C(1s) binding energy shifts which are unusual because they are influenced by atoms which are several bonds away from the probed atom. In this work, the influence of the trifluoroacetate substituent on the 1s ionization potential of the carbon atoms of the polyethylene chain is investigated theoretically using mono-substituted, diad and triad models of trimers representing the polymer. Carbon 1s ionization energies are calculated by the Hartree-Fock theory employing Koopmans' theorem. The influence of the configuration and conformation of the functional groups as well as the degree of substitution are found to be important determinants of XPS spectra. It is further found that the 1s binding energy correlates in a linear fashion, with the total electrostatic potential at the position of the probe atom, and depends not only on nearest neighbor effects. This may have implications for the interpretation of high-resolution XP spectra.
Action spectroscopy has emerged as an analytical tool to probe excited states in the gas phase. Although comparison of gas-phase absorption properties with quantum-chemical calculations is, in principle, straightforward, popular methods often fail to describe many molecules of interest-such as xanthene analogues. We, therefore, face their nano-and picosecond laser-induced photofragmentation with excited-state computations by using the CC2 method and time-dependent density functional theory (TDDFT). Whereas the extracted absorption maxima agree with CC2 predictions, the TDDFT excitation energies are blueshifted. Lowering the amount of Hartree-Fock exchange in the DFT functional can reduce this shift but at the cost of changing the nature of the excited state. Additional bandwidth observed in the photofragmentation spectra is rationalized in terms of multiphoton processes. Observed fragmentation from higher-lying excited states conforms to intense excited-to-excited state transitions calculated with CC2. The CC2 method is thus suitable for the comparison with photofragmentation in xanthene analogues.
Thermally stable photoswitches that are driven with low-energy light are rare, yet crucial for extending the applicability of photoresponsive molecules and materials towards, e.g., living systems. Combined ortho-fluorination and -amination couples high visible light absorptivity of o-aminoazobenzenes with the extraordinary bistability of o-fluoroazobenzenes. Herein, we report a library of easily accessible o-aminofluoroazobenzenes and establish structure-property relationships regarding spectral qualities, visible light isomerization efficiency and thermal stability of the cis-isomer with respect to the degree of o-substitution and choice of amino substituent. We rationalize the experimental results with quantum chemical calculations, revealing the nature of low-lying excited states and providing insight into thermal isomerization. The synthesized azobenzenes absorb at up to 600 nm and their thermal cis-lifetimes range from milliseconds to months. The most unique example can be driven from trans to cis with any wavelength from UV up to 595 nm, while still exhibiting a thermal cis-lifetime of 81 days. <br /> [GRAPHICS] <br /> .
In recent simulations of femtosecond laser induced desorption of molecular oxygen from the Ag(110) surface, it has been shown that depending on the properties (depth and electronic environment) of the well in which 02 is adsorbed, the desorption can be either induced dominantly by hot electrons or via excitations of phonons. In this work we explore whether the ratios between the desorption yields from different adsorption wells can be tuned by changing initial surface temperature and laser pulse properties. We show that the initial surface temperature is an important parameter, and that by using low initial surface temperatures the electronically mediated process can be favored. In contrast, laser properties seem to have only a modest influence on the results. (C) 2016 Elsevier B.V. All rights reserved.
We simulate the femtosecond-laser-induced desorption dynamics of a diatomic molecule from a metal surface by including the effect of the electron and phonon excitations created by the laser pulse. Following previous models, the laser-induced surface excitation is treated through the two temperature model, while the multidimensional dynamics of the molecule is described by a classical Langevin equation, in which the friction and random forces account for the action of the heated electrons. In this work we propose the additional use of the generalized Langevin oscillator model to also include the effect of the energy exchange between the molecule and the heated surface lattice in the desorption dynamics. The model is applied to study the laser-induced desorption of O-2 from the Ag(110) surface, making use of a six-dimensional potential energy surface calculated within density functional theory. Our results reveal the importance of the phonon mediated process and show that, depending on the value of the electronic density in the surroundings of the molecule adsorption site, its inclusion can significantly enhance or reduce the desorption probabilities.
Complete sticking at low incidence energies and broad angular scattering distributions at higher energies are often observed in molecular beam experiments on gas-surface systems which feature a deep chemisorption well and lack early reaction barriers. Although CO binds strongly on Ru(0001), scattering is characterized by rather narrow angular distributions and sticking is incomplete even at low incidence energies. We perform molecular dynamics simulations, accounting for phononic (and electronic) energy loss channels, on a potential energy surface based on first-principles electronic structure calculations that reproduce the molecular beam experiments. We demonstrate that the mentioned unusual behavior is a consequence of a very strong rotational anisotropy in the molecule-surface interaction potential. Beyond the interpretation of scattering phenomena, we also discuss implications of our results for the recently proposed role of a precursor state for the desorption and scattering of CO from ruthenium.
We present a rigorous method to set up a system-bath Hamiltonian for the coupling of adsorbate vibrations (the system) to surface phonons (the bath). The Hamiltonian is straightforward to derive and exact up to second order in the environment coordinates, thus capable of treating one- and two-phonon contributions to vibration-phonon coupling. The construction of the Hamiltonian uses orthogonal coordinates for system and bath modes, is based on an embedded cluster approach, and generalizes previous Hamiltonians of a similar type, but avoids several (additional) approximations. While the parametrization of the full Hamiltonian is in principle feasible by a first principles quantum mechanical treatment, here we adopt in the spirit of a QM/MM model a combination of density functional theory (“QM”, for the system) and a semiempirical forcefield (“MM”, for the bath). We apply the Hamiltonian to a fully H-covered Si(100)-(2 × 1) surface, using Fermi’s Golden Rule to obtain vibrational relaxation rates of various H–Si bending modes of this system. As in earlier work it is found that the relaxation is dominated by two-phonon contributions because of an energy gap between the Si–H bending modes and the Si phonon bands. We obtain vibrational lifetimes (of the first excited state) on the order of 2 ps at K. The lifetimes depend only little on the type of bending mode (symmetric vs. antisymmetric, parallel vs. perpendicular to the Si2H2 dimers). They decrease by a factor of about two when heating the surface to 300 K. We also study isotope effects by replacing adsorbed H atoms by deuterium, D. The Si–D bending modes are shifted into the Si phonon band of the solid, opening up one-phonon decay channels and reducing the lifetimes to few hundred fs.
System-bath problems in physics and chemistry are often described by Markovian master equations. However, the Markov approximation, i.e., neglect of bath memory effects is not always justified, and different measures of non-Markovianity have been suggested in the literature to judge the validity of this approximation. Here we calculate several computable measures of non-Markovianity for the non-trivial problem of a harmonic oscillator coupled to a large number of bath oscillators. The Multi Configurational Time Dependent Hart ree nietliod is used to provide a numerically converged solution of the system-bath Schrodinger equation, from which the appropriate quantities can be calculated. In particular, we consider measures based on trace-distances and quantum discord for a variety of initial states. These quantities have proven useful in the case of two-level and other small model systems Tpically encountered in quantum optics; but are less straightforward to interpret for the more complex model systems that are relevant for chemical physics.
Comparing thermal wave function methods for multi-configuration time-dependent Hartree simulations
(2014)
We compare two methods for creating stochastic temperature wave functions that can be used for Multi-Configuration Time-Dependent Hartree (MCTDH) simulations. In the first method, the MCTDH coefficients are chosen randomly, while the other method uses a single Hartree product of random single-particle functions (SPFs). We find that using random SPFs dramatically improves convergence for a model system for surface sticking.
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.
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.
We report on photoinduced remote control of work function and surface potential of a silicon surface modified with a photosensitive self-assembled monolayer consisting of chemisorbed azobenzene molecules (4-nitroazobenzene). Itwas found that the attachment of the organic monolayer increases the work function by hundreds of meV due to the increase in the electron affinity of silicon substrates. The change in the work function on UV light illumination is more pronounced for the azobenzene jacketed silicon substrate (ca. 250 meV) in comparison to 50 meV for the unmodified surface. Moreover, the photoisomerization of azobenzene results in complex kinetics of thework function change: immediate decrease due to light-driven processes in the silicon surface followed by slower recovery to the initial state due to azobenzene isomerization. This behavior could be of interest for electronic devices where the reaction on irradiation should be more pronounced at small time scales but the overall surface potential should stay constant over time independent of the irradiation conditions. Published by AIP Publishing.
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.
Femtosecond-laser pulse driven non-adiabatic spectroscopy and dynamics in molecular and condensed phase systems continue to be a challenge for theoretical modelling. One of the main obstacles is the "curse of dimensionality" encountered in non-adiabatic, exact wavepacket propagation. A possible route towards treating complex molecular systems is via semiclassical surface-hopping schemes, in particular if they account not only for non-adiabatic post-excitation dynamics but also for the initial optical excitation. One such approach, based on initial condition filtering, will be put forward in what follows. As a simple test case which can be compared with exact wavepacket dynamics, we investigate the influence of the different parameters determining the shape of a laser pulse (e.g., its finite width and a possible chirp) on the predissociation dynamics of a NaI molecule, upon photoexcitation of the A(0(+)) state. The finite-pulse effects are mapped into the initial conditions for semiclassical surface-hopping simulations. The simulated surface-hopping diabatic populations are in qualitative agreement with the quantum mechanical results, especially concerning the subpicosend photoinduced dynamics, the main deviations being the relative delay of the non-adiabatic transitions in the semiclassical picture. Likewise, these differences in the time-dependent electronic populations calculated via the semiclassical and the quantum methods are found to have a mild influence on the overall probability density distribution. As a result, the branching ratios between the bound and the dissociative reaction channels and the time-evolution of the molecular wavepacket predicted by the semiclassical method agree with those computed using quantum wavepacket propagation. Implications for more challenging molecular systems are given. (C) 2015 AIP Publishing LLC.
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
A multi-reference study of the byproduct formation for a ring-closed dithienylethene photoswitch
(2015)
Photodriven molecular switches are sometimes hindered in their performance by forming byproducts which act as dead ends in sequences of switching cycles, leading to rapid fatigue effects. Understanding the reaction pathways to unwanted byproducts is a prerequisite for preventing them. This article presents a study of the photochemical reaction pathways for byproduct formation in the photochromic switch 1,2-bis-(3-thienyl)-ethene. Specifically, using single-and multi-reference methods the post-deexcitation reaction towards the byproduct in the electronic ground state S-0 when starting from the S-1-S-0 conical intersection (CoIn), is considered in detail. We find an unusual low-energy pathway, which offers the possibility for the formation of a dyotropic byproduct. Several high-energy pathways can be excluded with high probability.
A multi-reference study of the byproduct formation for a ring-closed dithienylethene photoswitch
(2015)
Photodriven molecular switches are sometimes hindered in their performance by forming byproducts which act as dead ends in sequences of switching cycles, leading to rapid fatigue effects. Understanding the reaction pathways to unwanted byproducts is a prerequisite for preventing them. This article presents a study of the photochemical reaction pathways for byproduct formation in the photochromic switch 1,2-bis-(3-thienyl)-ethene. Specifically, using single- and multi-reference methods the post-deexcitation reaction towards the byproduct in the electronic ground state S0 when starting from the S1–S0 conical intersection (CoIn), is considered in detail. We find an unusual low-energy pathway, which offers the possibility for the formation of a dyotropic byproduct. Several high-energy pathways can be excluded with high probability.
A multi-reference study of the byproduct formation for a ring-closed dithienylethene photoswitch
(2015)
Photodriven molecular switches are sometimes hindered in their performance by forming byproducts which act as dead ends in sequences of switching cycles, leading to rapid fatigue effects. Understanding the reaction pathways to unwanted byproducts is a prerequisite for preventing them. This article presents a study of the photochemical reaction pathways for byproduct formation in the photochromic switch 1,2-bis-(3-thienyl)-ethene. Specifically, using single- and multi-reference methods the post-deexcitation reaction towards the byproduct in the electronic ground state S0 when starting from the S1–S0 conical intersection (CoIn), is considered in detail. We find an unusual low-energy pathway, which offers the possibility for the formation of a dyotropic byproduct. Several high-energy pathways can be excluded with high probability.
Following excited-state chemical shifts in molecular ultrafast x-ray photoelectron spectroscopy
(2022)
The conversion of photon energy into other energetic forms in molecules is accompanied by charge moving on ultrafast timescales. We directly observe the charge motion at a specific site in an electronically excited molecule using time-resolved x-ray photoelectron spectroscopy (TR-XPS). We extend the concept of static chemical shift from conventional XPS by the excited-state chemical shift (ESCS), which is connected to the charge in the framework of a potential model. This allows us to invert TR-XPS spectra to the dynamic charge at a specific atom. We demonstrate the power of TR-XPS by using sulphur 2p-core-electron-emission probing to study the UV-excited dynamics of 2-thiouracil. The method allows us to discover that a major part of the population relaxes to the molecular ground state within 220–250 fs. In addition, a 250-fs oscillation, visible in the kinetic energy of the TR-XPS, reveals a coherent exchange of population among electronic states.
Following excited-state chemical shifts in molecular ultrafast x-ray photoelectron spectroscopy
(2022)
The conversion of photon energy into other energetic forms in molecules is accompanied by charge moving on ultrafast timescales. We directly observe the charge motion at a specific site in an electronically excited molecule using time-resolved x-ray photoelectron spectroscopy (TR-XPS). We extend the concept of static chemical shift from conventional XPS by the excited-state chemical shift (ESCS), which is connected to the charge in the framework of a potential model. This allows us to invert TR-XPS spectra to the dynamic charge at a specific atom. We demonstrate the power of TR-XPS by using sulphur 2p-core-electron-emission probing to study the UV-excited dynamics of 2-thiouracil. The method allows us to discover that a major part of the population relaxes to the molecular ground state within 220–250 fs. In addition, a 250-fs oscillation, visible in the kinetic energy of the TR-XPS, reveals a coherent exchange of population among electronic states.
Water can adsorb molecularly or dissociatively onto different sites of metal oxide surfaces. These adsorption sites can be disentangled using surface-sensitive vibrational spectroscopy. Here, we model Vibrational Sum Frequency (VSF) spectra for various forms of dissociated, deuterated water on a reconstructed, Al-terminated α-Al2O3(0001) surface at submonolayer coverages (the so-called 1-2, 1-4, and 1-4′ modes). Using an efficient scheme based on velocity-velocity autocorrelation functions, we go beyond previous normal mode analyses by including anharmonicity, mode coupling, and thermal surface motion in the framework of ab initio molecular dynamics. In this way, we calculate vibrational density of states curves, infrared, and VSF spectra. Comparing computed VSF spectra with measured ones, we find that relative frequencies of resonances are in quite good agreement and linewidths are reasonably well represented, while VSF intensities coincide not well. We argue that intensities are sensitively affected by local interactions and thermal fluctuations, even at such low coverage, while absolute peak positions strongly depend on the choice of the electronic structure method and on the appropriate inclusion of anharmonicity.
Vibrational relaxation of adsorbates is a sensitive tool to probe energy transfer at gas/solid and liquid/solid interfaces. The most direct way to study relaxation dynamics uses time-resolved spectroscopy. Here we report on a non-equilibrium ab initio molecular dynamics (NE-AIMD) methodology to model vibrational relaxation of OH vibrations on a hydroxylated, water-covered alpha-Al2O3(0001) surface. In our NE-AIMD approach, after exciting selected O-H bonds their coupling to surface phonons and to the water adlayer is analyzed in detail, by following both the energy flow in time, as well as the time-evolution of Vibrational Density of States (VDOS) curves. The latter are obtained from Time-dependent Correlation Functions (TCFs) and serve as prototypical, generic representatives of time-resolved vibrational spectra. As most important results, (i) we find a few-picosecond lifetime of the excited modes and (ii) identify both hydrogen-bonded aluminols and water molecules in the adsorbed water layer as main dissipative channels, while the direct coupling to Al2O3 surface phonons is of minor importance on the timescales of interest. Our NE-AIMD/TCF methodology is powerful for complex adsorbate systems, in principle even reacting ones, and opens a way towards time-resolved vibrational spectroscopy.
Using gradient- and dispersion-corrected density functional theory in connection with ab initio molecular dynamics and efficient, parametrized Velocity-Velocity Autocorrelation Function (VVAF) methodology, we study the vibrational spectra (Vibrational Sum Frequency, VSF, and infrared, IR) of hydroxylated alpha-Al2O3(0001) surfaces with and without additional water. Specifically, by considering a naked hydroxylated surface and the same surface with a particularly stable, "ice-like" hexagonal water later allows us to identify and disentangle main spectroscopic bands of OH bonds, their orientation and dynamics, and the role of water adsorption. In particular, we assign spectroscopic signals around 3700 cm(-1) as being dominated by perpendicularly oriented non-hydrogen bonded aluminol groups, with and without additional water. Furthermore, the thin water layer gives spectroscopic signals which are already comparable to previous theoretical and experimental findings for the solid/(bulk) liquid interface, showing that water molecules closest to the surface play a decisive role in the vibrational response of these systems. From a methodological point of view, the effects of temperature, anharmonicity, hydrogen-bonding, and structural dynamics are taken into account and analyzed, allowing us to compare the calculated IR and VSF spectra with the ones based on normal mode analysis and vibrational density of states. The VVAF approach employed in this work appears to be a computationally accurate yet feasible method to address the vibrational fingerprints and dynamical properties of water/metal oxide interfaces. Published by AIP Publishing.
The quest for "chemical accuracy" is becoming more and more demanded in the field of structure and kinetics of molecules at solid surfaces. In this paper, as an example, we focus on the barrier for hydrogen diffusion on a alpha-Al2O3 (0001) surface, aiming for a couple cluster singles, doubles, and perturbative triples [CCSD(T)]-level benchmark. We employ the density functional theory (DFT) optimized minimum and transition state structures reported by Heiden, Usvyat, and Saalfrank [J. Phys. Chem. C 123, 6675 (2019)]. The barrier is first evaluated at the periodic Hartree-Fock and local Moller-Plesset second-order perturbation (MP2) level of theory. The possible sources of errors are then analyzed, which includes basis set incompleteness error, frozen core, density fitting, local approximation errors, as well as the MP2 method error. Using periodic and embedded fragment models, corrections to these errors are evaluated. In particular, two corrections are found to be non-negligible (both from the chemical accuracy perspective and at the scale of the barrier value of 0.72 eV): the correction to the frozen core-approximation of 0.06 eV and the CCSD(T) correction of 0.07 eV. Our correlated wave function results are compared to barriers obtained from DFT. Among the tested DFT functionals, the best performing for this barrier is B3LYP-D3.
Azobenzene-based molecular photoswitches are becoming increasingly important for the development of photoresponsive, functional soft-matter material systems. Upon illumination with light, fast interconversion between a more stable trans and a metastable cis configuration can be established resulting in pronounced changes in conformation, dipole moment or hydrophobicity. A rational design of functional photosensitive molecules with embedded azo moieties requires a thorough understanding of isomerization mechanisms and rates, especially the thermally activated relaxation. For small azo derivatives considered in the gas phase or simple solvents, Eyring’s classical transition state theory (TST) approach yields useful predictions for trends in activation energies or corresponding half-life times of the cis isomer. However, TST or improved theories cannot easily be applied when the azo moiety is part of a larger molecular complex or embedded into a heterogeneous environment, where a multitude of possible reaction pathways may exist. In these cases, only the sampling of an ensemble of dynamic reactive trajectories (transition path sampling, TPS) with explicit models of the environment may reveal the nature of the processes involved. In the present work we show how a TPS approach can conveniently be implemented for the phenomenon of relaxation–isomerization of azobenzenes starting with the simple examples of pure azobenzene and a push–pull derivative immersed in a polar (DMSO) and apolar (toluene) solvent. The latter are represented explicitly at a molecular mechanical (MM) and the azo moiety at a quantum mechanical (QM) level. We demonstrate for the push–pull azobenzene that path sampling in combination with the chosen QM/MM scheme produces the expected change in isomerization pathway from inversion to rotation in going from a low to a high permittivity (explicit) solvent model. We discuss the potential of the simulation procedure presented for comparative calculation of reaction rates and an improved understanding of activated states.
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 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 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 present quantum dynamical calculations on electron correlation dynamics in atoms and molecules using explicitly time-dependent ab initio configuration interaction theory. The goals are (i) to show that in which cases it is possible to switch off the electronic correlation by ultrashort laser pulses, and (ii) to understand the temporal evolution and the time scale on which it reappears. We characterize the appearance of correlation through electron-electron scattering when starting from an uncorrelated state, and we identify pathways for the preparation of a Hartree-Fock state from the correlated, true ground state. Exemplary results for noble gases, alkaline earth elements, and selected molecules are provided. For Mg we show that the uncorrelated state can be prepared using a shaped ultrashort laser pulse.
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
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.