Marek Z. Zgierski

Electronic relaxation dynamics in DNA and RNA bases studied by time-resolved photoelectron spectroscopy

We present femtosecond time-resolved photoelectron spectra (TRPES) of the DNA and RNA bases adenine, cytosine, thymine, and uracil in a molecular beam. We discuss in detail the analysis of our adenine TRPES spectra. A global two-dimensional fit of the time and energy-resolved spectra allows for reliable separation of photoelectron spectra from several channels, even for overlapping bands. Ab initio calculations of Koopmans’ ionization correlations and He(I) photoelectron spectra aid the assignment of electronically excited states involved in the relaxation dynamics. Based upon our results, we propose the following mechanism for electronic relaxation dynamics in adenine: Pump wavelengths of 250, 267 and 277 nm lead to initial excitation of the bright S2(pp*) state. Close to the band origin (277 nm), the lifetime is several picoseconds. At higher vibronic levels, i.e. 250 and 267 nm excitation, rapid internal conversion (t < 50 fs) populates the lower lying S1(np*) state which has a lifetime of 750 fs. At 267 nm, we found evidence for an additional channel which is consistent with the dissociative S3(ps*) state, previously proposed as an ultrafast relaxation pathway from S2(pp*). We present preliminary results from TRPES measurements of the other DNA bases at 250 nm excitation.

Discerning vibronic molecular dynamics using time-resolved photoelectron spectroscopy

Dynamic processes at the molecular level occur on ultrafast time scales and are often associated with structural as well as electronic changes. These can in principle be studied by time-resolved scattering and spectroscopic methods, respectively. In polyatomic molecules, however, excitation results in the rapid mixing of vibrational and electronic motions, which induces both charge redistribution and energy flow in the molecule. This ‘vibronic’ or ‘non-adiabatic’ coupling is a key step in photochemical and photobiological processes and underlies many of the concepts of molecular electronics, but it obscures the notion of distinct and readily observable vibrational and electronic states. Here we report time-resolved photoelectron spectroscopy measurements that distinguish vibrational dynamics from the coupled electronic population dynamics, associated with the photo-induced internal conversion, in a linear unsaturated hydrocarbon chain. The vibrational resolution of our photoelectron spectra allows for a direct observation of the underlying nuclear dynamics, demonstrating that it is possible to obtain detailed insights into ultrafast non-adiabatic processes.

Primary processes underlying the photostability of isolated DNA bases: adenine.

The UV chromophores in DNA are the nucleic bases themselves, and it is their photophysics and photochemistry that govern the intrinsic photostability of DNA. Because stability is related to the conversion of dangerous electronic to less-dangerous vibrational energy, we study ultrafast electronic relaxation processes in the DNA base adenine. We excite adenine, isolated in a molecular beam, to its ππ* state and follow its relaxation dynamics using femtosecond time-resolved photoelectron spectroscopy. To discern which processes are important on which timescales, we compare adenine with 9-methyl adenine. Methylation blocks the site of the much-discussed πσ* state that had been thought, until now, minor. Time-resolved photoelectron spectroscopy reveals that, although adenine and 9-methyl adenine show almost identical timescales for the processes involved, the decay pathways are quite different. Importantly, we confirm that in adenine at 267-nm excitation, the πσ* state plays a major role. We discuss these results in the context of recent experimental and theoretical studies on adenine, proposing a model that accounts for all known results, and consider the relationship between these studies and electron-induced damage in DNA.

Franck–Condon effects in resonance Raman spectra and excitation profiles

Resonance Raman spectra and excitation profiles are calculated for totally symmetric vibrations not involved in vibronic coupling and thus deriving all their intensity from Franck–Condon effects. Theoretical results are derived for harmonic oscillators undergoing displacements and frequency shifts upon electronic excitation of the molecule. The model does not only consider the effect of interference between several totally symmetric modes but also includes a number of basic refinements absent from most previous treatments such as inhomogeneous line broadening, perturbation of a weak resonance transition by the preresonance spectrum of a strong neighboring transition, and normal coordinate rotation (Dushinsky effect). The model calculations are used to interpret observed Raman spectra and excitation profiles of totally symmetric modes in the chromate ion and the β‐carotene molecule.

The structure of Nb3O and Nb3O+ determined by pulsed field ionization–zero electron kinetic energy photoelectron spectroscopy and density functional theory

The geometrical structures of the ground states of triniobium monoxide, Nb3O, and its cation, Nb3O+, have been determined by an experimental and theoretical study. Vibrationally resolved photoelectron spectra of an Nb3O cluster beam were obtained at 100 and 300 K using the pulsed field ionization‐zero electron kinetic energy technique. The spectra were simulated by calculating multidimensional Franck–Condon factors using the geometries and harmonic vibrational frequencies obtained from density functional theory for the minimum energy structures of the ion and neutral molecule. The rather remarkable agreement between the experiment and the simulated spectra establishes that Nb3O and Nb3O+ have planar C2v structures with the oxygen atom bridging two niobium atoms. These are the most complex transition metal cluster structures to date to be characterized by gas phase spectroscopic techniques.

Photochromism of salicylideneaniline (SA). How the photochromic transient is created: A theoretical approach

The theoretical ab initio studies of the singlet states of salicylideneaniline (SA) are presented. The enol, cis-keto and trans-keto tautomers were treated by the HF/6-31G* (geometries and force fields of the ground states), and the CIS (excited states), methods. For the dynamic calculations of the rates of proton transfer (PT) in S1 states, the instanton approach was applied. It was found that the SA molecule in S0 and S1 states of both tautomers needs nonplanarity to stabilize. In the ground state the corresponding angle was calculated as 44° vs the experimental value, 49°. Upon twist of the excited system, the conical intersection of (π,π*) and (n,π*) potential surfaces takes place. In enol form the absolute minimum on the S1 potential energy surface belongs to a strongly twisted (n,π*) state. In keto-form this minimum corresponds to a planar (π,π*) state, while the twisted (n,π*) has the energy ≈1055 cm−1 higher. The angles of distortion are equal 93° and 80°, for the enol and keto form, respectively....

Dynamics of excited-state proton transfer systems via time-resolved photoelectron spectroscopy

We investigate the applicability of time-resolved photoelectron spectroscopy to excited state intramolecular proton transfer (ESIPT) and internal conversion dynamics in the model system o-hydroxybenzaldehyde (OHBA) and related compounds. Photoelectron spectra of both the excited state enol and keto tautomers were obtained as a function of pump laser wavelength and pump-probe time delay. The ESIPT was found to occur in less than 50 fs over the whole absorption range of the S1(ππ*) state for both OHBA and its monodeuterated analog, suggestive of a small or nonexistent barrier. The subsequent keto internal conversion rate in OHBA varies from 0.63 to 0.17 ps−1 over the S1(ππ*) absorption band and the OD-deuterated analog shows no significant isotope effect. Based upon ab initio calculations and comparison with the two-ring analog, 1-hydroxy-2-acetonaphthone (HAN), we suggest that the internal conversion dynamics in OHBA is influenced by interactions with a close-lying nπ* state.

Theoretical study of the force fields of the three lowest singlet electronic states of linear polyenes

The potential energy surfaces of all trans hexatriene and octatetraene are investigated within the harmonic approximation in the diabatic and adiabatic representations for the 1A−g, 2A−g, and 1B+u electronic states by an extended Pople–Pariser–Parr (PPP/CI) model. The effect of excitation and of vibronic coupling on the molecular force fields of the three states is examined. While electronic excitation affects only diagonal force constants of local oscillators, vibronic coupling changes drastically the couplings between local oscillators. The calculations reproduce well the observed increase of the frequency of the in‐phase ag C=C stretch upon excitation to the 2A−g state.

Performance of DFT in Modeling Electronic and Structural Properties of Cobalamins

Computational modeling of the enzymatic activity of B12‐dependent enzymes requires a detailed understanding of the factors that influence the strength of the CoC bond and the limits associated with a particular level of theory. To address this issue, a systematic analysis of the electronic and structural properties of coenzyme B12 models has been performed to establish the performance of three different functionals including B3LYP, BP86, and revPBE. In particular the cobalt–carbon bond dissociation energies, axial bond lengths, and selected stretching frequencies have been analyzed in detail. Current analysis shows that widely used B3LYP functional significantly underestimates the strength of the CoC bond while the nonhybrid BP86 functional produces very consistent results in comparison to experimental data. To explain such different performance of these functionals molecular orbital analysis associated with axial bonds has been performed to show differences in axial bonding provided by hybrid and nonhybrid functionals.

An instanton approach to intramolecular hydrogen exchange: Tunneling splittings in malonaldehyde and the hydrogenoxalate anion

Calculations of hydrogen tunneling splittings are reported based on a combination of the instanton approach with quantum‐chemically computed potentials and force fields. The splittings are due to intramolecular hydrogen transfer in symmetric double‐minimum potentials in molecules such as malonaldehyde and the hydrogenoxalate anion. Potential‐energy curves along the tunneling coordinates and harmonic force fields at the stationary points are calculated at the HF/6‐31G** and HF/6‐31+G** level of theory, and combined to yield a complete multidimensional surface. All modes that are displaced between the equilibrium configuration and the transition state are included in the calculation. In the formalism, these modes are linearly coupled to the tunneling mode, the couplings being proportional to the displacements in dimensionless units. These couplings modify the instanton trajectory and subject it to fluctuations. It is argued that within the accuracy of the available potential‐energy surfaces, direct calculat...