Assessing the Nature of Chiral-Induced Spin Selectivity by Magnetic Resonance.

Understanding chiral-induced spin selectivity (CISS), resulting from charge transport through helical systems, has recently inspired many experimental and theoretical efforts but is still the object of intense debate. In order to assess the nature of CISS, we propose to focus on electron-transfer processes occurring at the single-molecule level. We design simple magnetic resonance experiments, exploiting a qubit as a highly sensitive and coherent magnetic sensor, to provide clear signatures of the acceptor polarization. Moreover, we show that information could even be obtained from time-resolved electron paramagnetic resonance experiments on a randomly oriented solution of molecules. The proposed experiments will unveil the role of chiral linkers in electron transfer and could also be exploited for quantum computing applications.

Charge migration in photo-ionized aromatic amino acids.

Attosecond pump-probe spectroscopy is a unique tool for the direct observation of the light-activated electronic motion in molecules and it offers the possibility to capture the first instants of a chemical reaction. Recently, advances in attosecond technology allowed the charge migration processes to be revealed in biochemically relevant molecules. Although this purely electronic process might be key for a future chemistry at the electron time scale, the influence of this ultrafast charge flow on the reactivity of a molecule is still debated. In this work, we exploit extreme ultraviolet attosecond pulses to activate charge migration in two aromatic amino acids, namely phenylalanine and tryptophan. Advanced numerical calculations are performed to interpret the experimental data and to discuss the effects of the nuclear dynamics on the activated quantum coherences. By comparing the experimental results obtained in the two molecules, we show that the presence of different functional groups strongly affects the fragmentation pathways, as well as the charge rearrangement. The observed charge dynamics indeed present peculiar aspects, including characteristic periodicities and decoherence times. Numerical results indicate that, even for a very large molecule such as tryptophan, the quantum coherences can survive the nuclear dynamics for several femtoseconds. These results open new and important perspectives for a deeper understanding of the photo-induced charge dynamics, as a promising tool to control the reactivity of bio-relevant molecules via photo-excitation. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.

Characterization of the Photochemical Properties of 5-Benzyluracil via Time-Dependent Density Functional Theory.

We present a detailed study of the excited state properties of 5-benzyluracil (5BU) in the gas phase and in implicit solvent using different electronic structure approaches ranging from time-dependent density functional theory in the linear response regime (LR-TDDFT) to a set of different wave-function-based methods for excited states, namely perturbed coupled cluster (CC2), algebraic diagrammatic construction method to second order (ADC(2)), and perturbed configuration interaction (CIS(D)). 5BU has been used to investigate DNA base-amino acid interactions. In particular, it served as a model of protein-DNA photoinduced cross-linking. While LR-TDDFT is computationally the most efficient first-principles approach for static and dynamic simulations of this bichromophoric system, its accuracy is difficult to assess due to the presence of excited states with charge transfer character. In this work, the performance of different exchange correlation functionals is compared against accurate benchmarks obtained either from high level wave-function-based methods or directly from experimental absorption spectra. Our investigation shows that accurate results for the excitation energies can be obtained using the hybrid meta-GGA functional M06. In view of dynamical studies of the relaxation of 5BU after photoexcitation, we also show that the PBE functional, while failing in the Franck-Condon region, provides qualitatively good results for the characterisation of a possible photocyclization path.

Photophysics of a copper phenanthroline elucidated by trajectory and wavepacket-based quantum dynamics: a synergetic approach.

On-the-fly excited state molecular dynamics is a valuable method for studying non-equilibrium processes in excited states and is beginning to emerge as a mature approach much like its ground state counterparts. In contrast to quantum wavepacket dynamics methods, it negates the need for modelling potential energy surfaces, which usually confine nuclear motion within a reduced number of vibrational modes. In addition, on-the-fly molecular dynamics techniques are easily combined with the atomistic description of the solvents (through the QM/MM approach) making it possible to explicitly address the effect of the environment. Herein, we study the nonadiabatic relaxation of photoexcited [Cu(dmp)2]+ (dmp = 2,9-dimethyl-1,10-phenanthroline) using QM/MM Trajectory Surface Hopping (TSH). We show that the decay of the initially excited singlet state into the lowest singlet (S1) state occurs within 100 fs, in agreement with previous experiments, and is slightly influenced by the solvent. Using a principal component analysis (PCA), we also identify the dominant normal modes activated during the excited state decay, which are then used to design the vibronic Hamiltonian for quantum wavepacket dynamics simulations.

Nonadiabatic dynamics with intersystem crossings: A time-dependent density functional theory implementation.

In this work, we derive a method to perform trajectory-based nonadiabatic dynamics that is able to describe both nonadiabatic transitions and intersystem crossing events (transitions between states of different spin-multiplicity) at the same level of theory, namely, time-dependent density functional theory (TDDFT). To this end, we combined our previously developed TDDFT-based trajectory surface hopping scheme with an accurate and efficient algorithm for the calculation of the spin-orbit coupling (SOC) matrix elements. More specifically, we designed two algorithms for the calculation of intersystem crossing transitions, one based on an extended Tully's surface hopping scheme including SOC and the second based on a Landau-Zener approximation applied to the spin sector of the electronic Hilbert space. This development allows for the design of an efficient on-the-fly nonadiabatic approach that can handle, on an equal footing, nonadiabatic and intersystem crossing transitions. The method is applied to the study of the photophysics of sulfur dioxide (SO2) in gas and liquid phases.

Theoretical Rationalization of the Emission Properties of Prototypical Cu(I)-Phenanthroline Complexes.

The excited state properties of transition metal complexes have become a central focus of research owing to a wide range of possible applications that seek to exploit their luminescence properties. Herein, we use density functional theory (DFT), time-dependent DFT (TDDFT), classical and quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations to provide a full understanding on the role of the geometric and electronic structure, spin-orbit coupling, singlet-triplet gap and the solvent environment on the emission properties of nine prototypical copper(I)-phenanthroline complexes. Our calculations reveal clear trends in the electronic properties that are strongly correlated to the luminescence properties, allowing us to rationalize the role of specific structural modifications. The MD simulations show, in agreement with recent experimental observations, that the lifetime shortening of the excited triplet state in donor solvents (acetonitrile) is not due to the formation of an exciplex. Instead, the solute-solvent interaction is transient and arises from solvent structures that are similar to the ones already present in the ground state. These results based on a subset of the prototypical mononuclear Cu(I) complexes shed general insight into these complexes that may be exploited for development of mononuclear Cu(I) complexes for applications as, for example, emitters in third generation OLEDs.

A quantum dynamics study of the ultrafast relaxation in a prototypical Cu(I)-phenanthroline.

The ultrafast nonadiabatic dynamics of a prototypical Cu(I)-phenanthroline complex, [Cu(dmp)2](+) (dmp = 2,9-dimethyl-1,10-phenanthroline), initiated after photoexcitation into the optically bright metal-to-ligand charge-transfer (MLCT) state (S3) is investigated using quantum nuclear dynamics. In agreement with recent experimental conclusions, we find that the system undergoes rapid (∼100 fs) internal conversion from S3 into the S2 and S1 states at or near the Franck-Condon (FC) geometry. This is preceded by a dynamic component with a time constant of ∼400 fs, which corresponds to the flattening of the ligands associated with the pseudo Jahn-Teller distortion. Importantly, our simulations demonstrate that this latter aspect is in competition with subpicosecond intersystem crossing (ISC). The mechanism for ISC is shown to be a dynamic effect, in the sense that it arises from the system traversing the pseudo Jahn-Teller coordinate where the singlet and triplet states become degenerate, leading to efficient crossing. These first-principles quantum dynamics simulations, in conjunction with recent experiments, allow us to clearly resolve the mechanistic details of the ultrafast dynamics within [Cu(dmp)2](+), which have been disputed in the literature.

X-ray spectroscopic study of solvent effects on the ferrous and ferric hexacyanide anions.

We present an Fe Kα resonant inelastic X-ray scattering (RIXS) and X-ray emission (XES) study of ferrous and ferric hexacyanide dissolved in water and ethylene glycol. We observe that transitions below the absorption edge show that the solvent has a distinct effect on the valence electronic structure. In addition, both the RIXS and XES spectra show a stabilization of the 2p levels when dissolved in water. Using molecular dynamics simulations, we propose that this effect arises from the hydrogen-bonding interactions between the complex and nearby solvent molecules. This withdraws electron density from the ligands, stabilizing the complex but also causing a slight increase in π-backbonding.

Photooxidation and photoaquation of iron hexacyanide in aqueous solution: A picosecond X-ray absorption study.

We present a picosecond Fe K-edge absorption study of photoexcited ferrous and ferric hexacyanide in water under 355 and 266 nm excitation. Following 355 nm excitation, the transient spectra for the ferrous and ferric complexes exhibit a red shift of the edge reflecting an increased electron density at the Fe atom. For the former, an enhanced pre-edge transition is also observed. These observations are attributed to the aquated [Fe(CN)5OH2](3-) species, based on quantum chemical calculations which also provide structural parameters. Upon 266 nm excitation of the ferric complex, a transient reminiscent of the aquated species is observed (appearance of a pre-edge feature and red shift of the edge) but it is different from that obtained under 355 nm excitation. This points to a new reaction channel occurring through an intermediate state lying between these two excitation energies. Finally, 266 nm excitation of the ferrous species is dominated by the photooxidation channel with formation of the ferric complex as main photoproduct. However, we observe an additional minor photoproduct, which is identical to the 266 nm generated photoproduct of the ferric species, suggesting that under our experimental conditions, the pump pulse photooxidises the ferrous complex and re-excites the primary ferric photoproduct.

Solvent-induced luminescence quenching: static and time-resolved X-ray absorption spectroscopy of a copper(I) phenanthroline complex.

We present a static and picosecond X-ray absorption study at the Cu K-edge of bis(2,9-dimethyl-1,10-phenanthroline)copper(I) ([Cu(dmp)2](+); dmp = 2,9-dimethyl-1,10-phenanthroline) dissolved in acetonitrile and dichloromethane. The steady-state photoluminescence spectra in dichloromethane and acetonitrile are also presented and show a shift to longer wavelengths for the latter, which points to a stronger stabilization of the excited complex. The fine structure features of the static and transient X-ray spectra allow an unambiguous assignment of the electronic and geometric structure of the molecule in both its ground and excited (3)MLCT states. Importantly, the transient spectra are remarkably similar for both solvents, and the spectral changes can be rationalized using the optimized ground- and excited-state structures of the complex. The proposed assignment of the lifetime shortening of the excited state in donor solvents (acetonitrile) to a metal-centered exciplex is not corroborated here. Molecular dynamics simulations confirm the lack of complexation; however, in both solvents the molecules come close to the metal but undergo rapid exchange with the bulk. The shortening of the lifetime of the title complex and nine additional related complexes can be rationalized by the decrease in the (3)MLCT energy. Deviations from this trend may be explained by means of the effects of the dihedral angle between the ligand planes, the solvent, and the (3)MLCT-(1)MLCT energy gap.

A wavelet analysis for the X-ray absorption spectra of molecules.

We present a Wavelet transform analysis for the X-ray absorption spectra of molecules. In contrast to the traditionally used Fourier transform approach, this analysis yields a 2D correlation plot in both R- and k-space. As a consequence, it is possible to distinguish between different scattering pathways at the same distance from the absorbing atom and between the contributions of single and multiple scattering events, making an unambiguous assignment of the fine structure oscillations for complex systems possible. We apply this to two previously studied transition metal complexes, namely iron hexacyanide in both its ferric and ferrous form, and a rhenium diimine complex, [ReX(CO)(3)(bpy)], where X = Br, Cl, or ethyl pyridine (Etpy). Our results demonstrate the potential advantages of using this approach and they highlight the importance of multiple scattering, and specifically the focusing phenomenon to the extended X-ray absorption fine structure (EXAFS) spectra of these complexes. We also shed light on the low sensitivity of the EXAFS spectrum to the Re-X scattering pathway.

X-ray absorption spectroscopy of ground and excited rhenium-carbonyl-diimine complexes: evidence for a two-center electron transfer.

Steady-state and picosecond time-resolved X-ray absorption spectroscopy is used to study the ground and lowest triplet states of [ReX(CO)(3)(bpy)](n+), X = Etpy (n = 1), Cl, or Br (n = 0). We demonstrate that the transient spectra at both the Re L(3)- and Br K-edges show the emergence of a pre-edge feature, absent in the ground-state spectrum, which is associated with the electron hole created in the highest occupied molecular orbital following photoexcitation. Importantly, these features have the same dynamics, confirming previous predictions that the low-lying excited states of these complexes involve a two-center charge transfer from both the Re and the ligand, X. We also demonstrate that the DFT optimized ground and excited structures allow us to reproduce the experimental XANES and EXAFS spectra. The ground-state structural refinement shows that the Br atom contributes very little to the latter, whereas the Re-C-O scattering paths are dominant due to the so-called focusing effect. For the excited-state spectrum, the Re-X bond undergoes one of the largest changes but still remains a weak contribution to the photoinduced changes of the EXAFS spectrum.

Ultrafast nonadiabatic fragmentation dynamics of doubly charged uracil in a gas phase.

A combination of time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods is used to investigate fragmentation of doubly charged gas-phase uracil in collisions with 100 keV protons. The results are in good agreement with ion-ion coincidence measurements. Orbitals of similar energy and/or localized in similar bonds lead to very different fragmentation patterns, thus showing the importance of intramolecular chemical environment. In general, the observed fragments do not correspond to the energetically most favorable dissociation path, which is due to dynamical effects occurring in the first few femtoseconds after electron removal.

Theoretical investigation of the ultrafast dissociation of ionised biomolecules immersed in water: direct and indirect effects.

Theoretical simulations are particularly well suited to investigate, at a molecular level, direct and indirect effects of ionising radiations in DNA, as in the particular case of irradiation by swift heavy ions such as those used in hadron therapy. In the past recent years, we have developed the modeling at the microscopic level of the early stages of the Coulomb explosion of DNA molecules immersed in liquid water that follows the irradiation by swift heavy ions. To that end, Time-Dependent Density Functional Theory molecular dynamics simulations (TD-DFT MD) have been developed where localised Wannier orbitals are propagated. This latter enables to separate molecular orbitals of each water molecule from the molecular orbitals of the biomolecule. Our main objective is to demonstrate that the double ionisation of one molecule of the liquid sample, either one water molecule from the solvent or the biomolecule, may be in some cases responsible for the formation of an atomic oxygen as a direct consequence of the molecule Coulomb explosion. Our hypothesis is that the molecular double ionisation arising from irradiation by swift heavy ions (about 10% of ionisation events by ions whose velocity is about the third of speed of light), as a primary event, though maybe less probable than other events resulting from the electronic cascading (for instance, electronic excitations, electron attachments), may be systematically more damageable (and more lethal), as supported by experiments that have been carried out in our group in the 1990s (in studies of damages created by K holes in DNA). The chemical reactivity of the produced atomic oxygen with other radicals present in the medium will ultimately lead to chemical products that are harmful to DNA. In the present paper, we review our theoretical methodology in an attempt that the community be familiar with our new approach. Results on the production of atomic oxygen as a result of the double ionisation of water or as a result of the double ionisation of the Uracil RNA base will be presented.

Dynamic properties of monomeric insect erythrocruorin III from Chironomus thummi-thummi: relationships between structural flexibility and functional complexity.

We have investigated the kinetics of geminate carbon monoxide binding to the monomeric component III of Chironomus thummi-thummi erythrocruorin, a protein that undergoes pH-induced conformational changes linked to a pronounced Bohr effect. Measurements were performed from cryogenic temperatures to room temperature in 75% glycerol and either 0.1 M potassium phosphate (pH 7) or 0.1 potassium borate (pH 9) after nanosecond laser photolysis. The distributions of the low temperature activation enthalpy g(H) for geminate ligand binding derived from the kinetic traces are quite narrow and are influenced by temperature both below and above approximately 170 K, the glass transition temperature. The thermal evolution of the CO binding kinetics between approximately 50 K and approximately 170 K indicates the presence of some degree of structural relaxation, even in this temperature range. Above approximately 220 K the width of the g(H) progressively decreases, and at 280 K geminate CO binding becomes exponential in time. Based on a comparison with analogous investigations of the homodimeric hemoglobin from Scapharca inaequivalvis, we propose a link between dynamic properties and functional complexity.