Electronic Control of Site Selective Reactivity: A Model Combining Charge Migration and Dissociation

Simulating Real-Time Molecular Electron Dynamics Efficiently Using the Time-Dependent Density Matrix Renormalization Group

Compared to ground-state electronic structure optimizations, accurate simulations of molecular real-time electron dynamics are usually much more difficult to perform. To simulate electron dynamics, the time-dependent density matrix renormalization group (TDDMRG) has been shown to offer an attractive compromise between accuracy and cost. However, many simulation parameters significantly affect the quality and efficiency of a TDDMRG simulation. So far, it is unclear whether common wisdom from ground-state DMRG carries over to the TDDMRG, and a guideline on how to choose these parameters is missing. Here, in order to establish such a guideline, we investigate the convergence behavior of the main TDDMRG simulation parameters, such as time integrator, the choice of orbitals, and the choice of matrix-product-state representation for complex-valued nonsinglet states. In addition, we propose a method to select orbitals that are tailored to optimize the dynamics. Lastly, we showcase the TDDMRG by applying it to charge migration ionization dynamics in furfural, where we reveal a rapid conversion from an ionized state with a σ character to one with a π character within less than a femtosecond.

Radiation-Induced Transfer of Charge, Atoms, and Energy within Isolated Biomolecular Systems

In biological tissues, ionizing radiation interacts with a variety of molecules and the consequences include cell killing and the modification of mechanical properties. Applications of biological radiation action are for instance radiotherapy, sterilization, or the tailoring of biomaterial properties. During the first femtoseconds to milliseconds after the initial radiation action, biomolecular systems typically respond by transfer of charge, atoms, or energy. In the condensed phase, it is usually very difficult to distinguish direct effects from indirect effects. A straightforward solution for this problem is the use of gas-phase techniques, for instance from the field of mass spectrometry. In this review, we survey mainly experimental but also theoretical work, focusing on radiation-induced intra- and inter-molecular transfer of charge, atoms, and energy within biomolecular systems in the gas phase. Building blocks of DNA, proteins, and saccharides, but also antibiotics are considered. The emergence of general processes as well as their timescales and mechanisms are highlighted.

Ultrafast chirality: the road to efficient chiral measurements

Today we are witnessing the electric-dipole revolution in chiral measurements. Here we reflect on its lessons and outcomes, such as the perspective on chiral measurements using the complementary principles of "chiral reagent" and "chiral observer", the hierarchy of scalar, vectorial and tensorial enantio-sensitive observables, the new properties of the chiro-optical response in the ultrafast and non-linear domains, and the geometrical magnetism associated with the chiral response in photoionization. The electric-dipole revolution is a landmark event. It has opened routes to extremely efficient enantio-discrimination with a family of new methods. These methods are governed by the same principles but work in vastly different regimes - from microwaves to optical light; they address all molecular degrees of freedom - electronic, vibrational and rotational, and use flexible detection schemes, i.e. detecting photons or electrons, making them applicable to different chiral phases, from gases to liquids to amorphous solids. The electric-dipole revolution has also enabled enantio-sensitive manipulation of chiral molecules with light. This manipulation includes exciting and controlling ultrafast helical currents in vibronic states of chiral molecules, enantio-sensitive control of populations in electronic, vibronic and rotational molecular states, and opens the way to efficient enantio-separation and enantio-sensitive trapping of chiral molecules. The word "perspective" has two meanings: an "outlook" and a "point of view". In this perspective article, we have tried to cover both meanings.

Observation of intra- and intermolecular vibrational coherences of the aqueous tryptophan radical induced by photodetachment

The study of the photodetachment of amino acids in aqueous solution is pertinent to the understanding of elementary processes that follow the interaction of ionizing radiation with biological matter. In the case of tryptophan, the tryptophan radical that is produced by electron ejection also plays an important role in numerous redox reactions in biology, although studies of its ultrafast molecular dynamics are limited. Here, we employ femtosecond optical pump-probe spectroscopy to elucidate the ultrafast structural rearrangement dynamics that accompany the photodetachment of the aqueous tryptophan anion by intense, ∼5-fs laser pulses. The observed vibrational wave packet dynamics, in conjunction with density functional theory calculations, identify the vibrational modes of the tryptophan radical, which participate in structural rearrangement upon photodetachment. Aside from intramolecular vibrational modes, our results also point to the involvement of intermolecular modes that drive solvent reorganization about the N-H moiety of the indole sidechain. Our study offers new insight into the ultrafast molecular dynamics of ionized biomolecules and suggests that the present experimental approach can be extended to investigate the photoionization- or photodetachment-induced structural dynamics of larger biomolecules.

Attochemistry: Is Controlling Electrons the Future of Photochemistry?

Controlling matter with light has always been a great challenge, leading to the ever-expanding field of photochemistry. In addition, since the first generation of light pulses of attosecond (1 as = 10^-18 s) duration, a great deal of effort has been devoted to observing and controlling electrons on their intrinsic time scale. Because of their short duration, attosecond pulses have a large spectral bandwidth populating several electronically excited states in a coherent manner, i.e., an electronic wavepacket. Because of interference, such a wavepacket has a new electronic distribution implying a potentially different and totally new reactivity as compared to traditional photochemistry, leading to the novel concept of "attochemistry". This nascent field requires the support of theory right from the start. In this Perspective, we discuss the opportunities offered by attochemistry, the related challenges, and the current and future state-of-the-art developments in theoretical chemistry needed to model it accurately.

Concluding remarks: The age of molecular movies

This Faraday Discussion has demonstrated enormous progress towards using advanced light sources, together with a variety of experimental and theoretical tools and techniques, to film the motion of both electrons and nuclei in molecules undergoing photo-induced reactions. The new tools are beginning to offer reliable opportunities for achieving the required spatio-temporal resolution, all the way to sub-femtosecond and sub-angstrom scales. The age of quantum molecular movies has arrived.

Ultrafast geometrical reorganization of a methane cation upon sudden ionization: an isotope effect on electronic non-equilibrium quantum dynamics

The ultrafast structural, Jahn-Teller (JT) driven, electronic coherence mediated quantum dynamics in the CH4+ and CD4+ cations that follows sudden ionization using an XUV attopulse exhibits a strong isotope effect. The JT effect makes the methane cation unstable in the Td geometry of the neutral molecule. Upon the sudden ionization the cation is produced in a coherent superposition of three electronic states that are strongly coupled and neither is in equilibrium with the nuclei. In the ground state of the cation the few femtosecond structural rearrangement leads first to a geometrically less distorted D2d minimum followed by a geometrical reorganization to a shallow C2v minimum. The dynamics is computed for an ensemble of 8000 ions randomly oriented with respect to the polarization of the XUV pulse. The ratio, about 3, of the CD4+ to CH4+ autocorrelation functions, is in agreement with experimental measurements of high harmonic spectra. The high value of the ratio is attributed to the faster electronic coherence dynamics in CH4+.

Attosecond science based on high harmonic generation from gases and solids

Recent progress in high power ultrafast short-wave and mid-wave infrared lasers has enabled gas-phase high harmonic generation (HHG) in the water window and beyond, as well as the demonstration of HHG in condensed matter. In this Perspective, we discuss the recent advancements and future trends in generating and characterizing soft X-ray pulses from gas-phase HHG and extreme ultraviolet (XUV) pulses from solid-state HHG. Then, we discuss their current and potential usage in time-resolved study of electron and nuclear dynamics in atomic, molecular and condensed matters.

Different methods are demonstrated in recent years to produce attosecond pulses. Here, the authors discuss recent development and future prospects of the generation of such pulses from gases and solids and their potential applications in spectroscopy and ultrafast dynamics in atoms, molecules and other complex systems.

Selective bond formation triggered by short optical pulses: quantum dynamics of a four-center ring closure

Making bonds with attopulses: quantum dynamics of the ring closure of norbornadiene to quadricyclane.

Addressing the Challenge of Molecular Change: An Interim Report

Invited by the editorial committee of the Annual Review of Physical Chemistry to "contribute my autobiography," I present it here, as I understand the term. It is about my parents, my mentors, my coworkers, and my friends in learning and the scientific problems that we tried to address. Courtesy of the editorial assistance of Annual Reviews, some of the science is in the figure captions and sidebars. I am by no means done: I am currently trying to fuse the quantitative rigor of physical chemistry with systems biology while also dealing with a post-Born-Oppenheimer regime in electronic dynamics and am attempting to instruct molecules to perform advanced logic.

Pumping and probing vibrational modulated coupled electronic coherence in HCN using short UV fs laser pulses: a 2D quantum nuclear dynamical study

The coupled electronic-nuclear coherent dynamics induced by a short strong VUV fs pulse in the low excited electronic states of HCN is probed by transient absorption spectroscopy with a second weaker fs UV pulse. The nuclear time-dependent Schrodinger equation is solved on a 2D nuclear grid with several electronic states with a Hamiltonian including the dipole coupling to the pump and the probe electric fields. The two internal nuclear coordinates describe the motion of the light H atom. There is a band of several excited electronic states at about 8 eV above the ground state (GS) that is transiently accessed by the pump pulse. We tailored the pump so as to selectively populate the lowest 1A'' electronic state thereby the pulse creates an electronic coherence with the GS. Our simulations show that this electronic coherence is modulated by the nuclear motion and persists all the way to dissociation on the 1A'' state. Transient absorption spectra computed as a function of the delay time between the pump and the probe pulses provide a detailed probe of the electronic amplitude and its phase, as well as of the modulation of the electronic coherence by the nuclear motion, both bound and dissociative.

Implementation of Multivariable Logic Functions in Parallel by Electrically Addressing a Molecule of Three Dopants in Silicon

To realize low-power, compact logic circuits, one can explore parallel operation on single nanoscale devices. An added incentive is to use multivalued (as distinct from Boolean) logic. Here, we theoretically demonstrate that the computation of all the possible outputs of a multivariate, multivalued logic function can be implemented in parallel by electrical addressing of a molecule made up of three interacting dopant atoms embedded in Si. The electronic states of the dopant molecule are addressed by pulsing a gate voltage. By simulating the time evolution of the non stationary electronic density built by the gate voltage, we show that one can implement a molecular decision tree that provides in parallel all the outputs for all the inputs of the multivariate, multivalued logic function. The outputs are encoded in the populations and in the bond orders of the dopant molecule, which can be measured using an STM tip. We show that the implementation of the molecular logic tree is equivalent to a spectral function decomposition. The function that is evaluated can be field-programmed by changing the time profile of the pulsed gate voltage.

Nuclear Motion Driven Ultrafast Photodissociative Charge Transfer of the PENNA Cation: An Experimental and Computational Study

Ultrafast nuclear driven charge transfer prior to dissociation is an important process in modular systems as was demonstrated experimentally in the bifunctional molecule 2-phenylethyl-N,N-dimethylamine (PENNA) in work by Lehr et al. ( J. Phys. Chem. A 2005 , 109 , 8074 ). The ultrafast dynamics of PENNA photoexcited to the three lowest electronic states of the cation (D₀, D₁, and D₂) was studied using quantum chemistry and surface hoping. We show that a conical intersection, localized in the Franck-Condon region, between the D₀ and the D₁ states, leads to an ultrafast charge transfer, computed here to be on a time scale of 65 fs, between the phenyl and the amine charged subunits. On the D₀ ground state, the dissociation proceeds on the 60 ps time scale through a 19 kcal/mol late barrier. The computed kinetic energy release is in good agreement with a new experimental measurement of PENNA ionization by an 800 nm 30 fs intense laser pulse.

Quantum Nuclear Dynamics Pumped and Probed by Ultrafast Polarization Controlled Steering of a Coherent Electronic State in LiH

The quantum wave packet dynamics following a coherent electronic excitation of LiH by an ultrashort, polarized, strong one-cycle infrared optical pulse is computed on several electronic states using a grid method. The coupling to the strong field of the pump and the probe pulses is included in the Hamiltonian used to solve the time-dependent Schrodinger equation. The polarization of the pump pulse allows us to control the localization in time and in space of the nonequilibrium coherent electronic motion and the subsequent nuclear dynamics. We show that transient absorption, resulting from the interaction of the total molecular dipole with the electric fields of the pump and the probe, is a very versatile probe of the different time scales of the vibronic dynamics. It allows probing both the ultrashort, femtosecond time scale of the electronic coherences as well as the longer dozens of femtoseconds time scales of the nuclear motion on the excited electronic states. The ultrafast beatings of the electronic coherences in space and in time are shown to be modulated by the different periods of the nuclear motion.

Electron and nuclear dynamics following ionisation of modified bismethylene-adamantane

We have simulated the coupled electron and nuclear dynamics using the Ehrenfest method upon valence ionisation of modified bismethylene-adamantane (BMA) molecules where there is an electron transfer between the two π bonds. We have shown that the nuclear motion significantly affects the electron dynamics after a few fs when the electronic states involved are close in energy. We have also demonstrated how the non-stationary electronic wave packet determines the nuclear motion, more precisely the asymmetric stretching of the two π bonds, illustrating “charge-directed reactivity”. Taking into account the nuclear wave packet width results in the dephasing of electron dynamics with a half-life of 8 fs; this eventually leads to the equal delocalisation of the hole density over the two methylene groups and thus symmetric bond lengths.

XUV excitation followed by ultrafast non-adiabatic relaxation in PAH molecules as a femto-astrochemistry experiment

Highly excited molecular species are at play in the chemistry of interstellar media and are involved in the creation of radiation damage in a biological tissue. Recently developed ultrashort extreme ultraviolet light sources offer the high excitation energies and ultrafast time-resolution required for probing the dynamics of highly excited molecular states on femtosecond (fs) (1 fs=10⁻¹⁵s) and even attosecond (as) (1 as=10⁻¹⁸ s) timescales. Here we show that polycyclic aromatic hydrocarbons (PAHs) undergo ultrafast relaxation on a few tens of femtoseconds timescales, involving an interplay between the electronic and vibrational degrees of freedom. Our work reveals a general property of excited radical PAHs that can help to elucidate the assignment of diffuse interstellar absorption bands in astrochemistry, and provides a benchmark for the manner in which coupled electronic and nuclear dynamics determines reaction pathways in large molecules following extreme ultraviolet excitation.

Extreme UV light sources allow us to study the dynamics of excited molecular stets over remarkably short timeframes. Here, the authors probe polyaromatic hydrocarbons—large organic molecules—and show their electronic excitation and subsequent ultrafast relaxation.

Length effects in VUV photofragmentation of protonated peptides

We have studied photoionization of protonated synthetic peptides YG(n)F (n = 0, 1, 3, 5, 10). Photon energies ranging from 8 to 30 eV were used. For YG(n)F peptides up to n = 5 small fragment ions related to the sidechains of the aromatic terminal amino acids Y and F dominate the fragmentation patterns. The associated yields scale with total photoabsorption cross section, demonstrating efficient hole migration towards the terminal amino acids upon photoionization of the peptide backbone. For n = 10 the side-chain loss channel is quenched and a series of large dications appear.

Electron capture dissociation product ion abundances at the X amino acid in RAAAA-X-AAAAK peptides correlate with amino acid polarity and radical stability

We present mechanistic studies aimed at improving the understanding of the product ion formation rules in electron capture dissociation (ECD) of peptides and proteins in Fourier transform ion cyclotron resonance mass spectrometry. In particular, we attempted to quantify the recently reported general correlation of ECD product ion abundance (PIA) with amino acid hydrophobicity. The results obtained on a series of model H-RAAAAXAAAAK-OH peptides confirm a direct correlation of ECD PIA with X amino acid hydrophobicity and polarity. The correlation factor (R) exceeds 0.9 for 12 amino acids (Ile, Val, His, Asn, Asp, Glu, Gln, Ser, Thr, Gly, Cys, and Ala). The deviation of ECD PIA for seven outliers (Pro is not taken into consideration) is explained by their specific radical stabilization properties (Phe, Trp, Tyr, Met, and Leu) and amino acid basicity (Lys, Arg). Phosphorylation of Ser, Thr, and Tyr decreases the efficiency of ECD around phosphorylated residues, as expected. The systematic arrangement of amino acids reported here indicates a possible route toward development of a predictive model for quantitative electron capture/transfer dissociation tandem mass spectrometry, with possible applications in proteomics.

Probing Ultrafast Purely Electronic Charge Migration in Small Peptides

A pump–probe experiment that can examine a pure charge migration on a time scale short compared to the onset of nuclear motion is discussed. The mass spectrometric studies of Schlag et al. suggest that short peptide terminated by an aromatic amino acid are particularly suitable test compounds. The pump pulse needs to ionize the molecule on a time scale short compared to the period of the electronic motion, typically sub-fs. However, ionization occurs preferentially when the electrical field of the light is maximal so that the duration of the pulse envelope can be somewhat longer. Detection by photoelectron spectrometry of the peptide cation, to produce a dication, is shown to be able to probe the electronic rearrangement.

Ionization and fragmentation of isomeric van der Waals complexes embedded in helium nanodroplets

The ionization and charge transfer processes, which occur when a doped helium droplet undergoes electron impact, are studied for droplets doped with van der Waals complexes with various structures and electrostatic moments. The mass spectra of the two isomers of hydrogen cyanide complexed with either cyanoacetylene or acetylene in helium droplets were obtained using optically selected mass spectrometry, and show that the structure of the complex has a large effect on the fragmentation pattern. The resulting fragmentation pattern is consistent with an ionization process in which charge steering strongly influences the site of initial ionization. The observed dissociation products may also be subject to caging by the helium matrix.

Distal charge transport in peptides

Biological systems often transport charges and reactive processes over substantial distances. Traditional models of chemical kinetics generally do not describe such extreme distal processes. In this Review, an atomistic model for a distal transport of information, which was specifically developed for peptides, is considered. Chemical reactivity is taken as the result of distal effects based on two-step bifunctional kinetics involving unique, very rapid motional properties of peptides in the subpicosecond regime. The bifunctional model suggests highly efficient transport of charge and reactivity in an isolated peptide over a substantial distance; conversely, a very low efficiency in a water environment was found. The model suggests ultrafast transport of charge and reactivity over substantial molecular distances in a peptide environment. Many such domains can be active in a protein.

The time scale for electronic reorganization upon sudden ionization of the water and water-methanol hydrogen bonded dimers and of the weakly bound NO dimer

When the valence molecular orbital is localized sudden ionization can cause the nascent hole to move rapidly even before any relaxation of the geometry occurs. Hydrogen bonded clusters offer suitable test systems where the hole is initially localized on one moiety. Computational studies are reported for the water dimer and water-methanol bimer. The local ionization potential of water is different in the methanol-water and water-methanol conformers and this difference is very clearly reflected in the dynamics of charge migration. For the NO dimer the results are that its structure is symmetric so that the two NO molecules are equivalent and do not exhibit the required localization. The role of symmetry is also evident in the charge propagation for holes created in different orbitals. Localization of the initial hole distribution even if absent in the bare molecule can still be induced by the intense electric field of a sudden photoionization. This effect is computationally studied for the NO dimer in the presence of a static electric field.

An electronic time scale in chemistry

Ultrafast, subfemtosecond charge migration in small peptides is discussed on the basis of computational studies and compared with the selective bond dissociation after ionization as observed by Schlag and Weinkauf. The reported relaxation could be probed in real time if the removal of an electron could be achieved on the attosecond time scale. Then the mean field seen by an electron would be changing rapidly enough to initiate the migration. Tyrosine-terminated tetrapeptides have a particularly fast charge migration where in <1 fs the charge arrives at the other end. A femtosecond pulse can be used to observe the somewhat slower relaxation induced by correlation between electrons of different spins. A slower relaxation also is indicated when removing a deeper-lying valence electron. When a chromophoric amino acid is at one end of the peptide, the charge can migrate all along the peptide backbone up to the N end, but site-selective ionization is probably easier to detect for tryptophan than for tyrosine.

Dissociation Kinetics of Peptide Ions

The dissociation of peptide ions has been found to have ultrafast components that in many ways are uniquely different from typical unimolecular kinetics. As such, some peptide reactions provide new channels, which do not conform to statistical models of reaction kinetics. When the dissociation rates are in the 100 fs range, they are in a time scale where statistical methods do not yet apply, although molecules that have not yet dissociated will later in time undergo statistical redistribution of their excess energy, which, however, may not lead to noticeable reactivity within the experimental time frames for large peptides and hence are simply dissipative. This work is meant to reconcile the long time statistical results of Lifshitz et al. (2003) with the work of Schlag et al. (1995/6) that suggests an alternate parallel and much faster time scale for dissociation. It is argued that the two sets of results and interpretations augment one another and in fact open up a most interesting new field of peptide kinetics in addition to the unimolecular behavior, which becomes de facto arrested by the shear size of the molecule being unable to find a transition state on any reasonable time scale.

Electrical transport in saturated and conjugated molecular wires

The mechanism for charge transport in dithio molecular wires tethered between two gold electrodes is investigated, using both a steady state and a time-dependent quantum mechanical approach. The interface with the electrodes is modeled by two gold clusters and the electronic structure of the entire Au(n)-S-bridge-S-Au(n) system is computed ab initio at the DFT level and semi-empirically, with the extended Hückel theory. Current vs. applied bias, I-V, curves are computed using a scattering Landauer-type formalism in a steady state picture. The applied source-drain and gate voltages are included at the ab initio level in the electronic Hamiltonian and found to influence strongly the I-V characteristics. The time evolution of a non stationary electronic wave packet initially localized on a gold atom at one end of the extended system shows that charge transfer proceeds sequentially, by a hopping mechanism, to the opposite end. Analysis of the effective one electron Hamiltonian matrix shows that the sulfur atom endows a resistive character to the Au-C-S junctions. The S atoms are however rather well coupled to both the gold and carbon atoms so that typically the super exchange limit for electron transfer is not reached unless the molecular bridge is saturated and the Fermi window function is narrow.

Femtosecond Dynamics after Ionization: 2-Phenylethyl-N,N-dimethylamine as a Model System for Nonresonant Downhill Charge Transfer in Peptides

The cation of 2-phenylethyl-N,N-dimethylamine (PENNA) offers two local sites for the charge: the amine group and 0.7 eV higher in energy the phenyl chromophore. In this paper, we investigate the dynamics of the charge transfer (CT) from the phenyl to the amine site. We present a femtosecond resonant two-color photoionization spectrum which shows that the femtosecond pump laser pulse is resonant in the phenyl chromophore. As shown previously with resonant wavelengths the aromatic phenyl chromophore can be then selectively ionized. Because the state "charge in the phenyl chromophore" is the first excited state in the PENNA cation, it can relax to the lower-energetic state "charge in the amine site". To follow this CT dynamics, femtosecond probe photoabsorption of green light (vis) is used. The vis light is absorbed by the charged phenyl chromophore, but not by the neutral phenyl and the neutral or cationic amine group. Thus, the absorption of vis photons of the probe laser pulse is switched off by the CT process. For detection of the resonant absorption of two or more vis photons in the cation the intensity of a fragmentation channel is monitored which opens only at high internal energy. The CT dynamics in PENNA cations has a time constant of 80 +/- 28 fs and is therefore not a purely electronic process. Because of its structural similarity to phenylalanine, PENNA is a model system for a downhill charge transfer in peptide cations.

Different chemical dynamics for different conformers of biological molecules: Photoionization of glycine

Single-photon ionization dynamics of two conformers of glycine is studied by classical trajectory simulations using the semiempirical PM3 potential surface in "on the fly" calculations. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for the initial vibrational ground state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. The dynamics of the two conformers are compared during the first 10 ps. The comparison shows very different dynamical behavior for the two conformers. In particular, the chemical fragmentation pathways differ in part. Also, one of the conformers gives much higher rates of conformational transitions, while the other conformer gives larger chemical fragmentation yields. The example shows significantly different chemical dynamics for two conformers close in energy and separated by a low barrier.

Formation of molecular radical cations of enkephalin derivatives via collision-induced dissociation of electrospray-generated copper (II) complex ions of amines and peptides

Fragmentation of some electrospray-generated complex ions, [63CuII(amine)M].2+, where M is an enkephalin derivative, produces the radical cation of the peptide, M.+. This ion has only been observed when M contains a tyrosyl or tryptophanyl residue plus a basic residue, typically arginyl or lysyl. A typical viable amine is diethylenetriamine. Collision-induced dissociation (CID) of the M.+ ion yields a prominent [M - 106].+ product ion for tyrosine-containing peptides, and a prominent [M - 129].+ ion for a tryptophan-containing peptide. These fragment ions are formed as a result of elimination of the tyrosyl and tryptophanyl side chains. Dissociation of these ions, in turn, produces second generation product ions, many of which are typically absent in the fragmentation of protonated peptide ions. Structures for some of these unusual ions are proposed.