Charge migration and control of site selective reactivity: The role of covalent and ionic states

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.

Systematic Investigation of the Reliability of the Frozen Nuclei Approximation for Short-Pulse Excitation: The Example of HCCI+

In this work we quantitatively study the reliability of the frozen nuclei approximation for ultrafast dynamics. Specifically we study laser excitation of HCCI⁺ from its ground state to the first electronically excited state. The population of the first excited state is obtained by both the frozen nuclei approximation and by multidimensional nuclear dynamics. Detailed comparison of the results by the two methods are performed to provide quantitative criteria for the reliability of the frozen nuclei approximation for this system.

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.

Theoretical description of charge migration with a single Slater-determinant and beyond

Triggered by the interest to study charge migration in large molecular systems, a simple methodology has recently been proposed based on straightforward density functional theory calculations. This approach describes the time evolution of the initially created hole density in terms of the time evolution of the ionized highest occupied molecular orbital (HOMO). Here we demonstrate that this time-dependent analog of Koopmans' theorem is not valid, and instead of the time evolution of the HOMO, the time evolution of the orbitals that remain occupied in the cation determines the evolution of the initially created hole in the framework of time-dependent single-determinant theories. Numerical examples underline that for a proper description of charge migration processes, an explicit treatment of the electron correlation is indispensable. Moreover, they also demonstrate that the attempts to describe charge migration based on Kohn-Sham density functional theory using conventional exchange-correlation functionals are doomed to fail due to the well-known self-interaction error.

Transcending binary logic by gating three coupled quantum dots

Physical considerations supported by numerical solution of the quantum dynamics including electron repulsion show that three weakly coupled quantum dots can robustly execute a complete set of logic gates for computing using three valued inputs and outputs. Input is coded as gating (up, unchanged, or down) of the terminal dots. A nanosecond time scale switching of the gate voltage requires careful numerical propagation of the dynamics. Readout is the charge (0, 1, or 2 electrons) on the central dot.

Molecular response properties from explicitly time-dependent configuration interaction methods

In this paper we report the calculation of molecular electric response properties with the help of explicitly time-dependent configuration interaction (TD-CI) methods. These methods have the advantage of being applicable (within the limitations of the time-dependent Schrodinger equation) to time-dependent perturbations of arbitrary shape and strength. Three variants are used to solve the time-dependent electronic Schrodinger equation, namely, the TD-CIS (inclusion of single excitations only), TD-CISD (inclusion of single and double excitations), and TD-CIS(D) (single excitations and perturbative treatment of double excitations) methods and applied for illustration to small molecules, H(2) and H(2)O. In the calculation, slowly varying off-resonant electric fields are applied to the molecules and linear (polarizabilities) and nonlinear (hyperpolarizabilities, harmonic generation) response properties are determined from the time-dependent dipole moments.

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.

Gauge symmetry, chirality and parity effects in four-particle systems: Coulomb's law as a universal function for diatomic molecules

Following recent work in search for a universal function (Van Hooydonk, Eur. J. Inorg. Chem., (1999), 1617), we test four symmetric +/- a(n)Rn potentials for reproducing molecular potential energy curves (PECs). Classical gauge symmetry for 1/R-potentials results in generic left right asymmetric PECs. A pair of symmetric perturbed Coulomb potentials is quantitatively in accordance with observed PECs. For a bond, a four-particle system, charge inversion (a parity effect, atom chirality) is the key to explain this shape generically. A parity adapted Hamiltonian reduces from ten to two terms and to a soluble Bohr-like formula, a Kratzer (1 - Re/R)2 potential. The result is similar to the combined action of spin and wave function symmetry upon the Hamiltonian in Heitler-London theory. Analytical perturbed Coulomb functions varying with (1 - Re/R) scale attractive and repulsive branches of PECs for 13 bonds H2, HF, LiH, KH, AuH, Li2, LiF, KLi, NaCs, Rb2, RbCs, Cs2 and I2 in a single straight line. The 400 turning points for 13 bonds are reproduced with a deviation of 0.007 A at both branches. For 230 points at the repulsive side, the deviation is 0.003 A. The perturbed electrostatic Coulomb law is a universal molecular function. Ab initio zero molecular parameter functions give PECs of acceptable quality, just using atomic ionisation energies. The function can be used as a model potential for inverting levels and gives a first principle's comparison of short- and long-range interactions, important for the study of cold atoms. Wave-packet dynamics, femto-chemistry applied to the crossing of covalent and ionic curves, can provide evidence for this theory. We anticipate this scale/shape invariant scheme applies to smaller scales in nuclear and high-energy particle physics. For larger gravitational scales (Newton 1/R potentials), problems with super-unification are discussed. Reactions between hydrogen and antihydrogen, feasible in the near future, will probably produce normal H2.

Architecture with designer atoms: simple theoretical considerations

The distinct electronic states of assemblies of metallic quantum dots are discussed in a simple approximation where each dot is mimicked as an "atom" that carries one valence electron. Because of their large size, the charging energy of the dots, I = energy required to add another electron, is much smaller than for ordinary atoms. The Coulomb blocking of charge migration is therefore easier to overcome. For the theory, however, this is a challenge, because ionic states, which are typically higher in energy, come down, so the density of electronic states is high, and special methods need to be adapted. Quantum dots are prepared by wet chemical methods and accordingly are not quite identical. They will have a size distribution that can be narrow (when the dots can be assembled into an ordered array) or broad. Other sources of disorder are packing imperfections, which are characteristic of a wider size distribution, ligand deformations, and chemical unevenness. Two experimental control parameters are the size of the dots and the spacing between them. We discuss the combined effects of the low charging energy and disorder and examine the distinct electronic phases that can be realized.