Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.

Electronic and Vibrational Manifold of Tetracyanoethylene-Chloronaphthalene Charge Transfer Complex in Solution: Insights from TD-DFT and Ab Initio Molecular Dynamics

The interplay between light absorption and the molecular environment has a central role in the observed photophysics of a wide range of photoinduced chemical and biological phenomena. The understanding of the interplay between vibrational and electronic transitions is the focus of this work, since it can provide a rationale to tune the optical properties of charge transfer (CT) materials used for technological applications. A clear description of these processes poses a nontrivial challenge from both the theoretical and experimental points of view, where the main issue is how to accurately describe and probe drastic changes in the electronic structure and the ultrafast molecular relaxation and dynamics. In this work we focused on the intermolecular CT reaction that occurs upon photon absorption in a π-stacked model system in dichloromethane solution, in which the 1-chloronaphthalene (1ClN) acts as the electron donor and tetracyanoethylene (TCNE) is the electron acceptor. Density functional theory calculations have been carried out to characterize both the ground-state properties and more importantly the low-lying CT electronic transition, and excellent agreement with recently available experimental results [Mathies, R. A.; et al. J. Phys. Chem. A 2018, 122 (14), 3594] was obtained. The minima of the ground state and first singlet excited state have been accurately characterized in terms of spatial arrangements and vibrational Raman frequencies, and the CT natures of the first two low-lying electronic transitions in the absorption spectra have been addressed and clarified too. Finally, by modeling the possible coordination sites of the TCNE electron acceptor with respect to monovalent ions (Na+, K+) in an implicit solution of acetonitrile, we find that TCNE can accommodate a counterion in two different arrangements, parallel and orthogonal to the C═C axis, leading to the formation of a contact ion pair. The nature of the counterion and its relative position entail structural modifications of the TCNE radical anion, mainly the central C═C and C≡N bonds, compared to the isolated case. An important red shift of the C═C stretching frequency was observed when the counterion is orthogonal to the double bond, to a greater extent for Na+. On the contrary, in the second case, where the counterion ion lies along the internuclear C═C axis, we find that K+ polarizes the electron density of the double bond more, resulting in a greater red shift than with Na+.

Exploring the Franck-Condon region of a photoexcited charge transfer complex in solution to interpret femtosecond stimulated Raman spectroscopy: excited state electronic structure methods to unveil non-radiative pathways

We present electronic structure methods to unveil the non-radiative pathways of photoinduced charge transfer (CT) reactions that play a main role in photophysics and light harvesting technologies. A prototypical π-stacked molecular complex consisting of an electron donor (1-chloronaphthalene, 1ClN) and an electron acceptor (tetracyanoethylene, TCNE) was investigated in dichloromethane solution for this purpose. The characterization of TCNE:π:1ClN in both its equilibrium ground and photoinduced low-lying CT electronic states was performed by using a reliable and accurate theoretical-computational methodology exploiting ab initio molecular dynamics simulations. The structural and vibrational time evolution of key vibrational modes is found to be in excellent agreement with femtosecond stimulated Raman spectroscopy experiments [R. A. Mathies et al., J. Phys. Chem. A, 2018, 122, 14, 3594], unveiling a correlation between vibrational fingerprints and electronic properties. The evaluation of nonadiabatic coupling matrix elements along generalized normal modes has made possible the interpretation on the molecular scale of the activation of nonradiative relaxation pathways towards the ground electronic state. In particular, two low frequency vibrational modes such as the out of plane bending and dimer breathing and the TCNE central C[double bond, length as m-dash]C stretching play a prominent role in relaxation phenomena from the electronic CT state to the ground state one.

Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method

Practical ways to calculate the tunneling matrix elements and analyze the tunneling pathways for protein electron-transfer (ET) reactions with a fragment molecular orbital (FMO) method are presented. The straightforward use of minimal basis sets only for the atoms involved in the covalent bond detachment in FMO can properly describe the ETs through the protein main-chains with the cost-effective two-body corrections (FMO2) without losing the quality of double-zeta basis sets. The current FMO codes have been interfaced with density functional theory, polarizable continuum model, and model core potentials, with which the FMO-based protein ET calculations can consider the effects of electron correlation, solvation, and transition-metal redox centers. The reasonable performance of the FMO-based ET calculations is demonstrated for three different sets of protein-ET model molecules: (1) hole transfer between two tryptophans covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, (2) ET between two plastoquinones covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, and (3) hole transfer between ruthenium (Ru) and copper (Cu) complexes covalently bridged by a stretch of a polyglycine linker as a model for Ru-modified derivatives of azurin.

Transgenic and Diet-Enhanced Silk Production for Reinforced Biomaterials: A Metamaterial Perspective

Silk fibers, which are protein-based biopolymers produced by spiders and silkworms, are fascinating biomaterials that have been extensively studied for numerous biomedical applications. Silk fibers often have remarkable physical and biological properties that typical synthetic materials do not exhibit. These attributes have prompted a wide variety of silk research, including genetic engineering, biotechnological synthesis, and bioinspired fiber spinning, to produce silk proteins on a large scale and to further enhance their properties. In this review, we describe the basic properties of spider silk and silkworm silk and the important production methods for silk proteins. We discuss recent advances in reinforced silk using silkworm transgenesis and functional additive diets with a focus on biomedical applications. We also explain that reinforced silk has an analogy with metamaterials such that user-designed atypical responses can be engineered beyond what naturally occurring materials offer. These insights into reinforced silk can guide better engineering of superior synthetic biomaterials and lead to discoveries of unexplored biological and medical applications of silk.

Charge-patching method for the calculation of electronic structure of polypeptides

Based on the CPM method, the charge densities of polypeptides can be generated and their electronic structure can be further calculated.

Constructive quantum interference in a bis-copper six-porphyrin nanoring

The exchange interaction, J, between two spin centres is a convenient measure of through bond electronic communication. Here, we investigate quantum interference phenomena in a bis-copper six-porphyrin nanoring by electron paramagnetic resonance spectroscopy via measurement of the exchange coupling between the copper centres. Using an analytical expression accounting for both dipolar and exchange coupling to simulate the time traces obtained in a double electron electron resonance experiment, we demonstrate that J can be quantified to high precision even in the presence of significant through-space coupling. We show that the exchange coupling between two spin centres is increased by a factor of 4.5 in the ring structure with two parallel coupling paths as compared to an otherwise identical system with just one coupling path, which is a clear signature of constructive quantum interference.

Quantum interference in charge transport is attracting interest with applications in nanoelectronics and quantum computing. Here, the authors present a method for quantifying electronic transmission through molecules, and demonstrate constructive quantum interference in a molecule with two identical, parallel coupling paths.

Vibronic coupling in organic semiconductors for photovoltaics

Ultrafast two-dimensional electronic spectroscopy reveals vibronically-assisted coherent charge transport and separation in organic materials and opens up new perspectives for artificial light-to-current conversion.

Quantifying electron transfer reactions in biological systems: what interactions play the major role?

Various biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve light absorption, excited electronic states formation, excitation energy transfer, electrons and protons tunnelling which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between quantum physics and biology. In this paper we consider electron transfer in biological processes, from a theoretical view-point; namely in terms of quantum mechanical and semi-classical models. We systematically characterize the interactions between the moving electron and its biological environment to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe specifically the electron transfer reactions in Arabidopsis thaliana cryptochrome-a signaling photoreceptor protein that became attractive recently due to its possible function as a biological magnetoreceptor.

Quantifying non-Markovianity for a chromophore-qubit pair in a super-Ohmic bath

An approach based on a non-Markovian time-convolutionless polaron master equation is used to probe the quantum dynamics of a chromophore-qubit in a super-Ohmic bath. Utilizing a measure of non-Markovianity based on dynamical fixed points, we study the effects of the environmental temperature and the coupling strength on the non-Markovian behavior of the chromophore in a super-Ohmic bath. It is found that an increase in the temperature results in a reduction in the backflow information from the environment to the chromophore, and therefore, a suppression of non-Markovianity. In the weak coupling regime, increasing the coupling strength will enhance the non-Markovianity, while the effect is reversed in the strong coupling regime.

Electrical conductivity equations derived with the rate process theory and free volume concept

Inspired by the Marcus theory of electron transfer, electrical conductivity equations without reference to any specific materials are derived on the basis of Eyring’s rate process theory and the free volume concept.

DFT-based Green's function pathways model for prediction of bridge-mediated electronic coupling

New LMO-GFM methodology enables intuitive understanding of electron tunneling in terms of through-bond and through-space interactions.

Non-adiabatic effects in thermochemistry, spectroscopy and kinetics: the general importance of all three Born–Oppenheimer breakdown corrections

Analytical and numerical solutions describing Born–Oppenheimer breakdown in a simple, widely applicable, model depict shortcomings in modern computational methods.

Investigation of the molecular mechanisms of electronic decoherence within a quinone cofactor

The notion of decoherence is particularly adapted to discuss the quantum-to-classical transition in the context of chemical reactions. Decoherence can be modeled by computing the time evolution of nuclear wave packets evolving on distinct potential energy surfaces, here using density functional theory (DFT) and Born–Oppenheimer molecular dynamics simulations. We investigate a redox cofactor of biological interest (tryptophan tryptophylquinone, TTQ) found in the enzyme methylamine dehydrogenase. We also report the first systematic comparison of semi-empirical DFT (tight-binding DFT) and classical force field approaches for estimating decoherence in molecular systems. In the TTQ cofactor, we find that decoherence combines structural and dynamical aspects: it is initiated by the divergent motions of few atoms and then propagates dynamically to the remaining atoms. It is the mass effect of all the atoms that leads to decoherence within a few femtosecond.

Can mitochondrial dysfunction be initiated by dissociative electron attachment to xenobiotics?

Resonance attachment of low-energy electrons to xenobiotic molecules, 2,4-dichlorophenoxyacetic acid (2,4-D), dichlorodiphenyltrichloroethane (DDT) and dichlorodiphenyldichloroethylene (DDE), was investigated under gas-phase conditions by means of complementary experimental techniques. Electron transmission spectroscopy (ETS) and dissociative electron attachment spectroscopy (DEAS), in the 0-6 eV and 0-15 eV energy range, respectively, were applied with the aim of modeling the behavior of these pesticide molecules under reductive conditions in vivo. Formation of long-lived parent molecular anions and fragment negative ions was observed at incident electron energies very close to zero, in agreement with the results of density functional theory calculations. The gas-phase DEA process, analogous to dissociative electron transfer in solution, was considered as a model for the initial step which occurs in the intermembrane space of mitochondria when a xenobiotic molecule captures an electron "leaked" from the respiratory chain. A possible involvement of the fragments produced by DEA to the pesticides under investigation into cellular processes is discussed. It is concluded that the free radicals and potential DNA adducts formed by DEA are expected to be dangerous for mitochondrial functionalities, while several of the products observed could act as messenger molecules, thus interfering with the normal cellular signaling pathways.

New insights into the mechanism of electron transfer within flavohemoglobins: tunnelling pathways, packing density, thermodynamic and kinetic analyses

Flavohemoglobins (FlavoHb) are metalloenzymes catalyzing the reaction of nitric oxide dioxygenation. The iron cation of the heme group needs to be preliminarily reduced to the ferrous state to be catalytically competent. This reduction is triggered by a flavin adenine dinucleotide (FAD) prosthetic group which is localized in a distinct domain of the protein. In this paper we obtain new insights into the internal long range electron transfer (over ca. 12 Å) using a combination of experimental and computational approaches. Employing a time-resolved pulse radiolysis technique we report the first direct measurement of the FADH˙→ HemeFe(III) electron transfer rate. A rate constant of (6.8 ± 0.5) × 10(3) s(-1) is found. A large panel of computational approaches are used to provide the first estimation of the thermodynamic characteristics of the internal electron transfer step within flavoHb: both the driving force and the reorganization energy are estimated as a function of the protonated state of the flavin semi-quinone. We also report an analysis of the electron pathways involved in the tunnelling of the electron through the aqueous interface between the globin and the flavin domains.