Electronic Excitation Response of DNA to High-Energy Proton Radiation in Water.

The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer therapies. In particular, the dependence of different types of DNA damage on high-energy protons represents a significant knowledge void. Here we employ first-principles real-time time-dependent density functional theory simulation, using a massively parallel supercomputer, to unravel the quantum-mechanical details of the energy transfer from high-energy protons to DNA in water. The calculations reveal that protons deposit significantly more energy onto the DNA sugar-phosphate side chains than onto the nucleobases, and greater energy transfer is expected onto the DNA side chains than onto water. As a result of this electronic stopping process, highly energetic holes are generated on the DNA side chains as a source of oxidative damage.

2D Monolayers for Superior Transparent Electromagnetic Interference Shielding.

With countless modern technologies utilizing wireless communication, materials that can selectively allow transmission of visible light and prevent transmission of low frequency GHz electromagnetic interference (EMI) are needed. Recently, 2D materials such as graphene, transition metal dichalcogenides, and MXenes have shown promise for such applications. Despite the rapid advances, little progress has been made in identifying 2D monolayers with intrinsically higher visible transmittance (Tvis) and shielding effectiveness (SE). With endless variations in structure and composition, the 2D materials space is too large for systematic experimental investigation. To tackle this challenge, we perform a high-throughput computational screening. Using an atomistic first-principles method, we simultaneously calculate Tvis and SE of 7000 2D monolayer materials. We identify 26 monolayer materials with excellent properties of >98% Tvis and >5 dB SE (∼70% EMI attenuation). The top candidate, an AgSe2 monolayer with predicted 98.53% Tvis and 12.53 dB SE (∼94% EMI attenuation), is a significant improvement over the state-of-the-art, graphene, with 96.7% Tvis and 3.04 dB SE (∼40% EMI attenuation). Additionally, we gain physical insights into the transparent EMI shielding performance of 2D monolayers and their electronic structure, elucidating the role of surface terminations and nearly free electron states.

Emerged Metallicity in Molecular Ferromagnetic Wires.

Supramolecular engineering bridges molecular assembly with macromolecular charge-transfer salts, promising the design to construct supramolecular architectures that integrate cooperative properties difficult or impossible to find in conventional lattices. Here, we report the crystal engineering design and kinetic growth of one-dimensional supramolecular wires composed of bis(ethylenedithio)tetrathiafulvalene (ET+) cation and polymeric Cu[N(CN)2]2- anion. A bulk ferromagnetic order is discovered for filling up the gap where strong ferromagnetism is missing in such ET molecule-based charge-transfer salts. Metallicity is induced by electric current from the semiconducting wire, which is attributed to strain effect by tuning its close molecular contact. This structural feature is evidenced through the combination of various mechanistic spectroscopic studies. Electric dipole is established from the close molecular contacts and is suggestive to stabilize ferromagnetic spin interaction through anions bridging spin sites. The breakthrough shown here provides a pathway to explore low-dimensional supramolecular materials exhibiting strong electron correlation, metallicity, and ferromagnetism.

Simulating electronic excitation and dynamics with real-time propagation approach to TDDFT within plane-wave pseudopotential formulation.

We give a perspective on simulating electronic excitation and dynamics using the real-time propagation approach to time-dependent density functional theory (RT-TDDFT) in the plane-wave pseudopotential formulation. RT-TDDFT is implemented in various numerical formalisms in recent years, and its practical application often dictates the most appropriate implementation of the theory. We discuss recent developments and challenges, emphasizing numerical aspects of studying real systems. Several applications of RT-TDDFT simulation are discussed to highlight how the approach is used to study interesting electronic excitation and dynamics phenomena in recent years.

First-Principles Demonstration of Nonadiabatic Thouless Pumping of Electrons in a Molecular System.

We demonstrate nonadiabatic Thouless pumping of electrons in trans-polyacetylene in the framework of Floquet engineering using first-principles theory. We identify the regimes in which the quantized pump is operative with respect to the driving electric field for a time-dependent Hamiltonian. By employing the time-dependent maximally localized Wannier functions in real-time time-dependent density functional theory simulation, we connect the winding number, a topological invariant, to a molecular-level understanding of the quantized pumping. While the pumping dynamics constitutes the opposing movement of the Wannier functions that represent both double and single bonds, the resulting current is unidirectional due to the greater number of double-bond electrons. Using a gauge-invariant formulation called dynamical transition orbitals, an alternative viewpoint on the nonequilibrium dynamics is obtained in terms of the particle-hole excitation. A single time-dependent transition orbital is found to be largely responsible for the observed quantized pumping. In this representation, the pumping dynamics manifests itself in the dynamics of this single orbital as it undergoes changes from its π bonding orbital character at equilibrium to acquiring resonance and antibonding character in the driving cycle. The work demonstrates the Floquet engineering of the nonadiabatic topological state in an extended molecular system, paving the way for experimental realization of the new quantum material phase.

First-Principles Modeling of Electronic Stopping in Complex Matter under Ion Irradiation.

Electronic stopping refers to the dynamical energy-transfer process to electrons in matter from highly energetic charged particles such as high-velocity protons. We discuss recent progress in theoretical studies of electronic stopping in condensed matter under ion irradiation, focusing on modern electronic structure theory's role in enabling the study of electronic excitation dynamics that result from the energy transfer. In the last few decades, first-principles simulation approaches based on real-time time-dependent density functional theory have greatly advanced the field. While linear response theory is widely used to study electronic stopping processes, especially for simple solids, novel first-principles dynamics approaches now allow us to study chemically complex systems and also yield detailed descriptions of electronic excitations at the molecular scale. Outstanding challenges for further advancement of electronic stopping modeling are also discussed from the viewpoint of electronic structure theory.

K-Shell Core-Electron Excitations in Electronic Stopping of Protons in Water from First Principles.

Understanding the role of core-electron excitation in liquid water under proton irradiation has become important due to the growing use of proton beams in radiation oncology. Using a first-principles, nonequilibrium simulation approach based on real-time, time-dependent density functional theory, we determine the electronic stopping power, the velocity-dependent energy transfer rate from irradiating ions to electrons. The electronic stopping power curve agrees quantitatively with experimental data over the velocity range available. At the same time, significant differences are observed between our first-principles result and commonly used perturbation theoretic models. Excitations of the water molecules' oxygen core electrons are a crucial factor in determining the electronic stopping power curve beyond its maximum. The core-electron contribution is responsible for as much as one third of the stopping power at the high proton velocity of 8.0 a.u. (1.6 MeV). K-shell core-electron excitations not only provide an additional channel for the energy transfer-they also significantly influence the valence electron excitations. In the excitation process, generated holes remain highly localized within a few angstroms around the irradiating proton path, whereas electrons are excited away from the path. In spite of their great contribution to the stopping power, K-shell electrons play a rather minor role in terms of the excitation density; only 1% of the hole population composes K-shell holes, even at the high proton velocity of 8.0 a.u. The excitation behavior revealed is distinctly different from that of photon-based ionizing radiation such as x or γ rays.

Excitation energy-dependent photocurrent switching in a single-molecule photodiode.

The direction of electron flow in molecular optoelectronic devices is dictated by charge transfer between a molecular excited state and an underlying conductor or semiconductor. For those devices, controlling the direction and reversibility of electron flow is a major challenge. We describe here a single-molecule photodiode. It is based on an internally conjugated, bichromophoric dyad with chemically linked (porphyrinato)zinc(II) and bis(terpyridyl)ruthenium(II) groups. On nanocrystalline, degenerately doped indium tin oxide electrodes, the dyad exhibits distinct frequency-dependent, charge-transfer characters. Variations in the light source between red-light (∼1.9 eV) and blue-light (∼2.7 eV) excitation for the integrated photodiode result in switching of photocurrents between cathodic and anodic. The origin of the excitation frequency-dependent photocurrents lies in the electronic structure of the chromophore excited states, as shown by the results of theoretical calculations, laser flash photolysis, and steady-state spectrophotometric measurements.

Propagation of maximally localized Wannier functions in real-time TDDFT.

Real-time, time-dependent density functional theory (RT-TDDFT) has gained popularity as a first-principles approach to study a variety of excited-state phenomena such as optical excitations and electronic stopping. Within RT-TDDFT simulations, the gauge freedom of the time-dependent electronic orbitals can be exploited for numerical and scientific convenience while the unitary transformation does not alter physical properties calculated from the quantum dynamics of electrons. Exploiting this gauge freedom, we demonstrate the propagation of maximally localized Wannier functions within RT-TDDFT. We illustrate its great utility through a number of examples including its application to optical excitation in extended systems using the so-called length gauge, interpreting electronic stopping excitation, and simulating electric field-driven quantized charge transport. We implemented the approach within our plane-wave pseudopotential RT-TDDFT module of the QB@LL code, and the performance of the implementation is also discussed.

Electronic Excitation Dynamics in DNA under Proton and α-Particle Irradiation.

Electronic excitations are produced when matter is exposed to ion irradiation comprising highly energetic ions. These electronic stopping excitations are responsible for ion beam-induced DNA damage by energetic protons and α-particles, the chemistry and physics of which are central to burgeoning radiation cancer therapies. By simulating the non-perturbative electronic response of DNA to irradiating protons and α-particles, our first-principles dynamics simulations enable us to test the validity of the commonly used linear response theory description, and they also reveal unprecedented details of the quantum dynamics of electronic excitations. In this work, we discuss the extent to which the linear response theory is valid by comparing to the first-principles determination of electronic stopping power, the energy-transfer rate from ions to electronic excitation. The simulations show that electronic excitations induced by proton and α-particle irradiation cause ionization of DNA, resulting in the generation of holes. By studying the excited hole generation in terms of both the energetic and spatial details in DNA, our work reveals remarkable differences with the excitation behavior of DNA under more commonly used ionizing irradiation sources such as X/γ-ray photons. Furthermore, we find that the generation of excited holes does not directly correlate with the energy-transfer rate as a function of the irradiating ion velocity, in contrast to what is often assumed in the chemistry and physics of radiation oncology.