Heavy element incorporation in nitroimidazole radiosensitizers: molecular-level insights into fragmentation dynamics.

The present study investigates the photofragmentation behavior of iodine-enhanced nitroimidazole-based radiosensitizer model compounds in their protonated form using near-edge X-ray absorption mass spectrometry and quantum mechanical calculations. These molecules possess dual functionality: improved photoabsorption capabilities and the ability to generate species that are relevant to cancer sensitization upon photofragmentation. Four samples were investigated by scanning the generated fragments in the energy regions around C 1s, N 1s, O 1s, and I 3d-edges with a particular focus on NO2+ production. The experimental summed ion yield spectra are explained using the theoretical near-edge X-ray absorption fine structure spectrum based on density functional theory. Born-Oppenheimer-based molecular dynamics simulations were performed to investigate the fragmentation processes.

Ultrafast manipulation of the NiO antiferromagnetic order via sub-gap optical excitation.

Wide-band-gap insulators such as NiO offer the exciting prospect of coherently manipulating electronic correlations with strong optical fields. Contrary to metals where rapid dephasing of optical excitation via electronic processes occurs, the sub-gap excitation in charge-transfer insulators has been shown to couple to low-energy bosonic excitations. However, it is currently unknown if the bosonic dressing field is composed of phonons or magnons. Here we use the prototypical charge-transfer insulator NiO to demonstrate that 1.5 eV sub-gap optical excitation leads to a renormalised NiO band-gap in combination with a significant reduction of the antiferromagnetic order. We employ element-specific X-ray reflectivity at the FLASH free-electron laser to demonstrate the reduction of the upper band-edge at the O 1s-2p core-valence resonance (K-edge) whereas the antiferromagnetic order is probed via X-ray magnetic linear dichroism (XMLD) at the Ni 2p-3d resonance (L2-edge). Comparing the transient XMLD spectral line shape to ground-state measurements allows us to extract a spin temperature rise of 65 ± 5 K for time delays longer than 400 fs while at earlier times a non-equilibrium spin state is formed. We identify transient mid-gap states being formed during the first 200 fs accompanied by a band-gap reduction lasting at least up to the maximum measured time delay of 2.4 ps. Electronic structure calculations indicate that magnon excitations significantly contribute to the reduction of the NiO band gap.

Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides.

X-ray free-electrons lasers have revolutionized the method of imaging biological macromolecules such as proteins, viruses and cells by opening the door to structural determination of both single particles and crystals at room temperature. By utilizing high intensity X-ray pulses on femtosecond timescales, the effects of radiation damage can be reduced. Achieving high resolution structures will likely require knowledge of how radiation damage affects the structure on an atomic scale, since the experimentally obtained electron densities will be reconstructed in the presence of radiation damage. Detailed understanding of the expected damage scenarios provides further information, in addition to guiding possible corrections that may need to be made to obtain a damage free reconstruction. In this work, we have quantified the effects of ionizing photon-matter interactions using first principles molecular dynamics. We utilize density functional theory to calculate bond breaking and charge dynamics in three ultracharged molecules and two different structural conformations that are important to the structural integrity of biological macromolecules, comparing to our previous studies on amino acids. The effects of the ultracharged states and subsequent bond breaking in real space are studied in reciprocal space using coherent diffractive imaging of an ensemble of aligned biomolecules in the gas phase.

X-ray Induced Fragmentation of Protonated Cystine.

We demonstrate site-specific X-ray induced fragmentation across the sulfur L-edge of protonated cystine, the dimer of the amino acid cysteine. Ion yield NEXAFS were performed in the gas phase using electrospray ionization (ESI) in combination with an ion trap. The interpretation of the sulfur L-edge NEXAFS spectrum is supported by Restricted Open-Shell Configuration Interaction (ROCIS) calculations. The fragmentation pathway of triply charged cystine ions was modeled by Molecular Dynamics (MD) simulations. We have deduced a possible pathway of fragmentation upon excitation and ionization of S 2p electrons. The disulfide bridge breaks for resonant excitation at lower photon energies but remains intact upon higher energy resonant excitation and upon ionization of S 2p. The larger fragments initially formed subsequently break into smaller fragments.

Protein orientation in time-dependent electric fields: orientation before destruction.

Proteins often have nonzero electric dipole moments, making them interact with external electric fields and offering a means for controlling their orientation. One application that is known to benefit from orientation control is single-particle imaging with x-ray free-electron lasers, in which diffraction is recorded from proteins in the gas phase to determine their structures. To this point, theoretical investigations into this phenomenon have assumed that the field experienced by the proteins is constant or a perfect step function, whereas any real-world pulse will be smooth. Here, we explore the possibility of orienting gas-phase proteins using time-dependent electric fields. We performed ab initio simulations to estimate the field strength required to break protein bonds, with 45 V/nm as a breaking point value. We then simulated ubiquitin in time-dependent electric fields using classical molecular dynamics. The minimal field strength required for orientation within 10 ns was on the order of 0.5 V/nm. Although high fields can be destructive for the structure, the structures in our simulations were preserved until orientation was achieved regardless of field strength, a principle we denote "orientation before destruction."

Tailoring the opto-electronic response of graphene nanoflakes by size and shape optimization.

The long spin-diffusion length, spin-lifetime and excellent optical absorption coefficient of graphene provide an excellent platform for building opto-electronic devices and spin-based logic in a nanometer regime. In this study, by using density functional theory and its time-dependent version, we provide a detailed analysis of how the size and shape of graphene nanoflakes can be used to alter their magnetic structures and optical properties. As the edges of zigzag graphene nanoribbons are known to align anti-ferromagnetically and armchair nanoribbons are typically non-magnetic, a combination of both in a nanoflake geometry can be used to optimize the ground-state magnetic structure and tailor the exchange coupling decisive for ferro- or anti-ferromagnetic edge magnetism, thereby offering the possibility to optimize the external fields needed to switch magnetic ordering. Most importantly, we show that the magnetic state alters the optical response of the flake leading to the possibility of opto-spintronic applications.

Femtosecond bond breaking and charge dynamics in ultracharged amino acids.

Historically, structure determination of nanocrystals, proteins, and macromolecules required the growth of high-quality crystals sufficiently large to diffract X-rays efficiently while withstanding radiation damage. The development of the X-ray free-electron laser has opened the path toward high resolution single particle imaging, and the extreme intensity of the X-rays ensures that enough diffraction statistics are collected before the sample is destroyed by radiation damage. Still, recovery of the structure is a challenge, in part due to the partial fragmentation of the sample during the diffraction event. In this study, we use first-principles based methods to study the impact of radiation induced ionization of six amino acids on the reconstruction process. In particular, we study the fragmentation and charge rearrangement to elucidate the time scales involved and the characteristic fragments occurring.

Theoretical Studies of Anisotropic Melting of Ice Induced by Ultrafast Nonthermal Heating.

Water and ice are routinely studied with X-rays to reveal their diverse structures and anomalous properties. We employ a hybrid collisional-radiative/molecular-dynamics method to explore how femtosecond X-ray pulses interact with hexagonal ice. We find that ice makes a phase transition into a crystalline plasma where its initial structure is maintained up to tens of femtoseconds. The ultrafast melting process occurs anisotropically, where different geometric configurations of the structure melt on different time scales. The transient state and anisotropic melting of crystals can be captured by X-ray diffraction, which impacts any study of crystalline structures probed by femtosecond X-ray lasers.

Nonequilibrium Phonon Dynamics and Its Impact on the Thermal Conductivity of the Benchmark Thermoelectric Material SnSe.

Thermoelectric materials play a vital role in the pursuit of a sustainable energy system by allowing the conversion of waste heat to electric energy. Low thermal conductivity is essential to achieving high-efficiency conversion. The conductivity depends on an interplay between the phononic and electronic properties of the nonequilibrium state. Therefore, obtaining a comprehensive understanding of nonequilibrium dynamics of the electronic and phononic subsystems as well as their interactions is key for unlocking the microscopic mechanisms that ultimately govern thermal conductivity. A benchmark material that exhibits ultralow thermal conductivity is SnSe. We study the nonequilibrium phonon dynamics induced by an excited electron population using a framework combining ultrafast electron diffuse scattering and nonequilibrium kinetic theory. This in-depth approach provides a fundamental understanding of energy transfer in the spatiotemporal domain. Our analysis explains the dynamics leading to the observed low thermal conductivity, which we attribute to a mode-dependent tendency to nonconservative phonon scattering. The results offer a penetrating perspective on energy transport in condensed matter with far-reaching implications for rational design of advanced materials with tailored thermal properties.

Optically controlling the competition between spin flips and intersite spin transfer in a Heusler half-metal on sub-100-fs time scales.

The direct manipulation of spins via light may provide a path toward ultrafast energy-efficient devices. However, distinguishing the microscopic processes that can occur during ultrafast laser excitation in magnetic alloys is challenging. Here, we study the Heusler compound Co2MnGa, a material that exhibits very strong light-induced spin transfers across the entire M-edge. By combining the element specificity of extreme ultraviolet high-harmonic probes with time-dependent density functional theory, we disentangle the competition between three ultrafast light-induced processes that occur in Co2MnGa: same-site Co-Co spin transfer, intersite Co-Mn spin transfer, and ultrafast spin flips mediated by spin-orbit coupling. By measuring the dynamic magnetic asymmetry across the entire M-edges of the two magnetic sublattices involved, we uncover the relative dominance of these processes at different probe energy regions and times during the laser pulse. Our combined approach enables a comprehensive microscopic interpretation of laser-induced magnetization dynamics on time scales shorter than 100 femtoseconds.

Influence of strain on an ultrafast phase transition.

The flexibility of 2D materials combined with properties highly sensitive to strain makes strain engineering a promising avenue for manipulation of both structure and function. Here we investigate the influence of strain, associated with microstructural defects, on a photo-induced structural phase transition in Td-WTe2. Above threshold photoexcitation of uniform, non-strained, samples result in an orthorhombic Td to a metastable orthorhombic 1T* phase transition facilitated by shear displacements of the WTe2 layers along the b axis of the material. In samples prepared with wrinkle defects WTe2 continue its trajectory through a secondary transition that shears the unit cell along the c axis towards a metastable monoclinic 1T' phase. The time scales and microstructural evolution associated with the transition and its subsequent recovery to the 1T* phase is followed in detail by a combination of ultrafast electron diffraction and microscopy. Our findings show how local strain fields can be employed for tailoring phase change dynamics in ultrafast optically driven processes with potential applications in phase change devices.

Manipulation of Stacking Order in Td-WTe2 by Ultrafast Optical Excitation.

Subtle changes in stacking order of layered transition metal dichalcogenides may have profound influence on the electronic and optical properties. The intriguing electronic properties of Td-WTe2 can be traced to the break of inversion symmetry resulting from the ground-state stacking sequence. Strategies for perturbation of the stacking order are actively pursued for intentional tuning of material properties, where optical excitation is of specific interest since it holds the potential for integration of ultrafast switches in future device designs. Here we investigate the structural response in Td-WTe2 following ultrafast photoexcitation by time-resolved electron diffraction. A 0.23 THz shear phonon, involving layer displacement along the b axis, was excited by a 515 nm laser pulse. Pump fluences in excess of a threshold of ∼1 mJ/cm2 result in formation, with an ∼5 ps time constant, of a new stacking order by layer displacement along the b axis in the direction toward the centrosymmetric 1T* phase. The shear displacement of the layers increases with pump fluence until saturation at ∼8 pm. We demonstrate that the excitation of the shear phonon and the stabilization of the metastable phase are decoupled when using an optical pump as evidenced by observation of a transition also in samples with a pinned shear phonon. The results are compared to dynamic first-principles simulations and the transition is interpreted in terms of a mechanism where transient local disorder is prominent before settling at the atomic positions of the metastable phase. This interpretation is corroborated by results from diffuse scattering. The correlation between excitation of intralayer vibrations and interlayer interaction demonstrates the importance of including both short- and long-range interactions in an accurate description of how optical fields can be employed to manipulate the stacking order in 2-dimensional transition metal dichalcogenides.

Data-Driven Studies of the Magnetic Anisotropy of Two-Dimensional Magnetic Materials.

A key issue in layered materials is the dependence of their properties on their chemical composition and crystal structure in addition to the dimensionality. For instance, atomically thin magnetic structures exhibit novel spin properties that do not exist in the bulk. We use first-principles calculations, based on density functional theory, and machine learning to study the magnetocrystalline anisotropy of a set of single-layer two-dimensional structures that are derived from changing the chemical composition of the ferromagnetic semiconductor Cr2Ge2Te6. We discuss trends and identify descriptors for the magnetocrystalline anisotropy in monolayers with the chemical formula A2B2X6. Our data-driven study aims to provide physical insights into the microscopic origins of magnetic anisotropy in two dimensions. For instance, we demonstrate that hybridization plays a key role in determining the magnetic anisotropy of the materials investigated in this study. In addition, we demonstrate that first-principles calculations can be combined with machine learning to create a high-throughput computational approach for the targeted design of quantum materials with potential applications in areas ranging from sensing to data storage.

In Situ Pseudopotentials for Electronic Structure Theory.

We present a general method of constructing in situ pseodopotentials from first-principles, all-electron, and full-potential electronic structure calculations of a solid. The method is applied to bcc Na, at low-temperature equilibrium volume. The essential steps of the method involve (i) calculating an all-electron Kohn-Sham eigenstate, (ii) replacing the oscillating part of the wave function (inside the muffin-tin spheres) of this state, with a smooth function, (iii) representing the smooth wave function in a Fourier series, and (iv) inverting the Kohn-Sham equation, to extract the pseudopotential that produces the state generated in steps i-iii. It is shown that an in situ pseudopotential can reproduce an all-electron full-potential eigenvalue up to the sixth significant digit. A comparison of the all-electron theory, in situ pseudopotential theory, and the standard nonlocal pseudopotential theory demonstrates good agreement, e.g., in the energy dispersion of the 3s band state of bcc Na.

Reproducibility in the unfolding process of protein induced by an external electric field.

The dynamics of proteins are crucial for their function. However, commonly used techniques for studying protein structures are limited in monitoring time-resolved dynamics at high resolution. Combining electric fields with existing techniques to study gas-phase proteins, such as single particle imaging using free-electron lasers and gas-phase small angle X-ray scattering, has the potential to open up a new era in time-resolved studies of gas-phase protein dynamics. Using molecular dynamics simulations, we identify well-defined unfolding pathways of a protein, induced by experimentally achievable external electric fields. Our simulations show that strong electric fields in conjunction with short-pulsed X-ray sources such as free-electron lasers can be a new path for imaging dynamics of gas-phase proteins at high spatial and temporal resolution.

Establishing the limits of efficiency of perovskite solar cells from first principles modeling.

The recent surge in research on metal-halide-perovskite solar cells has led to a seven-fold increase of efficiency, from ~3% in early devices to over 22% in research prototypes. Oft-cited reasons for this increase are: (i) a carrier diffusion length reaching hundreds of microns; (ii) a low exciton binding energy; and (iii) a high optical absorption coefficient. These hybrid organic-inorganic materials span a large chemical space with the perovskite structure. Here, using first-principles calculations and thermodynamic modelling, we establish that, given the range of band-gaps of the metal-halide-perovskites, the theoretical maximum efficiency limit is in the range of ~25-27%. Our conclusions are based on the effect of level alignment between the perovskite absorber layer and carrier-transporting materials on the performance of the solar cell as a whole. Our results provide a useful framework for experimental searches toward more efficient devices.

Real-Time TD-DFT with Classical Ion Dynamics: Methodology and Applications.

We present a method for real-time propagation of electronic wave functions, within time-dependent density functional theory (RT-TDDFT), coupled to ionic motion through mean-field classical dynamics. The goal of our method is to treat large systems and complex processes, in particular photocatalytic reactions and electron transfer events on surfaces and thin films. Due to the complexity of these processes, computational approaches are needed to provide insight into the underlying physical mechanisms and are therefore crucial for the rational design of new materials. Because of the short time step required for electron propagation (of order ∼10 attoseconds), these simulations are computationally very demanding. Our methodology is based on numerical atomic-orbital-basis sets for computational efficiency. In the computational package, to which we refer as TDAP-2.0 (Time-evolving Deterministic Atom Propagator), we have implemented a number of important features and analysis tools for more accurate and efficient treatment of large, complex systems and time scales that reach into a fraction of a picosecond. We showcase the capabilities of our method using four different examples: (i) photodissociation into radicals of opposite spin, (ii) hydrogen adsorption on aluminum surfaces, (iii) optical absorption of spin-polarized organic molecule containing a metal ion, and (iv) electron transfer in a prototypical dye-sensitized solar cell.

Reproducibility in density functional theory calculations of solids.

The widespread popularity of density functional theory has given rise to an extensive range of dedicated codes for predicting molecular and crystalline properties. However, each code implements the formalism in a different way, raising questions about the reproducibility of such predictions. We report the results of a community-wide effort that compared 15 solid-state codes, using 40 different potentials or basis set types, to assess the quality of the Perdew-Burke-Ernzerhof equations of state for 71 elemental crystals. We conclude that predictions from recent codes and pseudopotentials agree very well, with pairwise differences that are comparable to those between different high-precision experiments. Older methods, however, have less precise agreement. Our benchmark provides a framework for users and developers to document the precision of new applications and methodological improvements.

A new first principles approach to calculate phonon spectra of disordered alloys.

The lattice dynamics in substitutional disordered alloys with constituents having large size differences is driven by strong disorder in masses, inter-atomic force constants and local environments. In this paper, a new first principles approach based on special quasirandom structures and an itinerant coherent potential approximation to compute the phonon spectra of such alloys is proposed and applied to Ni0.5Pt0.5 alloy. The agreement between our results and experiments is found to be much better than for previous models of disorder due to an accurate treatment of the interplay of inter-atomic forces among various pairs of chemical species. This new formalism serves as a potential solution to the longstanding problem of a proper microscopic understanding of lattice dynamical behavior of disordered alloys.

Itinerant magnetic multipole moments of rank five as the hidden order in URu(2)Si(2).

A broken symmetry ground state without any magnetic moments has been calculated by means of the local-density approximation to density functional theory plus a local exchange term, the so-called LDA+U approach, for URu(2)Si(2). The solution is analyzed in terms of a multipole tensor expansion of the itinerant density matrix and is found to be a nontrivial magnetic multipole. Analysis and further calculations show that this type of multipole enters naturally in time reversal breaking in the presence of large effective spin-orbit coupling and coexists with magnetic moments for most magnetic actinides.