Manipulating ultrafast even-order nonlinear chiral responses of L-tryptophan by polarization pulse shaping.

Molecular chirality has long been monitored in the frequency domain in the ultraviolet, visible, and infrared regimes. Recently developed time-domain approaches can detect time-dependent chiral dynamics by enhancing intrinsically weak chiral signals. Even-order nonlinear signals in chiral molecules have gained attention thanks to their existence in the electric dipole approximation, without relying on the weaker higher-order multipole interactions. We illustrate the optimization of temporal polarization pulse-shaping in various frequency ranges (infrared/optical and optical/X ray) to enhance chiral nonlinear signals. These signals can be recast as an overlap integral of matter and field pseudoscalars which contain the relevant chiral information. Simulations are carried out for second- and fourth-order nonlinear spectroscopies in L-tryptophan.

X-ray and Optical Circular Dichroism as Local and Global Ultrafast Chiral Probes of [12]Helicene Racemization.

Chirality is a fundamental molecular property that plays a crucial role in biophysics and drug design. Optical circular dichroism (OCD) is a well-established chiral spectroscopic probe in the UV-visible regime. Chirality is most commonly associated with a localized chiral center. However, some compounds such as helicenes (Figure 1) are chiral due to their screwlike global structure. In these highly conjugated systems, some electric and magnetic allowed transitions are distributed across the entire molecule, and OCD thus probes the global molecular chirality. Recent advances in X-ray sources, in particular the control of their polarization and spatial profiles, have enabled X-ray circular dichroism (XCD), which, in contrast to OCD, can exploit the localized and element-specific nature of X-ray electronic transitions. XCD therefore is more sensitive to local structures, and the chirality probed with it can be referred to as local. During the racemization of helicene, between opposite helical structures, the screw handedness can flip locally, making the molecule globally achiral while retaining a local handedness. Here, we use the racemization mechanism of [12]helicene as a model to demonstrate the capabilities of OCD and XCD as time-dependent probes for global and local chiralities, respectively. Our simulations demonstrate that XCD provides an excellent spectroscopic probe for the time-dependent local chirality of molecules.

Vibrationally Hot Reactants in a Plasmon-Assisted Chemical Reaction.

Recent studies on plasmon-assisted chemical reactions postulate that the hot electrons of plasmon-excited nanostructures may induce a non-thermal vibrational activation of metal-bound reactants. However, the postulate has not been fully validated at the level of molecular quantum states. We directly and quantitatively prove that such activation occurs on plasmon-excited nanostructures: The anti-Stokes Raman spectra of reactants undergoing a plasmon-assisted reaction reveal that a particular vibrational mode of the reactant is selectively excited, such that the reactants possess >10 times more energy in the mode than is expected from the fully thermalized molecules at the given local temperature. Furthermore, a significant portion (∼20%) of the excited reactant is in vibrational overtone states with energies exceeding 0.5 eV. Such mode-selective multi-quantum excitation could be fully modeled by the resonant electron-molecule scattering theory. Such observations suggest that the vibrationally hot reactants are created by non-thermal hot electrons, not by thermally heated electrons or phonons of metals. The result validates the mechanism of plasmon-assisted chemical reactions and further offers a new method to explore the vibrational reaction control on metal surfaces.

Time-Evolving Chirality Loss in Molecular Photodissociation Monitored by X-ray Circular Dichroism Spectroscopy.

The ultrafast photoinduced chirality loss of 2-iodobutane is studied theoretically by time- and frequency-resolved X-ray circular dichroism (TRXCD) spectroscopy. Following an optical excitation, the iodine atom dissociates from the chiral center, which we capture by quantum non-adiabatic molecular dynamics simulations. At variable time delays after the pump, the resonant X-ray pulse selectively probes the iodine and carbon atom involved in the chiral dissociation through a selected core-to-valence transition. The TRXCD signal at the iodine L1 edge accurately captures the timing of C-I photodissociation and thereby chirality loss, c.a 70 fs. The strong electric dipole-electric quadrupole (ED-EQ) response makes this signal particularly sensitive to vibronic coherence at the high X-ray regime. At the carbon K-edges, the signals monitor the molecular chirality of the 2-butyl radical photoproduct and the spin state of the iodine atom. The ED-EQ response is masked under the strong electric dipole-magnetic dipole response, making this signal intuitive for the electronic population. The evolution of the core electronic states and its chiral sensitivity is discussed. Overall, the element-specific TRXCD signal provides a detailed picture of molecular dynamics and offers a unique sensitive window into the time-dependent chirality of molecules.

Monitoring early-stage ß-amyloid dimer aggregation by histidine site-specific two-dimensional infrared spectroscopy in a simulation study.

Monitoring early-stage ß-amyloid (Aß) dimerization is a formidable challenge for understanding neurological diseases. We compared ß-sheet formation and histidine site-specific two-dimensional infrared (2D IR) spectroscopic signatures of Aß dimers with different histidine states (δ; Nδ1-H, ε; Nε2-H, or π; both protonated). Molecular dynamics (MD) simulations revealed that ß-sheet formation is favored for the δδδ:δδδ and πππ:πππ tautomeric isomers showing strong couplings and frequent contacts between the central hydrophobic core and C-terminus compared with the εεε:εεε isomer. Characteristic blue-shifts in the 2D IR central bands were observed upon monomer-dimer transformation. The εεε:εεε dimer exhibited larger frequency shifts than δδδ:δδδ and πππ:πππ implying that the red-shift may have a correlation with Nδ1-H(δ) protonation. Our results support the tautomerization/protonation hypothesis that attributes Aß misfolding to histidine tautomers as a possible primary initiator for Aß aggregation and facilitates the application of histidine site-specific 2D IR spectroscopy for studying early-stage Aß self-assembly.

Tautomeric Effect of Histidine on ß-Sheet Formation of Amyloid Beta 1-40: 2D-IR Simulations.

Histidine state (protonated or δ or ε tautomer) has been considered the origin of abnormal misfolding and aggregation of ß-amyloid (Aß). Our previous studies reported that the δδδ isomer of Aß (1-40) has a greater propensity for ß-sheet conformation compared to other isomers. However, direct proof of the tautomeric effect has not been reported. In this context, we calculated histidine site-specific two-dimensional infrared spectroscopy of the δδδ, εεε, and πππ (all protonated histidine) systems within the framework of classical molecular dynamics simulations aiming at connecting our previous results with the current experimental observations. Our results showed that ß-sheet formation is favored for the δδδ and πππ tautomers compared with the εεε tautomer, consistent with our previous studies. This result was further supported by contact map analyses and the strength of dipole coupling between the amide-I bonds of each residue. The two-dimensional infrared diagonal trace for each tautomer included three distinctive spectrally resolvable peaks near 1680, 1686, and 1693 cm-1, as was also observed for histidine dipeptides. However, the peak positions at His6, His13, and His14 did not show a consensus trend with the histidine or protonation state but were instead affected by the presence of surrounding hydrogen bonds. Our study provides a deeper insight into the influence of tautomerism and protonation of histidine residues in Aß (1-40) on amyloid misfolding and provides a connection between our previous simulations and experimental observations.

Impact of A2V Mutation and Histidine Tautomerism on Aß42 Monomer Structures from Atomistic Simulations.

The self-assembly of amyloid-ß (Aß) peptides into senile plaques in the brain is a hallmark of Alzheimer's disease (AD) pathology. Mutation and histidine tautomerism are considered intrinsic origins in the accumulation of Aß. As a first step toward understanding the impact of A2V mutation and histidine tautomerism on the Aß42 isoform, we performed replica-exchange molecular dynamics (REMD) simulations to investigate the effects of histidine tautomerism on the structural properties of A2V Aß42 peptides. There are generally more ß-sheet and less α-helix secondary structures in A2V Aß42 monomers than in WT Aß42, implying a higher aggregation tendency in A2V Aß42, which is consistent with previous studies. The current research will help develop the histidine tautomerism hypothesis of misfolded protein aggregation and eventually elucidate the pathogenesis of AD.

Monitoring aromatic ring-currents in Mg-porphyrin by time-resolved circular dichroism.

Time-resolved circular dichroism signals (TRCD) in the X-ray regime can directly probe the magnitude and the direction of ring currents in molecules. The electronic ring currents in Mg-porphyrin, generated by a coherent superposition of electronic states induced by a circularly polarized UV pulse, are tracked by a time-delayed circularly polarized attosecond X-ray pulse. The signals are calculated using the minimal coupling Hamiltonian, which directly makes use of transition current densities. The TRCD signals obtained from the left and right circularly polarized light pump have opposite signs, revealing the direction of the ring current. Molecular aromaticity and its role in photochemical reactions such as ring opening or closure can be studied using this technique.

Electric field effect on the magnetic properties of zigzag MoS2 nanoribbons with different edge passivation.

Electrical control of magnetic exchange coupling interactions is central to designing magnetic materials. In this study, we performed density functional theory calculations to investigate the magnetic spin configuration, magnetic moment, and magnetic coupling strength of zigzag MoS2 nanoribbons (zMoS2NRs) with different edge passivation, that is, pristine (Pristine), hydrogen termination (H-tem), sulfur termination (S-term), and sulfhydryl termination (SH-term). Further, we investigated the influence of an external electric field (FExt) on the magnetic properties. Pristine and H-term showed an AFM ground configuration with considerably weak magnetic coupling strength while S-term and SH-term showed a single edge FM ground configuration in the absence of the electric field. When the external electric field was applied, the positive field intensified the original spin configuration, thus increasing the magnetic moment of the system while the negative field weakened the original spin configuration, thus decreasing the magnetic moment and further reversed the spin configuration from AFM to FM and vice versa in most systems. The magnetic coupling strength of the system increased for both Pristine and H-term regardless of the direction of the field. However, the extent of increase was much higher in Pristine due to the existence of relatively easily transferable dangling electrons compared with the constrained electrons of H-term restricted to chemical bonds. Our results demonstrate a possibility of reversible spin control from AFM to FM and vice versa by applying an electric field and the enhancement of the magnetic coupling strength of zMoS2NRs.

Time-resolved enantiomer-exchange probed by using the orbital angular momentum of X-ray light.

Molecular chirality, a geometric property of utmost importance in biochemistry, is now being investigated in the time-domain. Ultrafast chiral techniques can probe the formation or disappearance of stereogenic centers in molecules. The element-sensitivity of X-rays adds the capability to probe chiral nuclear dynamics locally within the molecular system. However, the implementation of ultrafast techniques for measuring transient chirality remains a challenge because of the intrinsic weakness of chiral-sensitive signals based on circularly polarized light. We propose a novel approach for probing the enantiomeric dynamics by using the orbital angular momentum (OAM) of X-ray light, which can directly monitor the real-time chirality of molecules. Our simulations probe the oscillations in excited chiral formamide on different potential energy surfaces and demonstrate that using the X-ray OAM can increase the measured asymmetry ratio. Moreover, combining the OAM and SAM (spin angular momentum) provides stronger dichroic signals than linearly polarized light, and offers a powerful scheme for chiral discrimination.

Attosecond Monitoring of Nonadiabatic Molecular Dynamics by Transient X-ray Transmission Spectroscopy.

Tracing the evolution of molecular coherences can provide a direct, unambiguous probe of nonadiabatic molecular processes, such as the passage through conical intersections of electronic states. Two techniques, attosecond transient absorption spectroscopy (ATAS) and Transient Redistribution of Ultrafast Electronic Coherences in Attosecond Raman Signals (TRUECARS), have been used or proposed for monitoring nonadiabatic molecular dynamics. Both techniques employ the transmission of a weak attosecond extreme-ultraviolet or X-ray probe to interrogate the molecule at controllable time delays with respect to an optical pump, thereby extracting dynamical information from transient spectral features. The connection between these techniques has not been firmly established yet. In this theoretical study, we provide a unified description of both transient transmission techniques, establishing their relationship as limits of the same pump-probe spectroscopy technique for different pulse parameter regimes. We demonstrate this by quantum dynamical simulations of thiophenol photodissociation and show how complementary coherence information can be revealed by the two techniques.

Quantum Interferometric Pathway Selectivity in Difference-Frequency-Generation Spectroscopy.

Even-order spectroscopies such as sum-frequency generation (SFG) and difference-frequency generation (DFG) can serve as direct probes of molecular chirality. Such signals are usually given by the sum of several interaction pathways that carry different information about matter. Here we focus on DFG, involving impulsive optical-optical-IR interactions, where the last IR pulse probes vibrational transitions in the ground or excited electronic state manifolds, depending on the interaction pathway. Spectroscopy with classical light can use phase matching to select the two pathways. In this theoretical study, we propose a novel quantum interferometric protocol that uses entangled photons to isolate individual pathways. This additional selectivity originates from engineering the state of light using a Zou-Wang-Mandel interferometer combined with coincidence detection.

Monitoring vibronic coherences and molecular aromaticity in photoexcited cyclooctatetraene with an X-ray probe: a simulation study.

Understanding conical intersection (CI) dynamics and subsequent conformational changes is key for exploring and controlling photo-reactions in aromatic molecules. Monitoring of their time-resolved dynamics remains a formidable experimental challenge. In this study, we simulate the photoinduced S3 to S1 non-adiabatic dynamics of cyclooctatetraene (COT), involving multiple CIs with relaxation times in good agreement with experiment. We further investigate the possibility to directly probe the CI passages in COT by off-resonant X-ray Raman spectroscopy (TRUECARS) and time-resolved X-ray diffraction (TRXD). We find that these signals sensitively monitor key chemical features during the ultrafast dynamics. First, we distinguish two CIs by using TRUECARS signals with their appearances at different Raman shifts. Second, we demonstrate that TRXD, where X-ray photons scatter off electron densities, can resolve ultrafast changes in the aromaticity of COT. It can further distinguish between planar and non-planar geometries explored during the dynamics, as e.g. two different tetraradical-type CIs. The knowledge gained from these measurements can give unique insight into fundamental chemical properties that dynamically change during non-adiabatic passages.

Time-Resolved Optical Pump-Resonant X-ray Probe Spectroscopy of 4-Thiouracil: A Simulation Study.

We theoretically monitor the photoinduced ππ* → nπ* internal conversion process in 4-thiouracil (4TU), triggered by an optical pump. The element-sensitive spectroscopic signatures are recorded by a resonant X-ray probe tuned to the sulfur, oxygen, or nitrogen K-edge. We employ high-level electronic structure methods optimized for core-excited electronic structure calculation combined with quantum nuclear wavepacket dynamics computed on two relevant nuclear modes, fully accounting for their quantum nature of nuclear motions. We critically discuss the capabilities and limitations of the resonant technique. For sulfur and nitrogen, we document a pre-edge spectral window free from ground-state background and rich with ππ* and nπ* absorption features. The lowest sulfur K-edge shows strong absorption for both ππ* and nπ*. In the lowest nitrogen K-edge window, we resolve a state-specific fingerprint of the ππ* and an approximate timing of the conical intersection via its depletion. A spectral signature of the nπ* transition, not accessible by UV-vis spectroscopy, is identified. The oxygen K-edge is not sensitive to molecular deformations and gives steady transient absorption features without spectral dynamics. The ππ*/nπ* coherence information is masked by more intense contributions from populations. Altogether, element-specific time-resolved resonant X-ray spectroscopy provides a detailed picture of the electronic excited-state dynamics and therefore a sensitive window into the photophysics of thiobases.

Nonadiabatic Molecular Dynamics Study of the Relaxation Pathways of Photoexcited Cyclooctatetraene.

In the current study, we present nonadiabatic (NAMD) and adiabatic molecular dynamics simulations of the transition-state dynamics of photoexcited cyclooctatetraene (COT). The equilibrium-state structure and absorption spectra are analyzed using the semiempirical Austin Model 1 potential. The NAMD simulations are obtained by a surface-hopping algorithm. We analyzed in detail an active excited to ground state relaxation pathway accompanied by an S2/S3(D2d) → S1(D8h) → S0(D4h) → S0(D2d) double-bond shifting mechanism. The simulated excitation lifetime is in good agreement with experiment. The first excited singlet state S1 plays a crucial role in the photochemistry. The obtained critical molecular conformations, energy barrier, and transition-state lifetime results will provide a basis for further investigations of the bond-order inversion and photoswitching process of COT.

Conical Intersection Passages of Molecules Probed by X-ray Diffraction and Stimulated Raman Spectroscopy.

Conical intersections (CoIns) play an important role in ultrafast relaxation channels. Their monitoring remains a formidable experimental challenge. We theoretically compare the probing of the S2 → S1 CoIn passage in 4-thiouracil by monitoring its vibronic coherences, using off-resonant X-ray-stimulated Raman spectroscopy (TRUECARS) and time-resolved X-ray diffraction (TRXD). The quantum nuclear wavepacket (WP) dynamics provides an accurate picture of the photoinduced dynamics. Upon photoexcitation, the WP oscillates among the Franck-Condon point, the S2 minimum, and the CoIn with a 70 fs period. A vibronic coherence first emerges at 20 fs and can be observed until the S2 state is fully depopulated. The distribution of the vibronic frequencies involved in the coherence is recorded by the TRUECARS spectrogram. The TRXD signal provides spatial images of electron densities associated with the CoIn. In combination, the two signals provide a complementary picture of the nonadiabatic passage, which helps in the study of the underlying photophysics in thiobases.

Strong Influence of Oxygen Vacancy Location on Charge Carrier Losses in Reduced TiO2 Nanoparticles.

Oxygen vacancies in TiO2 nanoparticles are important for charge carrier dynamics, with recent studies reporting contradictory results on TiO2 nanoparticle photocatalytic activity. We demonstrate that ground state multiplicity, defect levels, and formation energies depend strongly on vacancy location. Quantum dynamics simulations show that charges are trapped within several picoseconds and recombine over a broad range of time scales from tens of picoseconds to nanoseconds. Specifically, nanoparticles with missing partially coordinated surface oxygens showed fast recombination, while nanoparticles with missing highly coordinated subsurface oxygens or singly coordinated oxygens at tips showed slow recombination, even slower than in the pristine system. The results are rationalized by energy gaps and electron-hole localization, the latter determining nonadiabatic coupling and quantum coherence time. The diverse charge recombination scenarios revealed by the nonadiabatic dynamics simulations rationalize the contradictory experimental results for photocatalytic activity and provide guidelines for rational design of nanoscale metal oxides for solar energy harvesting and utilization.

Atomic layer etching of graphene through controlled ion beam for graphene-based electronics.

The electronic and optical properties of graphene are greatly dependent on the the number of layers. For the precise control of the graphene layers, atomic layer etching (ALE), a cyclic etching method achieved through chemical adsorption and physical desorption, can be the most powerful technique due to barely no damage and no contamination. In this study, we demonstrated the ALE process of graphene layers without noticeably damaging the graphene by using a controlled low energy oxygen (O2+/O+)-ion for chemical adsorption and a low energy Ar+-ion (11.2 eV) for physical desorption. In addition, using a trilayer graphene, mono- and bi-layer graphene could be successfully fabricated after one- and two-cycle ALE of the trilayer graphene, respectively. We believe that the ALE technique presented herein can be applicable to all layered materials such as graphene, black phosphorous and transition metal dichalcogenides which are important for next generation electronic devices.

Atomic Layer Etching Mechanism of MoS2 for Nanodevices.

Among the layered transition metal dichalcogenides (TMDs) that can form stable two-dimensional crystal structures, molybdenum disulfide (MoS2) has been intensively investigated because of its unique properties in various electronic and optoelectronic applications with different band gap energies from 1.29 to 1.9 eV as the number of layers decreases. To control the MoS2 layers, atomic layer etching (ALE) (which is a cyclic etching consisting of a radical-adsorption step such as Cl adsorption and a reacted-compound-desorption step via a low-energy Ar+-ion exposure) can be a highly effective technique to avoid inducing damage and contamination that occur during the reactive steps. Whereas graphene is composed of one-atom-thick layers, MoS2 is composed of three-atom-thick S(top)-Mo(mid)-S(bottom) layers; therefore, the ALE mechanisms of the two structures are significantly different. In this study, for MoS2 ALE, the Cl radical is used as the adsorption species and a low-energy Ar+ ion is used as the desorption species. A MoS2 ALE mechanism (by which the S(top), Mo(mid), and S(bottom) atoms are sequentially removed from the MoS2 crystal structure due to the trapped Cl atoms between the S(top) layer and the Mo(mid) layer) is reported according to the results of an experiment and a simulation. In addition, the ALE technique shows that a monolayer MoS2 field effect transistor (FET) fabricated after one cycle of ALE is undamaged and exhibits electrical characteristics similar to those of a pristine monolayer MoS2 FET. This technique is also applicable to all layered TMD materials, such as tungsten disulfide (WS2), molybdenum diselenide (MoSe2), and tungsten diselenide (WSe2).