Unraveling dynamic protein structures by two-dimensional infrared spectra with a pretrained machine learning model.

Dynamic protein structures are crucial for deciphering their diverse biological functions. Two-dimensional infrared (2DIR) spectroscopy stands as an ideal tool for tracing rapid conformational evolutions in proteins. However, linking spectral characteristics to dynamic structures poses a formidable challenge. Here, we present a pretrained machine learning model based on 2DIR spectra analysis. This model has learned signal features from approximately 204,300 spectra to establish a "spectrum-structure" correlation, thereby tracing the dynamic conformations of proteins. It excels in accurately predicting the dynamic content changes of various secondary structures and demonstrates universal transferability on real folding trajectories spanning timescales from microseconds to milliseconds. Beyond exceptional predictive performance, the model offers attention-based spectral explanations of dynamic conformational changes. Our 2DIR-based pretrained model is anticipated to provide unique insights into the dynamic structural information of proteins in their native environments.

Ultrafast transient absorption spectra and kinetics of human blue cone visual pigment at room temperature.

The ultrafast photochemical reaction mechanism, transient spectra, and transition kinetics of the human blue cone visual pigment have been recorded at room temperature. Ultrafast time-resolved absorption spectroscopy revealed the progressive formation and decay of several metastable photo-intermediates, corresponding to the Batho to Meta-II photo-intermediates previously observed with bovine rhodopsin and human green cone opsin, on the picosecond to millisecond timescales following pulsed excitation. The experimental data reveal several interesting similarities and differences between the photobleaching sequences of bovine rhodopsin, human green cone opsin, and human blue cone opsin. While Meta-II formation kinetics are comparable between bovine rhodopsin and blue cone opsin, the transition kinetics of earlier photo-intermediates and qualitative characteristics of the Meta-I to Meta-II transition are more similar for blue cone opsin and green cone opsin. Additionally, the blue cone photo-intermediate spectra exhibit a high degree of overlap with uniquely small spectral shifts. The observed variation in Meta-II formation kinetics between rod and cone visual pigments is explained based on key structural differences.

Coherent detection of hidden spin-lattice coupling in a van der Waals antiferromagnet.

Strong interactions between different degrees of freedom lead to exotic phases of matter with complex order parameters and emergent collective excitations. Conventional techniques, such as scattering and transport, probe the amplitudes of these excitations, but they are typically insensitive to phase. Therefore, novel methods with phase sensitivity are required to understand ground states with phase modulations and interactions that couple to the phase of collective modes. Here, by performing phase-resolved coherent phonon spectroscopy (CPS), we reveal a hidden spin-lattice coupling in a vdW antiferromagnet FePS3 that eluded other phase-insensitive conventional probes, such as Raman and X-ray scattering. With comparative analysis and analytical calculations, we directly show that the magnetic order in FePS3 selectively couples to the trigonal distortions through partially filled t2g orbitals. This magnetoelastic coupling is linear in magnetic order and lattice parameters, rendering these distortions inaccessible to inelastic scattering techniques. Our results not only capture the elusive spin-lattice coupling in FePS3 but also establish phase-resolved CPS as a tool to investigate hidden interactions.

Ultrafast electron localization and screening in a transition metal dichalcogenide.

The coupling of light to electrical charge carriers in semiconductors is the foundation of many technological applications. Attosecond transient absorption spectroscopy measures simultaneously how excited electrons and the vacancies they leave behind dynamically react to the applied optical fields. In compound semiconductors, these dynamics can be probed via any of their atomic constituents with core-level transitions into valence and conduction band. Typically, the atomic species forming the compound contribute comparably to the relevant electronic properties of the material. One therefore expects to observe similar dynamics, irrespective of the choice of atomic species via which it is probed. Here, we show in the two-dimensional transition metal dichalcogenide semiconductor MoSe2, that through a selenium-based core-level transition we observe charge carriers acting independently from each other, while when probed through molybdenum, the collective, many-body motion of the carriers dominates. Such unexpectedly contrasting behavior can be explained by a strong localization of electrons around molybdenum atoms following absorption of light, which modifies the local fields acting on the carriers. We show that similar behavior in elemental titanium metal [M. Volkov et al., Nat. Phys. 15, 1145-1149 (2019)] carries over to transition metal-containing compounds and is expected to play an essential role for a wide range of such materials. Knowledge of independent particle and collective response is essential for fully understanding these materials.

Elucidating interprotein energy transfer dynamics within the antenna network from purple bacteria.

In photosynthesis, absorbed light energy transfers through a network of antenna proteins with near-unity quantum efficiency to reach the reaction center, which initiates the downstream biochemical reactions. While the energy transfer dynamics within individual antenna proteins have been extensively studied over the past decades, the dynamics between the proteins are poorly understood due to the heterogeneous organization of the network. Previously reported timescales averaged over such heterogeneity, obscuring individual interprotein energy transfer steps. Here, we isolated and interrogated interprotein energy transfer by embedding two variants of the primary antenna protein from purple bacteria, light-harvesting complex 2 (LH2), together into a near-native membrane disc, known as a nanodisc. We integrated ultrafast transient absorption spectroscopy, quantum dynamics simulations, and cryogenic electron microscopy to determine interprotein energy transfer timescales. By varying the diameter of the nanodiscs, we replicated a range of distances between the proteins. The closest distance possible between neighboring LH2, which is the most common in native membranes, is 25 Šand resulted in a timescale of 5.7 ps. Larger distances of 28 to 31 Šresulted in timescales of 10 to 14 ps. Corresponding simulations showed that the fast energy transfer steps between closely spaced LH2 increase transport distances by ∼15%. Overall, our results introduce a framework for well-controlled studies of interprotein energy transfer dynamics and suggest that protein pairs serve as the primary pathway for the efficient transport of solar energy.

Probing phonon dynamics with multidimensional high harmonic carrier-envelope-phase spectroscopy.

We explore pump-probe high harmonic generation (HHG) from monolayer hexagonal-boron-nitride, where a terahertz pump excites coherent optical phonons that are subsequently probed by an intense infrared pulse that drives HHG. We find, through state-of-the-art ab initio calculations, that the structure of the emission spectrum is attenuated by the presence of coherent phonons and no longer comprises discrete harmonic orders, but rather a continuous emission in the plateau region. The HHG yield strongly oscillates as a function of the pump-probe delay, corresponding to ultrafast changes in the lattice such as specific bond compression or stretching dynamics. We further show that in the regime where the excited phonon period and the pulse duration are of the same order of magnitude, the HHG process becomes sensitive to the carrier-envelope phase (CEP) of the driving field, even though the pulse duration is so long that no such sensitivity is observed in the absence of coherent phonons. The degree of CEP sensitivity versus pump-probe delay is shown to be a highly selective measure for instantaneous structural changes in the lattice, providing an approach for ultrafast multidimensional HHG spectroscopy. Remarkably, the obtained temporal resolution for phonon dynamics is ∼1 femtosecond, which is much shorter than the probe pulse duration because of the inherent subcycle contrast mechanism. Our work paves the way toward routes of probing phonons and ultrafast material structural changes with subcycle temporal resolution and provides a mechanism for controlling the HHG spectrum.

Machine learning recognition of protein secondary structures based on two-dimensional spectroscopic descriptors.

Protein secondary structure discrimination is crucial for understanding their biological function. It is not generally possible to invert spectroscopic data to yield the structure. We present a machine learning protocol which uses two-dimensional UV (2DUV) spectra as pattern recognition descriptors, aiming at automated protein secondary structure determination from spectroscopic features. Accurate secondary structure recognition is obtained for homologous (97%) and nonhomologous (91%) protein segments, randomly selected from simulated model datasets. The advantage of 2DUV descriptors over one-dimensional linear absorption and circular dichroism spectra lies in the cross-peak information that reflects interactions between local regions of the protein. Thanks to their ultrafast (∼200 fs) nature, 2DUV measurements can be used in the future to probe conformational variations in the course of protein dynamics.

The photoprotection mechanism in the black-brown pigment eumelanin.

The natural black-brown pigment eumelanin protects humans from high-energy UV photons by absorbing and rapidly dissipating their energy before proteins and DNA are damaged. The extremely weak fluorescence of eumelanin points toward nonradiative relaxation on the timescale of picoseconds or shorter. However, the extreme chemical and physical complexity of eumelanin masks its photoprotection mechanism. We sought to determine the electronic and structural relaxation pathways in eumelanin using three complementary ultrafast optical spectroscopy methods: fluorescence, transient absorption, and stimulated Raman spectroscopies. We show that photoexcitation of chromophores across the UV-visible spectrum rapidly generates a distribution of visible excitation energies via ultrafast internal conversion among neighboring coupled chromophores, and then all these excitations relax on a timescale of ∼4 ps without transferring their energy to other chromophores. Moreover, these picosecond dynamics are shared by the monomeric building block, 5,6-dihydroxyindole-2-carboxylic acid. Through a series of solvent and pH-dependent measurements complemented by quantum chemical modeling, we show that these ultrafast dynamics are consistent with the partial excited-state proton transfer from the catechol hydroxy groups to the solvent. The use of this multispectroscopic approach allows the minimal functional unit in eumelanin and the role of exciton coupling and excited-state proton transfer to be determined, and ultimately reveals the mechanism of photoprotection in eumelanin. This knowledge has potential for use in the design of new soft optical components and organic sunscreens.

From antenna to reaction center: Pathways of ultrafast energy and charge transfer in photosystem II.

The photosystem II core complex (PSII-CC) is the smallest subunit of the oxygenic photosynthetic apparatus that contains core antennas and a reaction center, which together allow for rapid energy transfer and charge separation, ultimately leading to efficient solar energy conversion. However, there is a lack of consensus on the interplay between the energy transfer and charge separation dynamics of the core complex. Here, we report the application of two-dimensional electronic-vibrational (2DEV) spectroscopy to the spinach PSII-CC at 77 K. The simultaneous temporal and spectral resolution afforded by 2DEV spectroscopy facilitates the separation and direct assignment of coexisting dynamical processes. Our results show that the dominant dynamics of the PSII-CC are distinct in different excitation energy regions. By separating the excitation regions, we are able to distinguish the intraprotein dynamics and interprotein energy transfer. Additionally, with the improved resolution, we are able to identify the key pigments involved in the pathways, allowing for a direct connection between dynamical and structural information. Specifically, we show that C505 in CP43 and the peripheral chlorophyll ChlzD1 in the reaction center are most likely responsible for energy transfer from CP43 to the reaction center.

Ultrafast photooxidation of protein-bound anionic flavin radicals.

The photophysical properties of anionic semireduced flavin radicals are largely unknown despite their importance in numerous biochemical reactions. Here, we studied the photoproducts of these intrinsically unstable species in five different flavoprotein oxidases where they can be stabilized, including the well-characterized glucose oxidase. Using ultrafast absorption and fluorescence spectroscopy, we unexpectedly found that photoexcitation systematically results in the oxidation of protein-bound anionic flavin radicals on a time scale of less than ∼100 fs. The thus generated photoproducts decay back in the remarkably narrow 10- to 20-ps time range. Based on molecular dynamics and quantum mechanics computations, positively charged active-site histidine and arginine residues are proposed to be the electron acceptor candidates. Altogether, we established that, in addition to the commonly known and extensively studied photoreduction of oxidized flavins in flavoproteins, the reverse process (i.e., the photooxidation of anionic flavin radicals) can also occur. We propose that this process may constitute an excited-state deactivation pathway for protein-bound anionic flavin radicals in general. This hitherto undocumented photochemical reaction in flavoproteins further extends the family of flavin photocycles.

Picosecond energy transfer in a transition metal dichalcogenide-graphene heterostructure revealed by transient Raman spectroscopy.

Intense light­matter interactions and unique structural and electrical properties make van der Waals heterostructures composed by graphene (Gr) and monolayer transition metal dichalcogenides (TMD) promising building blocks for tunneling transistors and flexible electronics, as well as optoelectronic devices, including photodetectors, photovoltaics, and quantum light emitting devices (QLEDs), bright and narrow-line emitters using minimal amounts of active absorber material. The performance of such devices is critically ruled by interlayer interactions which are still poorly understood in many respects. Specifically, two classes of coupling mechanisms have been proposed, charge transfer (CT) and energy transfer (ET), but their relative efficiency and the underlying physics are open questions. Here, building on a time-resolved Raman scattering experiment, we determine the electronic temperature profile of Gr in response to TMD photoexcitation, tracking the picosecond dynamics of the G and 2D Raman bands. Compelling evidence for a dominant role of the ET process accomplished within a characteristic time of ∼4 ps is provided. Our results suggest the existence of an intermediate process between the observed picosecond ET and the generation of a net charge underlying the slower electric signals detected in optoelectronic applications.

Ultrafast Coherent Exciton Couplings and Many-Body Interactions in Monolayer WS2.

Transition metal dichalcogenides (TMDs) are quantum confined systems with interesting optoelectronic properties, governed by Coulomb interactions in the monolayer (1L) limit, where strongly bound excitons provide a sensitive probe for many-body interactions. Here, we use two-dimensional electronic spectroscopy (2DES) to investigate many-body interactions and their dynamics in 1L-WS2 at room temperature and with sub-10 fs time resolution. Our data reveal coherent interactions between the strongly detuned A and B exciton states in 1L-WS2. Pronounced ultrafast oscillations of the transient optical response of the B exciton are the signature of a coherent 50 meV coupling and coherent population oscillations between the two exciton states. Supported by microscopic semiconductor Bloch equation simulations, these coherent dynamics are rationalized in terms of Dexter-like interactions. Our work sheds light on the role of coherent exciton couplings and many-body interactions in the ultrafast temporal evolution of spin and valley states in TMDs.

Electroluminescence Rectification and High Harmonic Generation in Molecular Junctions.

The field of molecular electronics has emerged from efforts to understand electron propagation through single molecules and to use them in electronic circuits. Serving as a testbed for advanced theoretical methods, it reveals a significant discrepancy between the operational time scales of experiments (static to GHz frequencies) and theoretical models (femtoseconds). Utilizing a recently developed time-linear nonequilibrium Green function formalism, we model molecular junctions on experimentally accessible time scales. Our study focuses on the quantum pump effect in a benzenedithiol molecule connected to two copper electrodes and coupled with cavity photons. By calculating both electric and photonic current responses to an ac bias voltage, we observe pronounced electroluminescence and high harmonic generation in this setup. The mechanism of the latter effect is more analogous to that from solids than from isolated molecules, with even harmonics being suppressed or enhanced depending on the symmetry of the driving field.

Electronic Structure of Isolated Graphene Nanoribbons in Solution Revealed by Two-Dimensional Electronic Spectroscopy.

Structurally well-defined graphene nanoribbons (GNRs) are nanostructures with unique optoelectronic properties. In the liquid phase, strong aggregation typically hampers the assessment of their intrinsic properties. Recently we reported a novel type of GNRs, decorated with aliphatic side chains, yielding dispersions consisting mostly of isolated GNRs. Here we employ two-dimensional electronic spectroscopy to unravel the optical properties of isolated GNRs and disentangle the transitions underlying their broad and rather featureless absorption band. We observe that vibronic coupling, typically neglected in modeling, plays a dominant role in the optical properties of GNRs. Moreover, a strong environmental effect is revealed by a large inhomogeneous broadening of the electronic transitions. Finally, we also show that the photoexcited bright state decays, on the 150 fs time scale, to a dark state which is in thermal equilibrium with the bright state, that remains responsible for the emission on nanosecond time scales.

Fluorescence-Detected Two-Dimensional Electronic Spectroscopy of a Single Molecule.

Single-molecule fluorescence spectroscopy is a powerful method that avoids ensemble averaging, but its temporal resolution is limited by the fluorescence lifetime to nanoseconds at most. At the ensemble level, two-dimensional spectroscopy provides insight into ultrafast femtosecond processes, such as energy transfer and line broadening, even beyond the Fourier limit, by correlating pump and probe spectra. Here, we combine these two techniques and demonstrate coherent 2D spectroscopy of individual dibenzoterrylene (DBT) molecules at room temperature. We excite the molecule in a confocal microscope with a phase-modulated train of femtosecond pulses and detect the emitted fluorescence with single-photon counting detectors. Using a phase-sensitive detection scheme, we were able to measure the nonlinear 2D spectra of most of the DBT molecules that we studied. Our method is applicable to a wide range of single emitters and opens new avenues for understanding energy transfer in single quantum objects on ultrafast time scales.

Dynamic Ultrastrong Coupling in a 2 nm Gap Plasmonic Cavity at the Sub-Picosecond Scale.

Localized surface plasmon resonances (LSPRs) can enhance the electromagnetic fields on metallic nanostructures upon light illumination, providing an approach for manipulating light-matter interactions at the sub-wavelength scale. However, currently, there is no thorough investigation of the physical mechanism in the dynamic formation of the strongly coupled LSPRs on sub-5 nm plasmonic cavities at the sub-picosecond scale. In this work, through femtosecond broadband transient absorption spectroscopy, we reveal the dynamic ultrastrong coupling processes in a nanoparticle-in-trench (NPiT) structure containing 2 nm gap cavities, and demonstrate a coherent motional coupling between vibrating AuNPs and the nanogaps. We achieve a maximum Rabi splitting energy of ∼660 meV in the sub-picosecond hot-electron relaxation time scale under the resonant excitation of the nanogap cavity's LSPR, reaching the ultrastrong coupling regime. This leads to a change of global vibration modes for the 2 nm gap cavity, potentially related to the dynamical Casimir effect with nanogap resonators.

Light harvesting in purple bacteria does not rely on resonance fine-tuning in peripheral antenna complexes.

The ring-like peripheral light-harvesting complex 2 (LH2) expressed by many phototrophic purple bacteria is a popular model system in biological light-harvesting research due to its robustness, small size, and known crystal structure. Furthermore, the availability of structural variants with distinct electronic structures and optical properties has made this group of light harvesters an attractive testing ground for studies of structure-function relationships in biological systems. LH2 is one of several pigment-protein complexes for which a link between functionality and effects such as excitonic coherence and vibronic coupling has been proposed. While a direct connection has not yet been demonstrated, many such interactions are highly sensitive to resonance conditions, and a dependence of intra-complex dynamics on detailed electronic structure might be expected. To gauge the sensitivity of energy-level structure and relaxation dynamics to naturally occurring structural changes, we compare the photo-induced dynamics in two structurally distinct LH2 variants. Using polarization-controlled 2D electronic spectroscopy at cryogenic temperatures, we directly access information on dynamic and static disorder in the complexes. The simultaneous optimal spectral and temporal resolution of these experiments further allows us to characterize the ultrafast energy relaxation, including exciton transport within the complexes. Despite the variations in PPC molecular structure manifesting as clear differences in electronic structure and disorder, the energy-transport and-relaxation dynamics remain remarkably similar. This indicates that the light-harvesting functionality of purple bacteria within a single LH2 complex is highly robust to structural perturbations and likely does not rely on finely tuned electronic- or electron-vibrational resonance conditions.

Reinvestigation on primary processes of PSII-dimer from Thermosynechococcus vulcanus by femtosecond pump-probe spectroscopy.

Cyanobacterial photosynthetic apparatus efficiently capture sunlight, and the energy is subsequently transferred to photosystem I (PSI) and II (PSII), to produce electrochemical potentials. PSII is a unique membrane protein complex that photo-catalyzes oxidation of water and majorly contains photosynthetic pigments of chlorophyll a and carotenoids. In the present study, the ultrafast energy transfer and charge separation dynamics of PSII from a thermophilic cyanobacterium Thermosynechococcus vulcanus were reinvestigated by femtosecond pump-probe spectroscopic measurements under low temperature and weak intensity excitation condition. The results imply the two possible models of the energy transfers and subsequent charge separation in PSII. One is the previously suggested "transfer-to-trapped limit" model. Another model suggests that the energy transfers from core CP43 and CP47 antennas to the primary electron donor ChlD1 with time-constants of 0.71 ps and 3.28 ps at 140 K (0.17 and 1.33 ps at 296 K), respectively and that the pheophytin anion (PheoD1-) is generated with the time-constant of 43.0 ps at 140 K (14.8 ps at 296 K) upon excitation into the Qy band of chlorophyll a at 670 nm. The secondary electron transfer to quinone QA: PheoD1-QA → PheoD1QA- is observed with the time-constant of 650 ps only at 296 K. On the other hand, an inefficient ß-carotene → chlorophyll a energy transfer (33%) occurred after excitation to the S2 state of ß-carotene at 500 nm. Instead, the carotenoid triplet state appeared in an ultrafast timescale after excitation at 500 nm.

Boosting the Efficiency of Red Thermally Activated Delayed Fluorescence via Conjugation Enhancement in Push-Pull Naphthalimide Derivatives.

In this work, we synthesize a series of push-pull compounds bearing naphthalimide as the electron acceptor and tetraphenylethylene (TPE)/triphenylamine (TPA)/phenothiazine (PTZ) as the electron rich/electron donor units. These moieties are arranged in highly conjugated quadrupolar structures. The structure-property relationships are investigated through a joint experimental time-resolved spectroscopic and computational TD-DFT study. The femtosecond transient absorption and fluorescence up-conversion experiments reveal ultrafast photoinduced intramolecular charge transfer. This is likely the key factor leading to efficient spin-orbit CT-induced intersystem crossing for the TPA- and PTZ-derivatives as well as to small singlet-to-triplet energy gap. Consequently, evidence for a delayed fluorescence component is found together with the main prompt emission in the fluorescence kinetics both in solution and in thin film. The weight of the Thermally Activated Delayed Fluorescence (TADF) is greatly enhanced when these fluorophores are used as guests in solid-state host matrices. TADF is interestingly revealed in the orange-red region of the visible. Such long wavelength emission is here observed with surprisingly large fluorescence quantum yields, thanks to the conjugation enhancement achieved in these newly synthesized structures relative to previous studies. Our findings may be thus promising for the future development of efficient third generation TADF-based OLEDs.

Photoacid Dynamics in the Green Fluorescent Protein.

The photoacid dynamics of fluorescent proteins include both electronic excited- and ground-state mechanisms of proton transfer. The associated characteristic timescales of these reactions range over many orders of magnitude, and the tunneling, barrier crossing, and relevant thermodynamics have in certain cases been linked to coherent nuclear motion. We review the literature and summarize the experiments and theory that demonstrate proton tunneling in the electronic ground state of the green fluorescent protein (GFP). We also discuss the excited-state proton-transfer reaction of GFP that takes place on the picosecond timescale. Although this reaction has been investigated using several vibrational spectroscopic methods, the interpretation remains unsettled. We discuss recent advances as well as remaining questions, in particular those related to the vibrational mode couplings that involve low-frequency modulations of chromophore vibrations on the timescale of proton transfer.