Infrared and terahertz spectroscopy performed at synchrotron facilities offers unique opportunities for probing matter under extreme and well controlled conditions. At the AILES beamline of Synchrotron SOLEIL, two complementary experimental setups have recently been developed to enable spectroscopy of submillimetric samples across a broad range of temperatures and pressures. These platforms operate from 10 K to 600 K and from vacuum up to 100 GPa, while accommodating a variety of sample environments, including liquid cells, diamond anvil cells and uniaxial strain devices. Combined with the high brilliance and stability of synchrotron radiation and advanced detection schemes, these setups are particularly suited for in situ and operando investigations, allowing real-time monitoring of structural changes, phase transitions and reaction dynamics under external stimuli. Their performance is illustrated through far-infrared measurements of water and ice over different thermodynamic states, demonstrating sensitivity to structural reorganizations and hydrogen-bond dynamics. These developments significantly expand the experimental capabilities of the AILES beamline and provide versatile tools for a wide user community, opening new perspectives for studies of functional materials, molecular systems and emerging phenomena under extreme conditions.

Using the multi-reference configuration interaction method with the aug-cc-pV(Q/5)Z basis set, 7762 ab initio energy points were computed and used to construct an analytical potential energy surface (PES) for HCO(12A″). The fitted PES has an overall root-mean-square deviation of 0.833 kcal/mol. Based on this PES, the geometry, energy, and harmonic frequencies of stationary points were analyzed in detail, showing good agreement with other theoretical data. Subsequently, quantum time-dependent wave packet (TDWP) and quasi-classical trajectory (QCT) calculations were performed on this new PES to study the reaction C(3P) + OH(X2Π) → CO(a3Π) + H(2S). The reaction probabilities, integral cross sections, differential cross sections, product rot-vibrational distributions, and rate constants were obtained. TDWP results show a rich resonance structure, and the QCT calculations provide a qualitatively correct description of the reaction cross section. Discrepancies between the dynamical information derived from the two methods indicate pronounced quantum effects in this reaction. The reaction is predominantly governed by a complex-forming mechanism. Although increasing collision energy shortens the complex lifetime, the indirect mechanism remains operative across the studied energy range. This study provides fundamental insights into the microscopic reaction mechanisms and dynamics of carbon chemistry in interstellar environments and provides theoretical support for future experimental results.

The activation of CO2 at isolated transition-metal centers represents a prototypical problem for understanding elementary steps relevant to single-atom catalysis. Fundamental knowledge of such systems can be acquired by investigating gas phase reactions between transition-metal ions and molecules. Because open-shell transition-metal species often possess multiple accessible spin states, their reactions with CO2 can proceed along competing spin-changing and spin-conserving pathways. Understanding how spin-orbit coupling influences these competing pathways therefore calls for a direct comparison between scattering experiments and multi-state dynamical simulations. In this Perspective, we summarize our combined experimental and theoretical investigations of the Ta+, Nb+, and Zr+ + CO2 reactions. Crossed-beam velocity map imaging provides energy- and angle-resolved differential cross sections, while trajectory surface-hopping simulations on first-principles based full-dimensional multi-spin potential energy surfaces enable a dynamical treatment of intersystem crossing and spin-conserving channels on an equal footing. In all three systems, intersystem crossing competes with the spin-conserving channel for the control of the overall reaction dynamics and kinetics. These reactions all proceed predominantly via an indirect mechanism, as evidenced by the nearly isotropic differential cross sections consistent with long-lived complex formation, and the respective product energy distributions indicate substantial energy deposition into internal modes. Despite their similar potential-energy topographies, Ta+ and Nb+ + CO2 reactions are dominated by spin-changing pathways at all energies investigated, whereas in the Zr+ system the spin-conserving channel becomes competitive. This difference arises from the markedly different magnitudes of the spin-orbit coupling, which determines the efficiency of intersystem crossing and thereby the balance between the two pathways.

Photodissociation of diazines following UV excitation provides a prototypical system for examining unimolecular reaction dynamics on vibrationally excited ground-state potential energy surfaces. In this work, we present a comprehensive theoretical study of the isomerization and dissociation dynamics of the isomers of diazines (C4H4N2), with particular emphasis on pyrazine, after rapid internal conversion to the ground electronic state. A unified ground-state potential energy surface is constructed using CCSD(T)/CBS energies, and microcanonical rate constants and product branching ratios are evaluated using Rice-Ramsperger-Kassel-Marcus theory in combination with microcanonical variational transition-state theory. The results reveal a strong energy dependence of the photodissociation dynamics arising from the interplay between isomerization and competing fragmentation pathways. At lower excitation energies (248 nm), rapid isomerization funnels population into pyrimidine, and dissociation proceeds predominantly through pyrimidine-centered channels. At intermediate energies (193 nm), direct dissociation of pyrazine becomes competitive, with concerted three-body fragmentation producing acetylene and hydrogen cyanide accounting for approximately 36% of the total product yield. At higher energies (157 nm), the dynamics approach a statistical limit dominated by concerted three-body dissociation. These results demonstrate that product branching in diazine photodissociation is governed by a coupled isomerization-dissociation network and cannot be inferred from isolated reaction pathways.

Chemical oscillators such as the Belousov-Zhabotinsky (BZ) reaction offer a promising foundation for energy-efficient, biologically inspired chemical information processing. While optical and mechanical manipulation of BZ has been extensively studied, electrochemical control has remained largely elusive and lacks fundamental understanding, in spite of its superior energy efficiency. Here, we investigate how a platinum electrode influences the dynamics of a ruthenium-catalyzed BZ reaction. We observe a pronounced acceleration of the oscillation frequency that scales with the electrode's surface-to-solution-volume ratio. In addition, we demonstrate that small DC currents (<0.4 mA) further modulate the effect up to a full recovery of the natural period. To explain these findings, we develop a quantitative model based on mixed-potential theory, which accurately captures the observed behavior. This framework reveals how the low-volume electrochemical conversion of molecules at the electrode's surface gets amplified by the chemistry and finally causes a pronounced impact on the entire system. This surprising effect, controllable through small applied currents, offers new strategies for designing programmable chemical systems for sensing and computing applications.

Biological nanopores can be used to monitor the conformational dynamics of enzymatic reactions in real time and at the single-molecule level. However, the molecular basis of this process and the requirements for efficiently engineering a nanopore for measuring conformational transitions in proteins remain poorly understood. Here, we combine all-atom molecular dynamics simulations and electrophysiology experiments to determine the molecular mechanism and improve the resolution for the recognition of glutamine by a substrate-binding domain (SBD) protein using ClyA nanopores through mutagenesis. By matching the simulated and experimental currents, we found that the SBD protein most likely resides very close to the constriction of the nanopore, where the open and closed conformations induce large current differences. To amplify the signal, we introduced bulky tryptophan residues near the likely location of the SBD protein. This effectively narrowed the nanopore and resulted in a 3-fold signal amplification. Molecular dynamics simulations suggest that prolonged residence of the SBD protein within ClyA is likely caused by an electro-osmotic flow that imparts a restoring force on the protein, counteracting its displacement from an equilibrium location. Our work shows how nanopore systems can be engineered in a rational way for the monitoring of biochemical reactions at the single-molecule level.

Light-induced dehalogenation by flavoenzymes offers a promising route to generate acyl radicals in photoenzymatic catalysis, but current applications are largely limited to α-acyl halides. Mechanistic studies are needed to understand this substituent position effect to engineer flavoenzymes for broader applications. Here, we elucidate the ultrafast dynamics of photoinduced electron transfer (ET) and dehalogenation reactions in lactate monooxygenase (LMO) with α-, β-, and γ-acyl halides. We found that the ET from the excited reduced flavin cofactor (FMNH-*) to the substrates bifurcates into two pathways: direct tunneling to the C-X (X = Cl, Br) bond or direct hopping to the neighboring carbonyl group. The former leads to instantaneous dehalogenation; the latter forms an anionic (C-O-) radical that can either transfer the electron to the halogen for dehalogenation or undergo nonproductive back ET (BET). This finding contrasts with conventional understandings that the direct tunneling ET to the halogen atom is the only reaction channel. For α-halogenated substrates, both pathways lead to a dehalogenation reaction. For β-halogenated ones, direct tunneling causes effective dehalogenation and direct hopping leads to a futile BET. For γ-halogenated ones, direct tunneling is negligible and direct hopping results in BET. After dehalogenation, the resulting acyl radical bonds with flavin semiquinone (FMNH•) to form the photoproduct. Molecular simulations and docking indicate that these outcomes are governed by substrate orientation, structural configuration, and hydrogen-bonding networks. This bifurcating ET mechanism explains the substituent position effects on reactivity and provides a framework for engineering flavoenzymes for dehalogenative reactions.

Dioxazolones are important precursors for generating nitrenes (highly reactive intermediates widely used for carbon–nitrogen bond formation in organic synthesis) upon exposure to light or heat. The photochemical reaction dynamics of 3-phenyl-1,4,2-dioxazol-5-one in CHCl3 were investigated using femtosecond time-resolved infrared spectroscopy and electronic structure calculations. Photoexcitation at 267 nm rapidly populates an excited singlet state that serves as the key branching point for subsequent photophysical and photochemical processes. Transient infrared spectra reveal the formation of carbon dioxide, phenyl isocyanate, and singlet benzoyl nitrene through their characteristic vibrational features. Kinetic analysis shows that decarboxylation from the excited singlet state occurs with a time constant of 4.7 ± 1 ns, producing phenyl isocyanate and benzoyl nitrene with time constants of 8.1 ± 2 ns and 11 ± 3 ns, respectively. Competing relaxation pathways include internal conversion to the ground state (7.5 ± 2 ns) and intersystem crossing to the T1 state (25 ± 5 ns). The T1 state relaxes to the ground state (350 ± 30 ns) without contributing to product formation. These results demonstrate that both isocyanate and nitrene products originate from the S1 state and provide detailed mechanistic insight into the competing pathways governing dioxazolone photochemistry in solution.

Protein synthesis in cell-free protein synthesis systems often exhibits nonintuitive input-output relationships. In the PURE system, a reconstituted cell-free system, protein production peaked at low elongation factor Tu (EF-Tu) concentrations and decreased at higher concentrations, resulting in a characteristic bell-shaped profile. Here, we investigated the origin of this behavior using a detailed mechanistic model of translation in the PURE system, designated as ePURE, which describes the reaction dynamics of hundreds of molecular species and reactions. Our computational analysis suggested that excess EF-Tu sequesters the initiator tRNA (tRNAfMet) into nonproductive EF-Tu·GTP·Met-tRNAfMet complexes, thereby depleting the pool of initiator tRNA available for translation initiation. This suppression arises from competition for a limited molecular resource rather than from direct inhibition. Based on this mechanism, we predicted that increasing the concentrations of tRNAfMet and methionyl-tRNA formyltransferase would eliminate the bell-shaped dependence, and experimentally confirmed this prediction. Under these modified conditions, the bell-shaped response disappeared and protein production was enhanced. These findings demonstrate how mechanistic computational models can reveal hidden constraints underlying nonintuitive input-output relationships in complex biochemical networks and guide the rational optimization of cell-free protein synthesis systems.

Branching ratios for fragmentation channels of important meta- and unstable species are essential for a molecular-level characterization of atmospheric chemistry. Here, the molecular product channels for the decomposition dynamics of the smallest Criegee intermediate, H2COO, are investigated. Using a high-quality, full-dimensional machine learned potential energy surface (CASPT2/aug-cc-pVTZ), the translational, rotational, and vibrational energy distributions of the CO2 + H2, H2O + CO, and HCO + OH fragmentation channels were analyzed to elucidate energy partitioning. The CO2+H2 product forms through two pathways that bifurcate after formation of the OCH2O intermediate. The first is a "direct pathway", for which CO2 is preferentially vibrationally excited and H2 remains in its vibrational ground state. Alternatively, along an "indirect pathway" passes through formic acid, whereby H2 can populate levels with v > 0. For all channels passing through energized formic acid, lifetime distributions are described by stretched exponentials with β ranging from 0.9 to 1.3, indicating non-RRKM effects and the need for explicit molecular dynamics.

The reaction dynamics of O(3P) + O2(3Σg-) collisions in the O3(X1A') electronic ground state is characterized on a high-level MRCI+Q/aug-cc-pVQZ potential energy surface (PES) represented as a reproducing kernel. For the atom exchange reactions involving the 16O and 18O isotopes with rates k6exch(T) and k8exch(T), a negative temperature dependence of kexch(T), consistent with experiments was found. The absolute rates typically underestimate measured rates by ∼50%. For the ratio R(T) = k8exch(T)/k6exch(T), the measured T dependence was correctly captured with a maximum at ∼300 K. The differences between experiments and computations are primarily due to neglect of zero-point effects. For the dissociation reaction, the rate is lower by approximately 1 order of magnitude compared with experiments, which is a clear improvement over simulations using previous PESs. The present results support an electronic degeneracy factor of gediss ∈ [1/27, 1] with a preference for values toward the lower end of the interval. Nonadiabatic effects are deemed to play only a minor role in the atom-exchange reaction.

Hydrogenases are metalloenzymes that catalyze the reversible splitting of dihydrogen (H2), a clean and sustainable fuel. In this study, we investigate the reversible photodissociation and rebinding of an extrinsic carbon monoxide (CO) ligand at the active site of a [NiFe] model hydrogenase. CO acts as a catalytic inhibitor of the enzyme, whereas its photolysis restores an active state capable of H2 binding. Using UVpump-IRprobe spectroscopy in a multiple-probe configuration that allows covering picosecond to millisecond time scales, we characterize the reaction dynamics following CO photolysis. The results reveal a large temporal window between rapid CO dissociation and slow rebinding, enabling the detailed investigation of H2 binding and activation at the active site, unaffected by H2 mass transport limitation.

Identifying key vibrational modes directly coupled to a chemical reaction is essential for understanding molecular reaction dynamics in condensed phases, yet remains challenging because of mode mixing, rapid dephasing, and strong multimode effects. Here, we combine ultrahigh-time-resolution fluorescence measurements with Born-Oppenheimer molecular dynamics simulations to study excited-state intramolecular proton transfer (ESIPT) in salophen. Notably, nuclear motions following photoexcitation are described by projecting simulated trajectories onto the normal modes of the relevant chemical species. Contrary to the common expectation that multimode effects dominate for such a large molecule in the condensed phase, we find that a single skeletal vibrational mode almost exclusively shortens the distance between the proton donor (oxygen) and acceptor (nitrogen) significantly, rendering the reaction potential energy surface effectively barrierless. This approach provides a practical route to identifying mode-specific driving motions in condensed-phase coherent reaction dynamics.

Liquid-phase transmission electron microscopy (LPTEM) enables real-time visualization of nanoscale dynamics in electrochemical, biological, and catalytic reactions. However, accelerated electrons employed as probes can perturb the chemical environment through electron-liquid interactions, thereby complicating reliable data acquisition and interpretation. Although these interactions have been studied based on kinetic modeling of water radiolysis, a comprehensive understanding of the influence of interfaces and confinement within microfluidic liquid cells remains less understood. Prior γ-irradiation and electron-beam studies have shown that adsorbed water on solid-liquid interfaces can dramatically modify radical yields, yet the effect of specific interfaces in liquid cells on radiolysis has been less understood. Herein, we reveal effects at interfaces and their influence on water radiolysis by liquid-cell interface engineering using radiolysis-driven oxidative etching of palladium nanocubes as a probing system. Complementary density functional theory calculations show that graphene coatings suppress interfacial water dissociation and electron transfer, thereby modulating beam interaction pathways.

Structural diversity in nitrobenzene trimer anions: messenger-tagged infrared photodissociation spectroscopy and theoretical study.

The dynamics of homogeneous electrochemical proton-coupled electron transfer (PCET) are governed by the complex interactions among the continuous electronic states of the electrode, molecular vibrational modes, and the solvent environment. Here, we study this process within a Newns-Anderson model using the hierarchical equations of motion (HEOM) method combined with matrix product states (MPS) for hybrid fermionic and bosonic baths. The simulations reveal how the reaction dynamics depend on a variety of parameters, including the proton-transfer distance, electrode chemical potential, molecule-electrode coupling strength, and solvent reorganization energy. Comparison with Fermi's Golden Rule shows that the perturbative rate theory is reliable in the weak-coupling regime, but may become inaccurate at strong molecule-electrode coupling. Rates extracted from population dynamics yield Tafel plots whose shapes depend on both solvent and electrode couplings. The calculations also reproduce a primary kinetic isotope effect, with hydrogen transfer faster than deuterium transfer and with a larger effective transfer coefficient. These results highlight the capability of the hybrid-bath MPS-HEOM method to provide a unified description of electrochemical PCET in a wide range of parameter regimes.

Biomolecules suffering birth and death in living cells often exhibit non-exponential lifetime distributions. However, the chemical dynamics of these biomolecules cannot be described by conventional chemical kinetics or chemical master equations. Here, we present exact results for the mean, time correlation function, and power spectrum of the copy number of biomolecules in living cells, establishing their relationship to product creation dynamics and lifetime distributions. The correctness of these results is confirmed against accurate stochastic simulations. This work establishes the power spectrum of the copy number of biomolecules as a quantitative probe of their intracellular reaction dynamics.

In this study, we present a rational donor-acceptor-donor (D-A-D) molecular design strategy to develop high-performance organic cathodes by enhancing the intramolecular charge transfer (ICT) effect. We designed and synthesized two organic molecules: 2,6-bis(10H-phenothiazin-10-yl)benzo[1,2-d:4,5-d']diimidazole-4,8-dione (PTZBQ), featuring a strong quinone-type acceptor core, and the control compound 2,6-bis(10H-phenothiazin-10-yl)benzo[1,2-d:4,5-d']diimidazole (PTZTAB), without a quinone core. The strong push-pull electronic structure of PTZBQ not only results in a significantly narrowed bandgap and improved electrode kinetics, but also allows the quinone core to contribute extra n-type capacity, thereby remarkably boosting the electrode's specific capacity and reaction dynamics. Moreover, the extended π-conjugation and D-A-D configuration-induced polarity endow both small molecules with exceptional electrolyte dissolution resistance. Consequently, PTZBQ exhibits bipolar redox activity, delivering a high discharge potential of 3.05V, a high specific capacity of 163.3 mAh g-1at 0.1 A g-1,an excellent rate capability (77.6% retention at 5 A g-1), and exceptional long-term cycling stability with 89.4% retention after 5000 cycles at 1 A g-1. DFT calculations and ex situ spectroscopy confirm that the unique D-A-D architecture possesses spatially separated n-type and p-type redox centers, facilitating the redox process. Our findings highlight that quinone-core engineering enhances intramolecular charge transfer and represents a powerful approach for developing high-performance cathode materials.

Tin-based metal-oxide resist (Sn-MOR) is a promising candidate material for next-generation photolithography, yet its shelf and in-process stability are significantly undermined by reactions with ambient moisture. While an in-depth computational study is required to understand the reaction mechanism and provide design rules balancing moisture stability and photospeed, the long time scale of degradation reactions hampers ab initio calculations. In this work, we introduce a two-phase active learning (2P-AL) framework, which couples deep potential molecular dynamics with well-tempered metadynamics (WT-MetaD) to capture the rare-event reaction dynamics of solvated Sn-MOR molecules in aqueous solution. The first phase focuses on exploration to broaden structural diversity under a fixed simulation budget, and the subsequent phase focuses on convergence to systematically improve force field fidelity and ultimately achieve ab initio-level accuracy. WT-MetaD simulations with this model successfully constructed the free energy landscape of moisture-induced degradation of Sn-MOR molecules and uncovered a plausible pathway by which ambient moisture can promote degradation in Sn-MORs, offering molecular-level insight into their stability challenges. In parallel, the proposed 2P-AL framework offers an adaptable and efficient approach to investigate reaction dynamics in solution-phase reactive systems, yielding direct molecular insight into moisture-induced degradation in disordered Sn-MOR materials.

Excited state potential energy surfaces are essential for understanding molecular behavior in excited states, including electronic transitions, reaction dynamics, and other photochemical and photophysical properties. When excited state minima or reaction dynamics are of interest, the gradients of the total excited state energy are required. Time-dependent density functional theory (TDDFT) is a widely used method, as it provides reasonably accurate excited state energies compared to experiment; however, its computational cost scales unfavorably with molecule size. To address this limitation, methods that maintain TDDFT accuracy while reducing the computational cost are needed. The time-dependent density functional theory plus tight binding (TDDFT+TB) method offers comparable accuracy to TDDFT with significantly improved efficiency. Previously, Havenridge etal. implemented TDDFT+TB analytical excited state gradients for closed-shell molecules. This was achieved using a Lagrangian-based approach by taking analytical derivatives of the excitation energies with respect to nuclear coordinates. In this study, we extend this implementation to handle open-shell molecular systems. Our unrestricted TDDFT+TB analytical gradient implementation follows the framework of the unrestricted TDDFT analytical gradient code in the Amsterdam Density Functional engine within the Amsterdam Modeling Suite. Building on the existing closed-shell implementation, we focus on key modifications to the coupling matrix and the incorporation of spin indices in the gradient expressions required for open-shell systems. We validate the method through calculations on various molecular systems, comparing gradient accuracy, emission energies, and computational cost to demonstrate that it delivers reliable results for open-shell molecular excited states with improved efficiency compared to the standard TDDFT method.