Mapping the emergence of molecular vibrations mediating bond formation.

Fundamental studies of chemical reactions often consider the molecular dynamics along a reaction coordinate using a calculated or suggested potential energy surface1-5. But fully mapping such dynamics experimentally, by following all nuclear motions in a time-resolved manner-that is, the motions of wavepackets-is challenging and has not yet been realized even for the simple stereotypical bimolecular reaction6-8: A-B + C â†’ A + B-C. Here we track the trajectories of these vibrational wavepackets during photoinduced bond formation of the gold trimer complex [Au(CN)2-]3 in an aqueous monomer solution, using femtosecond X-ray liquidography9-12 with X-ray free-electron lasers13,14. In the complex, which forms when three monomers A, B and C cluster together through non-covalent interactions15,16, the distance between A and B is shorter than that between B and C. Tracking the wavepacket in three-dimensional nuclear coordinates reveals that within the first 60 femtoseconds after photoexcitation, a covalent bond forms between A and B to give A-B + C. The second covalent bond, between B and C, subsequently forms within 360 femtoseconds to give a linear and covalently bonded trimer complex A-B-C. The trimer exhibits harmonic vibrations that we map and unambiguously assign to specific normal modes using only the experimental data. In principle, more intense X-rays could visualize the motion not only of highly scattering atoms such as gold but also of lighter atoms such as carbon and nitrogen, which will open the door to the direct tracking of the atomic motions involved in many chemical reactions.

High level ab initio and density functional study of TeF6+ and TeCl6+: Attainability of +7 oxidation state for tellurium.

Discovery of a new oxidation state for an element expands its chemistry. A high oxidation state, such as +7, is rare for sp-block elements except for halogens. In this study, we determined that Te can attain a +7 oxidation state through the existence of a distorted octahedron (DOH) structure of TeCl6+ based on coupled cluster singles and doubles with perturbative triples calculations. We propose a new type of isomerization that resembles pseudorotation. The octahedron structure of TeF6+ bearing one elongated axial bond isomerizes to a DOH via an associated pseudorotation.

Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering.

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.

Direct observation of bond formation in solution with femtosecond X-ray scattering.

The making and breaking of atomic bonds are essential processes in chemical reactions. Although the ultrafast dynamics of bond breaking have been studied intensively using time-resolved techniques, it is very difficult to study the structural dynamics of bond making, mainly because of its bimolecular nature. It is especially difficult to initiate and follow diffusion-limited bond formation in solution with ultrahigh time resolution. Here we use femtosecond time-resolved X-ray solution scattering to visualize the formation of a gold trimer complex, [Au(CN)2(-)]3 in real time without the limitation imposed by slow diffusion. This photoexcited gold trimer, which has weakly bound gold atoms in the ground state, undergoes a sequence of structural changes, and our experiments probe the dynamics of individual reaction steps, including covalent bond formation, the bent-to-linear transition, bond contraction and tetramer formation with a time resolution of ∼500 femtoseconds. We also determined the three-dimensional structures of reaction intermediates with sub-ångström spatial resolution. This work demonstrates that it is possible to track in detail and in real time the structural changes that occur during a chemical reaction in solution using X-ray free-electron lasers and advanced analysis of time-resolved solution scattering data.

Regulation of Protein Structural Changes by Incorporation of a Small-Molecule Linker.

Proteins have the potential to serve as nanomachines with well-controlled structural movements, and artificial control of their conformational changes is highly desirable for successful applications exploiting their dynamic structural characteristics. Here, we demonstrate an experimental approach for regulating the degree of conformational change in proteins by incorporating a small-molecule linker into a well-known photosensitive protein, photoactive yellow protein (PYP), which is sensitized by blue light and undergoes a photo-induced N-terminal protrusion coupled with chromophore-isomerization-triggered conformational changes. Specifically, we introduced thiol groups into specific sites of PYP through site-directed mutagenesis and then covalently conjugated a small-molecule linker into these sites, with the expectation that the linker is likely to constrain the structural changes associated with the attached positions. To investigate the structural dynamics of PYP incorporated with the small-molecule linker (SML-PYP), we employed the combination of small-angle X-ray scattering (SAXS), transient absorption (TA) spectroscopy and experiment-restrained rigid-body molecular dynamics (MD) simulation. Our results show that SML-PYP exhibits much reduced structural changes during photo-induced signaling as compared to wild-type PYP. This demonstrates that incorporating an external molecular linker can limit photo-induced structural dynamics of the protein and may be used as a strategy for fine control of protein structural dynamics in nanomachines.

Protein structural dynamics revealed by time-resolved X-ray solution scattering.

One of the most important questions in biological science is how a protein functions. When a protein performs its function, it undergoes regulated structural transitions. In this regard, to better understand the underlying principle of a protein function, it is desirable to monitor the dynamic evolution of the protein structure in real time. To probe fast and subtle motions of a protein in physiological conditions demands an experimental tool that is not only equipped with superb spatiotemporal resolution but also applicable to samples in solution phase. Time-resolved X-ray solution scattering (TRXSS), discussed in this Account, fits all of those requirements needed for probing the movements of proteins in aqueous solution. The technique utilizes a pump-probe scheme employing an optical pump pulse to initiate photoreactions of proteins and an X-ray probe pulse to monitor ensuing structural changes. The technical advances in ultrafast lasers and X-ray sources allow us to achieve superb temporal resolution down to femtoseconds. Because X-rays scatter off all atomic pairs in a protein, an X-ray scattering pattern provides information on the global structure of the protein with subangstrom spatial resolution. Importantly, TRXSS is readily applicable to aqueous solution samples of proteins with the aid of theoretical models and therefore is well suited for investigating structural dynamics of protein transitions in physiological conditions. In this Account, we demonstrate that TRXSS can be used to probe real-time structural dynamics of proteins in solution ranging from subtle helix movement to global conformational change. Specifically, we discuss the photoreactions of photoactive yellow protein (PYP) and homodimeric hemoglobin (HbI). For PYP, we revealed the kinetics of structural transitions among four transient intermediates comprising a photocycle and, by applying structural analysis based on ab initio shape reconstruction, showed that the signaling of PYP involves the protrusion of the N-terminus with significant increase of the overall protein size. For HbI, we elucidated the dynamics of complex allosteric transitions among transient intermediates. In particular, by applying structural refinement analysis based on rigid-body modeling, we found that the allosteric transition of HbI accompanies the rotation of quaternary structure and the contraction between two heme domains. By making use of the experimental and analysis methods presented in this Account, we envision that the TRXSS can be used to probe the structural dynamics of various proteins, allowing us to decipher the working mechanisms of their functions. Furthermore, when combined with femtosecond X-ray pulses generated from X-ray free electron lasers, TRXSS will gain access to ultrafast protein dynamics on sub-picosecond time scales.

Combined probes of X-ray scattering and optical spectroscopy reveal how global conformational change is temporally and spatially linked to local structural perturbation in photoactive yellow protein.

Real-time probing of structural transitions of a photoactive protein is challenging owing to the lack of a universal time-resolved technique that can probe the changes in both global conformation and light-absorbing chromophores of the protein. In this work, we combine time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) spectroscopy to investigate how the global conformational changes involved in the photoinduced signal transduction of photoactive yellow protein (PYP) is temporally and spatially related to the local structural change around the light-absorbing chromophore. In particular, we examine the role of internal proton transfer in developing a signaling state of PYP by employing its E46Q mutant (E46Q-PYP), where the internal proton transfer is inhibited by the replacement of a proton donor. The comparison of TRXSS and TA spectroscopy data directly reveals that the global conformational change of the protein, which is probed by TRXSS, is temporally delayed by tens of microseconds from the local structural change of the chromophore, which is probed by TA spectroscopy. The molecular shape of the signaling state reconstructed from the TRXSS curves directly visualizes the three-dimensional conformations of protein intermediates and reveals that the smaller structural change in E46Q-PYP than in wild-type PYP suggested by previous studies is manifested in terms of much smaller protrusion, confirming that the signaling state of E46Q-PYP is only partially developed compared with that of wild-type PYP. This finding provides direct evidence of how the environmental change in the vicinity of the chromophore alters the conformational change of the entire protein matrix.

Role of thermal excitation in ultrafast energy transfer in chlorosomes revealed by two-dimensional electronic spectroscopy.

Chlorosomes are the largest light harvesting complexes in nature and consist of many bacteriochlorophyll pigments forming self-assembled J-aggregates. In this work, we use two-dimensional electronic spectroscopy (2D-ES) to investigate ultrafast dynamics of excitation energy transfer (EET) in chlorosomes and their temperature dependence. From time evolution of the measured 2D electronic spectra of chlorosomes, we directly map out the distribution of the EET rate among the manifold of exciton states in a 2D energy space. In particular, it is found that the EET rate varies gradually depending on the energies of energy-donor and energy-acceptor states. In addition, from comparative 2D-ES measurements at 77 K and room temperature, we show that the EET rate exhibits subtle dependence on both the exciton energy and temperature, demonstrating the effect of thermal excitation on the EET rate. This observation suggests that active thermal excitation at room temperature prevents the excitation trapping at low-energy states and thus promotes efficient exciton diffusion in chlorosomes at ambient temperature.

Identifying the major intermediate species by combining time-resolved X-ray solution scattering and X-ray absorption spectroscopy.

Identifying the intermediate species along a reaction pathway is a first step towards a complete understanding of the reaction mechanism, but often this task is not trivial. There has been a strong on-going debate: which of the three intermediates, the CHI2 radical, the CHI2-I isomer, and the CHI2(+) ion, is the dominant intermediate species formed in the photolysis of iodoform (CHI3)? Herein, by combining time-resolved X-ray liquidography (TRXL) and time-resolved X-ray absorption spectroscopy (TR-XAS), we present strong evidence that the CHI2 radical is dominantly formed from the photolysis of CHI3 in methanol at 267 nm within the available time resolution of the techniques (∼20 ps for TRXL and ∼100 ps for TR-XAS). The TRXL measurement, conducted using the time-slicing scheme, detected no CHI2-I isomer within our signal-to-noise ratio, indicating that, if formed, the CHI2-I isomer must be a minor intermediate. The TR-XAS transient spectra measured at the iodine L1 and L3 edges support the same conclusion. The present work demonstrates that the application of these two complementary time-resolved X-ray methods to the same system can provide a detailed understanding of the reaction mechanism.

Sub-100-ps structural dynamics of horse heart myoglobin probed by time-resolved X-ray solution scattering.

Here we report sub-100-ps structural dynamics of horse heart myoglobin revealed by time-resolved X-ray solution scattering. By applying the time-slicing scheme to the measurement and subsequent deconvolution, we investigate the protein structural dynamics that occur faster than the X-ray temporal pulse width of synchrotrons (~100 ps). The singular value decomposition analysis of the experimental data suggests that two structurally distinguishable intermediates are formed within 100 ps. In particular, the global structural change occurring on the time scale of 70 ps is identified.

Aloe vera-derived graphene-coupled phenosafranin photocatalyst for generation and regeneration of ammonia and NADH by mimicking natural photosynthetic route.

Aloe vera-derived graphene (ADG) coupled system photocatalyst, mimicking natural photosynthesis, is one of the most promising ways for converting solar energy into ammonia (NH3 ) and nicotinamide adenine dinucleotide (NADH) that have been widely used to make the numerous chemicals such as fertilizer and fuel. In this study, we report the synthesis of the aloe vera-derived graphene-coupled phenosafranin (ADGCP) acting as a highly efficient photocatalyst for the generation of NH3 and regeneration of NADH from nitrogen (N2 ) and oxidized form of nicotinamide adenine dinucleotide (NAD+ ). The results show a benchmark instance for mimicking natural photosynthesis activity as well as the practical applications for the solar-driven selective formation of NH3 and the regeneration of NADH by using the newly designed photocatalyst.

Solar Light Responsive Graphitic Carbon Nitride Coupled Porphyrin Photocatalyst that Uses for Solar Fine Chemical Production.

Photocatalysis is a defendable manner for production of several organic chemicals, energy and its storage from solar energy. For the evolution of metal free, cost-effective catalyst a 2D composite has been appear as a photocatalyst. Here, we had reported the synthesis of a light harvesting composite as a photocatalyst which was assembled by a poly-condensation mechanism between graphitic carbon nitride and tetrakis(4-nitrophenyl) porphyrin and the resulting composite manifest the excellent light harvesting properties, suitable energy band and low charge recombination. The photocatalyst [(NO2 )4 TPP@g-C3 N4 ] enables the efficient photocatalytic production of nicotinamide adenine dinucleotide (NADH) from consumed NAD+ also the production of organic chemicals like 4-methoxybenzylimines from 4-methoxybenzylamines. The photocatalytic efficiency of the photocatalyst was estimated by the percentage of NADH regeneration and the percentage yield of organic transformations. It shows the tetrakis(4-nitrophenyl) porphyrin could enhance the charge transfer capacity of graphitic carbon nitride which shows excellent photocatalysis activities and organic transformations.

Dye Degradation and Sulfur Oxidation of Methyl Orange and Thiophenol via Newly Designed Nanocomposite GQDs/NiSe-NiO Photocatalyst Under Homemade LED Light.

Photocatalytic processes triggered by graphene-based photocatalysts under solar light have sparked interest as a new sort of instrument for solar chemical synthesis. Herein we investigated self-assembled graphene quantum dots (GQDs)/NiSe-NiO composite photocatalyst for organic transformation as well as dye degradation. The synthesized GQDs/NiSe-NiO composite photocatalyst has an excellent suitable band gap, high molar extinction coefficient, low toxicity and chemical/thermal stability. The GQDs/NiSe-NiO composite photocatalyst emerges as a new standard for sulfur oxidation and dye degradation reactions under homemade LED light with high yield.

Revolutionizing carbon chemistry: Solar-powered C(sp3 )-N bond activation and CO2 transformation via newly designed SBE-Y cutting-edge dynamic photocatalyst.

A solvent-free sulfur-bridge-eosin-Y (SBE-Y) polymeric framework photocatalyst was prepared for the first time through an in situ thermal polymerization route using elemental sulfur (S8 ) as a bridge. The addition of a sulfur bridge to the polymeric framework structure resulted in an allowance of the harvesting range of eosin-Y (E-Y) for solar light. This shows that a wider range of solar light can be used by the bridge material's photocatalytic reactions. In this context, supercharged solar spectrum: enhancing light absorption and hole oxidation with sulfur bridges. This suggests that the excited electrons and holes through solar light can contribute to oxidation-reduction reactions more potently. As a result, the photocatalyst-enzyme attached artificial photosynthesis system developed using SBE-Y as a photocatalyst performs exceptionally well, resulting in high 1,4-NADH regeneration (86.81%), followed by its utilization in the exclusive production of formic acid (210.01 µmol) from CO2 and synthesis of fine chemicals with 99.9% conversion yields. The creation of more effective photocatalytic materials for environmental clean-up and other applications that depend on the solar light-driven absorption spectrum of inorganic and organic molecules could be one of the practical ramifications of this research.

Transformation of PMMA from sunlight-blocking to sunlight-activated coupled with DNH photocatalytic platform for oxidative coupling of amines and generation/regeneration of LDC/NADH.

The photocatalytic oxidation and generation/regeneration of amines to imines and leucodopaminechrome (LDC)/NADH are subjects of intense interest in contemporary research. Imines serve as crucial intermediates for the synthesis of solar fuels, fine chemicals, agricultural chemicals, and pharmaceuticals. While significant progress has been made in developing efficient processes for the oxidation and generation/regeneration of secondary amines, the oxidation of primary amines has received comparatively less attention until recently. This discrepancy can be attributed to the high reactivity of imines generated from primary amines, which are prone to dehydrogenation into nitriles. In this study, we present the synthesis and characterization of a novel polymer-based photocatalyst, denoted as PMMA-DNH, designed for solar light-harvesting applications. PMMA-DNH incorporates the light-harvesting molecule dinitrophenyl hydrazine (DNH) at varying concentrations (5%, 10%, 20%, 30%, and 40%). Leveraging its high molar extinction coefficient and slow charge recombination, the 30% DNH-incorporated PMMA photocatalyst proves to be particularly efficient. This photocatalytic system demonstrates exceptional yields (96.5%) in imine production and high generation/regeneration rates for LDC/NADH (65.27%/78.77%). The research presented herein emphasizes the development and application of a newly engineered polymer-based photocatalyst, which holds significant promise for direct solar-assisted chemical synthesis in diverse commercial applications.

Photocatalytic oxygenation of sulfide using solar light and ingenious GQDs@AQ catalyst: Mechanistic and synthetic investigations.

The combination of excellent electronic properties and thermal stability positions orange-derived graphene quantum dots (GQDs) as promising materials for solar light-based applications. Researchers are actively exploring their potential in fields such as photovoltaics, photocatalysis, optoelectronics, and energy storage. Their abundance, cost-effectiveness, and eco-friendly nature further contribute to their growing relevance in cutting-edge scientific research. Furthermore, only GQDs are not much more effective in the UV-visible region, therefore, required band gap engineering in GQDs material. In this context, we designed GQDs-based light harvesting materials, which is active in UV-visible region. Herein we synthesized GQDs coupled with 2,6-diaminoanthrquninone (AQ), that is, GQDs@AQ light harvesting photocatalyst the first time for the oxidation of sulfide to sulfoxide under visible light. For the integrating reactions of sulfide in aerobic conditions under visible light by GQDs@AQ photocatalyst exhibit utmost higher photocatalytic activity than simple GQDs due to low molar extinction coefficient and slow recombination charges. The use of GQDs@AQ light harvesting photocatalyst, showed the excellent organic transformation efficiency of sulfide to sulfoxide with excellent yield (94%). The high efficiency and excellent yield of 94% indicate the effectiveness of GQDs@AQ as a photocatalyst for these specific organic transformations.

Protein structural dynamics of photoactive yellow protein in solution revealed by pump-probe X-ray solution scattering.

Photoreceptor proteins play crucial roles in receiving light stimuli that give rise to the responses required for biological function. However, structural characterization of conformational transition of the photoreceptors has been elusive in their native aqueous environment, even for a prototype photoreceptor, photoactive yellow protein (PYP). We employ pump-probe X-ray solution scattering to probe the structural changes that occur during the photocycle of PYP in a wide time range from 3.16 µs to 300 ms. By the analysis of both kinetics and structures of the intermediates, the structural progression of the protein in the solution phase is vividly visualized. We identify four structurally distinct intermediates and their associated five time constants and reconstructed the molecular shapes of the four intermediates from time-independent, species-associated difference scattering curves. The reconstructed structures of the intermediates show the large conformational changes such as the protrusion of N-terminus, which is restricted in the crystalline phase due to the crystal contact and thus could not be clearly observed by X-ray crystallography. The protrusion of the N-terminus and the protein volume gradually increase with the progress of the photocycle and becomes maximal in the final intermediate, which is proposed to be the signaling state. The data not only reveal that a common kinetic mechanism is applicable to both the crystalline and the solution phases, but also provide direct evidence for how the sample environment influences structural dynamics and the reaction rates of the PYP photocycle.

Direct observation of cooperative protein structural dynamics of homodimeric hemoglobin from 100 ps to 10 ms with pump-probe X-ray solution scattering.

Proteins serve as molecular machines in performing their biological functions, but the detailed structural transitions are difficult to observe in their native aqueous environments in real time. For example, despite extensive studies, the solution-phase structures of the intermediates along the allosteric pathways for the transitions between the relaxed (R) and tense (T) forms have been elusive. In this work, we employed picosecond X-ray solution scattering and novel structural analysis to track the details of the structural dynamics of wild-type homodimeric hemoglobin (HbI) from the clam Scapharca inaequivalvis and its F97Y mutant over a wide time range from 100 ps to 56.2 ms. From kinetic analysis of the measured time-resolved X-ray solution scattering data, we identified three structurally distinct intermediates (I(1), I(2), and I(3)) and their kinetic pathways common for both the wild type and the mutant. The data revealed that the singly liganded and unliganded forms of each intermediate share the same structure, providing direct evidence that the ligand photolysis of only a single subunit induces the same structural change as the complete photolysis of both subunits does. In addition, by applying novel structural analysis to the scattering data, we elucidated the detailed structural changes in the protein, including changes in the heme-heme distance, the quaternary rotation angle of subunits, and interfacial water gain/loss. The earliest, R-like I(1) intermediate is generated within 100 ps and transforms to the R-like I(2) intermediate with a time constant of 3.2 ± 0.2 ns. Subsequently, the late, T-like I(3) intermediate is formed via subunit rotation, a decrease in the heme-heme distance, and substantial gain of interfacial water and exhibits ligation-dependent formation kinetics with time constants of 730 ± 120 ns for the fully photolyzed form and 5.6 ± 0.8 µs for the partially photolyzed form. For the mutant, the overall kinetics are accelerated, and the formation of the T-like I(3) intermediate involves interfacial water loss (instead of water entry) and lacks the contraction of the heme-heme distance, thus underscoring the dramatic effect of the F97Y mutation. The ability to keep track of the detailed movements of the protein in aqueous solution in real time provides new insights into the protein structural dynamics.

Structural dynamics of 1,2-diiodoethane in cyclohexane probed by picosecond X-ray liquidography.

We investigate the structural dynamics of iodine elimination reaction of 1,2-diiodoethane (C(2)H(4)I(2)) in cyclohexane by applying time-resolved X-ray liquidography (TRXL). The TRXL technique combines structural sensitivity of X-ray diffraction and 100 ps time resolution of X-ray pulses from synchrotron and allows direct probing of transient structure of reacting molecules. From the analysis of time-dependent X-ray solution scattering patterns using global fitting based on DFT calculation and MD simulation, we elucidate the kinetics and structure of transient intermediates resulting from photodissociation of C(2)H(4)I(2). In particular, the effect of solvent on the reaction kinetics and pathways is examined by comparison with an earlier TRXL study on the same reaction in methanol. In cyclohexane, the C(2)H(4)I radical intermediate undergoes two branched reaction pathways, formation of C(2)H(4)I-I isomer and direct dissociation into C(2)H(4) and I, while only isomer formation occurs in methanol. Also, the C(2)H(4)I-I isomer has a shorter lifetime in cyclohexane by an order of magnitude than in methanol. The difference in the reaction dynamics in the two solvents is accounted for by the difference in solvent polarity. In addition, we determine that the C(2)H(4)I radical has a bridged structure, not a classical structure, in cyclohexane.