Structural analysis of transient reaction intermediate in formic acid dehydrogenation catalysis using two-dimensional IR spectroscopy.

The molecular structure of a catalytically active key intermediate is determined in solution by employing 2D IR spectroscopy measuring vibrational cross-angles. The formate intermediate (2) in the formic acid dehydrogenation reaction catalyzed by a phosphorus-nitrogen PN3P-Ru catalyst is elucidated. Our spectroscopic studies show that the complex features a formate ion directly attached to the Ru center as a ligand, and a proton added to the imine arm of the dearomatized PN3P* ligand. During the catalytic process, the imine arms are not only reversibly protonated and deprotonated, but also interacting with the protic substrate molecules, effectively serving as the local proton buffer to offer remarkable stability with a turnover number (TON) over one million.

Two distinctive energy migration pathways of monolayer molecules on metal nanoparticle surfaces.

Energy migrations at metal nanomaterial surfaces are fundamentally important to heterogeneous reactions. Here we report two distinctive energy migration pathways of monolayer adsorbate molecules on differently sized metal nanoparticle surfaces investigated with ultrafast vibrational spectroscopy. On a 5 nm platinum particle, within a few picoseconds the vibrational energy of a carbon monoxide adsorbate rapidly dissipates into the particle through electron/hole pair excitations, generating heat that quickly migrates on surface. In contrast, the lack of vibration-electron coupling on approximately 1 nm particles results in vibrational energy migration among adsorbates that occurs on a twenty times slower timescale. Further investigations reveal that the rapid carbon monoxide energy relaxation is also affected by the adsorption sites and the nature of the metal but to a lesser extent. These findings reflect the dependence of electron/vibration coupling on the metallic nature, size and surface site of nanoparticles and its significance in mediating energy relaxations and migrations on nanoparticle surfaces.

Comparison Studies on Sub-Nanometer-Sized Ion Clusters in Aqueous Solutions: Vibrational Energy Transfers, MD Simulations, and Neutron Scattering.

In this work, MD simulations with two different force fields, vibrational energy relaxation and resonant energy transfer experiments, and neutron scattering data are used to investigate ion pairing and clustering in a series of GdmSCN aqueous solutions. The MD simulations reproduce the major features of neutron scattering experimental data very well. Although no information about ion pairing or clustering can be obtained from the neutron scattering data, MD calculations clearly demonstrate that substantial amounts of ion pairs and small ion clusters (subnanometers to a few nanometers) do exist in the solutions of concentrations 0.5 M*, 3 M*, and 5 M* (M* denotes mole of GdmSCN per 55.55 mole of water). Vibrational relaxation experiments suggest that significant amounts of ion pairs form in the solutions. Experiments measuring the resonant energy transfers among the thiocyanate anions in the solutions suggest that the ions form clusters and in the clusters the average anion distance is 5.6 Å (5.4 Å) in the 3 M* (5 M*) Gdm-DSCN/D2O solution.

The molecular origin of high DNA-repair efficiency by photolyase.

The primary dynamics in photomachinery such as charge separation in photosynthesis and bond isomerization in sensory photoreceptor are typically ultrafast to accelerate functional dynamics and avoid energy dissipation. The same is also true for the DNA repair enzyme, photolyase. However, it is not known how the photoinduced step is optimized in photolyase to attain maximum efficiency. Here, we analyse the primary reaction steps of repair of ultraviolet-damaged DNA by photolyase using femtosecond spectroscopy. With systematic mutations of the amino acids involved in binding of the flavin cofactor and the cyclobutane pyrimidine dimer substrate, we report our direct deconvolution of the catalytic dynamics with three electron-transfer and two bond-breaking elementary steps and thus the fine tuning of the biological repair function for optimal efficiency. We found that the maximum repair efficiency is not enhanced by the ultrafast photoinduced process but achieved by the synergistic optimization of all steps in the complex repair reaction.

Electron-phonon interactions in MoS2 probed with ultrafast two-dimensional visible/far-infrared spectroscopy.

An ultrafast two-dimensional visible/far-IR spectroscopy based on the IR/THz air biased coherent detection method and scanning the excitation frequencies is developed. The method allows the responses in the far-IR region caused by various electronic excitations in molecular or material systems to be observed in real time. Using the technique, the relaxation dynamics of the photo-excited carriers and electron/phonon coupling in bulk MoS2 are investigated. It is found that the photo-generation of excited carriers occurs within two hundred fs and the relaxation of the carriers is tens of ps. The electron-phonon coupling between the excitations of electrons and the phonon mode E1u of MoS2 is also directly observed. The electron excitation shifts the frequency of the phonon mode 9 cm(-1) higher, resulting in an absorption peak at 391 cm(-1) and a bleaching peak at 382 cm(-1). The frequency shift diminishes with the relaxation of the carriers.

Dynamics and mechanism of UV-damaged DNA repair in indole-thymine dimer adduct: molecular origin of low repair quantum efficiency.

Many biomimetic chemical systems for repair of UV-damaged DNA showed very low repair efficiency, and the molecular origin is still unknown. Here, we report our systematic characterization of the repair dynamics of a model compound of indole-thymine dimer adduct in three solvents with different polarity. By resolving all elementary steps including three electron-transfer processes and two bond-breaking and bond-formation dynamics with femtosecond resolution, we observed the slow electron injection in 580 ps in water, 4 ns in acetonitrile, and 1.38 ns in dioxane, the fast back electron transfer without repair in 120, 150, and 180 ps, and the slow bond splitting in 550 ps, 1.9 ns, and 4.5 ns, respectively. The dimer bond cleavage is clearly accelerated by the solvent polarity. By comparing with the biological repair machine photolyase with a slow back electron transfer (2.4 ns) and a fast bond cleavage (90 ps), the low repair efficiency in the biomimetic system is mainly determined by the fast back electron transfer and slow bond breakage. We also found that the model system exists in a dynamic heterogeneous C-clamped conformation, leading to a stretched dynamic behavior. In water, we even identified another stacked form with ultrafast cyclic electron transfer, significantly reducing the repair efficiency. Thus, the comparison of the repair efficiency in different solvents is complicated and should be cautious, and only the dynamics by resolving all elementary steps can finally determine the total repair efficiency. Finally, we use the Marcus electron-transfer theory to analyze all electron-transfer reactions and rationalize all observed electron-transfer dynamics.

Nonresonant energy transfers independent on the phonon densities in polyatomic liquids.

Energy-gap-dependent vibrational-energy transfers among the nitrile stretches of KSCN/KS(13)CN/KS(13)C(15)N in D2O, DMF, and formamide liquid solutions at room temperature were measured by the vibrational-energy-exchange method. The energy transfers are slower with a larger energy donor/acceptor gap, independent of the calculated instantaneous normal mode ("phonons" in liquids) densities or the terahertz absorption spectra. The energy-gap dependences of the nonresonant energy transfers cannot be described by phonon compensation mechanisms with the assumption that phonons are the instantaneous normal modes of the liquids. Instead, the experimental energy-gap dependences can be quantitatively reproduced by the dephasing mechanism. A simple theoretical derivation shows that the fast molecular motions in liquids randomize the modulations on the energy donor and acceptor by phonons and diminish the phonon compensation efficiency on energy transfer. Estimations based on the theoretical derivations suggest that, for most nonresonant intermolecular vibrational-energy transfers in liquids with energy gaps smaller than the thermal energy, the dephasing mechanism dominates the energy-transfer process.

Intermolecular vibrational energy transfers in liquids and solids.

Resonant and nonresonant intermolecular vibrational energy transfers in KSCN/KSC(13)N/KS(13)C(15)N aqueous and DMF solutions and crystals are studied. Both energy-gap and temperature dependent measurements reveal some surprising results, e.g. inverted energy-gap dependent energy transfer rates and opposite temperature dependences of resonant and nonresonant energy transfer rates. Two competing mechanisms are proposed to be responsible for the experimental observations. The first one is the dephasing mechanism in which the measured energy transfer rate originates from the dephasing of the energy donor-acceptor coherence, and the second one is the phonon-compensation mechanism derived from the second order perturbation. It is found that both the nonresonant energy transfers in the liquids and resonant energy transfers in both liquids and solids can be well described by the first mechanism. The second mechanism explains the nonresonant energy transfers in one series of the solid samples very well.

Dynamic Determination of Active-Site Reactivity in Semiquinone Photolyase by the Cofactor Photoreduction.

Photolyase contains a flavin cofactor in a fully reduced form as its functional state to repair ultraviolet-damaged DNA upon blue light absorption. However, after purification, the cofactor exists in its oxidized or neutral semiquinone state. Such oxidization eliminates the repair function, but it can be reverted by photoreduction, a photoinduced process with a series of electron-transfer (ET) reactions. With femtosecond absorption spectroscopy and site-directed mutagenesis, we completely recharacterized such photoreduction dynamics in the semiquinone state. Comparing with all previous studies, we identified a new intramolecular ET pathway, determined stretched ET behaviors, refined all ET time scales, and finally evaluated the driving forces and reorganization energies for eight elementary ET reactions. Combined with the oxidized-state photoreduction dynamics, we elucidated the different active-site properties of the reduction ability and structural flexibility in the oxidized and semiquinone states, leading to the dramatically different ET dynamics and photoreduction efficiency in the two states.

Femtosecond dynamics of short-range protein electron transfer in flavodoxin.

Intraprotein electron transfer (ET) in flavoproteins is important for understanding the correlation of their redox, configuration, and reactivity at the active site. Here, we used oxidized flavodoxin as a model system and report our complete characterization of a photoinduced redox cycle from the initial charge separation in 135-340 fs to subsequent charge recombination in 0.95-1.6 ps and to the final cooling relaxation of the product(s) in 2.5-4.3 ps. With 11 mutations at the active site, we observed that these ultrafast ET dynamics, much faster than active-site relaxation, mainly depend on the reduction potentials of the electron donors with minor changes caused by mutations, reflecting a highly localized ET reaction between the stacked donor and acceptor at a van der Waals distance and leading to a gas-phase type of bimolecular ET reaction confined in the active-site nanospace. Significantly, these ultrafast ET reactions ensure our direct observation of vibrationally excited reaction product(s), suggesting that the back ET barrier is effectively reduced because of the decrease in the total free energy in the Marcus inverted region, leading to the accelerated charge recombination. Such vibrationally coupled charge recombination should be a general feature of flavoproteins with similar configurations and interactions between the cofactor flavin and neighboring aromatic residues.

Molecular conformations of crystalline L-cysteine determined with vibrational cross angle measurements.

The molecular conformations of crystalline L-cysteine prepared in its orthorhombic form were determined by the vibrational cross angle measurements. Its major dihedral angles of chemical bonds determined by this method are consistent with the results from diffraction experiments. In addition, the relative orientations of the chemical bonds associated with the hydrogen atoms of the NH3(+) group and the thiol group are also determined. The results demonstrate that the vibrational cross angle method based on the multiple-mode approach can potentially become a structural tool for determining molecular conformations. The major challenges for the method to become a general molecular structural tool are discussed, and some approaches to address them are proposed.

Dynamic determination of the functional state in photolyase and the implication for cryptochrome.

The flavin adenine dinucleotide cofactor has an unusual bent configuration in photolyase and cryptochrome, and such a folded structure may have a functional role in initial photochemistry. Using femtosecond spectroscopy, we report here our systematic characterization of cyclic intramolecular electron transfer (ET) dynamics between the flavin and adenine moieties of flavin adenine dinucleotide in four redox forms of the oxidized, neutral, and anionic semiquinone, and anionic hydroquinone states. By comparing wild-type and mutant enzymes, we have determined that the excited neutral oxidized and semiquinone states absorb an electron from the adenine moiety in 19 and 135 ps, whereas the excited anionic semiquinone and hydroquinone states donate an electron to the adenine moiety in 12 ps and 2 ns, respectively. All back ET dynamics occur ultrafast within 100 ps. These four ET dynamics dictate that only the anionic hydroquinone flavin can be the functional state in photolyase due to the slower ET dynamics (2 ns) with the adenine moiety and a faster ET dynamics (250 ps) with the substrate, whereas the intervening adenine moiety mediates electron tunneling for repair of damaged DNA. Assuming ET as the universal mechanism for photolyase and cryptochrome, these results imply anionic flavin as the more attractive form of the cofactor in the active state in cryptochrome to induce charge relocation to cause an electrostatic variation in the active site and then lead to a local conformation change to initiate signaling.

Determining complete electron flow in the cofactor photoreduction of oxidized photolyase.

The flavin cofactor in photoenzyme photolyase and photoreceptor cryptochrome may exist in an oxidized state and should be converted into reduced state(s) for biological functions. Such redox changes can be efficiently achieved by photoinduced electron transfer (ET) through a series of aromatic residues in the enzyme. Here, we report our complete characterization of photoreduction dynamics of photolyase with femtosecond resolution. With various site-directed mutations, we identified all possible electron donors in the enzyme and determined their ET timescales. The excited cofactor behaves as an electron sink to draw electron flow from a series of encircling aromatic molecules in three distinct layers from the active site in the center to the protein surface. The dominant electron flow follows the conserved tryptophan triad in a hopping pathway across the layers with multiple tunneling steps. These ET dynamics occur ultrafast in less than 150 ps and are strongly coupled with local protein and solvent relaxations. The reverse electron flow from the flavin is slow and in the nanosecond range to ensure high reduction efficiency. With 12 experimentally determined elementary ET steps and 6 ET reaction pairs, the enzyme exhibits a distinct reduction-potential gradient along the same aromatic residues with favorable reorganization energies to drive a highly unidirectional electron flow toward the active-site center from the protein surface.

Ultrafast dynamics of nonequilibrium electron transfer in photoinduced redox cycle: solvent mediation and conformation flexibility.

We report here our systematic characterization of a photoinduced electron-transfer (ET) redox cycle in a covalently linked donor-spacer-acceptor flexible system, consisting of N-acetyl-tryptophan methylester as an electron donor and thymine as an electron acceptor in three distinct solvents of water, acetonitrile, and dioxane. With femtosecond resolution, we determined all the ET time scales, forward and backward, by following the complete reaction evolution from reactants to intermediates and finally to products. Surprisingly, we observed two distinct ET dynamics in water, corresponding to a stacked configuration with ultrafast ET in 0.7 ps and back ET in 4.5 ps and a partially folded C-clamp conformation with ET in 322 ps but back ET in 17 ps. In acetonitrile and dioxane, only the C-clamp conformations were observed with ET in 470 and 1068 ps and back ET in 110 and 94 ps, respectively. These relatively slow ET dynamics in hundreds of picoseconds all showed significant conformation heterogeneity and followed a stretched decay behavior. With both forward and back ET rates determined, we derived solvent reorganization energies and coupling constants. Significantly, we found that solvent molecules intercalated in the cleft of the C-clamp structure mediate electron transfer with a tunneling parameter (ß) of 1.0-1.4 Å(-1) and the high-frequency vibration modes in the product(s) couple with the back ET process, leading to the ultrafast back ET dynamics in tens of picoseconds. These findings provide mechanistic insights of nonequilibrium ET dynamics modulated by conformation flexibility, mediated by unique solvent configuration, and accelerated by vibrational coupling.

Electron tunneling pathways and role of adenine in repair of cyclobutane pyrimidine dimer by DNA photolyase.

Electron tunneling pathways in enzymes are critical to their catalytic efficiency. Through electron tunneling, photolyase, a photoenzyme, splits UV-induced cyclobutane pyrimidine dimer into two normal bases. Here, we report our systematic characterization and analyses of photoinitiated three electron transfer processes and cyclobutane ring splitting by following the entire dynamical evolution during enzymatic repair with femtosecond resolution. We observed the complete dynamics of the reactants, all intermediates and final products, and determined their reaction time scales. Using (deoxy)uracil and thymine as dimer substrates, we unambiguously determined the electron tunneling pathways for the forward electron transfer to initiate repair and for the final electron return to restore the active cofactor and complete the catalytic photocycle. Significantly, we found that the adenine moiety of the unusual bent flavin cofactor is essential to mediating all electron-transfer dynamics through a superexchange mechanism, leading to a delicate balance of time scales. The cyclobutane ring splitting takes tens of picoseconds, while electron-transfer dynamics all occur on a longer time scale. The active-site structural integrity, unique electron tunneling pathways, and the critical role of adenine ensure the synergy of these elementary steps in this complex photorepair machinery to achieve maximum repair efficiency which is close to unity. Finally, we used the Marcus electron-transfer theory to evaluate all three electron-transfer processes and thus obtained their reaction driving forces (free energies), reorganization energies, and electronic coupling constants, concluding that the forward and futile back-electron transfer is in the normal region and that the final electron return of the catalytic cycle is in the inverted region.

Dynamics and mechanism of cyclobutane pyrimidine dimer repair by DNA photolyase.

Photolyase uses blue light to restore the major ultraviolet (UV)-induced DNA damage, the cyclobutane pyrimidine dimer (CPD), to two normal bases by splitting the cyclobutane ring. Our earlier studies showed that the overall repair is completed in 700 ps through a cyclic electron-transfer radical mechanism. However, the two fundamental processes, electron-tunneling pathways and cyclobutane ring splitting, were not resolved. Here, we use ultrafast UV absorption spectroscopy to show that the CPD splits in two sequential steps within 90 ps and the electron tunnels between the cofactor and substrate through a remarkable route with an intervening adenine. Site-directed mutagenesis reveals that the active-site residues are critical to achieving high repair efficiency, a unique electrostatic environment to optimize the redox potentials and local flexibility, and thus balance all catalytic reactions to maximize enzyme activity. These key findings reveal the complete spatio-temporal molecular picture of CPD repair by photolyase and elucidate the underlying molecular mechanism of the enzyme's high repair efficiency.

Dynamics and mechanism of repair of ultraviolet-induced (6-4) photoproduct by photolyase.

One of the detrimental effects of ultraviolet radiation on DNA is the formation of the (6-4) photoproduct, 6-4PP, between two adjacent pyrimidine rings. This lesion interferes with replication and transcription, and may result in mutation and cell death. In many organisms, a flavoenzyme called photolyase uses blue light energy to repair the 6-4PP (ref. 3). The molecular mechanism of the repair reaction is poorly understood. Here, we use ultrafast spectroscopy to show that the key step in the repair photocycle is acyclic proton transfer between the enzyme and the substrate. By femtosecond synchronization of the enzymatic dynamics with the repair function, we followed the function evolution and observed direct electron transfer from the excited flavin cofactor to the 6-4PP in 225 picoseconds, but surprisingly fast back electron transfer in 50 picoseconds without repair. We found that the catalytic proton transfer between a histidine residue in the active site and the 6-4PP, induced by the initial photoinduced electron transfer from the excited flavin cofactor to 6-4PP, occurs in 425 picoseconds and leads to 6-4PP repair in tens of nanoseconds. These key dynamics define the repair photocycle and explain the underlying molecular mechanism of the enzyme's modest efficiency.

Determination of the formation of dark state via depleted spontaneous emission in a complex solvated molecule.

We present a general two-color two-pulse femtosecond pump-dump approach to study the specific population transfer along the reaction coordinate through the higher vibrational energy levels of excited states of a complex solvated molecule via the depleted spontaneous emission. The time-dependent fluorescence depletion provides the correlated dynamical information between the monitored fluorescence state and the SEP "dumped" dark states, and therefore allow us to obtain the dynamics of the formation of the dark states corresponding to the ultrafast photoisomerization processes. The excited-state dynamics of LDS 751 have been investigated as a function of solvent viscosity and solvent polarity, where a cooperative two-step isomerization process is clearly identified within LDS 751 upon excitation.

Photophysical properties of photoactive molecules with conjugated push-pull structures.

The photophysical properties of two newly synthesized photoactive compounds with asymmetrical D-pi-A structure and symmetrical D-pi-A-pi-D structure are investigated in different aprotic solvents by steady-state and femtosecond fluorescence depletion measurements. It is found that the asymmetrical DA compound has larger dipole moment change than that of the symmetrical DAD compound upon excitation, where the dipole moments of the two compounds have been estimated using the Lippert-Mataga equation. Furthermore, the steady-state spectral results show that increasing solvent polarity results in small solvatochromic shift in the absorption maxima but a large red shift in the fluorescence maxima for them, indicating that the dipole moment changes mainly reflect the changes of dipole moment in excited-state rather than in ground state. The red-shifted fluorescence band is attributed to an intramolecular charge transfer (ICT) state upon photoexcitation, which could result in a strong interaction with the surrounding solvents to cause the fast solvent reorganization. The resulting ICT states of symmetrical compounds are less polar than the asymmetrical compounds, indicating the different extents of stabilization of solute-solvent interaction in the excited state. Femtosecond fluorescence depletion measurements are further employed to investigate the fast solvation effects and dynamics of the ICT state of these two novel compounds. The femtosecond fluorescence depletion results show that the DA compound has faster solvation time than that of DAD compound, which corresponds to the formation of relaxed ICT state (i.e., a final ICT state with rearranged solvent molecules after solvation) in polar solvents. It is therefore reasonably understood that the ICT compounds with asymmetrical (D-pi-A) structure have better performance for those photovoltaic devices, which strongly rely on the nature of the electron push-pull ability, compared to those symmetrical compounds (D-pi-A-pi-D).