Visualizing Heterogeneous Protein Conformations with Multi-Tilt Nanoparticle-Aided Cryo-Electron Microscopy Sampling.

Obtaining the heterogeneous conformation of small proteins is important for understanding their biological role, but it is still challenging. Here, we developed a multi-tilt nanoparticle-aided cryo-electron microscopy sampling (MT-NACS) technique that enables the observation of heterogeneous conformations of small proteins and applied it to calmodulin. By imaging the proteins labeled by two gold nanoparticles at multiple tilt angles and analyzing the projected positions of the nanoparticles, the distributions of 3D interparticle distances were obtained. From the measured distance distributions, the conformational changes associated with Ca2+ binding and salt concentration were determined. MT-NACS was also used to track the structural change accompanied by the interaction between amyloid-beta and calmodulin, which has never been observed experimentally. This work offers an alternative platform for studying the functional flexibility of small proteins.

Photoinduced Group Transposition via Iridium-Nitrenoid Leading to Amidative Inner-Sphere Aryl Migration.

We herein report a fundamental mechanistic investigation into photochemical metal-nitrenoid generation and inner-sphere transposition reactivity using organometallic photoprecursors. By designing Cp*Ir(hydroxamate)(Ar) complexes, we induced photo-initiated ligand activation, allowing us to explore the amidative σ(Ir-aryl) migration reactivity. A combination of experimental mechanistic studies, femtosecond transient absorption spectroscopy, and density functional theory (DFT) calculations revealed that the metal-to-ligand charge transfer enables the σ(N-O) cleavage, followed by Ir-acylnitrenoid generation. The final inner-sphere σ(Ir-aryl) group migration results in a net amidative group transposition.

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.

Inter-Ligand Energy Transfer Process in an Ir-Complex with Expanding π-Conjugated Ligand.

The inter-ligand energy transfer (ILET) process in heteroleptic iridium complex, [Ir(dfppy)2 (bpy-Im2 )]+ , where dfppy=2-(2,4-difluorophenyl)pyridine and bpy-Im2 =4,4'-bis(1,2-diphenyl-1H-benzo[d]imidazole)-2,2',-bipyridine, was investigated using a femtosecond transient absorption (fs-TA) spectroscopic technique. The photophysical properties of [Ir(dfppy)2 (bpy-Im2 )]+ with significantly expanding π-conjugated ligand are compared to those of [Ir(dfppy)2 (bpy)]+ (bpy=2,2'-bipyridine) and a free bpy-Im2 ligand. The emission spectrum of [Ir(dfppy)2 (bpy-Im2 )]+ shows no shift upon changing the solvent polarity, whereas the free ligand bpy-Im2 showed bathochromic fluorescence shifts with increasing solvent polarity, which is attributed to intramolecular charge transfer (ICT). The unique photophysical properties of [Ir(dfppy)2 (bpy-Im2 )]+ are due to the fast ILET process from 3 MLCTdfppy to 3 MLCT/3 LCbpy-Im2 , resulting in the phosphorescence emission originating from 3 MLCT/3 LCbpy-Im2 . On the other hand, the TA bands of bpy-Im2 are observed at 540 and 480 nm, corresponding to the singlet and triplet manifolds, respectively. In contrast, the TA spectrum of [Ir(dfppy)2 (bpy-Im2 )]+ showes broad bands centered at 420 and 600 nm, attributed to the transitions from 3 MLCTdfppy and 3 MLCT/3 LCbpy-Im2 , respectively. Time-resolved spectroscopic results confirm the efficient ILET dynamics from 3 MLCTdfppy to 3 MLCT/3 LCbpy-Im2 in [Ir(dfppy)2 (bpy-Im2 )]+ . From the relaxation times determined by singular value decomposition analysis and simple sequential kinetic model, we infer that the ILET process from 3 MLCTdfppy to 3 MLCT/3 LCbpy-Im2 occurs with a time constant of ca. 4 ps. The presented results in this study show that the introduction of an expanding π-conjugated ligand can lead to the efficient ILET dynamics for improving the OLED performance.

Control of Chemoselectivity of SET-Promoted Photoaddition Reactions of Fullerene C60 with α-Trimethylsilyl Group-Containing N-Alkylglycinates Yielding Aminomethyl-1,2-dihydrofullerenes or Fulleropyrrolidines.

Knowledge about factors that govern chemoselectivity is pivotal to the design of reactions that are utilized to produce complex organic substances. In the current study, single-electron transfer (SET)-promoted photoaddition reactions of fullerene C60 with both trimethylsilyl and various alkyl group-containing glycinates and ethyl N-alkyl-N-((trimethylsilyl)methyl)glycinates were explored to evaluate how the nature of N-alkyl substituents of glycinate substrates and reaction conditions govern the chemoselectivity of reaction pathways followed. The results showed that photoreactions of C60 with glycinates, performed in deoxygenated conditions, produced aminomethyl-1,2-dihydrofullerenes efficiently through a pathway involving the addition of α-amino radical intermediates that are generated by sequential SET-solvent-assisted desilylation of glycinate substrates to C60. Under oxygenated conditions, photoreactions of glycinate substrates, except N-benzyl-substituted analogues, did not take place efficiently owing to quenching of 3C60* by oxygen. Interestingly, N-benzyl-substituted glycinates did react under these conditions to form fulleropyrrolidines through a pathway involving 1,3-dipolar cycloaddition of in situ formed azomethine ylides to C60. The ylide intermediates were formed by regioselective H-atom transfer from glycinates by singlet oxygen. Furthermore, methylene blue (MB)-photosensitized reactions of C60 with glycinates under oxygenated conditions took place efficiently to produce fulleropyrrolidines independent of the nature of N-alkyl substituents of glycinates.

Charge transfer induced by electronic state mixing in a symmetric X-Y-X-type multi-chromophore system.

Charge transfer (CT) from electron donor (D) to acceptor (A) plays an important role in photoelectric or electrochemical devices and is a useful concept for a molecule with D and A well distinguishable. Here, we report our finding that even in a molecule with D and A not resolvable, CT can be induced by electronic state mixing (ESM) in a symmetric multi-chromophore system (MCS), namely 1,4-di(1-pyrenyl)benzene (Py-Benz-Py). Unlike Py and Py-Benz, Py-Benz-Py exhibits unique photophysical properties attributable to the reduction of the energy gap between two electronic states induced by ESM. The ESM for Py-Benz-Py is due to the extended π-conjugation owing to the further introduction of Py into Py-Benz, and consequently leads to the favorable intramolecular CT, followed by the planarization due to the twisting motion between Py and phenyl moieties. Time-resolved spectroscopic data demonstrate that the twisting process of the Py moiety in acetonitrile occurs with two unequal time constants, suggesting the localized CT state and the asynchronous twisting dynamics of two Py moieties unlike the delocalized CT state in nonpolar and low-polarity solvents leading to the synchronous twisting of two Py moieties. This means that the symmetry-breaking CT in MCSs can induce an asynchronous twisting motion. The results reported here support that a molecule without CT can be turned into another molecule with CT induced by ESM and demonstrate that the excited-state relaxation dynamics can be regulated through the ESM induced by introducing the substituents or changing the environmental factors such as solvent polarities.

Elongated Lifetime and Enhanced Flux of Hot Electrons on a Perovskite Plasmonic Nanodiode.

A fundamental understanding of hot electron transport is critical for developing efficient hot-carrier-based solar cells. There have been significant efforts to enhance hot electron flux, and it has been found that a key factor affecting the hot electron flux is the lifetime of the hot electrons. Here, we report a combined study of hot electron flux and the lifetime of hot carriers using a perovskite-modified plasmonic nanodiode. We found that perovskite deposition on a plasmonic nanodiode can considerably improve hot electron generation induced by photon absorption. The perovskite plasmonic nanodiode consists of MAPbI3 layers covering a plasmonic-Au/TiO2 Schottky junction that is composed of randomly connected Au nanoislands deposited on a TiO2 layer. The measured incident photon-to-electron conversion efficiency and the short-circuit photocurrent show a significantly improved solar-to-electrical conversion performance of this nanodiode. Such an improvement is ascribed to the improved hot electron flux in MAPbI3 caused by effective light absorption from near-field enhancement of plasmonic Au and the efficient capture of hot electrons from Au nanoislands via the formation of a three-dimensional Schottky interface. The relation between the lifetime and flux of hot electrons was confirmed by femtosecond transient absorption spectroscopy that showed considerably longer hot electron lifetimes in MAPbI3 combined with the plasmonic Au structure. These findings can provide a fundamental understanding of hot electron generation and transport in perovskite, which can provide helpful guidance to designing efficient hot carrier photovoltaics.

Gold Nanoparticle Formation via X-ray Radiolysis Investigated with Time-Resolved X-ray Liquidography.

We report the generation of gold nanoparticles (AuNPs) from the aqueous solution of chloro(2,2',2″-terpyridine)gold(III) ion ([Au(tpy)Cl]2+) through X-ray radiolysis and optical excitation at a synchrotron. The original purpose of the experiment was to investigate the photoinduced structural changes of [Au(tpy)Cl]2+ upon 400 nm excitation using time-resolved X-ray liquidography (TRXL). Initially, the TRXL data did not show any signal that would suggest structural changes of the solute molecule, but after an induction time, the TRXL data started to show sharp peaks and valleys. In the early phase, AuNPs with two types of morphology, dendrites, and spheres, were formed by the reducing action of hydrated electrons generated by the X-ray radiolysis of water, thereby allowing the detection of TRXL data due to the laser-induced lattice expansion and relaxation of AuNPs. Along with the lattice expansion, the dendritic and spherical AuNPs were transformed into smaller, raspberry-shaped AuNPs of a relatively uniform size via ablation by the optical femtosecond laser pulse used for the TRXL experiment. Density functional theory calculations confirm that the reduction potential of the metal complex relative to the hydration potential of X-ray-generated electrons determines the facile AuNP formation observed for [Au(tpy)Cl]2+.

Formation of the Charge-Localized Dimer Radical Cation of 2-Ethyl-9,10-dimethoxyanthracene in Solution Phase.

Although dimer radical ions of aromatic molecules in the liquid-solution phase have been intensely studied, the understanding of charge-localized dimers, in which the extra charge is localized in a single monomer unit instead of being shared between two monomer units, is still elusive. In this study, the formation of a charge-localized dimer radical cation of 2-ethyl-9,10-dimethoxyanthracene (DMA), (DMA)2 .+ is investigated by transient absorption (TA) and time-resolved resonance Raman (TR3 ) spectroscopic methods combined with a pulse radiolysis technique. Visible- and near-IR TA signals in highly concentrated DMA solutions supported the formation of non-covalent (DMA)2 .+ by association of DMA and DMA.+ . TR3 spectra obtained from 30 ns to 300 µs time delays showed that the major bands are quite similar to those of DMA except for small transient bands, even at 30 ns time delay, suggesting that the positive charge of non-covalent (DMA)2 .+ is localized in a single monomer unit. From DFT calculations for (DMA)2 .+ , our TR3 spectra showed the best agreement with the calculated Raman spectrum of charge-localized edge-to-face T-shaped (DMA)2 .+ , termed DT.+ , although the charge-delocalized asymmetric π-stacked face-to-face (DMA)2 .+ , termed DF3.+ , is the most stable structure of (DMA)2 .+ according to the energetics from DFT calculations. The calculated potential energy curves for the association between DMA.+ and DMA showed that DT.+ is likely to be efficiently formed and contribute significantly to the TR3 spectra as a result of the permanent charge-induced Coulombic interactions and a dynamic equilibrium between charge localized and delocalized structures.

Proton Transfer Accompanied by the Oxidation of Adenosine.

Despite numerous experimental and theoretical studies, the proton transfer accompanying the oxidation of 2'-deoxyadenosine 5'-monophosphate 2'-deoxyadenosine 5'-monophosphate (5'-dAMP, A) is still under debate. To address this issue, we have investigated the oxidation of A in acidic and neutral solutions by using transient absorption (TA) and time-resolved resonance Raman (TR3 ) spectroscopic methods in combination with pulse radiolysis. The steady-state Raman signal of A was significantly affected by the solution pH, but not by the concentration of adenosine (2-50 mm). More specifically, the A in acidic and neutral solutions exists in its protonated (AH+ (N1+H+ )) and neutral (A) forms, respectively. On the one hand, the TA spectral changes observed at neutral pH revealed that the radical cation (A.+ ) generated by pulse radiolysis is rapidly converted into A. (N6-H) through the loss of an imino proton from N6. In contrast, at acidic pH (<4), AH.2+ (N1+H+ ) generated by pulse radiolysis of AH+ (N1+H+ ) does not undergo the deprotonation process owing to the pKa value of AH.2+ (N1+H+ ), which is higher than the solution pH. Furthermore, the results presented in this study have demonstrated that A, AH+ (N1+H+ ), and their radical species exist as monomers in the concentration range of 2-50 mm. Compared with the Raman bands of AH+ (N1+H+ ), the TR3 bands of AH.2+ (N1+H+ ) are significantly down-shifted, indicating a decrease in the bond order of the pyrimidine and imidazole rings due to the resonance structure of AH.2+ (N1+H+ ). Meanwhile, A. (N6-H) does not show a Raman band corresponding to the pyrimidine+NH2 scissoring vibration due to diprotonation at the N6 position. These results support the final products generated by the oxidation of adenosine in acidic and neutral solutions being AH.2+ (N1+H+ ) and A. (N6-H), respectively.

Fate of transient isomer of CH2I2: Mechanism and origin of ionic photoproducts formation unveiled by time-resolved x-ray liquidography.

Diiodomethane, CH2I2, in a polar solvent undergoes a unique photoinduced reaction whereby I2 - and I3 - are produced from its photodissociation, unlike for other iodine-containing haloalkanes. While previous studies proposed that homolysis, heterolysis, or solvolysis of iso-CH2I-I, which is a major intermediate of the photodissociation, can account for the formation of I2 - and I3 -, there has been no consensus on its mechanism and no clue for the reason why those negative ionic species are not observed in the photodissociation of other iodine-containing chemicals in the same polar solvent, for example, CHI3, C2H4I2, C2F4I2, I3 -, and I2. Here, using time-resolved X-ray liquidography, we revisit the photodissociation mechanism of CH2I2 in methanol and determine the structures of all transient species and photoproducts involved in its photodissociation and reveal that I2 - and I3 - are formed via heterolysis of iso-CH2I-I in the photodissociation of CH2I2 in methanol. In addition, we demonstrate that the high polarity of iso-CH2I-I is responsible for the unique photochemistry of CH2I2.

Influence of Charge Distribution on Structural Changes of Aromatic Imide Derivatives upon One-Electron Reduction Revealed by Time-Resolved Resonance Raman Spectroscopy during Pulse Radiolysis.

Structural changes of aromatic imides upon one-electron reduction are investigated by time-resolved resonance Raman spectroscopy during pulse radiolysis. Significant downshifts are observed for both the aromatic ring stretching and carbonyl stretching modes, which are related to a reduction of the bond order and increase of the charge density on these moieties. For three aromatic imides, i.e., 1,8-naphthalene imide (1,8-NI), 2,3-naphthalene imide (2,3-NI), and naphthalene diimide (NDI), the extent of structural changes is found to follow the order: 2,3-NI > 1,8-NI > NDI, reflecting the influence of charge distribution on molecular structure. To further investigate this phenomenon, a series of homologous NDI derivatives with a substituted phenyl group at the imide position are studied. The Raman peaks between 1550 and 1600 cm-1, which are assigned to aromatic stretching vibrations of the NDI moieties, are found to be sensitive to the charge distribution: stronger electron-withdrawing substituents result in these peaks shifting to slightly higher wavenumbers. As supported by a spin density analysis, despite the fact that the added charge is mostly localized on the NDI moiety, in the presence of an electron-withdrawing group, the subtle charge is likely to delocalize on the phenyl fragment, alleviating the effect of one-electron reduction on the molecular structure.

The time scale of the quaternary structural changes in hemoglobin revealed using the transient grating technique.

The quaternary structural transition between the R and T states of human hemoglobin was investigated using the transient grating technique. The results presented herein reveal that the quaternary structural change accompanied by the R-T transition occurs within a few microseconds.

Detection of Structural Changes upon One-Electron Oxidation and Reduction of Stilbene Derivatives by Time-Resolved Resonance Raman Spectroscopy during Pulse Radiolysis and Theoretical Calculations.

Stilbene (St) derivatives have been investigated for many years because of their interesting photochemical reactions such as cis-trans isomerization in the excited states and charged states and their relation to poly(p-phenylenevinylene)s. To clarify their charged state properties, structural information is indispensable. In the present study, radical cations and radical anions of St derivatives were investigated by radiation chemical methods. Absorption spectra of radical ion states were obtained by transient absorption measurements during pulse radiolysis; theoretical calculations that included the solvent effect afforded reasonable assignments. The variation in the peak position was explained by using HOMO and LUMO energy levels. Structural changes upon one-electron oxidation and reduction were detected by time-resolved resonance Raman measurements during pulse radiolysis. Significant downshifts were observed with the CC stretching mode of the ethylenic groups, indicative of the decrease in the bonding order. It was confirmed that the downshifts observed with reduction were larger than those with oxidation. On the other hand, the downshift caused by oxidation depends significantly on the electron-donating or electron-withdrawing nature of the substituents.

Structural study of various substituted biphenyls and their radical anions based on time-resolved resonance Raman spectroscopy combined with pulse radiolysis.

The structures of various para-substituted biphenyls (Bp-X; X = -OH, -OCH3, -CH3, -H, -CONH2, -COOH, and -CN) and their radical anions (Bp-X(•-)) were investigated by time-resolved resonance Raman spectroscopy combined with pulse radiolysis. The inter-ring C1-C1' stretching modes (ν6) of Bp-X were observed at ∼1285 cm(-1), whereas the ν6 modes of Bp-X(•-) with an electron-donating or -withdrawing substituent were significantly up-shifted. The difference (Δf) between the ν6 frequencies of Bp-X and Bp-X(•-) showed a significant dependence on the electron affinity of the substituent and exhibited a correlation with the Hammett substituent constants (σp). In contrast to Bp-H(•-) with a planar geometry, the theoretical and experimental results reveal that all Bp-X(•-) with an electron-donating or -withdrawing substituent have a slightly twisted structure. The twisted structure of Bp-X(•-) is due to the localization of the unpaired electron and negative charge density on one phenyl moiety in Bp-X(•-).

Radical cation of star-shaped condensed oligofluorenes having isotruxene as a core: importance of rigid planar structure on charge delocalization.

Because of their excellent optical and electronic properties, oligofluorenes and polyfluorenes have been investigated for years. Recently developed star-shaped oligomers bearing a truxene or isotruxene core are interesting two-dimensional oligomers. Since employment of a condensed ring system will be effective in further extension of π-conjugation system, we studied electronic and vibrational properties of radical cation of CITFn, star-shaped condensed oligomer with isotruxene core and fluorene unit, by means of the radiation chemical methods. Absorption spectra of radical cation of CITFn were measured in the wide spectral range, which revealed extended π-conjugation of CITFn. Furthermore, time-resolved resonance Raman spectra during pulse radiolysis revealed that the oxidation of CITFn induced structural change to enhance quinoidal character. The Raman data and theoretical calculation indicated that the rigid framework of the present star-shaped oligomer which makes the oligomer a planar structure is quite important in extension of the conjugation pathway.

Efficient electron transfer in i-motif DNA with a tetraplex structure.

Electron transfer through DNA: The electron-transfer dynamics of i-motif DNA conjugated with pyrene (Py) and anthraquinone (AQ) has been investigated by fluorescence up-conversion and transient absorption spectroscopic methods. Electron transfer (see red arrows) in i-motif DNA is more efficient than in duplex DNA, suggesting that i-motif DNA can be used as electron carrier in nanoelectronic devices.

Length and Charge of the N-terminus Regulate the Lifetime of the Signaling State of Photoactive Yellow Protein.

Photoactive yellow protein (PYP) is one of the most extensively studied photoreceptors. Nevertheless, the role of the N-terminus in the photocycle and structural transitions is still elusive. Here, we attached additional amino acids to the N-terminus of PYP and investigated the effect of the length and charge of additional N-terminal residues using circular dichroism, two-dimensional nuclear magnetic resonance (2D-NMR), transient absorption (TA), and transient grating (TG) spectroscopic techniques. TA experiments showed that, except for negatively charged residues (5D-PYP), additional N-terminal residues of PYP generally enable faster dark recovery from the putative signaling state (pB2) to the ground state (pG). TG data showed that although the degree of structural changes can be controlled by adjusting specific amino acid residues in the extended N-terminus of N-terminal extended PYPs (NE-PYPs), the dark recovery times of wt-PYP and NE-PYPs, except for 5D-PYP, are independent of the structural differences between pG and pB2 states. These results demonstrate that the recovery time and the degree of structural change can be regulated by controlling the length and sequence of N-terminal residues of PYP. The findings in this study emphasize the need for careful attention to the remaining amino acid residues when designing recombinant proteins for genetic engineering purposes.

Singlet fission dynamics modulated by molecular configuration in covalently linked pyrene dimers, Anti- and Syn-1,2-di(pyrenyl)benzene.

Covalently linked dimers (CLDs) and their structural isomers have attracted much attention as potential materials for improving power conversion efficiencies through singlet fission (SF). Here, we designed and synthesized two covalently ortho-linked pyrene (Py) dimers, anti- and syn-1,2-di(pyrenyl)benzene (Anti-DPyB and Syn-DPyB, respectively), and investigated the effect of molecular configuration on SF dynamics using steady-state and time-resolved spectroscopies. Both Anti-DPyB and Syn-DPyB, which have different Py-stacking configurations, form excimers, which then relax to the correlated triplet pair ((T1T1)) state, indicating the occurrence of SF. Unlike previous studies where the excimer formation inhibited an SF process, the (T1T1)'s of Anti-DPyB and Syn-DPyB are formed through the excimer state. The dissociation of (T1T1)'s to 2T1 in Anti-DPyB is more favorable than in Syn-DPyB. Our results showcase that the molecular configuration of a CLD plays an important role in SF dynamics.

Folding dynamics of cytochrome c using pulse radiolysis.

Pulse radiolysis is a powerful method to realize real-time observation of various redox processes, which induces various structural and functional changes occurring in biological systems. However, its application has been mainly limited to studies of the redox reactions of rather smaller biological systems such as DNA because of an undesired reaction due to various free radicals generated by pulse radiolysis. For application of pulse radiolysis to generate plenty of redox reactions of biological systems, selective redox reactions induced by electron pulses have to be developed. In this study, we report that in the presence of the high concentration of the denaturant, guanidine HCl (GdHCl), the selective reduction of the oxidized cytochrome c (Cyt c) takes place in time scales of a few microseconds by the electron transfer from the guanidine radical that is formed by the fast reaction of e(aq)(-) with GdHCl, consequently leading to folding kinetics of Cyt c. By providing insight into the folding dynamics of Cyt c, we show that the pulse radiolysis technique can be used to track the folding dynamics of various biomolecules in the presence of a denaturant including GdHCl.