Time-resolved Resonance Raman Spectroscopy Research Articles

Structural dynamics of the heme pocket and intersubunit coupling in the dimeric hemoglobin from Scapharca inaequivalvis.

Cooperativity is essential for the proper functioning of numerous proteins by allosteric interactions. Hemoglobin from Scapharca inaequivalvis (HbI) is a homodimeric protein that can serve as a minimal unit for studying cooperativity. We investigated the structural changes in HbI after carbon monoxide dissociation using time-resolved resonance Raman spectroscopy and observed structural rearrangements in the Fe-proximal histidine bond, the position of the heme in the pocket, and the hydrogen bonds between heme and interfacial water upon ligand dissociation. Some of the spectral changes were different from those observed for human adult hemoglobin due to differences in subunit assembly and quaternary changes. The structural rearrangements were similar for the singly and doubly dissociated species but occurred at different rates. The rates of the observed rearrangements indicated that they occurred synchronously with subunit rotation and are influenced by intersubunit coupling, which underlies the positive cooperativity of HbI.

Transient Absorption Spectroscopic Investigation of the Photocyclization-Deprotection Reaction of 3',5'-Dimethoxybenzoin Fluoride.

The 3',5'-dimethoxybenzoin (DMB) system has been widely investigated as a photoremovable protecting group (PRPG) for the elimination of various functional groups and has been applied in many fields. The photolysis of DMB fluoride leads to a highly efficient photocyclization-deprotection reaction, resulting in a high yield of 3',5'-dimethoxybenzofuran (DMBF) in a MeCN solution, while there is a competitive reaction that produces DMB in an aqueous solution. The yield of DMB increased as the volume ratio of water increased. To understand the solvent effect of the photolysis of selected DMB-based compounds, a combination of femtosecond to nanosecond transient absorption spectroscopies (fs-TA and ns-TA), nanosecond time-resolved resonance Raman spectroscopy (ns-TR3) and quantum chemical calculation was employed to study the photophysical and photochemical reaction mechanisms of DMB fluoride in different solutions. Facilitated by the bichromophoric nature of DMB fluoride with electron-donating and -withdrawing chromophores, the cyclized intermediates could be found in a pure MeCN solution. The deprotection of a cyclic biradical intermediate results in the simultaneous formation of DMBF and a cyclic cation species. On the other hand, in aqueous solution, fs-TA experiments revealed that α-keto cations could be observed after excitation directly, which could easily produce the DMB through the addition of a hydroxyl within 8.7 ps. This work provides comprehensive photo-deactivation mechanisms of DMB fluoride in MeCN and aqueous conditions and provides critical insights regarding the biomedical application of DMB-based PRPG compounds.

Cis-Trans Reisomerization Preceding Reprotonation of the Retinal Chromophore Is Common to the Schizorhodopsin Family: A Simple and Rational Mechanism for Inward Proton Pumping.

The creation of unidirectional ion transporters across membranes represents one of the greatest challenges in chemistry. Proton-pumping rhodopsins are composed of seven transmembrane helices with a retinal chromophore bound to a lysine side chain via a Schiff base linkage and provide valuable insights for designing such transporters. What makes these transporters particularly intriguing is the discovery of both outward and inward proton-pumping rhodopsins. Surprisingly, despite sharing identical overall structures and membrane topologies, these proteins facilitate proton transport in opposite directions, implying an underlying rational mechanism that can transport protons in different directions within similar protein structures. In this study, we unraveled this mechanism by examining the chromophore structures of deprotonated intermediates in schizorhodopsins, a recently discovered subfamily of inward proton-pumping rhodopsins, using time-resolved resonance Raman spectroscopy. The photocycle of schizorhodopsins revealed the cis-trans thermal isomerization that precedes reprotonation at the Schiff base of the retinal chromophore. Notably, this order has not been observed in other proton-pumping rhodopsins, but here, it was observed in all seven schizorhodopsins studied across the archaeal domain, strongly suggesting that cis-trans thermal isomerization preceding reprotonation is a universal feature of the schizorhodopsin family. Based on these findings, we propose a structural basis for the remarkable order of events crucial for facilitating inward proton transport. The mechanism underlying inward proton transport by schizorhodopsins is straightforward and rational. The insights obtained from this study hold great promise for the design of transmembrane unidirectional ion transporters.

Twisting and Protonation of Retinal Chromophore Regulate Channel Gating of Channelrhodopsin C1C2.

Channelrhodopsins (ChRs) are light-gated ion channels and central optogenetic tools that can control neuronal activity with high temporal resolution at the single-cell level. Although their application in optogenetics has rapidly progressed, it is unsolved how their channels open and close. ChRs transport ions through a series of interlocking elementary processes that occur over a broad time scale of subpicoseconds to seconds. During these processes, the retinal chromophore functions as a channel regulatory domain and transfers the optical input as local structural changes to the channel operating domain, the helices, leading to channel gating. Thus, the core question on channel gating dynamics is how the retinal chromophore structure changes throughout the photocycle and what rate-limits the kinetics. Here, we investigated the structural changes in the retinal chromophore of canonical ChR, C1C2, in all photointermediates using time-resolved resonance Raman spectroscopy. Moreover, to reveal the rate-limiting factors of the photocycle and channel gating, we measured the kinetic isotope effect of all photoreaction processes using laser flash photolysis and laser patch clamp, respectively. Spectroscopic and electrophysiological results provided the following understanding of the channel gating: the retinal chromophore highly twists upon the retinal Schiff base (RSB) deprotonation, causing the surrounding helices to move and open the channel. The ion-conducting pathway includes the RSB, where inflowing water mediates the proton to the deprotonated RSB. The twisting of the retinal chromophore relaxes upon the RSB reprotonation, which closes the channel. The RSB reprotonation rate-limits the channel closing.

Time-Resolved Spectroscopic Study of a Photoinduced Intramolecular Chloride Exchange Reaction of 3',5'-Dimethoxybenzoin Chloride.

Photoremovable protecting groups are of great importance due to their remote control over the liberation of diverse reactive species temporally and spatially, including biologically active compounds and functional groups. Here, an in-depth investigation on the heterolysis-solvolysis reaction mechanisms of a photoremovable protecting group, 3',5'-dimethoxybenzoin (DMB) chloride, has been accomplished. With the aid of transient absorption and time-resolved resonance Raman spectroscopies, the features of the intermediates that emerged from the photolysis process were directly observed. Elaborate optical and theoretical studies on DMB chloride have suggested a long-lived α-keto cation intermediate (0.9 ms) exists as a key intermediate, unlike the radical intermediates that are typically generated in such photocyclization reactions. After undergoing nucleophilic addition and isomerization, the intermediate species eventually leads to the formation of the final product(s).

Time-resolved spectroscopic mapping of vibrational energy flow in proteins: Understanding thermal diffusion at the nanoscale.

Vibrational energy exchange between various degrees of freedom is critical to barrier-crossing processes in proteins. Hemeproteins are well suited for studying vibrational energy exchange in proteins because the heme group is an efficient photothermal converter. The released energy by heme following photoexcitation shows migration in a protein moiety on a picosecond timescale, which is observed using time-resolved ultraviolet resonance Raman spectroscopy. The anti-Stokes ultraviolet resonance Raman intensity of a tryptophan residue is an excellent probe for the vibrational energy in proteins, allowing the mapping of energy flow with the spatial resolution of a single amino acid residue. This Perspective provides an overview of studies on vibrational energy flow in proteins, including future perspectives for both methodologies and applications.

Ultrafast Time-Resolved Spectroscopic Study on the Photophysical and Photochemical Reaction Mechanisms of ortho-Methylbenzophenone in Selected Solutions.

The photophysical and photochemical reaction pathways of ortho-methylbenzophenone (o-MeBP) in different solutions were investigated by employing femtosecond to nanosecond transient absorption and nanosecond time-resolved resonance Raman spectroscopy methods. In pure acetonitrile, neutral or pH 1 aqueous solutions, o-MeBP exhibit similar excited-state evolutions upon excitation in which o-MeBP will experience excitation to an excited state then undergo intersystem crossing and solvent arrangement followed by 1,5 hydrogen atom transfer processes to form the first singlet excited state, triplet state (n, π*), biradical intermediates, and enol form transients, respectively. However, in a pH 0 acidic solution, the protonation of o-MeBP will form the cation biradical intermediate that facilitates radical coupling to generate a benzocyclobutanol product, which causes a dramatic reduction of the lifetime of the enol form transients. In contrast, in sodium bicarbonate solution, the biradical intermediate may be quenched by the bicarbonate ion to construct a C-C bond and form the carboxylic acid that causes a fast decay of biradical intermediate. These results demonstrate that the photophysical and photochemical reaction pathways of o-MeBP are pH-dependent in aqueous solution which may be very useful for the capture of CO2 capture by photoexcitation of aromatic ketones.

Contact-Mediated Retinal-Opsin Coupling Enables Proton Pumping in Gloeobacter Rhodopsin.

When a chromophore embedded in a photoreceptive protein undergoes a reaction upon photoexcitation, the photoreaction triggers structural changes in the protein moiety that are necessary for the function of the protein. It is thus essential to elucidate the coupling between the chromophore and protein moiety to understand the functional mechanism for photoreceptive proteins, but the mechanism by which this coupling occurs remains poorly understood. Here, we show that nonbonded atomic contacts play an essential role in driving functionally important structural changes following photoisomerization of the chromophore in Gloeobacter rhodopsin (GR). Time-resolved ultraviolet resonance Raman spectroscopy revealed that the substitution of Trp222, which contacts with methyl groups of the retinal chromophore, with a Phe residue reduced the extent of structural change. The proton-pumping activity of the GR mutant was as small as 9% of that of the wild type. Time-resolved visible absorption and resonance Raman spectra showed that the photocycle of the mutant proceeded to the L intermediate following the all-trans to 13-cis photoisomerization step but did not result in the deprotonation of the chromophore. The present results demonstrate that the atomic contacts between the chromophore and the Trp222 side chain induce the structural changes necessary for proton transfer. The requirement for dense atomic packing in a protein structure for the efficient propagation of structural changes through a coupling mechanism is discussed.

Dependence of Vibrational Energy Transfer on Distance in a Four-Helix Bundle Protein: Equidistant Increments with the Periodicity of α Helices.

Vibrational energy exchanges between various degrees of freedom are critical to barrier-crossing processes in proteins. Heme proteins are highly suitable for studies of the vibrational energy exchanges in proteins. The migration of excess energy released by heme in a protein moiety can be observed using time-resolved anti-Stokes ultraviolet resonance Raman spectroscopy. The anti-Stokes resonance Raman intensity of a tryptophan residue is an excellent probe for the excess energy and the spatial resolution of a single amino acid residue can be achieved. Here, we studied dependence of vibrational energy transfer on the distance in cytochrome b562, which is a heme-containing, four-helix bundle protein. The vibrational energy transfer from the heme group to a single tryptophan residue introduced by site-directed mutagenesis was examined for different heme-tryptophan distances by a quasi-constant length with the periodicity of α helices. Taken together with structural data obtained by molecular dynamics simulations, the energy transfer could be well described by the model of classical thermal diffusion, which suggests that continuum media provide a good approximation of the protein interior, of which the atomic packing density is very high.

Time-Resolved Raman Spectroscopy of Polaron Formation in a Polymer Photocatalyst

Polymer photocatalysts are a synthetically diverse class of materials that can be used for the production of solar fuels such as H2, but the underlying mechanisms by which they operate are poorly understood. Time-resolved vibrational spectroscopy provides a powerful structure-specific probe of photogenerated species. Here we report the use of time-resolved resonance Raman (TR3) spectroscopy to study the formation of polaron pairs and electron polarons in one of the most active linear polymer photocatalysts for H2 production, poly(dibenzo[b,d]thiophene sulfone), P10. We identify that polaron-pair formation prior to thermalization of the initially generated excited states is an important pathway for the generation of long-lived photoelectrons.

Resonance Raman Determination of Chromophore Structures of Heliorhodopsin Photointermediates.

Light is utilized as energy or information by rhodopsins (membrane proteins that contain a retinal chromophore). Heliorhodopsins (HeRs) are a new class of rhodopsins with low sequence identity (<15%) to microbial and animal rhodopsins. Their physiological roles remain unknown, although the involvement of a long-lived intermediate in the photocycle suggests a light-sensor function. Characterization of the molecular structures of the intermediates is essential to an understanding of the roles and mechanisms of HeRs. We determined the chromophore structures of the intermediates in HeR 48C12 by time-resolved resonance Raman spectroscopy and observed that the hydrogen bond of the protonated Schiff base strengthened prior to deprotonation. The chromophore is photoisomerized from the all-trans to the 13-cis form and is reisomerized in the transition from the O intermediate to the unphotolyzed state. Our results demonstrate that the chromophore structure evolves similarly to microbial rhodopsins, despite the dissimilarity in amino acid residues surrounding the chromophore.

Time-Resolved Spectroscopic Observation of Diphenylnitrenium Ion Reactions with Guanosine.

Arylnitrenium ions have gained attention for their high reactivity toward guanosine, which in some cases has been linked to carcinogenesis. Although many studies have examined covalent addition reactions between arylnitrenium ions and guanosine, there is still some uncertainty regarding the attack position of nitrenium ions on guanosine and its derivatives. In this paper, we employ nanosecond transient absorption and nanosecond time-resolved resonance Raman spectroscopy to investigate the reaction between the N,N-di(4-bromophenyl) nitrenium ion (2) and guanosine. Our time-resolved spectroscopic results and photochemical product analysis results show that the reaction of guanosine with 2 generates an N7 intermediate that subsequently undergoes rearrangement and deprotonation to produce a C8 adduct. Comparing these results to our previous study between the 2-fluorenylnitrenium ion and guanosine indicates that the structure and properties of arylnitrenium ions are able to influence the reaction pathways and intermediate structures.

Role of atomic contacts in vibrational energy transfer in myoglobin.

Heme proteins are ideal systems to investigate vibrational energy flow at the atomic level. Upon photoexcitation, a large amount of excess vibrational energy is selectively deposited on heme due to extremely fast internal conversion. This excess energy is redistributed to the surrounding protein moiety and then to water. Vibrational energy flow in myoglobin (Mb) was examined using picosecond time-resolved anti-Stokes ultraviolet resonance Raman (UVRR) spectroscopy. We used the Trp residue directly contacting the heme group as a selective probe for vibrationally excited populations. Trp residues were placed at different position close to the heme by site-directed mutagenesis. This technique allows us to monitor the excess energy on residue-to-residue basis. Anti-Stokes UVRR measurements for Mb mutants suggest that the dominant channel for energy transfer in Mb is the pathway through atomic contacts between heme and nearby amino acid residues as well as that between the protein and solvent water. It is found that energy flow through proteins is analogous to collisional exchange processes in solutions.

Does the photoredox reaction affect the photorelease of anthraquinone protected benzaldehyde? A time-resolved spectroscopic study.

In this study, combined time-resolved spectroscopies of femtosecond transient absorption, nanosecond transient absorption, and nanosecond time-resolved resonance Raman spectroscopies as well as DFT calculations were performed to unravel the photorelease reaction mechanism of anthraquinon-2-ylethyl-1,2-diol protected carbonyl compound (Aqe-diol-PPG). It was shown that the triplet state of Aqe-diol-PPG underwent a PCET process to form a xylylene intermediate. After the C-O bond cleavage, a diradical intermediate was generated, which further released the protected benzaldehyde with the by-product Aqe-diol. A comparison work suggested that Aqe-diol underwent a further photoredox reaction in aqueous solutions.

Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy

The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.

Time-Resolved Spectroscopic Study of N,N-Di(4-bromo)nitrenium Ions in Acidic Aqueous Solution.

Nitrenium ions are common reactive intermediates with high activities towards some biological nucleophiles. In this paper, we employed femtosecond transient absorption (fs-TA) and nanosecond transient absorption (ns-TA) as well as nanosecond time-resolved resonance Raman (ns-TR3) spectroscopy and density function theory (DFT) calculations to study the spectroscopic properties of the N(4,4′–dibromodiphenylamino)–2,4,6–trimethylpyridinium BF4− salt (1) in an acidic aqueous solution. Efficient cleavage of the N–N bond (4 ps) to form the N,N–di(4–bromophenyl)nitrenium ion (DN) was also observed in the acidic aqueous solution. As a result, the dication intermediate 4 appears more likely to be produced after abstracting a proton for the nitrenium ion DN in the acid solution first, followed by an electron abstraction to form the radical cation intermediate 3. These new and more extensive time-resolved spectroscopic data will be useful to help to develop an improved understanding of the identity, nature, and properties of nitrenium ions involved in reactions under acidic aqueous conditions.

Distortion and a Strong Hydrogen Bond in the Retinal Chromophore Enable Sodium-Ion Transport by the Sodium-Ion Pump KR2.

We conducted a comprehensive time-resolved resonance Raman spectroscopy study of the structures of the retinal chromophore during the photocycle of the sodium-ion pump Krokinobacter rhodopsin 2 (KR2). We succeeded in determining the structure of the chromophore in the unphotolyzed state and in the K, L, M, and O intermediates, by overcoming the problem that only a small fraction of the M intermediate is accumulated in the KR2 photocycle. The Schiff base in the retinal chromophore forms a strong hydrogen bond in the unphotolyzed state and in the K, L, and O intermediates and is deprotonated in the M intermediate. Formation of this strong hydrogen bond facilitates deprotonation of the Schiff base, which is necessary for the sodium ion to move past the Schiff base. The polyene chain in the chromophore of KR2 is twisted in all of the states of the photocycle: the portion near the Schiff base is largely twisted in the unphotolyzed state and in the K intermediate, whereas the middle portion of the polyene chain becomes largely twisted in the L, M, and O intermediates. During the photocycle, the twisted structure of the polyene chain and strong hydrogen bond at the Schiff base are advantageous for transient relocation of the Schiff base proton. The obtained resonance Raman data clarified the unique structural features of the KR2 chromophore, which are not accessible by other methods.

Time-Resolved Spectroscopic Observation and Characterization of Water-Assisted Photoredox Reactions of Selected Aromatic Carbonyl Compounds.

In recent years, unusual and efficient self-photoredox reactions were detected for selected benzophenone derivatives (BPs) and anthraquinone derivatives (AQs) in aqueous environments by Wan and co-workers, where the carbonyl undergoes reduction to the corresponding alcohol and a side-chain alcohol group undergoes oxidation to the corresponding carbonyl. To unravel the photoredox reaction mechanisms of these types of BPs and AQs in aqueous environments, we have utilized a combination of time-resolved spectroscopy techniques such as femtosecond transient absorption, nanosecond transient absorption, and nanosecond time-resolved resonance Raman spectroscopy to detect and characterize the electronic absorption and vibrational spectra of the intermediates and transient species from the femtosecond to microsecond time region after they are generated in the photoredox reactions. With the assistance of density functional theory calculations to simulate the electronic absorption and Raman spectra, the structural and kinetic information on the key reactive intermediates is described. Furthermore, the reaction pathways were calculated by finding the transition states connecting with the reactant and product complexes to better understand the photoredox reaction mechanism. In this Account, we summarize some of our time-resolved spectroscopic observations and characterization of water-assisted photoredox reactions of selected BPs and AQs. In the strong hydrogen-donor solvent isopropanol, the commonly studied photoreduction reaction for aromatic carbonyls via an intermolecular hydrogen atom tranfer process was observed for BPs and AQs. The photoredox reactions for the investigated BPs and AQs in aqueous environments occur on the triplet excited-state surface. Under moderately acidic aqueous conditions, the photoredox reactions for BPs and AQs are triggered by a proton transfer (PT) pathway. In neutral aqueous solutions, AQs may also undergo proton-coupled electron transfer (PCET) leading to the photoredox reaction, while BPs generate the ketyl radical species. Both BPs and AQs prefer the photohydration reaction in high-proton-concentration aqueous solutions (pH 0). The PT and PCET processes were found to offer more possibilities for the aromatic carbonyl compounds to lead to new photochemical reactions like the unusual photoredox reactions associated with BPs and AQs described here. Clear characterization of the photophysical pathways and the photochemical reactions of representative aromatic carbonyl compounds in aqueous environments not only provides fundamental information to better understand the photochemistry of carbonyl-containing compounds but also will facilitate the development of applications of these systems, like photochemical synthesis, drugs, and photolabile protecting groups. In addition, the importance of water molecules in the photochemical reactions of interest here may also lead to further understanding of how water influences the photochemistry of related carbonyl-containing compounds in aqueous environments.

Time-Resolved Spectroscopic and Density Functional Theory Investigation of the Photogeneration of a Bifunctional Quinone Methide in Neutral and Basic Aqueous Solutions.

Binol quinone methides (BQMs) can be generated from 1,1′-(2,2′-dihydroxy-1,1′-binaphthyl-6,6′-diyl)bis(N,N,N-trimethylmethanamiuium) bromide (BQMP-b) in a 1:1 MeCN:H2O mixed solution via a ground state intramolecular proton transfer (GSIPT), as mentioned in our previously reported studies. Here, the photoreaction of BQMP-b in neutral and basic aqueous solution (pH = 7, 10, 12) was investigated to explore the possible mechanisms and the key intermediates produced in the process of the photoreaction and to examine whether they are different from those in a neutral mild-mixed MeCN:H2O solution. The studies were conducted using femtosecond transient absorption (fs-TA), nanosecond transient absorption (ns-TA), and nanosecond time-resolved resonance Raman spectroscopy (ns-TR3) in conjunction with results from density functional theory (DFT) computations. The results showed that BQMP-b was deprotonated initially and produced BQMs species more effectively through an E1bc elimination reaction in a strong basic aqueous condition (pH = 12), which differed from the reaction pathway that took place in the solution with pH = 7 or 10. A related single naphthol ring molecule 1-(6-hydroxynaphthalen-2-yl)-N,N,N-trimethylmethanaminium bromide (QMP-b) that did not contain a second naphthol ring was also investigated. The related reaction mechanisms are elucidated in this work, and it is briefly discussed how the mechanisms vary as a function of aqueous solution pH conditions.

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.