Time-resolved Infrared Spectroscopy Research Articles

Effect of isotope substitution on the Fermi resonance and vibrational lifetime of unnatural amino acids modified with IR probe: A 2D-IR and pump-probe study of 4-azido-L-phenyl alanine.

The infrared (IR) probe often suffers from an unexpected complex absorption profile due to the Fermi resonance and short vibrational lifetime, which restricts the application of time-resolved IR spectroscopy to investigate the site-specific structural dynamics of the protein. Researchers have found that isotope substitution to the IR probe not only removes the Fermi resonance but also extends the dynamic observation window with a prolonged vibrational lifetime. This method has been successfully applied to modify the vibrational properties of many IR probes for time-resolved spectroscopy and imaging. In this study, the effect of isotope substitution (15N) on the vibrational properties of the azide stretching band in 4-azido-L-phenylalanine has been investigated using ultrafast pump-probe and 2D-IR spectroscopy. In contrast to the earlier reports, it has been observed that the Fermi resonance remains unchanged even after isotope substitution, and there is very little change in the vibrational relaxation dynamics as well. Anharmonic frequency analysis reveals that the α-N atom of N3 is being shared between the two transitions participating in the Fermi resonance and gets affected similarly due to isotope labeling. Hence, this study unveils the specific circumstance at which the isotope labeling strategy may not be successful in eliminating the Fermi resonance band and explains the molecular origin behind it. This study also suggests definitive approaches on how to overcome the limitations related to the Fermi resonance to extend the development and application of this IR probe for biological research.

A Time-Resolved Spectroscopic Investigation of a Novel BODIPY Copolymer and Its Potential Use as a Photosensitiser for Hydrogen Evolution.

A novel 4,4-difuoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) copolymer with diethynylbenzene has been synthesised, and its ability to act as a photosensitiser for the photocatalytic generation of hydrogen was investigated by time-resolved spectroscopic techniques spanning the ps- to ns-timescales. Both transient absorption and time-resolved infrared spectroscopy were used to probe the excited state dynamics of this photosensitising unit in a variety of solvents. These studies indicated how environmental factors can influence the photophysics of the BODIPY polymer. A homogeneous photocatalytic hydrogen evolution system has been developed using the BODIPY copolymer and cobaloxime which provides hydrogen evolution rates of 319 μmol h−1 g−1 after 24 h of visible irradiation.

Time-Resolved Vibrational Fingerprints for Two Silver Cluster-DNA Fluorophores.

DNA-templated silver clusters are chromophores in which the nucleobases encode the cluster spectra and brightness. We describe the coordination environments of two nearly identical Ag106+ clusters that form with 18-nucleotide strands CCCCA CCCCT CCCX TTTT, with X = guanosine and inosine. For the first time, femtosecond time-resolved infrared (TRIR) spectroscopy with visible excitation and mid-infrared probing is used to correlate the response of nucleobase vibrational modes to electronic excitation of the metal cluster. A rich pattern of transient TRIR peaks in the 1400-1720 cm-1 range decays synchronously with the visible emission. Specific infrared signatures associated with the single guanosine/inosine along with a subset of cytidines, but not the thymidines, are observed. These fingerprints suggest that the network of bonds between a silver cluster adduct and its polydentate DNA ligands can be deciphered to rationally tune the coordination and thus spectra of molecular silver chromophores.

Structural Characterization and Lifetimes of Triple-Stranded Helical Coinage Metal Complexes: Synthesis, Spectroscopy and Quantum Chemical Calculations.

This work reports on a series of polynuclear complexes containing a trinuclear Cu, Ag, or Au core in combination with the fac‐isomer of the metalloligand [Ru(pypzH)3](PF6)2 (pypzH=3‐(pyridin‐2‐yl)pyrazole). These (in case of the Ag and Au containing species) newly synthesized compounds of the general formula [{Ru(pypz)3}2M3](PF6) (2: M=Cu; 3: M=Ag; 4: M=Au) contain triple‐stranded helical structures in which two ruthenium moieties are connected by three N‐M‐N (M=Cu, Ag, Au) bridges. In order to obtain a detailed description of the structure both in the electronic ground and excited states, extensive spectroscopic and quantum chemical calculations are applied. The equilateral coinage metal core triangle in the electronic ground state of 2–4 is distorted in the triplet state. Furthermore, the analyses offer a detailed description of electronic excitations. By using time‐resolved IR spectroscopy from the microsecond down to the nanosecond regime, both the vibrational spectra and the lifetime of the lowest lying electronically excited triplet state can be determined. The lifetimes of these almost only non‐radiative triplet states of 2–4 show an unusual effect in a way that the Au‐containing complex 4 has a lifetime which is by more than a factor of five longer than in case of the Cu complex 2. Thus, the coinage metals have a significant effect on the electronically excited state, which is localized on a pypz ligand coordinated to the Ru atom indicating an unusual cooperative effect between two moieties of the complex.

Folding and Unfolding of the Short Light-Triggered β-Hairpin Peptide AzoChignolin Occurs within 100 ns.

To map the underlying molecular mechanisms of folding dynamics in proteins, light-operated peptides have emerged as promising tools. In this study, we reveal the complete sequence of light-induced structural changes of AzoChignolin, a short β-hairpin peptide containing an azobenzene photoswitch in its loop region. Light-triggered structural changes were monitored by time-resolved IR spectroscopy. Formation and destruction of the hairpin structure is very fast and occurs within 100 ns for AzoChignolin in methanol. Atomistic molecular dynamics simulations using two explicit solvents, methanol and water, revealed the underlying molecular processes and allowed us to gain further insight into the reaction mechanism. Despite its rapid reaction time, hairpin formation in these solvents is not force-driven by the molecular switch but proceeded via formation of interstrand hydrogen bonds and contacts between aromatic residues. Moreover, the combined experimental and theoretical study demonstrates that the solvent (methanol vs water) does not dictate the velocity of β-hairpin formation in the AzoChignolin peptide comprising only a few hydrophobic residues in the strands.

Theoretical Insights into the Excited State Decays of a Donor-Acceptor Dyad: Is the Twisted and Rehybridized Intramolecular Charge-Transfer State Involved?

The twisted intramolecular charge transfer has been proposed for a number of years and widely accepted to explain the excited-state dynamics of organic molecules. Recently, a new state termed as "twisted and rehybridized intramolecular charge transfer" has been proposed to explain the excited-state dynamics of an aniline-triazine electron donor-acceptor dyad with an alkyne spacer based on ultrafast time-resolved spectroscopy. However, the change of the geometries along the excited-state decay pathway remains unknown. In this study, by optimization of the excited-state geometry of the donor-acceptor dyad and potential energy surface scan along the twisting angle, we successfully reproduce the experimentally observed band in time-resolved infrared absorption spectroscopy. Our calculation results demonstrated that the rehybridization process is not involved and only the twisted intramolecular charge transfer state is formed. Moreover, we located a minimum energy conical intersection between the ground and first excited-state of the donor-acceptor dyad, which is easily reached and corresponding to the primary nonradiative decay pathway of the donor-acceptor dyad. The energy of minimum energy conical intersection is solvent-dependent and consistent with the experimentally observed solvent-dependent lifetime of excited state.

Photo-activated CO-release in the amino tungsten Fischer carbene complex, [(CO)5WC(NC4H8)Me], picosecond time resolved infrared spectroscopy, time-dependent density functional theory, and an antimicrobial study

Picosecond time-resolved infrared spectroscopy was used to probe the photo-induced early state dynamics preceding CO loss in the Fischer carbene complex, [(CO)5WC(NC4H8)CH3]. Time-dependent density functional theory calculations were employed to help in understanding the photochemical and photophysical processes leading to CO-loss. Electrochemical initiated CO release was quantified using gas chromatography. The potential of [(CO)5WC(NC4H8)CH3], as an antimicrobial agent under irradiation conditions was studied using a Staphylococcus aureus strain.

Nitro End Groups: Remarkable Vibrational Reporters for Charge Transfer in the Excited States of Oligo(p-phenyleneethynylene)-Bridged Donor–Acceptor Dyads

The D-π-A dyads [(n-Hex)2N(1,4-C6H4)]CC[(1,4-C6H4)NO2] (1) and [(n-Hex)2N(1,4-C6H4)]CC(1,4-C6H4)CC[(1,4-C6H4)NO2] (2) have been studied by ultrafast time-resolved infrared absorption spectroscopy. After excitation into their singlet charge-transfer (1CT) state, a fast decay (ca. 6 ps for 1 and 1 ps for 2) of the initially populated singlet state into a ground state (major pathway) and a longer lived excited state (possibly the triplet state) is observed. The nitro and alkyne groups were used as vibrational reporters to probe the changes induced by the charge-transfer process. For the first time, we confirm experimentally that these changes are consistent with expectations based on the traditional valence-bond representations of the CT states of these push-pull chromophores. An almost identical charge transfer takes place in the two dyads, despite π-bridges of different lengths between the donor and acceptor groups. Complementary DFT calculations support the experimental assignments and have helped clarify the photophysical behavior of 1 and 2.

Time-Resolved Temperature-Jump Infrared Spectroscopy at a High Repetition Rate.

Time-resolved temperature-jump infrared absorption spectroscopy at a 0.5 to 1 kHz repetition rate is presented. A 1 kHz neodymium-doped yttrium aluminum garnet (Nd:YAG) laser pumping an optical parametric oscillator provided >70 µJ, 3.75 µm pump pulses, which delivered a temperature jump via excitation of the O-D stretch of a D2O solution. A 10 kHz train of mid-infrared probe pulses was used to monitor spectral changes following the temperature jump. Calibration with trifluoroacetic acid solution showed that a temperature jump of 10 K lasting for tens of microseconds was achieved, sufficient to observe fast processes in functionally relevant biomolecular mechanisms. Modeling of heating profiles across ≤10 µm path length cells and subsequent cooling dynamics are used to describe the initial <100 ns cooling at the window surface and subsequent, >10 µs cooling dynamics of the bulk solution.

Uranium(VI) Complexes of Glutathione Disulfide Forming in Aqueous Solution.

The interactions between glutathione disulfide, GSSG, the redox partner and dimer of the intracellular detoxification agent glutathione, GSH, and hexavalent uranium, U(VI), were extensively studied by solution NMR (in D2O), complemented by time-resolved laser-induced fluorescence and IR spectroscopies. As expected for the hard Lewis acid U(VI), coordination facilitates by the ligands' O-donor carboxyl groups. However, owing to the adjacent cationic α-amino group, the glutamyl-COO reveal monodentate binding, while the COO of the glycyl residues show bidentate coordination. The log K value for the reaction UO22+ + H3GSSG- → UO2(H3GSSG)+ (pH 3, 0.1 M NaClO4) was determined for the first time, being 4.81 ± 0.08; extrapolation to infinite dilution gave log K⊖ = 5.24 ± 0.08. U(VI) and GSSG form precipitates in the whole pD range studied (2-8), showing least solubility for 4 < pD < 6.5. Thus, particularly GSSG, hereby representing also other peptides and small proteins, affects the mobility of U(VI), strongly depending on the speciation of either component.

Oxidized Derivatives of 5-Methylcytosine Alter the Stability and Dehybridization Dynamics of Duplex DNA.

The naturally occurring nucleobase 5-methylcytosine (mC) and its oxidized derivatives 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxylcytosine (caC) play important roles in epigenetic regulation and, along with cytosine (C), represent nucleobases currently implicated in the active cytosine demethylation pathway. Despite considerable interest in these modified bases, their impact on the thermodynamic stability of double-stranded DNA (dsDNA) remains ambiguous and their influence on hybridization kinetics and dynamics is even less well-understood. To address these unknowns, we employ steady-state and time-resolved infrared spectroscopy to measure the influence of cytosine modification on the thermodynamics and kinetics of hybridization by assessing the impact on local base pairing dynamics, shifts in the stability of the duplex state, and changes to the hybridization transition state. Modification with mC leads to more tightly bound base pairing below the melting transition and stabilizes the duplex relative to canonical DNA, but the free energy barrier to dehybridization at physiological temperature is nevertheless reduced slightly. Both hmC and fC lead to an increase in local base pair fluctuations, a reduction in the cooperativity of duplex melting, and a lowering of the dissociation barrier, but these effects are most pronounced when the 5-position is formylated. The caC nucleobase demonstrates little impact on dsDNA under neutral conditions, but we find that this modification can dynamically switch between C-like and fC-like behavior depending on the protonation state of the 5-position carboxyl group. Our results provide a consistent thermodynamic and kinetic framework with which to describe the modulation of the physical properties of double-stranded DNA containing these modified nucleobases.

Relationship Between Cognitive Dysfunction and Systemic Metabolic Disorders in Elderly: Dementia Might be a Systematic Disease.

Vascular cognitive impairment (VCI) plays an important role in dementia in elderly people, and refers to the contribution of vascular pathology to the entire spectrum of cognitive disorders, ranging from mild cognitive impairment to severe dementia, as well as the pathological spectrum, from 'pure' Alzheimer disease through degrees of vascular comorbidity to 'pure' vascular dementia. In the present study, we investigated the relationship between cognitive dysfunction and systemic metabolic disorders, by employing deep learning (DL). We studied 202 patients (73.4±13.0years), 94.6% of whom were undergoing treatment for lifestyle diseases, and 68.8% of whom had a history of cerebrovascular disorder. We evaluated cognitive dysfunction by performing a Mini Mental State Examination (MMSE). We performed general blood examination, including Complete Blood Count and Basic Metabolic Panel, and measured cerebral blood oxygenation in the prefrontal cortex (PFC) using time-resolved near infrared spectroscopy (TNIRS). We then used deep neural networks to assess the MMSE scores of the subjects based on the TNIRS parameters and the blood examination data, independently. Next, we compared predicted MMSE scores based on the TNIRS and the blood examination. There was a significant positive correlation between the TNIRS parameters and the blood examination data (r=0.6, p<0.01). These observations suggest that cognitive dysfunction in patients with VCI may be caused by combinations of systemic metabolic disorders such as energy and oxygen metabolisms and cerebral circulatory disturbance due to arteriosclerosis resulting from lifestyle-related diseases.

Correction: Time-resolved infra-red spectroscopy reveals competitive water and dinitrogen coordination to a manganese(i) carbonyl complex.

Correction for 'Time-resolved infra-red spectroscopy reveals competitive water and dinitrogen coordination to a manganese(i) carbonyl complex' by Jonathan B. Eastwood et al., Dalton Trans., 2020, DOI: .

Time-resolved infra-red spectroscopy reveals competitive water and dinitrogen coordination to a manganese(i) carbonyl complex.

Time-resolved infra-red (TRIR) spectroscopy has been used to demonstrate that photolysis of [Mn(C^N)(CO)4] (C^N = bis-(4-methoxyphenyl)methanimine) in heptane solution results in ultra-fast CO dissociation and ultimate formation of a rare Mn-containing dinitrogen complex fac-[Mn(C^N)(CO)3(N2)] with a diagnostic stretching mode for a terminal-bound N[triple bond, length as m-dash]N ligand at 2249 cm-1. An isotopic shift to 2174 cm-1 was observed when the reaction was performed under 15N2 and the band was not present when the experiment was undertaken under an atmosphere of argon, reinforcing this assignment. An intermediate solvent complex fac-[Mn(C^N)(CO)3(heptane)] was identified which is formed in less than 2 ps, indicating that CO-release occurs on an ultra-fast timescale. The heptane ligand is labile and is readily displaced by both N2 and water to give fac-[Mn(C^N)(CO)3(N2)] and fac-[Mn(C^N)(CO)3(OH2)] respectively. The fac-[Mn(C^N)(CO)3(heptane)] framework showed a significant affinity for N2, as performing the reaction under air produced significant amounts of fac-[Mn(C^N)(CO)3(N2)]. Kinetic analysis reveals that the substitution of heptane by N2 (k = (1.028 ± 0.004) × 109 mol-1 dm3 s-1), and H2O is competitive on fast (<1 μs) time scales. The binding of water is reversible and, under an atmosphere of N2, some fac-[Mn(C^N)(CO)3(OH2)] converts to fac-[Mn(C^N)(CO)3(N2)].

Photoinduced Terminal Hydride of [FeFe]-Hydrogenase Biomimetic Complexes.

The active site of the [FeFe]-hydrogenase ([FeFe]-H2ase) has a bridging carbonyl ligand and a terminal hydride in the key H-cluster intermediate Hhyd. However, nearly all of the synthetic mimics reported, so far, prefer a hydride bridging the two irons, and only few mimics with a terminal hydride were achieved by tuning the steric effects of bulky diphosphine ligands. Moreover, although intermediates with either a terminal hydride or a protonated bridging thiolate ligand were proposed to exist during protonation processes or hydrogen exchange in the [FeFe]-H2ase mimic, [Fe2(μ-pdt)(μ-H)(CO)4(PMe3)2]+ (1H+), only bridging hydrides were observed by time-resolved IR spectroscopy. In this report, FTIR spectroscopy of 1H+, under CO with longer irradiation time, revealed several new photoinduced species. In addition to the CO loss species, many of the photoinduced products can be assigned to 1H+ with a terminal hydride by comparison of their CO vibrational frequencies with density functional theory calculations.

Uncovering the Early Stages of Domain Melting in Calmodulin with Ultrafast Temperature-Jump Infrared Spectroscopy

The signaling protein calmodulin (CaM) undergoes a well-known change in secondary structure upon binding Ca2+, but the structural plasticity of the Ca2+-free apo state is linked to CaM functionality. Variable temperature studies of apo-CaM indicate two structural transitions at 46 and 58 °C that are assigned to melting of the C- and N-terminal domains, respectively, but the molecular mechanism of domain unfolding is unknown. We report temperature-jump time-resolved infrared (IR) spectroscopy experiments designed to target the first steps in the C-terminal domain melting transition of human apo-CaM. A comparison of the nonequilibrium relaxation of apo-CaM with the more thermodynamically stable holo-CaM, with 4 equiv of Ca2+ bound, shows that domain melting of apo-CaM begins on microsecond time scales with α-helix destabilization. These observations enable the assignment of previously reported dynamics of CaM on hundreds of microsecond time scales to thermally activated melting, producing a complete mechanism for thermal unfolding of CaM.

Investigating the Kinetic Competency of CrHydA1 [FeFe] Hydrogenase Intermediate States via Time-Resolved Infrared Spectroscopy.

Hydrogenases are metalloenzymes that catalyze the reversible oxidation of H2. The [FeFe] hydrogenases are generally biased toward proton reduction and have high activities. Several different catalytic mechanisms have been proposed for the [FeFe] enzymes based on the identification of intermediate states in equilibrium and steady state experiments. Here, we examine the kinetic competency of these intermediate states in the [FeFe] hydrogenase from Chlamydomonas reinhardtii (CrHydA1), using a laser-induced potential jump and time-resolved IR (TRIR) spectroscopy. A CdSe/CdS dot-in-rod (DIR) nanocrystalline semiconductor is employed as the photosensitizer and a redox mediator efficiently transfers electrons to the enzyme. A pulsed laser induces a potential jump, and TRIR spectroscopy is used to follow the population flux through each intermediate state. The results clearly establish the kinetic competency of all intermediate populations examined: Hox, Hred, HredH+, HsredH+, and Hhyd. Additionally, a new short-lived intermediate species with a CO peak at 1896 cm-1 was identified. These results establish a kinetics framework for understanding the catalytic mechanism of [FeFe] hydrogenases.

Kinetics and Mechanism of Intramolecular Electron Transfer in Ru(II)-Re(I) Supramolecular CO2-Reduction Photocatalysts: Effects of Bridging Ligands.

The supramolecular photocatalysts in which a Ru(II) complex as a molecular redox photosensitizer unit and a Re(I) complex as a molecular catalyst unit are connected with a various alkyl or ether chain have attracted attention because they can efficiently photocatalyze CO2 reduction with high durability and high selectivity of CO formation, especially on various solid materials such as semiconductor electrodes and mesoporous organosilica. The intramolecular electron transfer from the one-electron reduced photosensitizer unit to the catalyst unit, which follows excitation of the photosensitizer unit and subsequent reductive quenching of the excited photosensitizer unit by a reductant, is one of the most important processes in the photocatalytic reduction of CO2. We succeeded in determining the rate constants of this intramolecular electron transfer process by using subnanosecond time-resolved IR spectroscopy. The logarithm of rate constants shows a linear relationship with the lengths of the bridging chain in the supramolecular photocatalysts with one bridging alkyl or ether chain. In conformity with the exponential decay of the wave function and the coupling element in the long-distance electron transfer, the apparent decay coefficient factor (β) in the supramolecular photocatalysts with one bridging chain was determined to be 0.74 Å-1. In the supramolecular photocatalyst with two ethylene chains connecting between the photosensitizer and catalyst units, on the other hand, the intramolecular electron transfer rate is much faster than that with only one ethylene chain. These results strongly indicate that the intramolecular electron transfer from the one-electron reduced species of the Ru photosensitizer unit to the Re catalyst unit proceeds by the through-bond mechanism.

Direct Spectroscopic Detection of Key Intermediates and the Turnover Process in Catalytic H2 Formation by a Biomimetic Diiron Catalyst

[FeFe(Cl2 -bdt)(CO)6 ] (1; Cl2 -bdt=3,6-dichlorobenzene-1,2-dithiolate), inspired by the active site of FeFe-hydrogenase, shows a chemically reversible 2 e- reduction at -1.20 V versus the ferrocene/ferrocenium couple. The rigid and aromatic bdt bridging ligand lowers the reduction potential and stabilizes the reduced forms, compared with analogous complexes with aliphatic dithiolates; thus allowing details of the catalytic process to be characterized. Herein, time-resolved IR spectroscopy is used to provide kinetic and structural information on key catalytic intermediates. This includes the doubly reduced, protonated complex 1H- , which has not been previously identified experimentally. In addition, the first direct spectroscopic observation of the turnover process for a molecular H2 evolving catalyst is reported, allowing for straightforward determination of the turnover frequency.

Capturing the Long-Lived Photogenerated Electrons in Au/TiO2 upon UV or Visible Irradiation by Time-Resolved Infrared Spectroscopy

Gold nanoparticle modifications for TiO2 (Au/TiO2) can extend the absorption wavelength from UV to visible (Vis) and enhance the photocatalytic performance, thus fueling increasing attention as an emerging photocatalysis strategy. To explore the plasmon-enhanced photocatalytic mechanism and directly unveil the intrinsic properties of Au/TiO2, the decay kinetics of photoelectrons upon UV (355 nm) or Vis (532 nm) excitation are monitored by means of nanosecond time-resolved infrared spectroscopy, which is a unique tool offering observations without interference of the holes. Under UV irradiation, the longer lifetime of photoelectrons observed in Au/TiO2 compared to that in bare TiO2 provides unambiguous evidence for the enhanced charge separation by AuNPs. Under Vis irradiation, the long-lived (hundreds of microseconds) electrons produced by injection from AuNPs into TiO2 upon plasmon excitation are here detected for the first time. Moreover, the effects of TiO2 phase composition and the amount of AuNPs loa...