Genetic Code Expansion: Recent Developments and Emerging Applications

The concept of genetic code expansion (GCE) has revolutionized the field of chemical and synthetic biology, enabling the site-specific incorporation of noncanonical amino acids (ncAAs) into proteins, thus opening new avenues in research and applications across biology and medicine. In this review, we cover the principles of GCE, including the optimization of the aminoacyl-tRNA synthetase (aaRS)/tRNA system and the advancements in translation system engineering. Notable developments include the refinement of aaRS/tRNA pairs, enhancements in screening methods, and the biosynthesis of noncanonical amino acids. The applications of GCE technology span from synthetic biology, where it facilitates gene expression regulation and protein engineering, to medicine, with promising approaches in drug development, vaccine production, and gene editing. The review concludes with a perspective on the future of GCE, underscoring its potential to further expand the toolkit of biology and medicine. Through this comprehensive review, we aim to provide a detailed overview of the current state of GCE technology, its challenges, opportunities, and the frontier it represents in the expansion of the genetic code for novel biological research and therapeutic applications.

Unraveling the excited-state vibrational cooling dynamics of chlorophyll-a using femtosecond broadband fluorescence spectroscopy

Understanding the dynamics of excited-state vibrational energy relaxation in photosynthetic pigments is crucial for elucidating the mechanisms underlying energy transfer processes in light-harvesting complexes. Utilizing advanced femtosecond broadband transient fluorescence (TF) spectroscopy, we explored the excited-state vibrational dynamics of Chlorophyll-a (Chl-a) both in solution and within the light-harvesting complex II (LHCII). We discovered a vibrational cooling (VC) process occurring over ∼6 ps in Chl-a in ethanol solution following Soret band excitation, marked by a notable ultrafast TF blueshift and spectral narrowing. This VC process, crucial for regulating the vibronic lifetimes, was further elucidated through the direct observation of the population dynamics of higher vibrational states within the Qy electronic state. Notably, Chl-a within LHCII demonstrated significantly faster VC dynamics, unfolding within a few hundred femtoseconds and aligning with the ultrafast energy transfer processes observed within the complex. Our findings shed light on the complex interaction between electronic and vibrational states in photosynthetic pigments, underscoring the pivotal role of vibrational dynamics in enabling efficient energy transfer within light-harvesting complexes.

Nickel(II) Analogues of Phosphorescent Platinum(II) Complexes with Picosecond Excited-State Decay

Square-planar NiII complexes are interesting as cheaper and more sustainable alternatives to PtII luminophores widely used in lighting and photocatalysis. We investigated the excited-state behavior of two NiII complexes, which are isostructural with two luminescent PtII complexes. The initially excited singlet metal-to-ligand charge transfer (1 MLCT) excited states in the NiII complexes decay to metal-centered (3 MC) excited states within less than 1 picosecond, followed by non-radiative relaxation of the 3 MC states to the electronic ground state within 9-21 ps. This contrasts with the population of an emissive triplet ligand-centered (3 LC) excited state upon excitation of the PtII analogues. Structural distortions of the NiII complexes are responsible for this discrepant behavior and lead to dark 3 MC states far lower in energy than the luminescent 3 LC states of PtII compounds. Our findings suggest that if these structural distortions could be restricted by more rigid coordination environments and stronger ligand fields, the excited-state relaxation in four-coordinate NiII complexes could be decelerated such that luminescent 3 LC or 3 MLCT excited states become accessible. These insights are relevant to make NiII fit for photophysical and photochemical applications that relied on PtII until now.

Primary Photophysics of Nicotinamide Chromophores in Their Oxidized and Reduced Forms

Nicotinamide adenine dinucleotide (NADH) is an important enzyme cofactor with emissive properties that allow it to be used in fluorescence microscopies to study cell metabolism. Its oxidized form NAD+, on the other hand, is considered to produce negligible fluorescence. In this contribution, we describe the photophysics of the isolated nicotinamidic system in both its reduced and oxidized states. This was achieved through the study of model molecules that do not carry the adenine nucleotide since its absorbance would overlap with the absorption spectrum of the nicotinamidic chromophores. We studied three model molecules: nicotinamide (niacinamide, an oxidized form without nitrogen substitution), the oxidized chromophore 1-benzyl-3-carbamoyl-pyridinium bromide (NBzOx), and its reduced form 1-benzyl-1,4-dihydronicotinamide (NBz). For a full understanding of the dynamics, we performed both femtosecond-resolved emission and transient absorption experiments. The oxidized systems, nicotinamide and NBzOx, have similar photophysics, where the originally excited bright state decays on an ultrafast timescale of less than 400 fs. The depopulation of this state is followed by excited-state positive absorption signals, which evolve in two timescales: the first one is from 1 to a few picoseconds and is followed by a second decaying component of 480 ps for nicotinamide in water and of 80-90 ps for nicotinamide in methanol and NBzOx in aqueous solution. The long decay times are assigned as the S1 lifetimes populated from the original higher-lying bright singlet, where this state is nonemissive but can be detected by transient absorption. While for NBzOx in aqueous solution and for nicotinamide in methanol, the S1 signal decays to the solvent-only level, for the aqueous solutions of nicotinamide, a small transient absorption signal remains after the 480 ps decay. This residual signal was assigned to a small population of triplet states formed during the slower S1 decay for nicotinamide in water. The experimental results were complemented by XMS-CASPT2 calculations, which reveal that in the oxidized forms, the rapid evolution of the initial π-π* state is due to a direct crossing with lower-energy dark n-π* singlet states. This coincides with the experimental observation of long-lived nonemissive states (80 to 480 ps depending on the system). On the other hand, the reduced model compound NBz has a long-lived emissive π-π* S1 state, which decays with a 510 ps time constant, similarly to the parent compound NADH. This is consistent with the XMS-CASPT2 calculations, which show that for the reduced chromophore, the dark states lie at higher energies than the bright π-π* S1 state.

Understanding Carotenoid Dynamics via the Vibronic Energy Relaxation Approach

Carotenoids are an integral part of natural photosynthetic complexes, with tasks ranging from light harvesting to photoprotection. Their underlying energy deactivation network of optically dark and bright excited states is extremely efficient: after excitation of light with up to 2.5 eV of photon energy, the system relaxes back to ground state on a time scale of a few picoseconds. In this article, we summarize how a model based on the vibrational energy relaxation approach (VERA) explains the main characteristics of relaxation dynamics after one-photon excitation with special emphasis on the so-called S* state. Lineshapes after two-photon excitation are beyond the current model of VERA. We outline this future line of research in our article. In terms of experimental method development, we discuss which techniques are needed to better describe energy dissipation effects in carotenoids and within the first solvation shell.

Photocycle of point defects in highly- and weakly-germanium doped silica revealed by transient absorption measurements with femtosecond tunable pump

We report pump-probe transient absorption measurements addressing the photocycle of the Germanium lone pair center (GLPC) point defect with an unprecedented time resolution. The GLPC is a model point defect with a simple and well-understood electronic structure, highly relevant for several applications. Therefore, a full explanation of its photocycle is fundamental to understand the relaxation mechanisms of such molecular-like systems in solid state. The experiment, carried out exciting the sample resonantly with the ultraviolet (UV) GLPC absorption band peaked at 5.1 eV, gave us the possibility to follow the defect excitation-relaxation dynamics from the femto-picosecond to the nanosecond timescale in the UV–visible range. Moreover, the transient absorption signal was studied as a function of the excitation photon energy and comparative experiments were conducted on highly- and weakly-germanium doped silica glasses. The results offer a comprehensive picture of the relaxation dynamics of GLPC and allow observing the interplay between electronic transitions localized on the defect and those related to bandgap transitions, providing a clear evidence that the role of dopant high concentration is not negligible in the earliest dynamics.

The excited-state dynamics of the radical anions of cyanoanthracenes

The radical anion of 9,10-dicyanoanthracene (DCA) has been suggested to be a promising chromophore for photoredox chemistry, due to its nanosecond excited-state lifetime determined from indirect measurements. Here, we investigate the excited-state dynamics of the radical anion of three cyanoanthracenes, including DCA˙-, produced by photoinduced electron transfer in liquid using both pump-probe and pump-pump probe transient electronic absorption spectroscopy. All three excited radical ions are characterised by a 3-5 ps lifetime, due to efficient non-radiative deactivation to the ground state. The decay pathway most probably involves D1/D0 conical intersection(s), whose presence is favoured by the enhanced flexibility of the radical anions relative to their neutral counterparts. The origin of the discrepancy with the nanosecond lifetime of DCA˙-* reported previously is discussed. These very short lifetimes limit, but do not preclude, photochemical applications of the cyanoanthracene anions.

Recent Advances in Fluorescence Imaging by Genetically Encoded Non-canonical Amino Acids

Technical innovations in protein labeling with a fluorophore at the specific residue have played a significant role in studying protein dynamics. The genetic code expansion (GCE) strategy enabled the precise installation of fluorophores at the tailored site of proteins in live cells with minimal perturbation of native functions. Considerable advances have been achieved over the past decades in fluorescent imaging using GCE strategies along with bioorthogonal chemistries. In this review, we discuss advances in the GCE-based strategies to site-specifically introduce fluorophore at a defined position of the protein and their bio-imaging applications.

Two-dimensional ultrafast transient absorption spectrograph covering deep-ultraviolet to visible spectral region optimized for biomolecules

We report on the implementation of a multi-kHz single-shot referenced non-coherent two-dimensional UV spectrograph based on conventional pump-probe geometry. It has the capability to cover a broad spectral region in excitation from 270-to-380 nm and in the detection from 270-to-390 nm and 320-to-720 nm. Other setups features are: an unprecedented time resolution of 33 fs (standard deviation); signals are photometrically corrected; a single-shot noise of <1 mOD. It has the capability to operate with sample volumes as small as few μl which is an accomplishment in studying biological or biomimetic systems. To show its performances and potentials, we report two preliminary studies on the photophysics of phenanthrenes hosted in a multichromophoric antenna system and of aromatic amino acids in a blue-copper azurin.

Enhancing the analysis of disorder in X-ray absorption spectra: application of deep neural networks to T-jump-X-ray probe experiments

Many chemical and biological reactions, including ligand exchange processes, require thermal energy for the reactants to overcome a transition barrier and reach the product state. Temperature-jump (T-jump) spectroscopy uses a near-infrared (NIR) pulse to rapidly heat a sample, offering an approach for triggering these processes and directly accessing thermally-activated pathways. However, thermal activation inherently increases the disorder of the system under study and, as a consequence, can make quantitative interpretations of structural changes challenging. In this Article, we optimise a deep neural network (DNN) for the instantaneous prediction of Co K-edge X-ray absorption near-edge structure (XANES) spectra. We apply our DNN to analyse T-jump pump/X-ray probe data pertaining to the ligand exchange processes and solvation dynamics of Co2+ in chlorinated aqueous solution. Our analysis is greatly facilitated by machine learning, as our DNN is able to predict quickly and cost-effectively the XANES spectra of thousands of geometric configurations sampled from ab initio molecular dynamics (MD) using nothing more than the local geometric environment around the X-ray absorption site. We identify directly the structural changes following the T-jump, which are dominated by sample heating and a commensurate increase in the Debye-Waller factor.

Direct Observation of Different One- and Two-Photon Fluorescent States in a Pyrrolo[3,2-b]pyrrole Fluorophore

Two-photon fluorophores are frequently employed to obtain superior spatial resolution in optical microscopy applications. To guide the rational design of these molecules, a detailed understanding of their excited-state deactivation pathways after two-photon excitation is beneficial, especially to assess the often-assumed presumption that the one- and two-photon excited-state dynamics are similar after excitation. Here, we showcase the breakdown of this assumption for one- and two-photon excitation of a centrosymmetric pyrrolo[3,2-b]pyrrole chromophore by combining time-resolved fluorescence and broadband femtosecond transient absorption spectroscopy. Compared to one-photon excitation, where radiative decay dominates the photodynamics, two-photon excitation leads to dynamics arising from increased nonradiative decay pathways. These different photodynamics are manifest to different quantum yields, thus highlighting the types of time-resolved studies described here to be valuable guideposts in the design of two-photon fluorophores for imaging applications.

Understanding and Designing Thermally Activated Delayed Fluorescence Emitters: Beyond the Energy Gap Approximation

In this article recent progress in the development of molecules exhibiting Thermally Activated Delayed Fluorescence (TADF) is discussed with a particular focus upon their application as emitters in highly efficient organic light emitting diodes (OLEDs). The key aspects controlling the desirable functional properties, e. g. fast intersystem crossing, high radiative rate and unity quantum yield, are introduced with a particular focus upon the competition between the key requirements needed to achieve high performance OLEDs. The design rules required for organic and metal organic materials are discussed, and the correlation between them outlined. Recent progress towards understanding the influence of the interaction between a molecule and its environment are explained as is the role of the mechanism for excited state formation in OLEDs. Finally, all of these aspects are combined to discuss the ability to implement high level design rules for achieving higher quality materials for commercial applications. This article highlights the significant progress that has been made in recent years, but also outlines the significant challenges which persist to achieve a full understanding of the TADF mechanism and improve the stability and performance of these materials.

A multi-scale time-resolved study of photoactivated dynamics in 5-benzyl uracil, a model for DNA/protein interactions

We combine fluorescence up-conversion and time correlated single photon counting experiments to investigate the 5-benzyl uracil excited state dynamics in methanol from 100 fs up to several ns. This molecule has been proposed as a model for DNA/protein interactions. Our results show emission bands at about 310 and 350 nm that exhibit bi-exponential sub-ps decays. Calculations, including solvent effects by a mixed discrete-continuum model, indicate that the Franck Condon region is characterized by significant coupling between the excited states of the benzyl and the uracil moieties, mirrored by the short-lived emission at 310 nm. Two main ground state recovery pathways are identified, both contributing to the 350 nm emission. The first 'photophysical' decay path involves a ππ* excited state localized on the uracil and is connected to the ground electronic state by an easily accessible crossing with S0, accounting for the short lifetime component. Simulations indicate that a possible second pathway is characterized by exciplex formation, with partial benzene → uracil charge transfer character, that may lead instead to photocyclization. The relevance of our results is discussed in view of the photoactivated dynamics of DNA/protein complexes, with implications on their interaction mechanisms.

Mapping of Wave Packet Dynamics at Conical Intersections by Time- and Frequency-Resolved Fluorescence Spectroscopy: A Computational Study

Monitoring of wave packet dynamics at conical intersections by time- and frequency-resolved fluorescence spectroscopy has been investigated theoretically for a three-state two-mode model of a conical intersection coupled to a dissipative environment. The ideal and the actually measurable time- and frequency-gated fluorescence spectra are accurately and efficiently simulated by combining the hierarchy equations-of-motion method for dissipative quantum dynamics with the methodology of the equation-of-motion phase-matching approach for the calculation of spectroscopic signals. It is shown that time- and frequency-resolved fluorescence spectra reveal essential aspects of the wave packet dynamics at conical intersections and the effects of environment-induced dissipation. The results of the present work indicate that fluorescence up-conversion spectroscopy with femtosecond time resolution is an efficient tool for the characterization of ultrafast dynamics at conical intersections.

Ground-State Structural Disorder and Excited-State Symmetry Breaking in a Quadrupolar Molecule

The influence of torsional disorder around the ethynyl π-bridges of a linear D-π-A-π-D molecule on the nature of its S₁ excited state was investigated using ultrafast time-resolved infrared spectroscopy. By tuning the pump wavelength throughout the S₁ ← S₀ absorption band, subpopulations with different extents of asymmetry could be excited. In nonpolar solvents, the equilibrated S₁ state is symmetric and quadrupolar independently of the initial degree of distortion. Photoexcitation of distorted molecules is followed by planarization and symmetrization of the S₁ state. Excited-state symmetry breaking is only observed in polar environments, where the equilibrated S₁ state has a strong dipolar character. However, neither the extent nor the rate of symmetry breaking are enhanced in an initially distorted molecule. They are only determined by the polarity and the dynamic properties of the solvent.

Picosecond Switchable Azo Dyes

Azo dyes that combine electron-withdrawing thiazole/benzothiazole heterocycles and electron-donating amino groups within the very same covalent skeleton exhibit relaxation times for their thermal isomerization kinetics within milli- and microsecond timescales at room temperature. Notably, the thermal back reaction of the corresponding benzothiazolium and thiazolium salts occurred much faster, within the picosecond temporal domain. In fact, these new light-sensitive platforms are the first molecular azo derivatives capable of reversible switching between their trans and cis isomers in a subnanosecond timescale under ambient conditions. In addition, theoretical calculations revealed very low activation energies for the isomerization process, in accordance with the fast subnanosecond kinetics that were observed experimentally.

The full dynamics of energy relaxation in large organic molecules: from photo-excitation to solvent heating

In some molecular systems, such as nucleobases, polyenes or sunscreens, substantial amounts of photo-excitation energy are dissipated on a sub-picosecond time scale. Where does this energy go or among which degrees of freedom it is being distributed at such early times?

In some molecular systems, such as nucleobases, polyenes or the active ingredients of sunscreens, substantial amounts of photo-excitation energy are dissipated on a sub-picosecond time scale, raising questions such as: where does this energy go or among which degrees of freedom it is being distributed at such early times? Here we use transient absorption spectroscopy to track excitation energy dispersing from the optically accessible vibronic subsystem into the remaining vibrational subsystem of the solute and solvent. Monitoring the flow of energy during vibrational redistribution enables quantification of local molecular heating. Subsequent heat dissipation away from the solute molecule is characterized by classical thermodynamics and molecular dynamics simulations. Hence, we present a holistic approach that tracks the internal temperature and vibronic distribution from the act of photo-excitation to the restoration of the global equilibrium. Within this framework internal vibrational redistribution and vibrational cooling are emergent phenomena. We demonstrate the validity of the framework by examining a highly controversial example, carotenoids. We show that correctly accounting for the local temperature unambiguously explains their energetically and temporally congested spectral dynamics without the ad hoc postulation of additional ‘dark’ states. An immediate further application of this approach would be to monitor the excitation and thermal dynamics of pigment–protein systems.

Ultrafast dynamics in polycyclic aromatic hydrocarbons: the key case of conical intersections at higher excited states and their role in the photophysics of phenanthrene monomer

Proper interpretation of phenanthrene's and similar PAHs’ photocycle relies on two higher excited state relaxations due to the simultaneous presence of non-adiabatic and adiabatic transitions.

Vibrational coherence transfer in the ultrafast intersystem crossing of a diplatinum complex in solution

We investigate the ultrafast transient absorption response of tetrakis(μ-pyrophosphito)diplatinate(II), [Pt₂(μ-P₂O₅H₂)₄]^4- [hereafter abbreviated Pt(pop)], in acetonitrile upon excitation of its lowest singlet ¹A_2u state. Compared with previously reported solvents [van der Veen RM, Cannizzo A, van Mourik F, Vlček A, Jr, Chergui M (2011) J Am Chem Soc 133:305-315], a significant shortening of the intersystem crossing (ISC) time (<1 ps) from the lowest singlet to the lowest triplet state is found, allowing for a transfer of vibrational coherence, observed in the course of an ISC in a polyatomic molecule in solution. Density functional theory (DFT) quantum mechanical/molecular mechanical (QM/MM) simulations of Pt(pop) in acetonitrile and ethanol show that high-lying, mostly triplet, states are strongly mixed and shifted to lower energies due to interactions with the solvent, providing an intermediate state (or manifold of states) for the ISC. This suggests that the larger the solvation energies of the intermediate state(s), the shorter the ISC time. Because the latter is smaller than the pure dephasing time of the vibrational wave packet, coherence is conserved during the spin transition. These results underscore the crucial role of the solvent in directing pathways of intramolecular energy flow.

Influence of the hydrogen-bond interactions on the excited-state dynamics of a push–pull azobenzene dye: the case of Methyl Orange

H-bonding with the solvent affects significantly the photoisomerisation of Methyl Orange.

Optical transient absorption experiments reveal the failure of formal kinetics in diffusion assisted electron transfer reactions

The charge separation yield is shown to be strongly influenced by the distance dependence of the reactivity, viscosity and concentration and cannot be disentangled from the preceding events.

Observing ground state vibrational coherence and excited state relaxation dynamics of a cyanine dye in pure solvents

Using a degenerate pump probe technique at 800 nm, Ground State Vibrational Coherence (GSVC) of a cyanine dye (IR780) is explored in various solvents.

Thousandfold Enhancement of Photoreduction Lifetime in Re(bpy)(CO)3 via Spin-Dependent Electron Transfer from a Perylenediimide Radical Anion Donor

Spin-dependent intramolecular electron transfer is revealed in the Re^I(CO)₃(py)(bpy-Ph)-perylenediimide radical anion (Re^I-bpy-PDI^-•) dyad, a prototype model system for artificial photosynthesis. Quantum chemical calculations and ultrafast transient absorption spectroscopy experiments demonstrate that selective photoexcitation of Re^I-bpy results in electron transfer from PDI^-• to Re^I-bpy, forming two distinct charge-shifted states. One is an overall doublet whose return to the ground state is spin-allowed. The other, high-spin quartet state, persists for 67 ns due to spin-forbidden back-electron transfer, constituting a more than thousandfold lifetime improvement compared to the low-spin state. Exploiting this spin dependency holds promise for artificial photosynthetic systems requiring long-lived reduced states to perform multi-electron chemistry.

Direct local solvent probing by transient infrared spectroscopy reveals the mechanism of hydrogen-bond induced nonradiative deactivation

The hydrogen-bond induced quenching of an excited chromophore is visualised by probing O–H vibrations of the interacting solvent molecules.

The fluorescence quenching of organic dyes via H-bonding interactions is a well-known phenomenon. However, the mechanism of this Hydrogen-Bond Induced Nonradiative Deactivation (HBIND) is not understood. Insight into this process is obtained by probing in the infrared the O–H stretching vibration of the solvent after electronic excitation of a dye with H-bond accepting cyano groups. The fluorescence lifetime of this dye was previously found to decrease from 1.5 ns to 110 ps when going from an aprotic solvent to the strongly protic hexafluoroisopropanol (HFP). Prompt strengthening of the H-bond with the dye was identified by the presence of a broad positive O–H band of HFP, located at lower frequency than the O–H band of the pure solvent. Further strengthening occurs within a few picoseconds before the excited H-bonded complex decays to the ground state in 110 ps. The latter process is accompanied by the dissipation of energy from the dye to the solvent and the rise of a characteristic hot solvent band in the transient spectrum. Polarization-resolved measurements evidence a collinear alignment of the nitrile and hydroxyl groups in the H-bonded complex, which persists during the whole excited-state lifetime. Measurements in other fluorinated alcohols and in chloroform/HFP mixtures reveal that the HBIND efficiency depends not only on the strength of the H-bond interactions between the dye and the solvent but also on the ability of the solvent to form an extended H-bond network. The HBIND process can be viewed as an enhanced internal conversion of an excited complex consisting of the dye molecule connected to a large H-bond network.

Tracking Ultrafast Vibrational Cooling during Excited-State Proton Transfer Reaction with Anti-Stokes and Stokes Femtosecond Stimulated Raman Spectroscopy

Energy dissipation following photoexcitation is foundational to photophysics and chemistry. Consequently, understanding such processes on molecular time scales holds paramount importance. Femtosecond stimulated Raman spectroscopy (FSRS) has been used to study the molecular structure-function relationships but usually on the Stokes side. Here, we perform both Stokes and anti-Stokes FSRS to track energy dissipation and excited-state proton transfer (ESPT) for the photoacid pyranine in aqueous solution. We reveal biphasic vibrational cooling on fs-ps time scales during ESPT. Characteristic low-frequency motions (<800 cm^-1) exhibit initial energy dissipation (∼2 ps) that correlates with functional events of forming contact ion pairs via H-bonds between photoacid and water, which lengthens to ∼9 ps in methanol where ESPT is inhibited. The interplay between photoinduced dissipative and reactive channels is implied. Thermal cooling to bulk solvent occurs on the ∼50 ps time scale. These results demonstrate the combined Stokes and anti-Stokes FSRS as a powerful toolset to elucidate structural dynamics.

Trypanocidal Activity of 2,5-Diphenyloxazoles Isolated from the Roots of Oxytropis lanata

Eleven 2,5-diphenyloxazole derivatives (1-11), together with six known isoflavonoid derivatives, were isolated from the roots of Oxytropis lanata. The 2,5-diphenyloxazole (1) obtained proved to be identical to a standard sample used as a scintillator and liquid laser dye. The other oxazole derivatives isolated were found to have one to four hydroxy and/or O-methyl groups in their phenyl rings. Seven of the oxazole derivatives obtained are new (3-9). The inhibitory activity of the isolated compounds was evaluated against Trypanosoma congolense, the causative agent of African trypanosomosis in animals. Oxazoles with di- and trihydroxy groups showed trypanocidal activity, and 2-(2',3'-dihydroxyphenyl)-5-(2″-hydroxyphenyl)oxazole (4) exhibited the most potent inhibitory activity (IC₅₀ 1.0 μM).

Evolution of Nonmirror Image Fluorescence Spectra in Conjugated Polymers and Oligomers

The nonmirror image relationship between absorption and fluorescence spectra of conjugated polymers contrasts with most organic chromophores and is widely considered a signature of interchromopohore energy funneling. We apply broad-band ultrafast fluorescence spectroscopy to resolve the evolution of fluorescence spectra for dilute solutions of conjugated oligothiophenes, where no energy transfer is possible. Fluorescence spectra evolve from a mirror image of absorption, which lacks vibronic structure, toward a spectrally narrower and vibronically structured species on the hundreds of femtosecond to early picosecond time scale. Our analysis of this fluorescence spectral evolution shows that a broad distribution of torsional conformers is driven to rapidly planarize in the excited state, including in solid films, which is supported by Raman spectroscopy and quantum chemical modeling. Our data have important implications for understanding different energy-transfer regimes that are delineated by structural relaxation.

Femtosecond broadband fluorescence upconversion spectroscopy: Spectral coverage versus efficiency

Sum frequency mixing of fluorescence and ∼1300 nm gate pulses, in a thin β-barium borate crystal and non-collinear type II geometry, is quantified as part of a femtosecond fluorimeter [X.-X. Zhang et al., Rev. Sci. Instrum. 82, 063108 (2011)]. For a series of fixed phasematching angles, the upconversion efficiency is measured depending on fluorescence wavelength. Two useful orientations of the crystal are related by rotation around the surface normal. Orientation A has higher efficiency (factor ∼3) compared to B at the cost of some loss of spectral coverage for a given crystal angle. It should be used when subtle changes of an otherwise stationary emission band are to be monitored. With orientation B, the fluorescence range λF > 420-750 nm is covered with a single setting of the crystal and less gate scatter around time zero. The accuracy of determining an instantaneous emission band shape is demonstrated by comparing results from two laboratories.

Micellar phase boundaries under the influence of ethyl alcohol

The Compton spectrum quenching technique is used to monitor the effect of ethyl alcohol (EtOH) additions on phase boundaries in two systems. In toluenic solutions of the nonionic surfactant, Triton X-100, EtOH shifts the boundary separating the first clear phase from the first turbid phase to higher water:surfactant ratios. In a commonly used scintillant, Ultima Gold AB, the critical micelle concentration is not shifted. The molecular interactions behind the observations and implications for liquid scintillation counting are discussed.

Ultrafast Electron Transfer in Complexes of Doxorubicin with Human Telomeric G-Quadruplexes and GC Duplexes Probed by Femtosecond Fluorescence Spectroscopy

Doxorubicin (DOX) is a natural anthracycline widely used in chemotherapy; its combined application as a chemotherapeutic and photodynamic agent has been recently proposed. In this context, understanding the photoinduced properties of DOX complexes with nucleic acids is crucial. Herein, the study of photoinduced electron transfer in DOX-DNA complexes by femtosecond fluorescence spectroscopy is reported. The behaviour of complexes with two model DNA structures, a G-quadruplex (G4) formed by the human telomeric sequence (Tel21) and a d(GC) duplex, is compared. The DOX affinity for these two sequences is similar. Although both 1:1 and 2:1 stoichiometries have been reported for DOX-G4 complexes, only 1:1 complexes form with the duplex. The steady-state absorption indicates a strong binding interaction with the duplex due to drug intercalation between the GC base pairs. In contrast, the interaction of DOX with Tel21 is much weaker and arises from drug binding on the G4 external faces at two independent binding sites. As observed for DOX-d(GC) complexes, fluorescence of the drug in the first binding site of Tel21 exhibits decays within a few picoseconds following a biphasic pattern; this is attributed to the existence of two drug conformations. The fluorescence of the drug in the second binding site of Tel21 shows slower decays within 150 ps. These timescales are consistent with electron transfer from the guanines to the excited drug, as favoured by the lower oxidation potential of the stacked guanines of G4 with respect to those in the duplex.

Novel luminescent β-ketoimine derivative of 2,1,3-benzothiadiazole: synthesis, complexation with Zn(ii) and photophysical properties in comparison with related compounds

2,1,3-Benzothiadiazoles and their Zn complexes show fluorescence in different wavelength regions, one of the complexes reveals white emission.

Characterization of dimethylsulfoxide/glycerol mixtures: a binary solvent system for the study of “friction-dependent” chemical reactivity

The properties of binary mixtures of dimethylsulfoxide and glycerol, measured using several techniques, are reported.

Ligand-centred fluorescence and electronic relaxation cascade at vibrational time scales in transition-metal complexes

Using femtosecond-resolved photoluminescence up-conversion, we report the observation of the fluorescence of the high-lying ligand-centered (LC) electronic state upon 266 nm excitation of an iridium complex, Ir(ppy)3, with a lifetime of 70 ± 10 fs. It is accompanied by a simultaneous emission of all lower-lying electronic states, except the lowest triplet metal-to-ligand charge-transfer ((3)MLCT) state that shows a rise on the same time scale. Thus, we observe the departure, the intermediate steps, and the arrival of the relaxation cascade spanning ∼1.6 eV from the (1)LC state to the lowest (3)MLCT state, which then yields the long-lived luminescence of the molecule. This represents the first measurement of the total relaxation time over an entire cascade of electronic states in a polyatomic molecule. We find that the relaxation cascade proceeds in ≤10 fs, which is faster than some of the highest-frequency modes of the system. We invoke the participation of the latter modes in conical intersections and their overdamping to low-frequency intramolecular modes. On the basis of literature, we also conclude that this behavior is not specific to transition-metal complexes but also applies to organic molecules.

Site-specific incorporation of a fluorescent terphenyl unnatural amino acid

The site-specific incorporation of unnatural amino acids into proteins has a wide range of biological implications. Of particular interest is the incorporation of fluorescent probes as a mechanism to track protein function, transport, and folding. Thus, the development of a novel system for the incorporation of new fluorescent unnatural amino acids has significant utility. Specifically, we have elucidated an aminoacyl-tRNA synthetase capable of recognizing a terphenyl UAA derivative, and charging a cognate tRNA with this amino acid for protein incorporation. Moreover, we have successfully incorporated this fluorescent UAA into GFP at several key residues, demonstrating a novel means to modulate fluorescence within the protein.

Ultrafast photophysics of transition metal complexes

The properties of transition metal complexes are interesting not only for their potential applications in solar energy conversion, OLEDs, molecular electronics, biology, photochemistry, etc. but also for their fascinating photophysical properties that call for a rethinking of fundamental concepts. With the advent of ultrafast spectroscopy over 25 years ago and, more particularly, with improvements in the past 10-15 years, a new area of study was opened that has led to insightful observations of the intramolecular relaxation processes such as internal conversion (IC), intersystem crossing (ISC), and intramolecular vibrational redistribution (IVR). Indeed, ultrafast optical spectroscopic tools, such as fluorescence up-conversion, show that in many cases, intramolecular relaxation processes can be extremely fast and even shorter than time scales of vibrations. In addition, more and more examples are appearing showing that ultrafast ISC rates do not scale with the magnitude of the metal spin-orbit coupling constant, that is, that there is no heavy-atom effect on ultrafast time scales. It appears that the structural dynamics of the system and the density of states play a crucial role therein. While optical spectroscopy delivers an insightful picture of electronic relaxation processes involving valence orbitals, the photophysics of metal complexes involves excitations that may be centered on the metal (called metal-centered or MC) or the ligand (called ligand-centered or LC) or involve a transition from one to the other or vice versa (called MLCT or LMCT). These excitations call for an element-specific probe of the photophysics, which is achieved by X-ray absorption spectroscopy. In this case, transitions from core orbitals to valence orbitals or higher allow probing the electronic structure changes induced by the optical excitation of the valence orbitals, while also delivering information about the geometrical rearrangement of the neighbor atoms around the atom of interest. With the emergence of new instruments such as X-ray free electron lasers (XFELs), it is now possible to perform ultrafast laser pump/X-ray emission probe experiments. In this case, one probes the density of occupied states. These core-level spectroscopies and other emerging ones, such as photoelectron spectroscopy of solutions, are delivering a hitherto unseen degree of detail into the photophysics of metal-based molecular complexes. In this Account, we will give examples of applications of the various methods listed above to address specific photophysical processes.

Direct observation of coherent oscillations in solution due to microheterogeneous environment

We report, for the first time, direct observation of coherent oscillations in the ground-state of IR775 dye due to microheterogeneous environment. Using ultrafast near-infrared degenerate pump-probe technique centered at 800 nm, we present the dynamics of IR775 in a binary mixture of methanol and chloroform at ultra-short time resolution of 30 fs. The dynamics of the dye in binary mixtures, in a time-scale of a few fs to ~740 ps, strongly varies as a function of solvent composition (volume fraction). Multi-oscillation behavior of the coherent vibration was observed, which increased with decreasing percentage of methanol in the dye mixture. Maximum number of damped oscillations were observed in 20% methanol. The observed vibrational wavepacket motion in the ground-state is periodic in nature. We needed two cosine functions to fit the coherent oscillation data as two different solvents were used. Dynamics of the dye molecule in binary mixtures can be explained by wavepacket motion in the ground potential energy surface. More is the confinement of the dye molecule in binary mixtures, more is the number of damped oscillations. The vibrational cooling time, τ₂, increases with increase in the confinement of the system. The observed wavepacket oscillations in ground-state dynamics continued until 1.6 ps.