Photoisomerization dynamics of stilbenes in polar solvents

On the third-order nonlinear optical responses of cis and trans stilbenes - a quantum chemistry investigation

The second hyperpolarizabilities (γ) of the stilbene molecular switch in its trans and cis forms have been calculated using quantum chemistry methods to address their third-order nonlinear optical contrasts, to assess the reliability of lower-cost DFT methods, and to make comparisons with experiments. First, the reference CCSD(T) method shows that trans-stilbene presents a γ‖ value twice larger than its cis isomer (its γTHS value is 2.7 times larger). Among more cost-effective methods, reliable results are obtained at MP2 as well as with DFT, provided the CAM-B3LYP or ωB97X-D XCFs are employed. Supplementary DFT calculations have investigated the relationships between the accuracy of the exchange-correlation functionals, the fulfillment of Koopmans' theorem, and the delocalization error, and they demonstrated that satisfying Koopmans' theorem is not the condition for the best accuracy but that functionals with small delocalization errors are generally efficient. Using the selected CAM-B3LYP, large γ enhancements by about 70% (trans-stilbene) and 50% (cis-stilbene) have been evidenced when accounting for solvent effects using an implicit solvation model (IEFPCM), even for apolar solvents. Then, the frequency dispersion of the γ responses has been described using Bishop polynomial expansions, allowing comparisons with a broad set of experimental data. To a certain extent, no systematic agreement between the calculations and the measured values was found. On the one hand, the agreement is satisfactory for the γ(-ω;ω,-ω,ω) quantities, provided that the dominant vibrational contribution is taken into account. On the other hand, the agreement is poor for the γ(-2ω;ω,ω,0) and γ(-3ω;ω,ω,ω) quantities, while some inconsistencies between experimental values are also highlighted.

Multicolor-Luminescence Including White Light by Photomodulation of Supramolecular Assemblies in Aqueous Media

Photo-responsive supramolecular systems offer intriguing functional aspects which have led to their applications in diverse fields such as optoelectronics and biomedicine. However, the modulation of the luminescence output in a spatiotemporal fashion by photo-controlled transformation still remains a challenging task. Herein, we report the controlled regulation of the emission color of supramolecular assemblies of amphiphilic cyanostilbenes (CSs) in water through in situ photomodulation employing UV and sunlight. Due to their aggregation-induced emission (AIE) features, the CS chromophores in the supramolecular assemblies exhibited bright greenish-yellow emission. Photoirradiation predominantly led to the formation of a cyclized product exhibiting aggregation-caused quenching (ACQ) features and having efficient cyan-blue emission in water but severely quenched emission in the solid state. Hence, starting from a unicomponent scaffold, photomodulation provided tunable emission ranging from greenish-yellow to cyan-blue including white light in water. Furthermore, using the contrasting AIE and ACQ behavior of the components in the photoirradiated mixtures, we were able to design rewritable fluorescent inks and encryption in solid films indicating the practical utility of these systems.

Different timescales during ultrafast stilbene isomerization in the gas and liquid phases revealed using time-resolved photoelectron spectroscopy

Directly contrasting ultrafast excited-state dynamics in the gas and liquid phases is crucial to understanding the influence of complex environments. Previous studies have often relied on different spectroscopic observables, rendering direct comparisons challenging. Here, we apply extreme-ultraviolet time-resolved photoelectron spectroscopy to both gaseous and liquid cis-stilbene, revealing the coupled electronic and nuclear dynamics that underlie its isomerization. Our measurements track the excited-state wave packets from excitation along the complete reaction path to the final products. We observe coherent excited-state vibrational dynamics in both phases of matter that persist to the final products, enabling the characterization of the branching space of the S₁-S₀ conical intersection. We observe a systematic lengthening of the relaxation timescales in the liquid phase and a red shift of the measured excited-state frequencies that is most pronounced for the complex reaction coordinate. These results characterize in detail the influence of the liquid environment on both electronic and structural dynamics during a complete photochemical transformation.

Physical stimuli-responsive cell-free protein synthesis

Cell-free protein synthesis has been developed as a critical platform in synthetic biology. Unlike the cell-based synthesis system, cell-free system activates transcriptional and translational mechanisms in vitro, and can control protein synthesis by artificially adding components or chemicals. However, the control method puts forward higher requirements in terms of accurate and non-toxic control, which cannot be achieved by chemical substances. For cell-free system, physical signal is a kind of ideal spatiotemporal control approach to replace chemical substances, realizing high accuracy with little side effect. Here we review the methods of using physical signals to control gene expression in cell-free systems, including studies based on light, temperature, electric field, and magnetic force. The transfer of these switches into cell-free system further expands the flexibility and controllability of the system, thus further expanding the application capability of cell-free systems. Finally, existing problems such as signal source and signal transmission are discussed, and future applications in pharmaceutical production, delivery and industrial production are further looked into.

Peptides and pseudopeptide ligands: a powerful toolbox for the affinity purification of current and next-generation biotherapeutics

Following the consolidation of therapeutic proteins in the fight against cancer, autoimmune, and neurodegenerative diseases, recent advancements in biochemistry and biotechnology have introduced a host of next-generation biotherapeutics, such as CRISPR-Cas nucleases, stem and car-T cells, and viral vectors for gene therapy. With these drugs entering the clinical pipeline, a new challenge lies ahead: how to manufacture large quantities of high-purity biotherapeutics that meet the growing demand by clinics and biotech companies worldwide. The protein ligands employed by the industry are inadequate to confront this challenge: while featuring high binding affinity and selectivity, these ligands require laborious engineering and expensive manufacturing, are prone to biochemical degradation, and pose safety concerns related to their bacterial origin. Peptides and pseudopeptides make excellent candidates to form a new cohort of ligands for the purification of next-generation biotherapeutics. Peptide-based ligands feature excellent target biorecognition, low or no toxicity and immunogenicity, and can be manufactured affordably at large scale. This work presents a comprehensive and systematic review of the literature on peptide-based ligands and their use in the affinity purification of established and upcoming biological drugs. A comparative analysis is first presented on peptide engineering principles, the development of ligands targeting different biomolecular targets, and the promises and challenges connected to the industrial implementation of peptide ligands. The reviewed literature is organized in (i) conventional (α-)peptides targeting antibodies and other therapeutic proteins, gene therapy products, and therapeutic cells; (ii) cyclic peptides and pseudo-peptides for protein purification and capture of viral and bacterial pathogens; and (iii) the forefront of peptide mimetics, such as β-/γ-peptides, peptoids, foldamers, and stimuli-responsive peptides for advanced processing of biologics.

Ultrafast trans → cis Photoisomerization Dynamics of Alkyl-Substituted Stilbenes in a Supramolecular Capsule

Ultrafast spectroscopy reveals the effects of confinement on the excited-state photoisomerization dynamics for a series of alkyl-substituted trans-stilbenes encapsulated in the hydrophobic cavity of an aqueous supramolecular organic host-guest complex. Compared with the solvated compounds, encapsulated trans-stilbenes have broader excited-state absorption spectra, excited-state lifetimes that are 3-4 times longer, and photoisomerization quantum yields that are 1.7-6.5 times lower in the restricted environment. The organic capsule disrupts the equilibrium structure and restricts torsional rotation around the central C═C double bond in the excited state, which is an important motion for the relaxation of trans-stilbene from S₁ to S₀. The location and identity of alkyl substituents play a significant role in determining the excited-state dynamics and photoisomerization quantum yields by tuning the relative crowding inside the capsule. The results are discussed in terms of distortions of the ground- and excited-state potential energy surfaces, including the topology of the S₁-S₀ conical intersection.

Polarization-dependent strong coupling between silver nanorods and photochromic molecules

Active plasmonics is a key focus for the development of advanced plasmonic applications. By selectively exciting the localized surface plasmon resonance sustained by the short or the long axis of silver nanorods, we demonstrate a polarization-dependent strong coupling between the plasmonic resonance and the excited state of photochromic molecules. By varying the width and the length of the nanorods independently, a clear Rabi splitting appears in the dispersion curves of both resonators.

Direct evidence for hula twist and single-bond rotation photoproducts

Photoisomerization reactions are quintessential processes driving molecular machines and motors, govern smart materials, catalytic processes, and photopharmacology, and lie at the heart of vision, phototaxis, or vitamin production. Despite this plethora of applications fundamental photoisomerization mechanisms are not well understood at present. The famous hula-twist motion—a coupled single and double-bond rotation—was proposed to explain proficient photoswitching in restricted environments but fast thermal follow-up reactions hamper identification of primary photo products. Herein we describe an asymmetric chromophore possessing four geometrically distinct diastereomeric states that do not interconvert thermally and can be crystallized separately. Employing this molecular setup direct and unequivocal evidence for the hula-twist photoreaction and for photoinduced single-bond rotation is obtained. The influences of the surrounding medium and temperature are quantified and used to favor unusual photoreactions. Based on our findings molecular engineers will be able to implement photo control of complex molecular motions more consciously.

Photoisomerization mechanisms govern important (bio)catalytic reactions and lie at the core of many functional materials. Here, the authors report a molecular setup that allows for the direct and separate observation of three fundamental photoreactions, namely the hula twist, single-bond rotation, as well as double-bond isomerization.

Recent developments in reversible photoregulation of oligonucleotide structure and function

There is a growing interest in the photoregulation of biological functions, due to the high level of spatiotemporal precision achievable with light. Additionally, light is non-invasive and waste-free. In particular, the photoregulation of oligonucleotide structure and function is a rapidly developing study field with relevance to biological, physical and material sciences. Molecular photoswitches have been incorporated in oligonucleotides for 20 years, and the field has currently grown beyond fundamental studies on photochemistry of the switches and DNA duplex stability, and is moving towards applications in chemical biology, nanotechnology and material science. Moreover, the currently emerging field of photopharmacology indicates the relevance of photocontrol in future medicine. In recent years, a large number of publications has appeared on photoregulation of DNA and RNA structure and function. New strategies are evaluated and novel, exciting applications are shown. In this comprehensive review, the key strategies for photoswitch inclusion in oligonucleotides are presented and illustrated with recent examples. Additionally the applications that have emerged in recent years are discussed, including gene regulation, drug delivery and materials design. Finally, we identify the challenges that the field currently faces and look forward to future applications.

Study of the E–Z stilbene isomerisation in perchlorotriphenyl-methane (PTM) derivatives

No reversibility in the E → Z isomerization of two vinylidene derivatives due to steric effects on the Z isomer is demonstrated.

Excited-State Proton Transfer in Resveratrol and Proposed Mechanism for Plant Resistance to Fungal Infection

Steady-state and time-resolved fluorescence techniques were employed to study the photophysics and photochemistry of trans-resveratrol. trans-Resveratrol is found in large quantities in fungi-infected grapevine-leaf tissue and plays a direct role in the resistance to plant disease. We found that trans-resveratrol in liquid solution undergoes a trans-cis isomerization process in the excited state at a rate that depends partially on the solvent viscosity, as was found in previous studies on trans-stilbene. The hydroxyl groups of the phenol moieties in resveratrol are weak photoacids. In water and methanol solutions containing weak bases such as acetate, a proton is transferred to the base within the lifetime of the excited state. When resveratrol is adsorbed on cellulose (also a component of the plant's cell wall), the cis-trans process is slow and the lifetime of the excited state increases from several tens of picoseconds in ethanol to about 1.5 ns. Excited-state proton transfer occurs when resveratrol is adsorbed on cellulose and acetate ions are in close proximity to the phenol moieties. We propose that proton transfer from excited resveratrol to the fungus acid-sensing chemoreceptor is one of the plant's resistance mechanisms to fungal infection.

Stereochemical modulation of emission behaviour in E/Z isomers of diphenyldipyrroethene from aggregation induced emission to crystallization induced emission

We have successfully separated and characterized E- and Z-isomers of diphenyldipyrroethene molecules and studies show that the E-isomer behaves as AIEgen, whereas the Z-isomer behaves as CIEgen.

Time-resolved emission spectra of 4-dimethylamino-4'-cyano-stilbene and resveratrol in high viscosity solvents and silica matrices

Time-resolved emission spectra of 4-dimethylamino-4'-cyano-stilbene (DMACS) and 3,5,4'-trihydroxy-stilbene (resveratrol, RSV) in propylene glycol and in rigid silica xerogel matrix at 23°C were studied. For the polar molecule DMACS in propylene glycol, a 66nm shift of maximum wavelength of emission spectra was observed within 1ns after excitation, and most of the shift occurred during the first 200ps. For resveratrol in propylene glycol no such a shift was observed. The rigid silica environment eliminates some deactivation pathways and stabilizes spectroscopic properties of both molecules. Spectral properties of nonpolar and high dipole moment molecules in viscous liquids and rigid environments are compared. Results are explained on the basis of intramolecular processes and solute-solvent relaxation, as well.

Anomalous photophysics of bis(hydroxystyryl)benzenes: a twist on the para/meta dichotomy

The dianions of two isomeric bis(hydroxystyryl)benzenes show dramatically different photophysical properties.

Watching Ultrafast Barrierless Excited-State Isomerization of Pseudocyanine in Real Time

The photoinduced excited-state processes in 1,1'-diethyl-2,2'-cyanine iodine are investigated using femtosecond time-resolved pump-probe spectroscopy. Using a broad range of probe wavelengths, the relaxation of the initially prepared excited-state wavepacket can be followed down to the sink region. The data directly visualize the directed downhill motion along the torsional reaction coordinate and suggest a barrierless excited-state isomerization in the short chain cyanine dye. Additionally, ultrafast ground-state hole and excited-state hole replica broadening is observed. While the narrow excited-state wavepacket broadens during pump-probe overlap, the ground-state hole burning dynamics takes place on a significantly longer time-scale. The experiment reported can be considered as a direct monitoring of the shape and the position of the photoprepared wavepacket on the excited-state potential energy surface.

Solvent Dependent Conformational Relaxation of cis-1,3,5-Hexatriene

Ultrafast transient absorption spectroscopy was used to study the conformational relaxation dynamics of 1,3,5-cis-hexatriene (Z-HT) produced in the photochemical ring-opening reaction of 1,3-cyclohexadiene (CHD) in methanol and n-propanol solvents. The results are compared with earlier investigations performed using cyclohexane and hexadecane solvents [Anderson, N. A.; Pullen, S. H.; Walker II, L. A.; Shiang, J. J.; Sension, R. J.; J. Phys. Chem. A 1998, 102, 10588-10598.]. The conformational relaxation between hot cZc-HT, cZt-HT, and tZt-HT, where the labels c and t designate cis and trans configurations about the single bonds, is much faster in alcohol solvents than in alkane solvents. The hot Z-HT produced in the photochemical ring-opening reaction evolves from the conformationally strained cZc-HT form to the more stable cZt-HT form on a time scale of 2 ps in alcohols compared with 6 ps in alkanes. The overall decay of the internal vibrational temperature of the hot Z-HT is faster in alcohols (5-6 ps) than alkanes (12-20 ps) and is weakly dependent on the specific alcohol or alkane solvent. A small population of cZt-HT (5-10%) is trapped as the solute equilibrates with the surrounding solvent following UV excitation of CHD or direct UV excitation of Z-HT. The influence of solvent on conformational relaxation of Z-HT was investigated further by probing the temperature dependence of the decay of this thermally equilibrated cZt-HT population. The apparent barrier for the cZt --> tZt conformational isomerization is lower in alcohols (17.4 kJ/mol) than in alkanes (23.5 kJ/mol). However the equilibrium Arrhenius prefactor (A(h)) is an order of magnitude smaller for alcohols (ca. 4 x 10(12)) than alkanes (ca. 6 x 10(13)) resulting in an absolute rate of decay that is faster in the alkane than in the alcohol solvents. These results are discussed in the context of transition state theory and Kramers' theory for condensed phase reaction dynamics.

Observation of Dynamic Solvent Effect for Electron Tunneling in U-Shaped Molecules

The electron-transfer rate constant is measured in two U-shaped donor-bridge-acceptor molecules over a wide range of temperature in acetonitrile and N-methylacetamide (NMA). The electron-transfer rate at high temperature can be well described by a nonadiabatic model of the reaction, but at low temperatures the rate in NMA becomes controlled by the solvent. The results are discussed in terms of theoretical models for the change in reaction mechanism and its dependence on the solute-solvent frictional coupling.

Temperature-dependent behavior of protein-chromophore interactions: a theoretical study of a blue fluorescent antibody

The unusual temperature-dependent excited-state dynamics of a stilbene-antibody complex reported by Simeonov et al. are explored using theoretical methods. The anomalous temperature-dependent fluorescence emission and lifetime are shown to be the result of interplay among temperature-modulated protein flexibility, the excited-state potential surface for the stilbene central twist, and changes in the stilbene charge distribution upon excitation. Stilbene is found to possess a similar geometry and orientation within the antibody binding pocket at all temperatures in the ground state and at low temperatures (approximately 240 K) in the excited state. At higher temperatures (approximately 260 K), the excited-state conformation twists around the central double bond and adopts an alternate orientation within the binding pocket. These changes result from protein side chain and loop motions that are frozen out at lower temperatures and account for the observed red shift of the fluorescence emission spectrum (a calculated shift of 3.8 kcal mol-1 compares favorably with the approximately 5 kcal.mol-1 observed experimentally). Approximately 3.0 kcal mol-1 of this stabilization is global in nature and is not attributable to specific local interactions. Local interactions between stilbene and Tyr-B39 contribute approximately 0.8 kcal mol-1 to the fluorescence shift. The primary structural change in simulations of the high temperature excited state involves a decrease in the stilbene-tyrosine distance and a relative change in orientation of the aromatic rings. We identify several nearby charged residues that contribute to the fluorescence emission shift and provide targets for mutagenesis to probe the temperature-dependent dynamics of protein-chromophore interactions.

Fluorescence Excitation Spectrum, Lifetimes and Photoisomerization of Jet-Cooled Conformers of 1,1´-bi(benzocyclobutylidene)

First measurements of fluorescence excitation spectra of the recently synthesized rigid stilbene analogue 1,1´-bi(benzocyclobutylidene) in asupersonic jet expansion show that, in contrast to the parent compound, both the