Gonçalves DP, Zhu C, Tilki T, Prévôt ME, Hegmann T. Controlling the Structure and Morphology of Organic Nanofilaments Using External Stimuli

In our continuing pursuit to generate, understand, and control the morphology of organic nanofilaments formed by molecules with a bent molecular shape, we here report on two bent-core molecules specifically designed to permit a phase or morphology change upon exposure to an applied electric field or irradiation with UV light. To trigger a response to an applied electric field, conformationally rigid chiral (S,S)-2,3-difluorooctyloxy side chains were introduced, and to cause a response to UV light, an azobenzene core was incorporated into one of the arms of the rigid bent core. The phase behavior as well as structure and morphology of the formed phases and nanofilaments were analyzed using differential scanning calorimetry, cross-polarized optical microscopy, circular dichroism spectropolarimetry, scanning and transmission electron microscopy, UV-vis spectrophotometry, as well as X-ray diffraction experiments. Both bent-core molecules were characterized by the coexistence of two nanoscale morphologies, specifically helical nanofilaments (HNFs) and layered nanocylinders, prior to exposure to an external stimulus and independent of the cooling rate from the isotropic liquid. The application of an electric field triggers the disappearance of crystalline nanofilaments and instead leads to the formation of a tilted smectic liquid crystal phase for the material featuring chiral difluorinated side chains, whereas irradiation with UV light results in the disappearance of the nanocylinders and the sole formation of HNFs for the azobenzene-containing material. Combined results of this experimental study reveal that in addition to controlling the rate of cooling, applied electric fields and UV irradiation can be used to expand the toolkit for structural and morphological control of suitably designed bent-core molecule-based structures at the nanoscale.

Photo-regulated genetic encoding of dibenzo[c,g][1,2]diazocine on proteins via configuration switching

We report two evolved Methanosarcina mazei pyrrolysine tRNA synthetases to genetically incorporate the isomers of dibenzo[c,g][1,2]diazocine-alanine (DBDAA) into proteins either in the dark or under regulation of 405 nm photo-stimulation. The genetic-encoded DBDAA realizes photo-tuning of enzymatic activity via the host-guest recognition of cucurbit[7]uril.

A Photochemical Reaction in Different Theoretical Representations

The Born–Oppenheimer picture has forged our representation and interpretation of photochemical processes, from photoexcitation down to the passage through a conical intersection, a funnel connecting different electronic states. In this work, we analyze a full in silico photochemical experiment, from the explicit electronic excitation by a laser pulse to the formation of photoproducts following a nonradiative decay through a conical intersection, by contrasting the picture offered by Born–Oppenheimer and that proposed by the exact factorization. The exact factorization offers an alternative understanding of photochemistry that does not rely on concepts such as electronic states, nonadiabatic couplings, and conical intersections. On the basis of nonadiabatic quantum dynamics performed for a two-state 2D model system, this work allows us to compare Born–Oppenheimer and exact factorization for (i) an explicit photoexcitation with and without the Condon approximation, (ii) the passage of a nuclear wavepacket through a conical intersection, (iii) the formation of excited stationary states in the Franck–Condon region, and (iv) the use of classical and quantum trajectories in the exact factorization picture to capture nonadiabatic processes triggered by a laser pulse.

Advances and opportunities in the exciting world of azobenzenes

Azobenzenes are archetypal molecules that have a central role in fundamental and applied research. Over the course of almost two centuries, the area of azobenzenes has witnessed great achievements; azobenzenes have evolved from simple dyes to 'little engines' and have become ubiquitous in many aspects of our lives, ranging from textiles, cosmetics, food and medicine to energy and photonics. Despite their long history, azobenzenes continue to arouse academic interest, while being intensively produced for industrial purposes, owing to their rich chemistry, versatile and straightforward design, robust photoswitching process and biodegradability. The development of azobenzenes has stimulated the production of new coloured and light-responsive materials with various applications, and their use continues to expand towards new high-tech applications. In this Review, we highlight the latest achievements in the synthesis of red-light-responsive azobenzenes and the emerging application areas of photopharmacology, photoswitchable adhesives and biodegradable materials for drug delivery. We show how the synthetic versatility and adaptive properties of azobenzenes continue to inspire new research directions, with limits imposed only by one's imagination.

Triazonine-based bistable photoswitches: synthesis, characterization and photochromic properties

We disclose here dibenzotriazonines as a new class of nine-membered cyclic azobenzenes displaying a nitrogen function in the saturated ring chain. The specific features of these compounds are (i) a preferred E-configuration, (ii) high bi-directional photoswitching and (iii) good thermal stability of both E- and Z-forms.

DNA Balance for Native Characterization of Chemically Modified DNA

Chemical modification is a powerful approach to expand the chemical diversity and functionality of natural DNA. However, when chemically modified oligonucleotides are employed in DNA-based reactions or structures, it becomes quite difficult to predict, understand, and control their kinetics and thermodynamics. To address this challenge, we introduce a rationally designed DNA balance capable of measuring critical thermodynamic and kinetic properties of chemically modified DNA in their native environment. Our DNA balance is operated using the principle of toehold-exchange, where a panel of weight probes were designed by tuning the lengths of forward and reverse toeholds. Once placed on the DNA balance, the chemical modification will be interrogated using the weight probes to determine changes in both Gibbs free energy and hybridization rate constant. Using cyclic-azobenzene (cAB)-modified DNA as a model system, we demonstrated that our DNA balance could not only measure stable chemical modifications, but also solve more challenging issues where unstable chemical modifications and transient isomerization reactions were involved. We anticipate that our DNA balance will find wide uses for measuring important thermodynamic and kinetic parameters for DNA carrying various chemical modifications, as well as for probing transient chemical changes in DNA.

Tuning the Thermal Stability and Photoisomerization of Azoheteroarenes through Macrocycle Strain*

Azobenzene and its derivatives are one of the most widespread molecular scaffolds used in a range of modern applications, as well as in fundamental research. After photoexcitation, azo-based photoswitches revert back to the most stable isomer on a timescale ( t 1 / 2 ) that determines the range of potential applications. Attempts to bring t 1 / 2 to extreme values prompted the development of azobenzene and azoheteroarene derivatives that either rebalance the E- and Z-isomer stabilities, or exploit unconventional thermal isomerization mechanisms. In the former case, one successful strategy has been the creation of macrocycle strain, which tends to impact the E/Z stability asymmetrically, and thus significantly modifyt 1 / 2 . On the bright side, bridged derivatives have shown an improved optical switching owing to the higher quantum yields and absence of degradation. However, in most (if not all) cases, bridged derivatives display a reversed thermal stability (more stable Z-isomer), and smaller t 1 / 2 than the acyclic counterparts, which restricts their potential interest to applications requiring a fast forward and backwards switch. In this paper, the impact of alkyl bridges on the thermal stability of phenyl-azoheteroarenes is investigated by using computational methods, and it is revealed that it is indeed possible to combine such improved photoswitching characteristics while preserving the regular thermal stability (more stable E-isomer), and increased t 1 / 2 values under the appropriate connectivity and bridge length.

The Photoisomerization Pathway(s) of Push-Pull Phenylazoheteroarenes*

Azoheteroarenes are the most recent derivatives targeted to further improve the properties of azo-based photoswitches. Their light-induced mechanism for trans-cis isomerization is assumed to be very similar to that of the parent azobenzene. As such, they inherited the controversy about the dominant isomerization pathway (rotation vs. inversion) depending on the excited state (nπ* vs. ππ*). Although the controversy seems settled in azobenzene, the extent to which the same conclusions apply to the more structurally diverse family of azoheteroarenes is unclear. Here, by means of non-adiabatic molecular dynamics, the photoisomerization mechanism of three prototypical phenyl-azoheteroarenes with increasing push-pull character is unraveled. The evolution of the rotational and inversion conical intersection energies, the preferred pathway, and the associated kinetics upon both nπ* and ππ* excitations can be linked directly with the push-pull substitution effects. Overall, the working conditions of this family of azo-dyes is clarified and a possibility to exploit push-pull substituents to tune their photoisomerization mechanism is identified, with potential impact on their quantum yield.

Efficient Conversion of Light to Chemical Energy: Directional, Chiral Photoswitches with Very High Quantum Yields

Photochromic systems have been used to achieve a number of engineering functions such as light energy conversion, molecular motors, pumps, actuators, and sensors. Key to practical applications is a high efficiency in the conversion of light to chemical energy, a rigid structure for the transmission of force to the environment, and directed motion during isomerization. We present a novel type of photochromic system (diindane diazocines) that converts visible light with an efficiency of 18 % to chemical energy. Quantum yields are exceptionally high with >70 % for the cis-trans isomerization and 90 % for the back-reaction and thus higher than the biochemical system rhodopsin (64 %). Two diastereomers (meso and racemate) were obtained in only two steps in high yields. Both isomers are directional switches with high conversion rates (76-99 %). No fatigue was observed after several thousands of switching cycles in both systems.

Nitrogen Bridged Diazocines: Photochromes Switching within the Near-Infrared Region with High Quantum Yields in Organic Solvents and in Water

Diazocines are bridged azobenzenes with superior photophysical properties. In contrast to azobenzenes the Z configuration is thermodynamically stable and the E isomer is metastable. We present a new class of nitrogen bridged diazocines with bathochromically shifted switching wavelengths and remarkably high quantum yields (-NH-CH₂- bridged diazocine: Φ_Z→E = 0.57, Φ_E→Z = 0.8). Z to E isomerization is induced by irradiation with blue light, whereas switching back to the Z isomer is accomplished with light in the near-infrared window (up to 740 nm), which is important for medical applications like photopharmacology (deep tissue penetration). Furthermore, substitution at the bridging nitrogen should provide access to widely applicable tricyclic, photoswitchable pharmacophores. The -NAc-CH₂- bridged derivative is soluble in water, and all photophysical properties (conversion rates, quantum yields, and thermal half-lives) are largely retained. Hence, this diazocine is an ideal photoswitch for applications in biochemical systems and in photopharmacology.

Azobenzene-based solar thermal fuels: design, properties, and applications

Development of renewable energy technologies has been a significant area of research amongst scientists with the aim of attaining a sustainable world society. Solar thermal fuels that can capture, convert, store, and release solar energy in the form of heat through reversible photoisomerization of molecular photoswitches such as azobenzene derivatives are currently in the limelight of research. Herein, we provide a state-of-the-art account on the recent advancements in solar thermal fuels based on azobenzene photoswitches. We begin with an overview on the importance of azobenzene-based solar thermal fuels and their fundamentals. Then, we highlight the recent advances in diverse azobenzene materials for solar thermal fuels such as pure azobenzene derivatives, nanocarbon-templated azobenzene, and polymer-templated azobenzene. The basic design concepts of these advanced solar energy storage materials are discussed, and their promising applications are highlighted. We then introduce the recent endeavors in the molecular design of azobenzene derivatives toward efficient solar thermal fuels, and conclude with new perspectives on the future scope, opportunities and challenges. It is expected that continuous pioneering research involving scientists and engineers from diverse technological backgrounds could trigger the rapid advancement of this important interdisciplinary field, which embraces chemistry, physics, engineering, nanoscience, nanotechnology, materials science, polymer science, etc.

Raman Microspectroscopic Evidence for the Metabolism of a Tyrosine Kinase Inhibitor, Neratinib, in Cancer Cells

Tyrosine kinase receptors are one of the main targets in cancer therapy. They play an essential role in the modulation of growth factor signaling and thereby inducing cell proliferation and growth. Tyrosine kinase inhibitors such as neratinib bind to EGFR and HER2 receptors and exhibit antitumor activity. However, little is known about their detailed cellular uptake and metabolism. Here, we report for the first time the intracellular spatial distribution and metabolism of neratinib in different cancer cells using label-free Raman imaging. Two new neratinib metabolites were detected and fluorescence imaging of the same cells indicate that neratinib accumulates in lysosomes. The results also suggest that both EGFR and HER2 follow the classical endosome lysosomal pathway for degradation. A combination of Raman microscopy, DFT calculations, and LC-MS was used to identify the chemical structure of neratinib metabolites. These results show the potential of Raman microscopy to study drug pharmacokinetics.

Arylazopyrazole Photoswitches in Aqueous Solution: Substituent Effects, Photophysical Properties, and Host-Guest Chemistry

Getting the green light! Substituted arylazopyrazoles (AAPs) have been investigated as supramolecular photoswitches in aqueous solution. Selective photostationary states (PSSs) and improved binding affinities to β-cyclodextrin have been determined. The experimental findings are supported by results from DFT calculations.

UV-Light-Induced Vibrational Coherences: The Key to Understand Kasha Rule Violation in trans-Azobenzene

We combine sub-20 fs transient absorption spectroscopy with state-of-the-art computations to study the ultrafast photoinduced dynamics of trans-azobenzene (AB). We are able to resolve the lifetime of the ππ* state, whose decay within ca. 50 fs is correlated to the buildup of the nπ* population and to the emergence of coherences in the dynamics, to date unobserved. Nonlinear spectroscopy simulations call for the CNN in-plane bendings as the active modes in the subps photoinduced coherent dynamics out of the ππ* state. Radiative to kinetic energy transfer into these modes drives the system to a high-energy planar nπ*/ground state conical intersection, inaccessible upon direct excitation of the nπ* state, that triggers an ultrafast (0.45 ps) nonproductive decay of the nπ* state and is thus responsible for the observed Kasha rule violation in UV excited trans-AB. On the other hand, cis-AB is built only after intramolecular vibrational energy redistribution and population of the NN torsional mode.

QM/MM Studies on Photoisomerization Dynamics of Azobenzene Chromophore Tethered to a DNA Duplex: Local Unpaired Nucleobase Plays a Crucial Role

The photoresponsive azobenzene-tethered DNAs have received growing experimental attention because of their potential applications in biotechnology and nanotechnology; however, little is known about the initial photoisomerization of azobenzene in these systems. Herein we have employed quantum mechanics/molecular mechanics (QM/MM) methods to explore the photoisomerization dynamics of an azobenzene-tethered DNA duplex. We find that in the S₁ state the trans-cis photoisomerization path is much steeper in DNA than in vacuo, which makes the photoisomerization much faster in the DNA environment. This acceleration is primarily caused by complex steric interactions between azobenzene and the nearby unpaired thymine nucleobase, which also change the photoisomerization mechanism of azobenzene in the DNA duplex.

Azobenzene photocontrol of peptides and proteins

The last few years have witnessed significant advances in the use of light as a stimulus to control biomolecular interactions. Great efforts have been devoted to the development of genetically encoded optobiological and small photochromic switches. Newly discovered small molecules now allow researchers to build molecular systems that are sensitive to a wider range of wavelengths of light than ever before with improved switching fidelities and increased lifetimes of the photoactivated states. Because these molecules are relatively small and adopt predictable conformations they are well suited as tools to interrogate cellular function in a spatially and temporally contolled fashion and for applications in photopharmacology.

Ultrafast unidirectional chiral rotation in the Z–E photoisomerization of two azoheteroarene photoswitches

Based on a large number of trajectories starting from the Z-isomer, for both azoheteroarenes, more than 99% of the trajectories decay through conical intersections with the same helicities as their initial geometries.

Strain, switching and fluorescence behavior of a nine-membered cyclic azobenzene

This work defines the smallest ring size for obtaining the trans form of cyclic azobenzene as the thermally stable form.

Modeling of Azobenzene-Based Compounds

Azobenzene is by far the most studied photochromic molecule and its applications range from optical storage to bio-engineering. To exploit the great potential of azobenzene, one must achieve deep understanding of its photochemistry as single molecule in solution AS WELL AS in-chain moiety and pendent group in macromolecular structures. With the advent of computer-aided simulation scientists have been able to match experimental data with computational models. In this chapter, a review on the modeling of azobenzene-containing molecules in different conditions and environments IS provided with a special focus on advanced applications of photo-controllable materials, such as molecular machines and photoactivation of bio-molecules.

Photoisomerization of Arylazopyrazole Photoswitches: Stereospecific Excited-State Relaxation

Electronic structure calculations and nonadiabatic dynamics simulations (more than 2000 trajectories) are used to explore the Z-E photoisomerization mechanism and excited-state decay dynamics of two arylazopyrazole photoswitches. Two chiral S1 /S0 conical intersections with associated enantiomeric S1 relaxation paths that are barrierless and efficient (timescale of ca. 50 fs) were found. For the parent arylazopyrazole (Z8) both paths contribute evenly to the S1 excited-state decay, whereas for the dimethyl derivative (Z11) each of the two chiral cis minima decays almost exclusively through one specific enantiomeric S1 relaxation path. To our knowledge, the Z11 arylazopyrazole is thus the first example for nearly stereospecific unidirectional excited-state relaxation.

Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis

In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.

Can Strained Hydrocarbons Be "Forced" To Be Stable?

Many strained hydrocarbons are prone to isomerization, dimerization, and trimerization under normal laboratory conditions. Here we investigate a method to stabilize angle-strained cycloalkynes by applying a mechanical pulling force to the carbon atoms adjacent to the triple bond, which partially linearizes the C≡C-C bond angles. We discuss various methods of applying such pulling forces, including photoswitches and incorporation into additional strained macrocycles. We use the computational JEDI (Judgement of Energy DIstribution) analysis to quantify the distribution of energy in strained cycloheptyne and judge the change in stability upon application of an external force via isodesmic and homodesmotic reactions. We find that cycloheptyne can indeed be stabilized by external forces. However, the force generated by photoswitches during isomerization is too low to lead to a significant stabilization of the molecule. Hence, stronger forces are needed, which can be achieved by incorporating cycloheptyne into a second strained macrocycle.

Stiff-stilbene photoswitch ruptures bonds not by pulling but by local heating

The forces generated by stiff-stilbene during photoswitching are too low to cause bond rupture, which is instead initiated by heating.

Chiral conversion and periodical decay in bridged-azobenzene photoisomerization: an ab initio on-the-fly nonadiabatic dynamics simulation

On-the-fly trajectory surface hopping dynamics simulations on the cis ↔ trans photoisomerization mechanisms of bridged-azobenzene upon S₁ excitation at the CASSCF level.

Electric field control of proton-transfer molecular switching: molecular dynamics study on salicylidene aniline

In this letter, we propose a novel, ultrafast, efficient molecular switch whose switching mechanism involves the electric field-driven intramolecular proton transfer. By means of ab initio quantum chemical calculations and on-the-fly dynamics simulations, we examine the switching performance of an isolated salicylidene aniline molecule and analyze the perspectives of its possible use as an electric field-controlled molecular electronics unit.

Generalized trajectory surface-hopping method for internal conversion and intersystem crossing

Trajectory-based fewest-switches surface-hopping (FSSH) dynamics simulations have become a popular and reliable theoretical tool to simulate nonadiabatic photophysical and photochemical processes. Most available FSSH methods model internal conversion. We present a generalized trajectory surface-hopping (GTSH) method for simulating both internal conversion and intersystem crossing processes on an equal footing. We consider hops between adiabatic eigenstates of the non-relativistic electronic Hamiltonian (pure spin states), which is appropriate for sufficiently small spin-orbit coupling. This choice allows us to make maximum use of existing electronic structure programs and to minimize the changes to available implementations of the traditional FSSH method. The GTSH method is formulated within the quantum mechanics (QM)/molecular mechanics framework, but can of course also be applied at the pure QM level. The algorithm implemented in the GTSH code is specified step by step. As an initial GTSH application, we report simulations of the nonadiabatic processes in the lowest four electronic states (S0, S1, T1, and T2) of acrolein both in vacuo and in acetonitrile solution, in which the acrolein molecule is treated at the ab initio complete-active-space self-consistent-field level. These dynamics simulations provide detailed mechanistic insight by identifying and characterizing two nonadiabatic routes to the lowest triplet state, namely, direct S1 → T1 hopping as major pathway and sequential S1 → T2 → T1 hopping as minor pathway, with the T2 state acting as a relay state. They illustrate the potential of the GTSH approach to explore photoinduced processes in complex systems, in which intersystem crossing plays an important role.

Amino-substituted diazocines as pincer-type photochromic switches

Azobenzenes are robust, reliable, and easy to synthesize photochromic switches. However, their high conformational flexibility is a disadvantage in machine-like applications. The almost free rotation of the phenyl groups can be restricted by bridging two ortho positions with a CH(2)CH(2) group, as realized in the dihydrodibenzo diazocine framework. We present the synthesis and properties of 3,3'-amino- and 3,3'-acetamido substituted diazocines. Upon irradiation with light of 405 and 530 nm they isomerize from the cis to the trans configuration and back, and thereby perform a pincer-like motion. In the thermodynamically more stable cis isomer the lone pairs of the amino nitrogen atoms point towards each other, and in the trans form they point in opposite directions. The distance between the amino nitrogen atoms changes between 8 Å (cis) and 11 Å (trans isomer).

Photoinduced ultrafast Wolff rearrangement: a non-adiabatic dynamics perspective

One reaction, two routes: full-dimensional non-adiabatic dynamics simulations shed light on the ultrafast photoinduced Wolff rearrangement in an α-diazocarbonyl compound. The trajectories show both concerted asynchronous and stepwise processes leading to the corresponding ketene.