On-the-fly simulation of time-resolved fluorescence spectra and anisotropy

We combine on-the-fly trajectory surface hopping simulations and the doorway-window representation of nonlinear optical response functions to create an efficient protocol for the evaluation of time- and frequency-resolved fluorescence (TFRF) spectra and anisotropies of the realistic polyatomic systems. This approach gives the effective description of the proper (e.g., experimental) pulse envelopes, laser field polarizations, and the proper orientational averaging of TFRF signals directly from the well-established on-the-fly nonadiabatic dynamic simulations without extra computational cost. To discuss the implementation details of the developed protocol, we chose cis-azobenzene as a prototype to simulate the time evolution of the TFRF spectra governed by its nonadiabatic dynamics. The results show that the TFRF is determined by the interplay of several key factors, i.e., decays of excited-state populations, evolution of the transition dipole moments along with the dynamic propagation, and scaling factor of the TFRF signals associated with the cube of emission frequency. This work not only provides an efficient and effective approach to simulate the TFRF and anisotropies of realistic polyatomic systems but also discusses the important relationship between the TFRF signals and the underlining nonadiabatic dynamics.

On the Effects of Different trans and cis Populations in Azobenzene Liquid Crystal Elastomers: A Monte Carlo Investigation

We investigate main-chain liquid crystal elastomers (LCEs) formed by photoresponsive azobenzene units with different populations of trans and cis conformers (from fully trans to fully cis). We study their macroscopic properties as well as their molecular organization using extensive Monte Carlo simulations of a simple coarse-grained model where the trans and cis conformers are represented by soft-core biaxial Gay-Berne particles with size and interaction energy parameters obtained by fitting a bare bone azobenzene moiety represented at atomistic level. We find that increasing the fraction of cis conformers, as could be obtained by near-UV irradiation, shifts the nematic-isotropic transition to a lower temperature, consistently with experiment, while generating internal stress in a clamped sample. An analysis of pair distributions shows that the immediate surroundings of a bent cis molecule are slightly less dense and more orientationally disordered in comparison with that of a trans conformer. Comparing nematic and smectic LCEs, actuation in the smectic phase proved less effective, disrupting the smectic layers to some extent but preserving orientational order of the azobenzene moieties.

Understanding the formation of surface relief gratings in azopolymers: A combined molecular dynamics and experimental study

The formation of surface relief gratings in thin azopolymeric films is investigated using atomistic molecular dynamics simulations and compared to experimental results for the specific case of poly-disperse-orange3-methyl-methacrylate. For this purpose, the film is illuminated with a light pattern of alternating bright and dark stripes in both cases. The simulations use a molecular mechanics switching potential to explicitly describe the photoisomerization dynamics between the E and Z isomers of the azo-units and take into account the orientation of the transition dipole moment with respect to the light polarization. Local heating and elevation of the illuminated regions with the subsequent movement of molecules into the neighboring dark regions are observed. This leads to the formation of valleys in the bright areas after re-cooling and is independent of the polarization direction. To verify these observations experimentally, the azopolymer film is illuminated with bright stripes of varying width using a spatial light modulator. Atomic force microscopy images confirm that the elevated areas correspond to the previously dark areas. In the experiment, the polarization of the incident light makes only a small difference since tiny grain-like structures form in the valleys only when the polarization is parallel to the stripes.

Cyclic Photoisomerization of Azobenzene in Atomistic Simulations: Modeling the Effect of Light on Columnar Aggregates of Azo Stars

This computational study investigates the influence of light on supramolecular aggregates of three-arm azobenzene stars. Every star contains three azobenzene (azo) moieties, each able to undergo reversible photoisomerization. In solution, the azo stars build column-shaped supramolecular aggregates. Previous experimental works report severe morphological changes of these aggregates under UV-Vis light. However, the underlying molecular mechanisms are still debated. Here we aim to elucidate how light affects the structure and stability of the columnar stacks on the molecular scale. The system is investigated using fully atomistic molecular dynamics (MD) simulations. To implement the effects of light, we first developed a stochastic model of the cyclic photoisomerization of azobenzene. This model reproduces the collective photoisomerization kinetics of the azo stars in good agreement with theory and previous experiments. We then apply light of various intensities and wavelengths on an equilibrated columnar stack of azo stars in water. The simulations indicate that the aggregate does not break into separate fragments upon light irradiation. Instead, the stack develops defects in the form of molecular shifts and reorientations and, as a result, it eventually loses its columnar shape. The mechanism and driving forces behind this order-disorder structural transition are clarified based on the simulations. In the end, we provide a new interpretation of the experimentally observed morphological changes.

Atomistic Insight Into the Host-Guest Interaction of a Photoresponsive Metal-Organic Framework

Photoresponsive functional materials have gained increasing attention due to their externally tunable properties. Molecular switches embedded in these materials enable the control of phenomena at the atomic level by light. Metal-organic frameworks (MOFs) provide a versatile platform to immobilize these photoresponsive units within defined molecular environments to optimize the intended functionality. For the application of these photoresponsive MOFs (pho-MOFs), it is crucial to understand the influence of the switching state on the host-guest interaction. Therefore, we present a detailed insight into the impact of molecular switching on the intermolecular interactions. By performing atomistic simulations, we revealed that due to different interactions of the guest molecules with the two isomeric states of an azobenzene-functionalized MOF, both the adsorption sites and the orientation of the molecules within the pores are modulated. By shedding light on the host-guest interaction, our study highlights the unique potential of pho-MOFs to tailor molecular interaction by light.

Do Columns of Azobenzene Stars Disassemble under Light Illumination?

The clustering properties of star-shaped molecules comprising three photochromic azobenzene-containing arms are investigated with specific focus on the influence of light on these structures. Previous experimental works report self-assembly of azobenzene stars in aqueous solution into long columnar clusters that are detectable using optical microscopy. These clusters appear to vanish under UV irradiation, which is known to induce trans-to-cis photoisomerization of the azobenzene groups. We have performed MD simulations, density functional theory, and density functional tight binding calculations to determine conformational properties and binding energies of these clusters. Our simulation data suggest that the binding strength of the clusters is large enough to prevent a breaking along their main axis. We conclude that very likely other mechanisms lead to the apparent disappearance of the clusters.

Molecular Dynamics Study on the Photothermal Actuation of a Glassy Photoresponsive Polymer Reinforced with Gold Nanoparticles with Size Effect

We investigated the optical and thermal actuation behavior of densely cross-linked photoresponsive polymer (PRP) and polymer nanocomposites containing gold nanoparticles (PRP/Au) using all-atom molecular dynamics (MD) simulations. The modeled molecular structures contain a large number of photoreactive mesogens with linear orientation. Flexible side chains are interconnected through covalent bonds under periodic boundary conditions. A switchable dihedral potential was applied on a diazene moiety to describe the photochemical trans-to-cis isomerization. To quantify the photoinduced molecular reorientation and its effect on the macroscopic actuation of the neat PRP and PRP/Au materials, we characterized the photostrain and other material properties including elastic stiffness and thermal stability according to the photoisomerization ratio of the reactive groups. We particularly examined the effect of nanoparticle size on the photothermal actuation by varying the diameter of the nanofiller (10-20 Å) under the same volume fraction of 1.62%. The results indicated that the insertion of the gold nanoparticles enlarges the photostrain of the material while enhancing its mechanical stiffness and thermal stability. When the diameter of the nanoparticle reaches a size similar to or smaller than the length of the mesogen, the interfacial energy between the nanofiller and the surrounding polymer matrix does not significantly affect the alignment of the mesogens, but rather the adsorption energy at the interface generates a stable interphase layer. Hence, these improvements were more effective as the size of the gold nanoparticle decreased. The present findings suggest a wider analysis of the nanofiller-reinforced PRP composites and could be a guide for the mechanical design of the PRP actuator system.

Local Density Fluctuations Predict Photoisomerization Quantum Yield of Azobenzene-Modified DNA

Azobenzene incorporated into DNA has a photoisomerization quantum yield that depends on the DNA sequence near the azobenzene attachment site. We use Molecular Dynamics computer simulations to elucidate which physical properties of the modified DNA determine the quantum yield. We show for a wide range of DNA sequences that the photoisomerization quantum yield is strongly correlated with the variance of the number of atoms in close proximity to the outer phenyl ring of the azobenzene group. We infer that quantum yield is controlled by the availability of fluctuations that enable the conformational change. We demonstrate that these simulations can be used as a qualitative predictive tool by calculating the quantum yield for several novel DNA sequences, and confirming these predictions using UV-vis spectroscopy. Our results will be useful for the development of a wide range of applications of photoresponsive DNA nanotechnology.

Excited-State Decay in the Photoisomerisation of Azobenzene: A New Balance between Mechanisms

The mechanism of the photoisomerisation of azobenzene has been studied by means of multiconfigurational ab initio calculations. Our results show that it is necessary to account for the dynamic electron correlation in the location of the critical points (CASPT2 optimizations) to obtain a correct description of the topography of the potential energy surfaces of the low energy singlet excited states. By using this methodology, we have found that the state populated by the initial excitation is the S₂ (ππ*) state, which decays very efficiently to the S₁ (nπ*) state at a pedal-like non-rotated geometry. In the S₁ state, relaxation leads to a rotated geometry where the system decays to the ground state, in which further relaxation can lead to either the trans or cis geometries. However, the S₁ /S₀ conical intersection seam also extends to planar geometries, so this reaction path is also accessible for rotation-constrained systems. Our results explain the experimental observations satisfactorily.

Adaptive switching of interaction potentials in the time domain: an extended Lagrangian approach tailored to transmute force field to QM/MM simulations and back

An extended Lagrangian formalism that allows for a smooth transition between two different descriptions of interactions during a molecular dynamics simulation is presented. This time-adaptive method is particularly useful in the context of multiscale simulation as it provides a sound recipe to switch on demand between different hierarchical levels of theory, for instance between ab initio ("QM") and force field ("MM") descriptions of a given (sub)system in the course of a molecular dynamics simulation. The equations of motion can be integrated straightforwardly using the usual propagators, such as the Verlet algorithm. First test cases include a bath of harmonic oscillators, of which a subset is switched to a different force constant and/or equilibrium position, as well as an all-MM to QM/MM transition in a hydrogen-bonded water dimer. The method is then applied to a smectic 8AB8 liquid crystal and is shown to be able to switch dynamically a preselected 8AB8 molecule from an all-MM to a QM/MM description which involves partition boundaries through covalent bonds. These examples show that the extended Lagrangian approach is not only easy to implement into existing code but that it is also efficient and robust. The technique moreover provides easy access to a conserved energy quantity, also in cases when Nosé-Hoover chain thermostatting is used throughout dynamical switching. A simple quadratic driving potential proves to be sufficient to guarantee a smooth transition whose time scale can be easily tuned by varying the fictitious mass parameter associated with the auxiliary variable used to extend the Lagrangian. The method is general and can be applied to time-adaptive switching on demand between two different levels of theory within the framework of hybrid scale-bridging simulations.

P3HT:DiPBI bulk heterojunction solar cells: morphology and electronic structure probed by multiscale simulation and UV/vis spectroscopy

The effect of different annealing protocols on the morphology and light absorption of a P3HT:DiPBI mixture is studied by theory and experiment.

Photoisomerization of azobenzenes isolated in cryogenic matrices

E–E and E–Z isomerization reactions were studied in azobenzene and its 2,2′ OH- and CH₃-derivatives isolated in cryogenic matrices.

Calculated photo-isomerization efficiencies of functionalized azobenzene derivatives in solar energy materials: azo-functional organic linkers for porous coordinated polymers

Recently, we used a local orbital density functional theory code called FIREBALL, to study the photoisomerization process in azobenzene derivatives for solar energy materials. Azobenzene functional groups undergo photoisomerization upon light irradiation or application of heat. Zhou et al (2012 J. Am. Chem. Soc. 134 99-102) showed that these azobenzenes can then be introduced into metal-organic frameworks via an organic linker in order to create a reversible switch for CO2 adsorption. In this manuscript, we examined how the addition of organic linkers (isophthalic acid) changes the relaxation times, isomerization mechanism, and quantum yield for both the cis↔trans pathways. We then tuned these properties by substituting functional groups, finding an increase in quantum yield as well as improved optical properties.

The photo-orientation of azobenzene in viscous solutions, simulated by a stochastic model

We report a computational study of the photo-orientation kinetics in a viscous solution of azobenzene in ethylene glycol, under irradiation with linearly polarized light. The development of anisotropy and its interplay with photoisomerization are simulated by a stochastic model. A distinctive feature of the model is that it takes into account the photo-orientation angular distributions, specific for each isomer, obtained by nonadiabatic dynamics simulations at the molecular level. We find that the anisotropy, as measured by optical absorption dichroism, does not necessarily increase monotonously with time. As expected, the photo-orientation turns out to be strongly coupled with photoisomerization, but the latter is not a mandatory ingredient of this phenomenon: we predict that any chromophore undergoing large amplitude geometry relaxation during its excited state dynamics can develop anisotropy under suitable conditions.

Unusual, photo-induced self-assembly of azobenzene-containing amphiphiles

Stimuli-responsive self-assembly is playing an increasingly important role in emerging applications, ranging from smart materials to biosensors. However, obtaining essential information for further development, such as molecular arrangement and interaction, is still experimentally challenging. A molecular-level understanding of the stimuli-responsive self-assembly is needed. Azobenzene-containing (azo-containing) amphiphiles organize into photo-responsive assemblies because of the cis-trans isomerization triggered by the irradiation of ultraviolet (UV) and visible light. In this study, we applied a coarse grained (CG) molecular dynamics (MD) simulation, with the necessary potential parameters fitted from theoretical calculation data, to study the photo-induced self-assembly of 4,4'-bis(hydroxymethyl)-azobenzene (AzoCO), a simple azo-containing amphiphile. An unusual "chaotic micelle" and "monolayer phase" were obtained with cis- and trans-AzoCO molecules, respectively. The structural information and formation mechanism were studied. The "chaotic micelle" possesses a chaotic but not a pure hydrophobic interior as commonly understood. Through comparative simulations, we found that the azo (-N[double bond, length as m-dash]N-) group of azobenzene plays a crucial role in the formation of the "chaotic micelle". The "monolayer phase" is arranged by abreast rod-like trans-AzoCO molecules; the axial symmetry of the trans-AzoCO molecule drives the formation of this structure. The novel "chaotic micelle" and "monolayer phase" have potential applications in nanotechnology and bioengineering. This work is expected to trigger further studies on stimuli-responsive phenomena and materials.

Azobenzene photoisomerization-induced destabilization of B-DNA

Molecular photoswitches provide a promising way for selective regulation of nanoscaled biological systems. It has been shown that conformational changes of azobenzene, one of the widely used photoswitches, can be used to reversibly control DNA duplex formation. Here, we investigate the conformational response of DNA upon azobenzene binding and isomerization, using a threoninol linker that has been experimentally investigated recently. To this end, nonequilibrium molecular dynamics simulations are carried out using a switching potential describing the photoinduced isomerization. Attachment of azobenzene leads to a distortion of the DNA helical conformation that is similar for the trans and cis forms. However, the trans form is stabilized by favorable stacking interactions whereas the cis form is found to remain flipped out of the basepair-stacked position. Multiple azobenzene attachment augments the distortion in DNA helical conformation. The distorted DNA retains nativelike pairing of bases at ambient temperatures, but shows weaker basepairing compared to native DNA at an elevated temperature.

Computational electrochemistry: prediction of liquid-phase reduction potentials

This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.

Photoisomerization in different classes of azobenzene

Azobenzene undergoes trans→cis isomerization when irradiated with light tuned to an appropriate wavelength. The reverse cis→trans isomerization can be driven by light or occurs thermally in the dark. Azobenzene's photochromatic properties make it an ideal component of numerous molecular devices and functional materials. Despite the abundance of application-driven research, azobenzene photochemistry and the isomerization mechanism remain topics of investigation. Additional substituents on the azobenzene ring system change the spectroscopic properties and isomerization mechanism. This critical review details the studies completed to date on the 3 main classes of azobenzene derivatives. Understanding the differences in photochemistry, which originate from substitution, is imperative in exploiting azobenzene in the desired applications.