Browse
Submit Data
Databases
API
Help

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Koch M

PROVIDER: S-EPMC8709326 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations.

Project description:We present a simulation study of supramolecular aggregates formed by three-arm azobenzene (Azo) stars with a benzene-1,3,5-tricarboxamide (BTA) core in water. Previous experimental works by other research groups demonstrate that such Azo stars assemble into needle-like structures with light-responsive properties. Disregarding the response to light, we intend to characterize the equilibrium state of this system on the molecular scale. In particular, we aim to develop a thorough understanding of the binding mechanism between the molecules and analyze the structural properties of columnar stacks of Azo stars. Our study employs fully atomistic molecular dynamics (MD) simulations to model pre-assembled aggregates with various sizes and arrangements in water. In our detailed approach, we decompose the binding energies of the aggregates into the contributions due to the different types of non-covalent interactions and the contributions of the functional groups in the Azo stars. Initially, we investigate the origin and strength of the non-covalent interactions within a stacked dimer. Based on these findings, three arrangements of longer columnar stacks are prepared and equilibrated. We confirm that the binding energies of the stacks are mainly composed of π-π interactions between the conjugated parts of the molecules and hydrogen bonds formed between the stacked BTA cores. Our study quantifies the strength of these interactions and shows that the π-π interactions, especially between the Azo moieties, dominate the binding energies. We clarify that hydrogen bonds, which are predominant in BTA stacks, have only secondary energetic contributions in stacks of Azo stars but remain necessary stabilizers. Both types of interactions, π-π stacking and H-bonds, are required to maintain the columnar arrangement of the aggregates.

| S-EPMC8703797 | biostudies-literature

Manipulating azobenzene photoisomerization through strong light-molecule coupling.

Project description:The formation of hybrid light-molecule states (polaritons) offers a new strategy to manipulate the photochemistry of molecules. To fully exploit its potential, one needs to build a toolbox of polaritonic phenomenologies that supplement those of standard photochemistry. By means of a state-of-the-art computational photochemistry approach extended to the strong-coupling regime, here we disclose various mechanisms peculiar of polaritonic chemistry: coherent population oscillations between polaritons, quenching by trapping in dead-end polaritonic states and the alteration of the photochemical reaction pathway and quantum yields. We focus on azobenzene photoisomerization, that encompasses the essential features of complex photochemical reactions such as the presence of conical intersections and reaction coordinates involving multiple internal modes. In the strong coupling regime, a polaritonic conical intersection arises and we characterize its role in the photochemical process. Our chemically detailed simulations provide a framework to rationalize how the strong coupling impacts the photochemistry of realistic molecules.

| S-EPMC6224570 | biostudies-other

Azobenzene photoisomerization-induced destabilization of B-DNA.

Project description: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.

| S-EPMC4142232 | biostudies-literature

New azobenzene liquid crystal with dihydropyrazole heterocycle and photoisomerization studies.

Project description:New azobenzene derivatives with dihydropyrazole heterocycle have been prepared and characterized. According to thermal polarizing microscopy and differential scanning calorimetry studies, the compounds consisting of four linearly linked rings and a long alkoxy chain on the azobenzene side (3a-8 and 3a-14) displayed no liquid crystal properties. When the length of mesogenic unit increased to five rings, except for compound 5a-8, all compounds from 5a-10 to 5a-16 containing a long chain of 10-16 carbon atoms on the side of ester group displayed liquid crystalline properties, and the mesogenic domain gradually narrowed with increase of the chain length. However, in the case of the molecule with long alkoxy chains on both sides, only 5c-16 with a long chain of 16 carbon atoms exhibited liquid crystal behaviour. In addition, these azo compounds underwent isomerization from E to Z under ultraviolet irradiation and then thermal back relaxation slowly in the dark, which can be recycled many times.

| S-EPMC7428282 | biostudies-literature

Reversible Photoisomerization in Thin Surface Films from Azo-Functionalized Guanosine Derivatives.

Project description:Two novel azo-functionalized guanosine derivatives were synthesized, and their photoisomerization process was investigated in molecular monolayers at the air-water interface and in the Langmuir-Blodgett (LB) films on solid substrates. Measurements of surface pressure vs area isotherms, surface potential measurements, UV-visible (vis) absorption spectroscopy, Brewster angle microscopy (BAM), and atomic force microscopy (AFM) were performed. Despite not having a typical amphiphilic molecular structure, the derivatives formed stable films on the water surface. They could also undergo repeated photoisomerization in all of the investigated thin-film configurations. The observations suggest that in the films at the air-water interface, the molecules first exhibit a conformational change, and then they reorient to an energetically more favored orientation. In the LB films transferred onto solid substrates, the isomerization process occurs on a similar time scale as in solution. However, the isomerization efficiency is about an order of magnitude lower than that in solution. Our results show that DNA nucleobases functionalized with azobenzene moieties are suitable candidates for the fabrication of photoactive two-dimensional (2D) materials that can provide all beneficial functionalities of DNA-based compounds.

| S-EPMC8210406 | biostudies-literature

Imaging conical intersection dynamics during azobenzene photoisomerization by ultrafast X-ray diffraction.

Project description:X-ray diffraction is routinely used for structure determination of stationary molecular samples. Modern X-ray photon sources, e.g., from free-electron lasers, enable us to add temporal resolution to these scattering events, thereby providing a movie of atomic motions. We simulate and decipher the various contributions to the X-ray diffraction pattern for the femtosecond isomerization of azobenzene, a textbook photochemical process. A wealth of information is encoded besides real-time monitoring of the molecular charge density for the cis to trans isomerization. In particular, vibronic coherences emerge at the conical intersection, contributing to the total diffraction signal by mixed elastic and inelastic photon scattering. They cause distinct phase modulations in momentum space, which directly reflect the real-space phase modulation of the electronic transition density during the nonadiabatic passage. To overcome the masking by the intense elastic scattering contributions from the electronic populations in the total diffraction signal, we discuss how this information can be retrieved, e.g., by employing very hard X-rays to record large scattering momentum transfers.

| S-EPMC7826416 | biostudies-literature

Atomistic simulations of bicelle mixtures.

Project description:Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C(14) tails) and dihexanoylphosphatidylcholine (DHPC, di-C(6) tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironments and the stabilization of the bilayer edge by DHPC. To approach equilibrium partitioning of lipids on an achievable simulation timescale, configuration-bias Monte Carlo mutation moves were used to allow individual lipids to change tail length within a semigrand-canonical ensemble. Since acceptance probabilities for direct transitions between DMPC and DHPC were negligible, a third component with intermediate tail length (didecanoylphosphatidylcholine, di-C(10) tails) was included at a low concentration to serve as an intermediate for transitions between DMPC and DHPC. Strong enrichment of DHPC is seen at ribbon and pore edges, with an excess linear density of approximately 3 nm(-1). The simulation model yields estimates for the onset of edge stability with increasing bilayer DHPC content between 5% and 15% DHPC at 300 K and between 7% and 17% DHPC at 323 K, higher than experimental estimates. Local structure and composition at points of close contact between pores suggest a possible mechanism for effective attractions between pores, providing a rationalization for the tendency of bicelle mixtures to aggregate into perforated vesicles and perforated sheets.

| S-EPMC2884235 | biostudies-other

How Does the Number of Arms Affect the Properties of Mikto-Arm Stars in a Selective Oligomeric Matrix? Insights from Atomistic Simulations.

Project description:We present a simulation study of amphiphilic mikto-arm star copolymers in a selective polymer host. By means of atomistic molecular dynamics simulations, we examine the structural and dynamical properties of mikto-arm stars with varying number, n, of poly(ethylene oxide) (PEO) and polystyrene (PS) arms, (PEO) n (PS) n in a 33% wt blend with an oligomeric PEO host (o-PEO). As the number of arms increases, the stars resemble more spherical particles with less separated PEO and PS intramolecular domains. As a result of their internal morphology and associated geometrical constraints, the mikto-arm stars self-assemble either into cylindrical-like objects or a percolated network with increasing n, within the o-PEO matrix. The segmental dynamics is mostly governed by the star architecture and the heterogeneous local environment, formed by the intra- and intermolecular nanosegregation. We discuss the role of each factor and compare the results with previously published studies on mikto-arm stars.

| S-EPMC7818313 | biostudies-literature

Miller experiments in atomistic computer simulations.

Project description:The celebrated Miller experiments reported on the spontaneous formation of amino acids from a mixture of simple molecules reacting under an electric discharge, giving birth to the research field of prebiotic chemistry. However, the chemical reactions involved in those experiments have never been studied at the atomic level. Here we report on, to our knowledge, the first ab initio computer simulations of Miller-like experiments in the condensed phase. Our study, based on the recent method of treatment of aqueous systems under electric fields and on metadynamics analysis of chemical reactions, shows that glycine spontaneously forms from mixtures of simple molecules once an electric field is switched on and identifies formic acid and formamide as key intermediate products of the early steps of the Miller reactions, and the crucible of formation of complex biological molecules.

| S-EPMC4183268 | biostudies-literature

Multisecond ligand dissociation dynamics from atomistic simulations.

Project description:Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and rate-limiting steps in protein-ligand unbinding is crucial for modern drug discovery. To achieve the enhanced sampling, we perform dissipation-corrected targeted molecular dynamics simulations, which yield free energy and friction profiles of molecular processes under consideration. Subsequently, we use these fields to perform temperature-boosted Langevin simulations which account for the desired kinetics occurring on multisecond timescales and beyond. Adopting the dissociation of solvated sodium chloride, trypsin-benzamidine and Hsp90-inhibitor protein-ligand complexes as test problems, we reproduce rates from molecular dynamics simulation and experiments within a factor of 2-20, and dissociation constants within a factor of 1-4. Analysis of friction profiles reveals that binding and unbinding dynamics are mediated by changes of the surrounding hydration shells in all investigated systems.

| S-EPMC7286908 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data