Azoarene photoswitches are versatile molecules that interconvert from their E-isomer to their Z-isomer with light. Azobenzene is a prototypical photoswitch but its derivatives can be poorly suited for in vivo applications such as photopharmacology due to undesired photochemical reactions promoted by ultraviolet light and the relatively short half-life (t1/2) of the Z-isomer (2 days). Experimental and computational studies suggest that these properties (λmax of the E isomer and t1/2 of the Z-isomer) are inversely related. We identified isomeric azobisthiophenes and azobisfurans from a high-throughput screening study of 1540 azoarenes as photoswitch candidates with improved λmax and t1/2 values relative to azobenzene. We used density functional theory to predict the activation free energies and vertical excitation energies of the E- and Z-isomers of 2,2- and 3,3-substituted azobisthiophenes and azobisfurans. The half-lives depend on whether the heterocycles are π-conjugated or cross-conjugated with the diazo π-bond. The 2,2-substituted azoarenes both have t1/2 values on the scale of 1 hour, while the 3,3-analogues have computed half-lives of 40 and 230 years (thiophene and furan, respectively). The 2,2-substituted heteroazoarenes have significantly higher λmax absorptions than their 3,3-substituted analogues: 76 nm for azofuran and 77 nm for azothiophene.
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Efficient discovery of visible light-activated azoarene photoswitches with long half-lives using active search
Photoswitches are molecules that undergo a reversible, structural isomerization after exposure to different wavelengths of light. The dynamic control offered by molecular photoswitches is favorable for applications in materials chemistry, photopharmacology, and catalysis. Ideal photoswitches absorb visible light and have long-lived metastable isomers. We used high throughput virtual screening to predict the absorption maxima (λmax) of the E-isomer and half-lives (t1/2) of the Z-isomer. However, computing the photophysical and kinetic properties of each entry of a virtual molecular library containing 103–106 entries with density functional theory is prohibitively time-consuming. We applied active search, a machine learning technique to intelligently search a chemical search space of 255991 photoswitches based on 29 known azoarenes and their derivatives. We iteratively trained the active search algorithm based on whether a candidate absorbed visible light (λmax > 450 nm). Active search was found to triple the discovery rate compared to random search. Further, we projected 1962 photoswitches to 2D using the Uniform Manifold Approximation and Projection (umap) algorithm and found that λmax depends on the core, which is tunable with substituents. We then incorporated a second stage of screening with to predict the stabilities of the Z-isomers for the top 1% of candidates. We identified four ideal photoswitches that concurrently satisfy λmax > 450 nm and t1/2 > 2 hours; the range of λmax and t1/2 range from 465 to 531 nm and hours to years, respectively.
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- Award ID(s):
- 1940224
- NSF-PAR ID:
- 10296606
- Date Published:
- Journal Name:
- ChemRxiv
- ISSN:
- 2573-2293
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract A new family of hydrazone modified cytidine phosphoramidite building block was synthesized and incorporated into oligodeoxynucleotides to construct photoswitchable DNA strands. The
E‐Z isomerization triggered by the irradiation of blue light with a wavelength of 450 nm was investigated and confirmed by1H NMR spectroscopy and HPLC in the contexts of both nucleoside and oligodeoxynucleotide. The light activatedZ form isomer of this hydrazone‐cytidine with a six‐member intramolecular hydrogen bond was found to inhibit DNA synthesis in the primer extension model by usingBst DNA polymerase. In addition, the hydrazone modification caused the misincorporation of dATP together with dGTP into the growing DNA strand with similar selectivity, highlighting a potential G to A mutation. This work provides a novel functional DNA building block and an additional molecular tool that has potential chemical biology and biomedicinal applications to control DNA synthesis and DNA‐enzyme interactions using the cell friendly blue light irradiation. -
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Context. In recent times, large organic molecules of exceptional complexity have been found in diverse regions of the interstellar medium.Aims. In this context, we aim to provide accurate frequencies of the ground vibrational state of two key aliphatic aldehydes,n -butanal and its branched-chain isomer, i-butanal, to enable their eventual detection in the interstellar medium. We also want to test the level of complexity that interstellar chemistry can reach in regions of star formation.Methods. We employ a frequency modulation millimeter-wave absorption spectrometer to measure the rotational features ofn - andi -butanal. We analyze the assigned rotational transitions of each rotamer separately using theA -reduced semirigid-rotor Hamiltonian. We use the spectral line survey ReMoCA performed with the Atacama Large Millimeter/submillimeter Array to search forn - andi -butanal toward the star-forming region Sgr B2(N). We also search for both aldehydes toward the molecular cloud G+0.693−0.027 with IRAM 30 m and Yebes 40 m observations. The observational results are compared with computational results from a recent gas-grain astrochemical model.Results. Several thousand rotational transitions belonging to the lowest-energy conformers of two distinct linear and branched isomers have been assigned in the laboratory spectra up to 325 GHz. A precise set of the relevant rotational spectroscopic constants has been determined for each structure as a first step toward identifying both molecules in the interstellar medium. We report non-detections ofn -and i-butanal toward both sources, Sgr B2(N1S) and G+0.693-0.027. We find thatn - andi -butanal are at least 2-6 and 6-18 times less abundant than acetaldehyde toward Sgr B2(N1S), respectively, and thatn -butanal is at least 63 times less abundant than acetaldehyde toward G+0.693−0.027. While propanal is not detected toward Sgr B2(N1S) either, with an abundance at least 5–11 lower than that of acetaldehyde, propanal is found to be 7 times less abundant than acetaldehyde in G+0.693−0.027. Comparison with astrochemical models indicates good agreement between observed and simulated abundances (where available). Grain-surface chemistry appears sufficient to reproduce aldehyde ratios in G+0.693−0.027; gas-phase production may play a more active role in Sgr B2(N1S). Model estimates for the larger aldehydes indicate that the observed upper limits may be close to the underlying values.Conclusions. Our astronomical results indicate that the family of interstellar aldehydes in the Galactic center region is characterized by a drop of one order of magnitude in abundance at each incrementation in the level of molecular complexity. -
null (Ed.)For many species, vision is one of the most important sensory modalities for mediating essential tasks that include navigation, predation and foraging, predator avoidance, and numerous social behaviors. The vertebrate visual process begins when photons of the light interact with rod and cone photoreceptors that are present in the neural retina. Vertebrate visual photopigments are housed within these photoreceptor cells and are sensitive to a wide range of wavelengths that peak within the light spectrum, the latter of which is a function of the type of chromophore used and how it interacts with specific amino acid residues found within the opsin protein sequence. Minor differences in the amino acid sequences of the opsins are known to lead to large differences in the spectral peak of absorbance (i.e. the λmax value). In our prior studies, we developed a new approach that combined homology modeling and molecular dynamics simulations to gather structural information associated with chromophore conformation, then used it to generate statistical models for the accurate prediction of λmax values for photopigments derived from Rh1 and Rh2 amino acid sequences. In the present study, we test our novel approach to predict the λmax of phylogenetically distant Sws2 cone opsins. To build a model that can predict the λmax using our approach presented in our prior studies, we selected a spectrally-diverse set of 11 teleost Sws2 photopigments for which both amino acid sequence information and experimentally measured λmax values are known. The final first-order regression model, consisting of three terms associated with chromophore conformation, was sufficient to predict the λmax of Sws2 photopigments with high accuracy. This study further highlights the breadth of our approach in reliably predicting λmax values of Sws2 cone photopigments, evolutionary-more distant from template bovine RH1, and provided mechanistic insights into the role of known spectral tuning sitesmore » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.33774/chemrxiv-2021-w32rs
