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1. Photostability of 2,6-diaminopurine and its 2′-deoxyriboside investigated by femtosecond transient absorption spectroscopy

   https://doi.org/10.1039/D1CP05269A  

   Caldero-Rodríguez, Naishka E. ; Ortiz-Rodríguez, Luis A. ; Gonzalez, Andres A. ; Crespo-Hernández, Carlos E. ( February 2022 , Physical Chemistry Chemical Physics)

   Ultraviolet radiation (UVR) from the sun is essential for the prebiotic syntheses of nucleotides, but it can also induce photolesions such as the cyclobutane pyrimidine dimers (CPDs) to RNA or DNA oligonucleotide in prebiotic Earth. 2,6-Diaminopurine (26DAP) has been proposed to repair CPDs in high yield under prebiotic conditions and be a key component in enhancing the photostability of higher-order prebiotic DNA structures. However, its electronic relaxation pathways have not been studied, which is necessary to know whether 26DAP could have survived the intense UV fluxes of the prebiotic Earth. We investigate the electronic relaxation mechanism of both 26DAP and its 2′-deoxyribonucleoside (26DAP-d) in aqueous solution using steady-state and femtosecond transient absorption measurements that are complemented with electronic-structure calculations. The results demonstrate that both purine derivatives are significantly photostable to UVR. It is shown that upon excitation at 287 nm, the lowest energy 1 ππ* state is initially populated. The population then branches following two relaxation coordinates in the 1 ππ* potential energy surface, which are identified as the C2- and C6-relaxation coordinates. The population following the C6-coordinate internally converts to the ground state nonradiatively through a nearly barrierless conical intersection within 0.7 ps in 26DAP or within 1.1 psmore »in 26DAP-d. The population that follows the C2-relaxation coordinate decays back to the ground state by a combination of nonradiative internal conversion via a conical intersection and fluorescence emission from the 1 ππ* minimum in 43 ps and 1.8 ns for the N9 and N7 tautomers of 26DAP, respectively, or in 70 ps for 26DAP-d. Fluorescence quantum yields of 0.037 and 0.008 are determined for 26DAP and 26DAP-d, respectively. Collectively, it is demonstrated that most of the excited state population in 26DAP and 26DAP-d decays back to the ground state via both nonradiative and radiative relaxation pathways. This result lends support to the idea that 26DAP could have accumulated in large enough quantities during the prebiotic era to participate in the formation of prebiotic RNA or DNA oligomers and act as a key component in the protection of the prebiotic genetic alphabet.« less
2. Transamidation of thioamides with nucleophilic amines: thioamide N–C(S) activation by ground-state-destabilization

   https://doi.org/10.1039/D2OB00412G  

   Zhang, Jin ; Zhao, Hui ; Li, Guangchen ; Zhu, Xinhao ; Shang, Linqin ; He, Yang ; Liu, Xin ; Ma, Yangmin ; Szostak, Michal ( January 2022 , Organic & Biomolecular Chemistry)

   Thioamides are ‘single-atom’ isosteres of amide bonds that have found broad applications in organic synthesis, biochemistry and drug discovery. In this New Talent themed issue, we present a general strategy for activation of N–C(S) thioamide bonds by ground-state-destabilization. This concept is outlined in the context of a full study on transamidation of thioamides with nucleophilic amines, and relies on (1) site-selective N -activation of the thioamide bond to decrease resonance and (2) highly chemoselective nucleophilic acyl addition to the thioamide CS bond. The follow-up collapse of the tetrahedral intermediate is favored by the electronic properties of the amine leaving group. The ground-state-destabilization concept of thioamides enables weakening of the N–C(S) bond and rationally modifies the properties of valuable thioamide isosteres for the development of new methods in organic synthesis. We fully expect that in analogy to the burgeoning field of destabilized amides introduced by our group in 2015, the thio amide bond ground-state-destabilization activation concept will find broad applications in various facets of chemical science, including metal-free, metal-catalyzed and metal-promoted reaction pathways.
3. Modifying the internal substituents of self-assembled cages controls their molecular recognition and optical properties

   https://doi.org/10.1039/D2DT01451C  

   Woods, Connor Z. ; Wu, Hoi-Ting ; Ngai, Courtney ; da Camara, Bryce ; Julian, Ryan R. ; Hooley, Richard J. ( July 2022 , Dalton Transactions)

   Self-assembled Fe4 L 6 cage complexes with variable internal functions can be synthesized from a 2,7-dibromocarbazole ligand scaffold, which orients six functional groups to the cage interior. Both ethylthiomethylether and ethyldimethylamino groups can be incorporated. The cages show strong ligand-centered fluorescence emission and a broad range of guest binding properties. Coencapsulation of neutral organic guests is favored in the larger, unfunctionalized cage cavity, whereas the thioether cage has a more sterically hindered cavity that favors 1 : 1 guest binding. Binding affinities up to 10 6 M −1 in CH3 CN are seen. The dimethylamino cage is more complex, as the internal amines display partial protonation and can be deprotonated by amine bases. This amine cage displays affinity for a broad range of neutral organic substrates, with affinities and stoichiometries comparable to that of the similarly sized thioether cage. These species show that simple variations in ligand backbone allow variations in the number and type of functions that can be displayed towards the cavity of self-assembled hosts, which will have applications in biomimetic sensing, catalysis and molecular recognition.
4. Large-scale investigation of the effects of nucleobase sequence on fluorescence excitation and Stokes shifts of DNA-stabilized silver clusters

   https://doi.org/10.1039/D0NR08300C  

   Copp, Stacy M. ; Gonzàlez-Rosell, Anna ( March 2021 , Nanoscale)

   DNA-stabilized silver clusters (Ag N -DNAs) exhibit diverse sequence-programmed fluorescence, making these tunable nanoclusters promising sensors and bioimaging probes. Recent advances in the understanding of Ag N -DNA structures and optical properties have largely relied on detailed characterization of single species isolated by chromatography. Because most Ag N -DNAs are unstable under chromatography, such studies do not fully capture the diversity of these clusters. As an alternative method, we use high-throughput synthesis and spectroscopy to measure steady state Stokes shifts of hundreds of Ag N -DNAs. Steady state Stokes shift is of interest because its magnitude is determined by energy relaxation processes which may be sensitive to specific cluster geometry, attachment to the DNA template, and structural engagement of solvent molecules. We identify 305 Ag N -DNA samples with single-peaked emission and excitation spectra, a characteristic of pure solutions and single emitters, which thus likely contain a dominant emissive Ag N -DNA species. Steady state Stokes shifts of these samples vary widely, are in agreement with values reported for purified clusters, and are several times larger than for typical organic dyes. We then examine how DNA sequence selects Ag N -DNA excitation energies and Stokes shifts, comment on possible mechanismsmore »for energy relaxation processes in Ag N -DNAs, and discuss how differences in Ag N -DNA structure and DNA conformation may result in the wide distribution of optical properties observed here. These results may aid computational studies seeking to understand the fluorescence process in Ag N -DNAs and the relations of this process to Ag N -DNA structure.« less
5. Excited state dynamics of 2′-deoxyisoguanosine and isoguanosine in aqueous solution

   https://doi.org/10.1039/D1CP05795B  

   Caldero-Rodríguez, Naishka E. ; Crespo-Hernández, Carlos E. ( March 2022 , Physical Chemistry Chemical Physics)

   Photostability is thought to be an inherent property of nucleobases required to survive the extreme ultraviolet radiation conditions of the prebiotic era. Previous studies have shown that absorption of ultraviolet radiation by the canonical nucleosides results in ultrafast internal conversion to the ground state, demonstrating that these nucleosides efficiently dissipate the excess electronic energy to the environment. In recent years, studies on the photophysical and photochemical properties of nucleobase derivatives have revealed that chemical substitution influences the electronic relaxation pathways of purine and pyrimidine nucleobases. It has been suggested that amino or carbonyl substitution at the C6 position could increase the photostability of the purine derivatives more than the substitution at the C2 position. This investigation aims to elucidate the excited state dynamics of 2′-deoxyisoguanosine (dIsoGuo) and isoguanosine (IsoGuo) in aqueous solution at pH 7.4 and 1.4, which contain an amino group at the C6 position and a carbonyl group at the C2 position of the purine chromophore. The study of these derivatives is performed using absorption and emission spectroscopies, broadband transient absorption spectroscopy, and density functional and time-dependent density functional levels of theory. It is shown that the primary relaxation mechanism of dIsoGuo and IsoGuo involves nonradiative decay pathways,more »where the population decays from the S 1 (ππ*) state through internal conversion to the ground state via two relaxation pathways with lifetimes of hundreds of femtoseconds and less than 2 ps, making these purine nucleosides photostable in aqueous solution.« less