More Like this

1. Time-Resolved Vibrational Fingerprints for Two Silver Cluster-DNA Fluorophores

   Y. Zhang, C. He ( October 2020 , The journal of physical chemistry letters)

   DNA-templated silver clusters are chromophores in which the nucleobases encode the cluster spectra and brightness. We describe the coordination environments of two nearly identical Ag106+ clusters that form with 18-nucleotide strands CCCCA CCCCT CCCX TTTT, with X = guanosine and inosine. For the first time, femtosecond time-resolved infrared (TRIR) spectroscopy with visible excitation and mid-infrared probing is used to correlate the response of nucleobase vibrational modes to electronic excitation of the metal cluster. A rich pattern of transient TRIR peaks in the 1400–1720 cm–1 range decays synchronously with the visible emission. Specific infrared signatures associated with the single guanosine/inosine along with a subset of cytidines, but not the thymidines, are observed. These fingerprints suggest that the network of bonds between a silver cluster adduct and its polydentate DNA ligands can be deciphered to rationally tune the coordination and thus spectra of molecular silver chromophores. 

   more » « less
2. Polarity-Dependent Twisted Intramolecular Charge Transfer in Diethylamino Coumarin Revealed by Ultrafast Spectroscopy

   https://doi.org/10.3390/chemosensors10100411  

   Liu, Jiawei ; Chen, Cheng ; Fang, Chong ( October 2022 , Chemosensors)

   Twisting intramolecular charge transfer (TICT) is a common nonradiative relaxation pathway for a molecule with a flexible substituent, effectively reducing the fluorescence quantum yield (FQY) by swift twisting motions. In this work, we investigate coumarin 481 (C481) that contains a diethylamino group in solution by femtosecond transient absorption (fs-TA), femtosecond stimulated Raman spectroscopy (FSRS), and theoretical calculations, aided by coumarin 153 with conformational locking of the alkyl arms as a control sample. In different solvents with decreasing polarity, the transition energy barrier between the fluorescent state and TICT state increases, leading to an increase of the FQY. Correlating the fluorescence decay time constant with solvent polarity and viscosity parameters, the multivariable linear regression analysis indicates that the chromophore’s nonradiative relaxation pathway is affected by both hydrogen (H)-bond donating and accepting capabilities as well as dipolarity of the solvent. Results from the ground- and excited-state FSRS shed important light on structural dynamics of C481 undergoing prompt light-induced intramolecular charge transfer from the diethylamino group toward –C=O and –CF3 groups, while the excited-state C=O stretch marker band tracks initial solvation and vibrational cooling dynamics in aprotic and protic solvents (regardless of polarity) as well as H-bonding dynamics in the fluorescent state for C481 in high-polarity protic solvents like methanol. The uncovered mechanistic insights into the molecular origin for the fluorogenicity of C481 as an environment-polarity sensor substantiate the generality of ultrafast TICT state formation of flexible molecules in solution, and the site-dependent substituent(s) as an effective route to modulate the fluorescence properties for such compact, engineerable, and versatile chemosensors. 

   more » « less
3. Excited State Lifetimes of Sulfur-Substituted DNA and RNA Monomers Probed Using the Femtosecond Fluorescence Up-Conversion Technique

   https://doi.org/10.3390/molecules25030584  

   Brister, M. M. ; Gustavsson, T. ; Crespo-Hernández, C. E. ( January 2020 , Molecules)

   Sulfur-substituted DNA and RNA nucleobase derivatives (a.k.a., thiobases) are an important family of biomolecules. They are used as prodrugs and as chemotherapeutic agents in medical settings, and as photocrosslinker molecules in structural-biology applications. Remarkably, excitation of thiobases with ultraviolet to near-visible light results in the population of long-lived and reactive triplet states on a time scale of hundreds of femtoseconds and with near-unity yields. This efficient nonradiative decay pathway explains the vanishingly small fluorescence yields reported for the thiobases and the scarcity of fluorescence lifetimes in the literature. In this study, we report fluorescence lifetimes for twelve thiobase derivatives, both in aqueous solution at physiological pH and in acetonitrile. Excitation is performed at 267 and 362 nm, while fluorescence emission is detected at 380, 425, 450, 525, or 532 nm. All the investigated thiobases reveal fluorescence lifetimes that decay in a few hundreds of femtoseconds and with magnitudes that depend and are sensitive to the position and degree of sulfur-atom substitution and on the solvent environment. Interestingly, however, three thiopyrimidine derivatives (i.e., 2-thiocytidine, 2-thiouridine, and 4-thiothymidine) also exhibit a small amplitude fluorescence component of a few picoseconds in aqueous solution. Furthermore, the N-glycosylation of thiobases to form DNA or RNA nucleoside analogues is demonstrated as affecting their fluorescence lifetimes. In aqueous solution, the fluorescence decay signals exciting at 267 nm are equal or slower than those collected exciting at 362 nm. In acetonitrile, however, the fluorescence decay signals recorded upon 267 nm excitation are, in all cases, faster than those measured exciting at 362 nm. A comparison to the literature values show that, while both the DNA and RNA nucleobase and thiobase derivatives exhibit sub-picosecond fluorescence lifetimes, the 1ππ* excited-state population in the nucleobase monomers primarily decay back to the ground state, whereas it predominantly populates long-lived and reactive triplet states in thiobase monomers. 

   more » « less
4. 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, 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. 

   more » « less
5. Shedding light on ultrafast ring-twisting pathways of halogenated GFP chromophores from the excited to ground state

   https://doi.org/10.1039/D1CP02140K  

   Boulanger, Sean A. ; Chen, Cheng ; Tang, Longteng ; Zhu, Liangdong ; Baleeva, Nadezhda S. ; Myasnyanko, Ivan N. ; Baranov, Mikhail S. ; Fang, Chong ( July 2021 , Physical Chemistry Chemical Physics)

   null (Ed.)

   Since green fluorescent protein (GFP) has revolutionized molecular and cellular biology for about three decades, there has been a keen interest in understanding, designing, and controlling the fluorescence properties of GFP chromophore ( i.e. , HBDI) derivatives from the protein matrix to solution. Amongst these cross-disciplinary efforts, the elucidation of excited-state dynamics of HBDI derivatives holds the key to correlating the light-induced processes and fluorescence quantum yield (FQY). Herein, we implement steady-state electronic spectroscopy, femtosecond transient absorption (fs-TA), femtosecond stimulated Raman spectroscopy (FSRS), and quantum calculations to study a series of mono- and dihalogenated HBDI derivatives (X = F, Cl, Br, 2F, 2Cl, and 2Br) in basic aqueous solution, gaining new insights into the photophysical reaction coordinates. In the excited state, the halogenated “floppy” chromophores exhibit an anti-heavy atom effect, reflected by strong correlations between FQY vs. Franck–Condon energy ( E FC ) or Stokes shift, and k nr vs. E FC , as well as a swift bifurcation into the I-ring (major) and P-ring (minor) twisting motions. In the ground state, both ring-twisting motions become more susceptible to sterics and exhibit spectral signatures from the halogen-dependent hot ground-state absorption band decay in TA data. We envision this type of systematic analysis of the halogenated HBDI derivatives to provide guiding principles for the site-specific modification of GFP chromophores, and expand design space for brighter and potentially photoswitchable organic chemical probes in aqueous solution with discernible spectral signatures throughout the photocycle. 

   more » « less