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1. Decoding the 2D IR spectrum of the aqueous proton with high-level VSCF/VCI calculations

   https://doi.org/10.1063/5.0020279  

   Carpenter, William B. ; Yu, Qi ; Hack, John H. ; Dereka, Bogdan ; Bowman, Joel M. ; Tokmakoff, Andrei ( September 2020 , The Journal of Chemical Physics)

   The aqueous proton is a common and long-studied species in chemistry, yet there is currently intense interest devoted to understanding its hydration structure and transport dynamics. Typically described in terms of two limiting structures observed in gas-phase clusters, the Zundel H₅O₂⁺and Eigen H₉O₄⁺ions, the aqueous structure is less clear due to the heterogeneity of hydrogen bonding environments and room-temperature structural fluctuations in water. The linear infrared (IR) spectrum, which reports on structural configurations, is challenging to interpret because it appears as a continuum of absorption, and the underlying vibrational modes are strongly anharmonically coupled to each other. Recent two-dimensional IR (2D IR) experiments presented strong evidence for asymmetric Zundel-like motifs in solution, but true structure–spectrum correlations are missing and complicated by the anharmonicity of the system. In this study, we employ high-level vibrational self-consistent field/virtual state configuration interaction calculations to demonstrate that the 2D IR spectrum reports on a broad distribution of geometric configurations of the aqueous proton. We find that the diagonal 2D IR spectrum around 1200 cm⁻¹is dominated by the proton stretch vibrations of Zundel-like and intermediate geometries, broadened by the heterogeneity of aqueous configurations. There is a wide distribution of multidimensional potential shapes for the proton stretching vibration with varying degrees of potential asymmetry and confinement. Finally, we find specific cross peak patterns due to aqueous Zundel-like species. These studies provide clarity on highly debated spectral assignments and stringent spectroscopic benchmarks for future simulations.

    

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2. Radical Complexes of Nickel(II)/Copper(II) and Redox Non‐innocent MB‐DIPY Ligands: Unusual Stability and Strong Near‐Infrared Absorption at λ max ∼1300 nm

   https://doi.org/10.1002/chem.202201181  

   Zatsikha, Yuriy V. ; Shamova, Liliya I. ; Shepit, Michael ; Berry, Steven M. ; Thomas, Fabrice ; Herbert, David E. ; van Lierop, Johan ; Nemykin, Victor N. ( June 2022 , Chemistry – A European Journal)

   The preparation of radicals with intense and redox‐switchable absorption beyond 1000 nm is a long‐standing challenge in the chemistry of functional dyes. Here we report the preparation of a series of unprecedented stable neutral nickel(II) and copper(II) complexes of “Manitoba dipyrromethenes” (MB‐DIPYs) in which the organic chromophore is present in the radical‐anion state. The new stable radicals have an intense absorption atλ_max∼1300 nm and can be either oxidized to regular [M^II(MB‐DIPY)]⁺(M=Cu or Ni) or reduced to [M^II(MB‐DIPY)]⁻compounds. The radical nature of the stable [M^II(MB‐DIPY)] complexes was confirmed by EPR spectroscopy with additional insight into their electronic structure obtained by UV‐Vis spectroscopy, electro‐ and spectroelectrochemistry, magnetic measurements, and X‐ray crystallography. The electronic structures and spectroscopic properties of the radical‐based chromophores were also probed by density functional theory (DFT) and time‐dependent DFT (TDDFT) calculations. These nickel(II) and copper(II) complexes represent the first stable radical compounds with a MB‐DIPY ligand.

    

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3. UV-Vis Photodissociation Action Spectroscopy Reveals Cytosine-Guanine Hydrogen Transfer in DNA Tetranucleotide Cation Radicals upon One-Electron Transfer

   https://doi.org/10.1021/acd.jpcb.0c01693  

   Huang, Shu R. ; Liu, Y. ; Turecek, Frantisek ( April 2020 , The journal of physical chemistry)

   ABSTRACT: We report the generation and spectroscopic study of hydrogen-rich DNA tetranucleotide cation radicals (GATC+2H)+• and (AGTC+2H)+•. The radicals were generated in the gas phase by one-electron reduction of the respective dications (GATC +2H)2+ and (AGTC+2H)2+ and characterized by collision-induced dissociation and photodissociation tandem mass spectrometry and UV−vis photodissociation action spectroscopy. Among several absorption bands observed for (GATC+2H)+•, the bands at 340 and 450 nm were assigned to radical chromophores. Timedependent density functional theory calculations including vibronic transitions in the visible region of the spectrum were used to provide theoretical absorption spectra of several low-energy tetranucleotide tautomers having cytosine-, adenine-, and thymine- based radical chromophores that did not match the experimental spectrum. Instead, the calculations indicated the formation of a new isomer with the 7,8-H-dihydroguanine cation radical moiety. The isomerization involved hydrogen migration from the cytosine N-3−H radical to the C-8 position in N-7-protonated guanine that was calculated to be 87 kJ mol−1 exothermic and had a low-energy transition state. Although the hydrogen migration was facilitated by the spatial proximity of the guanine and cytosine bases in the low-energy (GATC+2H)+• intermediate formed by electron transfer, the reaction was calculated to have a large negative activation entropy. Rice−Ramsperger−Kassel−Marcus (RRKM) and transition state theory kinetic analysis indicated that the isomerization occurred rapidly in hot cation radicals produced by electron transfer with the population-weighed rate constant of k = 8.9 × 103 s−1. The isomerization was calculated to be too slow to proceed on the experimental time scale in thermal cation radicals at 310 K. 

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4. Resonance Raman spectra and excited state properties of methyl viologen and its radical cation from time‐dependent density functional theory

   https://doi.org/10.1002/jcc.27207  

   Ozuguzel, Umut ; Aquino, Adelia J. A. ; Nieman, Reed ; Minteer, Shelley D. ; Korzeniewski, Carol ( August 2023 , Journal of Computational Chemistry)

   Time‐dependent density functional theory (TDDFT) was applied to gain insights into the electronic and vibrational spectroscopic properties of an important electron transport mediator, methyl viologen (MV²⁺). An organic dication, MV²⁺has numerous applications in electrochemistry that include energy conversion and storage, environmental remediation, and chemical sensing and electrosynthesis. MV²⁺is easily reduced by a single electron transfer to form a radical cation species (MV^•+), which has an intense UV–visible absorption near 600 nm. The redox properties of the MV²⁺/MV^•+couple and light‐sensitivity of MV^•+have made the system appealing for photo‐electrochemical energy conversion (e.g., solar hydrogen generation from water) and the study of photo‐induced charge transfer processes through electronic absorption and resonance Raman spectroscopic measurements. The reported work applies leading TDDFT approaches to investigate the electronic and vibrational spectroscopic properties of MV²⁺and MV^•+. Using a conventional hybrid exchange functional (B3‐LYP) and a long‐range corrected hybrid exchange functional (ωB97X‐D3), including with a conductor‐like polarizable continuum model to account for solvation, the electronic absorption and resonance Raman spectra predicted are in good agreement with experiment. Also analyzed are the charge transfer character and natural transition orbitals derived from the TDDFT vertical excitations calculated. The findings and models developed further the understanding of the electronic properties of viologens and related organic redox mediators important in renewable energy applications and serve as a reference for guiding the interpretation of electronic absorption and Raman spectra of the ions.

    

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5. On the Photostability of Cyanuric Acid and Its Candidature as a Prebiotic Nucleobase

   https://doi.org/10.3390/molecules27041184  

   Ortiz-Rodríguez, Luis A. ; Hoehn, Sean J. ; Crespo-Hernández, Carlos E. ( February 2022 , Molecules)

   Cyanuric acid is a triazine derivative that has been identified from reactions performed under prebiotic conditions and has been proposed as a prospective precursor of ancestral RNA. For cyanuric acid to have played a key role during the prebiotic era, it would have needed to survive the harsh electromagnetic radiation conditions reaching the Earth’s surface during prebiotic times (≥200 nm). Therefore, the photostability of cyanuric acid would have been crucial for its accumulation during the prebiotic era. To evaluate the putative photostability of cyanuric acid in water, in this contribution, we employed density functional theory (DFT) and its time-dependent variant (TD-DFT) including implicit and explicit solvent effects. The calculations predict that cyanuric acid has an absorption maximum at ca. 160 nm (7.73 eV), with the lowest-energy absorption band extending to ca. 200 nm in an aqueous solution and exhibiting negligible absorption at longer wavelengths. Excitation of cyanuric acid at 160 nm or longer wavelengths leads to the population of S5,6 singlet states, which have ππ* character and large oscillator strengths (0.8). The population reaching the S5,6 states is expected to internally convert to the S1,2 states in an ultrafast time scale. The S1,2 states, which have nπ* character, are predicted to access a conical intersection with the ground state in a nearly barrierless fashion (ca. ≤ 0.13 eV), thus efficiently returning the population to the ground state. Furthermore, based on calculated spin–orbit coupling elements of ca. 6 to 8 cm−1, the calculations predict that intersystem crossing to the triplet manifold should play a minor role in the electronic relaxation of cyanuric acid. We have also calculated the vertical ionization energy of cyanuric acid at 8.2 eV, which predicts that direct one-photon ionization of cyanuric acid should occur at ca. 150 nm. Collectively, the quantum-chemical calculations predict that cyanuric acid would have been highly photostable under the solar radiation conditions reaching the Earth’s surface during the prebiotic era in an aqueous solution. Of relevance to the chemical origin of life and RNA-first theories, these observations lend support to the idea that cyanuric acid could have accumulated in large quantities during the prebiotic era and thus strengthens its candidature as a relevant prebiotic nucleobase. 

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