Photophysical Deactivation Mechanisms of the Pyrimidine Analogue 1-Cyclohexyluracil

The photophysical relaxation mechanisms of 1-cyclohexyluracil, in vacuum and water, were investigated by employing the Multi-State CASPT2 (MS-CASPT2, Multi-State Complete Active-Space Second-Order Perturbation Theory) quantum chemical method and Dunning’s cc-pVDZ basis sets. In both environments, our results suggest that the primary photophysical event is the population of the S11(ππ*) bright state. Afterwards, two likely deactivation pathways can take place, which is sustained by linear interpolation in internal coordinates defined via Z-Matrix scans connecting the most important characteristic points. The first one (Route 1) is the same relaxation mechanism observed for uracil, its canonical analogue, i.e., internal conversion to the ground state through an ethylenic-like conical intersection. The other route (Route 2) is the direct population transfer from the S11(ππ*) bright state to the T23(nπ*) triplet state via an intersystem crossing process involving the (S11(ππ*)/T23(nπ*))STCP singlet-triplet crossing point. As the spin-orbit coupling is not too large in either environment, we propose that most of the electronic population initially on the S11(ππ*) state returns to the ground following the same ultrafast deactivation mechanism observed in uracil (Route 1), while a smaller percentage goes to the triplet manifold. The presence of a minimum on the S11(ππ*) potential energy hypersurface in water can help to understand why experimentally it is noticed suppression of the triplet states population in polar protic solvent.     

Galvano-Fenton Engineering Solution with Spontaneous Catalyst’s Generation from Waste: Experimental Efficiency,Parametric Analysis and Modeling Interpretation Applied to a Clean Technology for Dyes Degradation in Water

In this paper, the degradation of the diazo dye naphthol blue black (NBB) using the Galvano-Fenton process is studied experimentally and numerically. The simulations are carried out based on the anodic, cathodic, and 34 elementary reactions evolving in the electrolyte, in addition to the oxidative attack of NBB by HO• at a constant rate of 3.35×107 mol−1·m3·s−1 during the initiation stage of the chain reactions. The selection of the operating conditions including the pH of the electrolyte, the stirring speed, and the electrodes disposition is performed by assessing the kinetics of NBB degradation; these parameters are set to 3, 350 rpm and a parallel disposition with a 3 cm inter-electrode distance, respectively. The kinetics of Fe(III) in the electrolyte were monitored using the principles of Fricke dosimetry and simulated numerically. The model showed more than a 96% correlation with the experimental results in both the blank test and the presence of the dye. The effects of H2O2 and NBB concentrations on the degradation of the dye were examined jointly with the evolution of the simulated H2O2, Fe2+, and HO• concentrations in the electrolyte. The model demonstrated a good correlation with the experimental results in terms of the initial degradation rates, with correlation coefficients exceeding 98%.     

Incorporation of 4J-HMBC and NOE Data into Computer-Assisted Structure Elucidation with WebCocon

Over the past decades, different software programs have been developed for the Computer-Assisted Structure Elucidation (CASE) with NMR data using with various approaches. WebCocon is one of them that has been continuously improved over the past 20 years. Here, we present the inclusion of 4J_CH correlations (4J-HMBC) in the HMBC interpretation of Cocon and NOE data in WebCocon. The 4J-HMBC data is used during the structure generation process, while the NOE data is used in post-processing of the results. The marine natural product oxocyclostylidol was selected to demonstrate WebCocon’s enhanced HMBC data processing capabilities. A systematic study of the 4J_CH correlations of oxocyclostylidol was performed. The application of NOEs in CASE is demonstrated using the NOE correlations of the diterpene pyrone asperginol A known from the literature. As a result, we obtained a conformation that corresponds very well to the existing X-ray structure.     

Spectral Signatures of Hydrogen Thioperoxide (HOSH) and Hydrogen Persulfide (HSSH): Possible Molecular Sulfur Sinks in the Dense ISM

For decades, sulfur has remained underdetected in molecular form within the dense interstellar medium (ISM), and somewhere a molecular sulfur sink exists where it may be hiding. With the discovery of hydrogen peroxide (HOOH) in the ISM in 2011, a natural starting point may be found in sulfur-bearing analogs that are chemically similar to HOOH: hydrogen thioperoxide (HOSH) and hydrogen persulfide (HSSH). The present theoretical study couples the accuracy in the anharmonic fundamental vibrational frequencies from the explicitly correlated coupled cluster theory with the accurate rotational constants provided by canonical high-level coupled cluster theory to produce rovibrational spectra for use in the potential observation of HOSH and HSSH. The ν6 mode for HSSH at 886.1 cm−1 is within 0.2 cm−1 of the gas-phase experiment, and the B0 rotational constant for HSSH of 6979.5 MHz is within 9.0 MHz of the experimental benchmarks, implying that the unknown spectral features (such as the first overtones and combination bands) provided herein are similarly accurate. Notably, a previous experimentally-attributed 2ν1 mode, at 7041.8 cm−1, has been reassigned to the ν1+ν5 combination band based on the present work’s ν1+ν5 value at 7034.3 cm−1. The most intense vibrational transitions for each molecule are the torsions, with HOSH having a more intense transition of 72 km/mol compared to HSSH’s intensity of 14 km/mol. Furthermore, HOSH has a larger net dipole moment of 1.60 D compared to HSSH’s 1.15 D. While HOSH may be the more likely candidate of the two for possible astronomical observation via vibrational spectroscopy due to the notable difference in their intensities, both HSSH and HOSH have large enough net dipole moments to be detectable by rotational spectroscopy to discover the role these molecules may have as possible molecular sulfur sinks in the dense ISM.     

Fluorescent Liquid Tetrazines

Tetrazines with branched alkoxy substituents are liquids at ambient temperature that despite the high chromophore density retain the bright orange fluorescence that is characteristic of this exceptional fluorophore. Here, we study the photophysical properties of a series of alkoxy-tetrazines in solution and as neat liquids. We also correlate the size of the alkoxy substituents with the viscosity of the liquids. We show using time-resolved spectroscopy that intersystem crossing is an important decay pathway competing with fluorescence, and that its rate is higher for 3,6-dialkoxy derivatives than for 3-chloro-6-alkoxytetrazines, explaining the higher fluorescence quantum yields for the latter. Quantum chemical calculations suggest that the difference in rate is due to the activation energy required to distort the tetrazine core such that the nπ*S1 and the higher-lying ππ*T2 states cross, at which point the spin-orbit coupling exceeding 10 cm−1 allows for efficient intersystem crossing to occur. Femtosecond time-resolved anisotropy studies in solution allow us to measure a positive relationship between the alkoxy chain lengths and their rotational correlation times, and studies in the neat liquids show a fast decay of the anisotropy consistent with fast exciton migration in the neat liquid films.     

Synthesis and characterization of the azido-bound five-coordinate high-spin iron(II) “picket fence” porphyrin complex

An Fe(II)-azido five-coordinate picket fence porphyrin complex with the formula [Na(2,2,2-crypt)][Fe^II(TpivPP)(N₃)] · 3C₆H₅Cl (TpivPP = α,α,α,α-tetrakis(o-pivalamidophenyl)porphinato, known as a picket fence porphyrin, and 2,2,2-crypt is the cryptand-222) has been synthesized and characterized. The synthesis utilizes cryptand-222 to solubilize sodium azide in the preparation procedure. The UV–Vis and IR spectroscopic data are consistent with an azido ferrous porphyrinate. The X-ray structural analysis and the Mössbauer results indicate that the ion complex [Fe^II(TpivPP)(N₃)]⁻ is high-spin and has the (d_xy)²(d_xz)¹(d_yz)¹(d_z2)¹(d_x2-y2)¹$({\text{d}}_{\mathit{xy}}{)}^2({\text{d}}_{\mathit{xz}}{)}^1({\text{d}}_{\mathit{yz}}{)}^1({\text{d}}_{z^2}{)}^1({\text{d}}_{x^2-y^2}{)}^1$ ground state electronic configuration.     

Cn,CnH and their anions: Quest for linearity with n≤8 even versus odd,and beyond

Using the concept of quasi-molecule (“tile”) and the database of quasi-molecules embedded on a parent molecule, it is discussed whether the latter can attain linear form or otherwise. Besides anew accurate optimization of all tiles (quasi-triatomics) at various levels of ab initio theory and basis-sets, the nature of the predicted stationary points for the title parent molecules is probed through a priori calculations here too reported. Also discussed is the common rule that even- $n$ ${\text{C}}_n{\text{H}}^{-}$ anions are linear while odd-numbered ones tend to have nonlinear isomers. The reported quasi-molecule approach is general, and allow the prediction of linearity or otherwise of the parent systems prior to calculations on them. When based on an extension of the bisection method (Varandas, Int. J. Quantum Chem. 2023 , 123, e27036.), it is easy to use even for large parent molecules, as illustrated for neutral and anionic carbon clusters with $n\ge 9$.     

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller–Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers’ stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm−1–1700 cm−1 and 2300 cm−1–3400 cm−1 in the gas phase and 600 cm−1–1800 cm−1 and 2200 cm−1–3400 cm−1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm−1–1700 cm−1 and 2300 cm−1–3300 cm−1 for the gas phase and one broad absorption region in the solid state between 700 cm−1 and 3100 cm−1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.     

Anharmonic Vibrational Frequencies of Water Borane and Associated Molecules

Water borane (BH3OH2) and borinic acid (BH2OH) have been proposed as intermediates along the pathway of hydrogen generation from simple reactants: water and borane. However, the vibrational spectra for neither water borane nor borinic acid has been investigaged experimentally due to the difficulty of isolating them in the gas phase, making accurate quantum chemical predictions for such properties the most viable means of their determination. This work presents theoretical predictions of the full rotational and fundamental vibrational spectra of these two potentially application-rich molecules using quartic force fields at the CCSD(T)-F12b/cc-pCVTZ-F12 level with additional corrections included for the effects of scalar relativity. This computational scheme is further benchmarked against the available gas-phase experimental data for the related borane and HBO molecules. The differences are found to be within 3 cm−1 for the fundamental vibrational frequencies and as close as 15 MHz in the B0 and C0 principal rotational constants. Both BH2OH and BH3OH2 have multiple vibrational modes with intensities greater than 100 km mol−1, namely ν2 and ν4 in BH2OH, and ν1, ν3, ν4, ν9, and ν13 in BH3OH2. Finally, BH3OH2 has a large dipole moment of 4.24 D, which should enable it to be observable by rotational spectroscopy, as well.     

Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates

Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (μ) are necessary to optimize coupling within dye aggregates. Extinction coefficients (ε) can be used to determine the μ of dyes, and so dyes with a large ε (>150,000 M⁻¹cm⁻¹) should be engineered or identified. However, dye properties leading to a large ε are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations, can be time-consuming. In order to screen large datasets of molecules for desirable properties (i.e., large ε and μ), a computational workflow was established using machine learning (ML), DFT, time-dependent (TD-) DFT, and molecular dynamics (MD). ML models were developed through training and validation on a dataset of 8802 dyes using structural features. A Classifier was developed with an accuracy of 97% and a Regressor was constructed with an R2 of above 0.9, comparing between experiment and ML prediction. Using the Regressor, the ε values of over 18,000 dyes were predicted. The top 100 dyes were further screened using DFT and TD-DFT to identify 15 dyes with a μ relative to a reference dye, pentamethine indocyanine dye Cy5. Two benchmark MD simulations were performed on Cy5 and Cy5.5 dimers, and it was found that MD could accurately capture experimental results. The results of this study exhibit that our computational workflow for identifying dyes with a large μ for excitonic applications is effective and can be used as a tool to develop new dyes for excitonic applications.