The precise engineering of vacancies in nitrogen-doped graphene (NG) presents a promising strategy for stabilizing metal single-atom catalysts (SACs) and tuning their catalytic performance. We explore the role of vacancies in NG for stabilizing iron-based SACs (Fe-SACs) by using density functional theory (DFT). First, we examine the stability of various vacancy types in graphene and NG supports, addressing the question of preferential formation of specific structural defects as potential sites for metal binding. We reveal simple rules governing the stability of vacancies and show that nitrogen doping can bring about vacancy healing. We identify preferred binding sites for Fe atoms/ions, specifically single and double vacancies, and analyze how the nitrogen-doping pattern in a vacancy affects the interaction of Fe with the SAC support. The results show that the positions of nitrogen(s) and the local charge environment significantly influence the stability of the Fe-SACs. Notably, some Fe@NG configurations, although not the most thermodynamically stable, exhibit enhanced catalytic performance, particularly for a CO2 reduction reaction (CO2RR). These findings offer valuable insights into vacancy engineering as a strategy for designing high-performance Fe-SACs and emphasize the interplay among vacancy types, nitrogen concentration, and catalyst stability in driving the catalytic behavior.

• Klíčová slova
• Activity, CO2RR, SAC, Single-atom catalysis, Stability,
• Publikační typ
• časopisecké články MeSH

This study explores the structural and electronic factors affecting the absorption spectra of 5-carboxy-tetramethylrhodamine (TAMRA) in water, a widely used fluorophore in imaging and molecular labeling in biophysical studies. Through molecular dynamics (MD) simulations and density functional theory (DFT) calculations, we examine TAMRA UV absorption spectra together with TAMRA-labeled peptides (Arg9, Arg4, Lys9). We found that DFT calculations with different functionals underestimate TAMRA maximum UV absorption peak by ~100 nm, resulting in the maximum at ca. 450 nm instead of the experimental value of ca. 550 nm. However, incorporating MD simulation snapshots of TAMRA in water, the UV maximum peak shifts and is in close agreement with the experimental results due to the rotation of TAMRA N(CH3)2 groups, effectively captured in MD simulations. The method is used to estimate the UV absorption spectra of TAMRA-labeled peptides, matching experimental values.

• Klíčová slova
• UV absorption spectra, fluorescent probes, molecular dynamics simulations, time‐dependent density functional theory,
• MeSH
• fluorescenční barviva * chemie   MeSH
• peptidy * chemie   MeSH
• rhodaminy * chemie   MeSH
• simulace molekulární dynamiky * MeSH
• spektrofotometrie ultrafialová MeSH
• teorie funkcionálu hustoty * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• fluorescenční barviva * MeSH
• peptidy * MeSH
• rhodaminy * MeSH
• tetramethylrhodamine MeSH Prohlížeč

The binding free energy of hydrogen-bonded complexes is generally inversely proportional to the solvent dielectric constant. This occurs because the solvent-accessible surface area of the complex is always smaller than that of the individual subsystems, leading to a reduction in solvation energy. The present study explores the potential for stabilizing hydrogen-bonded complexes in a solvent with higher polarity. Contrary to the established understanding, we have demonstrated that the hydrogen-bonded complex (CH3CH2COOH⋅⋅⋅2,4,6-trimethylpyridine) can be better stabilized in a solvent with higher polarity. In this case, a significant charge transfer between the subsystems results in an increased dipole moment of the complex, leading to its stabilization in a more polar solvent. The expected inverse relationship between binding free energy and solvent dielectric constant is observed when the charge transfer between the subsystems is low. Thus, the magnitude of the charge transfer between subsystems is possibly the key factor in determining the stabilization or destabilization of H-bonded complexes in different solvents. Here, we present a comprehensive study that combines experimental and theoretical approaches, including nuclear magnetic resonance (NMR), infrared (IR) spectroscopies and quantum chemical calculations to validate the findings.

• Klíčová slova
• Hydrogen bonding, IR, Metadynamics, Micro-solvation, NMR, ONIOM, Solvent effect,
• Publikační typ
• časopisecké články MeSH

An activity-guided isolation study on the EtOH extract prepared from the bulbs of Prospero autumnale yielded four new phenolic compounds, including a new stilbenoid (1), a new homoisoflavonoid derivative (8), a new homoisoflavonoid dimer (9), and an unprecedented homoisoflavone-stilbene heterodimer (10), together with six known (2-7) analogs. Their chemical structures were elucidated by spectroscopic analysis and theoretical NMR and ECD calculations. Compounds 9 and 10 are unique in their scaffolds. The in vitro cytotoxic activity of purified compounds was evaluated against eight tumor cell lines (HCT116, LoVo, DU145, PC3, HEP3B, HEPG2, MCF7, and MDA-MB-231) and one nontumor cell line (L929) by the MTS assay. Compounds 1, 2, 4, and 10 exhibited inhibition with IC50 values ranging from 8.2 to 37.6 μM. Cytotoxic cell death mechanisms were further investigated, indicating variability in apoptosis, necrosis, or cell cycle arrest.

• MeSH
• apoptóza účinky léků   MeSH
• fytogenní protinádorové látky * farmakologie   chemie   MeSH
• isoflavony farmakologie   chemie   izolace a purifikace   MeSH
• kořeny rostlin chemie   MeSH
• lidé MeSH
• molekulární struktura MeSH
• nádorové buněčné linie MeSH
• screeningové testy protinádorových léčiv MeSH
• stilbeny * farmakologie   chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• fytogenní protinádorové látky * MeSH
• isoflavony MeSH
• stilbeny * MeSH

Two chiral bambusurils, which are diastereomers to each other, show remarkable differences in their binding affinity and selectivity toward inorganic anions as determined by isothermal titration calorimetry. These differences are explained by quantum-chemical calculations.

• Publikační typ
• časopisecké články MeSH

We report the design, synthesis, electrochemical, UV-vis, fluorescence, and computational study of nine π-linked donor-acceptor (D-π-A) chromophores. The series of novel compounds comprises a terphenyl, terthiophene, or 2,5-diphenyl thiophene linker, with one electron-donating group (methyl or p-N,N-diethyl) and one electron-withdrawing group (nitrone, formyl, or dicyanovinyl) at opposite ends of the molecule. The HOMO-LUMO gaps were determined via cyclic voltammetry and found to correspond well to DFT-calculated values. Furthermore, the influence of the π-linker character and substituent on the HOMO-LUMO gap was analysed and interpreted in terms of MO composition via DFT.

• Publikační typ
• časopisecké články MeSH

Herein, we report radical chlorination of cubane-1,4-dicarboxylic acid leading preferentially to one monochlorinated cubane dicarboxylate (ca. 70%) that is accompanied by four dichlorinated derivatives (ca. 20% in total). The exact positions of the chlorine atoms have been confirmed by X-ray diffraction of the corresponding single crystals. The acidity constants of all dicarboxylic acids in water were determined by capillary electrophoresis (3.17 ± 0.04 and 4.09 ± 0.05 for monochlorinated and ca. 2.71 ± 0.05 and 3.75 ± 0.05 for dichlorinated cubanes). All chlorinated derivatives as well as the parent diacid showed high thermal stability (decomposition above 250 °C) as documented by differential scanning calorimetry. The probable reaction pathways leading to individual isomers were proposed, and the energies of individual transition states and intermediates were obtained using density functional theory calculations (B3LYP-D3BJ/6-311+G(d,p)). The relative strain energies for all newly prepared derivatives as well as for hypothetical hexahalogenated (fluorinated, chlorinated, brominated, and iodinated) derivatives of cubane-1,4-dicarboxylic acids were predicted using wavefunction theory methods. The hexafluorinated derivative was identified as the most strained compound (57.5 kcal/mol), and the relative strain decreased as the size of halogen atoms increased (23.7 for hexachloro, 16.7 for hexabromo, and 4.0 kcal/mol for the hexaiodo derivative).

• Publikační typ
• časopisecké články MeSH

Polarons belong to a class of extensively studied quasiparticles that have found applications spanning diverse fields, including charge transport, colossal magnetoresistance, thermoelectricity, (multi)ferroism, optoelectronics, and photovoltaics. It is notable, though, that their interaction with the local environment has been overlooked so far. We report an unexpected phenomenon of the solvent-induced generation of polaronic spin active states in a two-dimensional (2D) material fluorographene under UV light. Furthermore, we present compelling evidence of the solvent-specific nature of this phenomenon. The generation of spin-active states is robust in acetone, moderate in benzene, and absent in cyclohexane. Continuous wave X-band electron paramagnetic resonance (EPR) spectroscopy experiments revealed a massive increase in the EPR signal for fluorographene dispersed in acetone under UV-light irradiation, while the system did not show any significant signal under dark conditions and without the solvent. The patterns appeared due to the generation of transient magnetic photoexcited states of polaronic character, which encompassed the net 1/2 spin moment detectable by EPR. Advanced ab initio calculations disclosed that polarons are plausibly formed at radical sites in fluorographene which interact strongly with acetone molecules in their vicinity. Additionally, we present a comprehensive scenario for multiplication of polaronic spin active species, highlighting the pivotal role of the photoinduced charge transfer from the solvent to the electrophilic radical centers in fluorographene. We believe that the solvent-tunable polaron formation with the use of UV light and an easily accessible 2D nanomaterial opens up a wide range of future applications, ranging from molecular sensing to magneto-optical devices.

• Publikační typ
• časopisecké články MeSH

Protonation states of molecules significantly influence the thermodynamics and kinetics of chemical reactions. This is especially important in biochemical processes, where appropriate protonation states of amino acids control the exo/endoergicity of practically all biochemical cycles. This paper is focused on appraisal of the impact of DFT functionals and PCM solvation models on the accuracy of pKa evaluations for all proteinogenic amino acids. Eight functionals (B3LYP, PBE0, revPBE0, M06-2X, M11, M11-L, TPSSh, and ωB97X-D) and four basis sets are considered, together with four kinds of implicit solvation models when additional attention is paid to a cavity construction. An influence of nonelectrostatic contributions and Wertz's corrections on Gibbs free energy is investigated together with accuracy of provided proton solvation energy. The best model is based on the M06-2X/6-311++G**/D-PCM/UAKS computational level. The fitting procedure is utilized to improve the accuracy of the evaluated models. All of these results are also compared with values obtained from the COSMOtherm program and CCSD(T) calculations. Results for cysteine and histidine are discussed individually, as they can be found in different protonation states at neutral pH.

• Publikační typ
• časopisecké články MeSH

Green hydrogen, by definition, must be produced with renewable energy sources without using fossil fuels. To transform the energy system, we need a fully sustainable production of green and renewable energy as well as the introduction of such "solar fuels" to tackle the chemical storage aspect of renewable energies. Conventional electrolysis of water splitting into oxygen and hydrogen gases is a clean and nonfossil method, but the use of massive noble-metal electrodes makes it expensive. Direct photocatalytic hydrogen evolution in water is an ideal approach, but an industrial scale is not available yet. In this paper, we intend to introduce flavins as metal-free organic photosensitizers for photoinduced reduction processes. Specifically, a flavin photosensitizer was employed for the photocatalytic evolution of hydrogen gas in aqueous media. The ratio of photosensitizer to cocatalyst concentration has been found to affect the efficiency of the hydrogen evolution reaction. Since flavins are nature-inspired molecules (like vitamin B2) with easily tunable properties through structure modification, this family of compounds opens the door for new possibilities in sustainable green hydrogen production.

• Publikační typ
• časopisecké články MeSH