Chemphyschem最新文献

Sulerythrins (SulE) are ferritin-like proteins from obligate aerobes such as Sulfolobus tokodaii, forming a domain-swapped dimer with a four-helix-bundle scaffold and a heterobimetallic Fe–Zn center. The diFe-SulE variant resembles diiron carboxylate proteins and contains two bimetallic active sites coordinated by histidines, glutamates, and bridging oxo ligands. High-resolution crystallography revealed slight differences in Fe–Fe distances and mixed-valence states, but the precise chemical nature of the oxo species remains unclear. To clarify the electronic and structural properties of diFe-SulE, we performed hybrid quantum mechanical/molecular mechanics (QM/MM) calculations on models varying in protonation, dioxo ligands, and iron redox states of the active site. Our results reveal at least three electronic states for diFe-SulE: (i) a diferrous center with an end-on di-μ-hydroperoxo ligand; (ii) a diferric center with hydroxo ligands interacting with protonated Glu95; and (iii) a diferrous center bridged by a di-μ-peroxo ligand, also interacting with protonated Glu95. These states are consistent with the structural heterogeneity observed experimentally. Overall, the hybrid QM/MM approach refines the crystallographic models and offers subatomic-level insight into the electronic structure and reactivity of the SulE diiron center, deepening our understanding of nonheme diiron enzymes.

In this study, constant potential molecular dynamics simulations have been employed to investigate the impact of sodium fluorosulfonyl(trifluoromethylsulfonyl)amide (NaFTA) salt on the interfacial properties of 1-methyl-1-propylpyrrolidinium fluorosulfonyl(trifluoromethylsulfonyl)amide (Pyrr_1,3FTA) ionic liquid (IL) confined between two graphite electrodes at different applied potential differences. For the pure IL, it is observed that at higher negative voltages, the FTA⁻ anions are completely replaced by Pyrr_1,3⁺ cations, resulting in an unsolvated cation near the negative electrode. In the salt–IL solutions, at 0.1 mole fraction of the salt, most of the Na⁺ ions are found to interact with the FTA⁻ near the positive electrode, and a moderate presence of Na⁺ ions is observed closer to the negative electrode. Interestingly, accumulation of Na⁺ ions near both the electrodes is observed in the solution having highest mole fraction of the salt (x^NaFTA = 0.3). A nonmonotonous change in the intensity of the peaks in the number density profile of the Na⁺ ions is observed near the positive electrode surface. Analysis of the average orientational order parameter for the Pyrr_1,3⁺ cations reveals a parallel arrangement of their ring closer to the negative electrode, which is minimally affected by the presence of NaFTA salt. The distribution of the C-S-S-F improper dihedral angle of the FTA⁻ ions near the positive electrode (+2.5 V) interfacial region shows that the probability of finding their $$ conformation increases up to 0.2 mole fraction of the salt.

By stabilizing weak and transient protein–protein interactions (PPIs), molecular glues address the challenge of targeting proteins previously considered undruggable. Rapamycin and WDB002 are molecular glues that bind to FK506-binding protein (FKBP12) and target the FKBP12-rapamycin-associated protein (FRAP) and the centrosomal protein 250 (CEP250), respectively. Herein, molecular dynamics simulations were used to gain insights into the effects of molecular glues on protein conformation and PPIs. The molecular glues modulated protein flexibility, leading to less flexibility in some regions, and changed the pattern and stability of water-mediated hydrogen bonds between the proteins. In the FKBP12-FRAP-rapamycin complex, two out of three water-mediated hydrogen bonds present in the crystallographic structure are more stable in the presence of the molecular glue, while in the FKBP12-CEP250-WDB002 complex, more water-mediated hydrogen bonds are present in the presence of the molecular glue, and they displayed higher stability. The findings highlight the importance of considering water-mediated hydrogen bonds in developing strategies for the rational design of molecular glues.

Exciton coupling model provides one of the most intuitive and powerful frameworks to directly connect molecular structure with chiroptical responses. This review focuses on rigid architectures with C₂ symmetry, in which conformational rigidity, symmetry constraints, and independent chromophores allow for direct correlations among molecular geometry, Davydov splitting, and electronic circular dichroism intensity. After introducing the theoretical basis of exciton coupling and its crucial role in absolute configuration assignment, we analyze how molecular design strategies control the conformational space, as well as how the electron transition dipole moments of interacting chromophores enable the modulation of dissymmetry factors (g-factors). Next, we expand these principles from isolated molecules to supramolecular assemblies, thin films, and polymers, where cooperative effects and new structural constraints can come into play to amplify or distort excitonic signatures. Overall, this review compiles transferable design principles to guide the development of next-generation chiroptical materials with broad relevance for sensing, optoelectronic, and spintronic applications.

Using combined geometry optimization and electronic analyses, it is examined how metal nature (alkali and Cu(I)), solvation (THF), ligands, and aggregation modulate the N- versus C-bonding balance in metalated acetonitrile. C-binding is energetically favored in covalent Cu(I) complexes, while lithiated species prefer N-binding. Surprisingly, N-metalated species do not all exhibit the expected ketenimine-like character (CCN, lone pair on N), but a nitrile-like one (C^bC≡N, lone pair on C^b) also emerges from the natural bond orbital analyses. Ketenimines are stabilized by polarizing or covalent MN bonds, while nitriles are obtained with weakly coordinating cations or in anionic species. Notably, an external electric field can induce a similar electronic reorganization, thus revealing the electronic flexibility of metalated nitriles.

Metal responsive transcription factors are essential for bacterial metal homeostasis, allowing cells to regulate metal uptake, efflux, and detoxification in response to fluctuating metal ion levels. Among these, CueR, a member of the MerR family, is widely found in Gram-negative bacteria. While E. coli CueR has been extensively studied, revealing that it adopts multiple conformational states to regulate transcription, P. aeruginosa CueR (PACueR) remains less characterized, with no resolved structure despite regulating a broader set of genes. In this study, we applied electron paramagnetic resonance (EPR) spectroscopy combined with DNA spin-labeling to investigate the conformational states of PACueR bound to two different promoter sequences, copZ2 and mexPQ-opmE. We examined the effects of PACueR binding and copper addition, capturing the transcription initiation stage that represents an essential step in copper homeostasis regulation of P. aeruginosa. Our results reveal promoter-specific differences in PACueR DNA interactions, suggesting that while the core transcription initiation mechanism is conserved, variations in promoter affinity and length of dyad symmetry fine-tune transcription levels in response to copper. These findings highlight the value of EPR spectroscopy in probing metal-dependent transcription mechanisms and offer new insights into copper regulation in P. aeruginosa, a clinically important pathogen.

The Front Cover shows how aromatic cyano compounds might have played an important role in the molecular complexity associated with the origin of life. Benzonitrile interacts with low-energy electrons to produce CN⁻ anions through coupling between π* and σ* orbitals, which leads to C─CN bond cleavage. More information can be found in the Research Article by L. M. Cornetta, F. Ferreira da Silva and co-workers (DOI: 10.1002/cphc.202500206).

Stimulated by recent findings of a beneficial effect of a high-temperature treatment on the activity and selectivity of highly active and selective Ru/TiO₂ catalysts in the CO_x methanation, a detailed study of the dynamic changes in the chemical and structural properties is performed, induced by this treatment and their correlation with the changes in the catalytic performance of the catalyst. These changes are characterized by time-resolved operando X-ray absorption spectroscopy at the Ru and Ti K-edges, together with structural characterization by high-resolution transmission electron microscopy. The observation of differently long times required for the reduction of the oxidic Ru nanoparticles in CO-free CO₂/H₂ gas mixtures (1000 min) and in trace amounts of CO containing CO/CO₂/H₂ gas mixtures (100 min) under reaction conditions (190 °C, atmospheric pressure) correlates very well with the different times required for catalyst activation in these reaction gas mixtures.

Modular synthetic modification to ligand scaffolds of metal complexes provides an approach to rational improvement of existing molecular catalytic systems. A previous report from the Marinescu group has shown that a cobalt phosphino thiolate complex ([Co(triphos)(bdt)]⁺) has excellent selectivity and activity for electrocatalytic CO₂ reduction to formate. Here, a multimetallic analogue, [Co₃(triphos)₃(tht)]³⁺, that is conjugated through a trinucleating dithiolene ligand in the form of triphenylene–2,3,6,7,10,11–hexathiolate is investigated. While voltammetric studies indicate enhanced current densities under similar conditions to [Co(triphos)(bdt)]⁺, electrolysis and ultraviolet–visible spectroscopy results suggest significant catalyst degradation and overall moderate faradaic yields.

The ionizing radiation acting on DNA results in various kinds of damage including base modifications. The Cover Feature illustrates the appearance of 8-oxo-guanine (OG) and 5-formyl-cytosine (5fC) as oxidation products resulting from the indirect effect of radiation on the DNA double helix. The picture highlights the high mutagenicity of the OG lesion, which can mispair with adenine, guanine, and thymine bases, leading to transition and transversion mutations after DNA replication. More information can be found in the Research Article by V. Poltev and co-workers (DOI: 10.1002/cphc.202400964). Cover design by V.D. and V.P.