Current Understanding of the Mechanism of Water Oxidation in Photosystem II and Its Relation to XFEL Data.

The investigation of water oxidation in photosynthesis has remained a central topic in biochemical research for the last few decades due to the importance of this catalytic process for technological applications. Significant progress has been made following the 2011 report of a high-resolution X-ray crystallographic structure resolving the site of catalysis, a protein-bound Mn4CaOx complex, which passes through ≥5 intermediate states in the water-splitting cycle. Spectroscopic techniques complemented by quantum chemical calculations aided in understanding the electronic structure of the cofactor in all (detectable) states of the enzymatic process. Together with isotope labeling, these techniques also revealed the binding of the two substrate water molecules to the cluster. These results are described in the context of recent progress using X-ray crystallography with free-electron lasers on these intermediates. The data are instrumental for developing a model for the biological water oxidation cycle.

Copper(II) coordination to the intrinsically disordered region of SARS-CoV-2 Nsp1.

The intrinsically disordered C-terminal peptide region of severe acute respiratory syndrome coronavirus 2 nonstructural protein-1 (Nsp1-CT) inhibits host protein synthesis by blocking messenger RNA (mRNA) access to the 40S ribosome entrance tunnel. Aqueous copper(II) ions bind to the disordered peptide with micromolar affinity, creating a possible strategy to restore protein synthesis during host infection. Electron paramagnetic resonance (EPR) and tryptophan fluorescence measurements on a 10-residue model of the disordered protein region (Nsp1-CT10), combined with advanced quantum mechanics calculations, suggest that the peptide binds to copper(II) as a multidentate ligand. Two optimized computational models of the copper(II)-peptide complexes were derived: One corresponding to pH 6.5 and the other describing the complex at pH 7.5 to 8.5. Simulated EPR spectra based on the calculated model structures are in good agreement with experimental spectra.

A robust computational quest: Discovering potential hits to improve the treatment of pyrazinamide-resistant Mycobacterium tuberculosis.

The rise of pyrazinamide (PZA)-resistant strains of Mycobacterium tuberculosis (MTB) poses a major challenge to conventional tuberculosis (TB) treatments. PZA, a cornerstone of TB therapy, must be activated by the mycobacterial enzyme pyrazinamidase (PZase) to convert its active form, pyrazinoic acid, which targets the ribosomal protein S1. Resistance, often associated with mutations in the RpsA protein, complicates treatment and highlights a critical gap in the understanding of structural dynamics and mechanisms of resistance, particularly in the context of the G97D mutation. This study utilizes a novel integration of computational techniques, including multiscale biomolecular and molecular dynamics simulations, physicochemical and medicinal chemistry predictions, quantum computations and virtual screening from the ZINC and Chembridge databases, to elucidate the resistance mechanism and identify lead compounds that have the potential to improve treatment outcomes for PZA-resistant MTB, namely ZINC15913786, ZINC20735155, Chem10269711, Chem10279789 and Chem10295790. These computational methods offer a cost-effective, rapid alternative to traditional drug trials by bypassing the need for organic subjects while providing highly accurate insight into the binding sites and efficacy of new drug candidates. The need for rapid and appropriate drug development emphasizes the need for robust computational analysis to justify further validation through in vitro and in vivo experiments.

Generation and Identification of the Trifluorosilylarsinidene F3SiAs and Isomeric Perfluorinated Arsasilene FAsSiF2.

The trifluorosilylarsinidene F3SiAs in the triplet ground state has been generated through the reaction of laser-ablated silicon atoms with AsF3 in cryogenic Ne- and Ar-matrices. The reactions proceed with the initial formation of perfluorinated arsasilene FAsSiF2 in the singlet ground state by two As-F bonds insertion reaction on annealing. The trifluorosilylarsinidene F3SiAs was formed via F-migration reactions of FAsSiF2 under irradiation at UV light (λ = 275 nm). The characterization of FAsSiF2 and F3SiAs by IR matrix-isolation spectroscopy is supported by computations at CCSD(T)-F12/aug-cc-pVTZ and B3LYP/aug-cc-pVTZ levels of theory.

On Haptotropic Rearrangements of Diphosphene and Diarsene Ligands in Titanium Complexes.

Dipnictenes of the type RE=ER (E=P, As, Sb, Bi) are the isovalence electronic heavier analogs of alkenes. Although diphosphenes and dipnictenes in general show a variety of binding modes in metal complexes, little is known about haptotropic shift reactions involving these ligands. Herein, we report an unprecedented η2 to η1 rearrangement of the dipnictene ligands in titanocene complexes of the type Cp2Ti(Pn2Ar2) (Pn=P, As; Ar=2,4,6-Me3-C6H2, Mes; 2,6-iPr2-C6H3, Dip; 2,4,6-iPr3-C6H2, Tip), initiated by Lewis basic ligands (L=MeCN, PMe3, AdNC, CO). In the presence of L the dipnictene ligand changes its hapticity from η2 to η1 and complexes of the general form Cp2Ti(L)(Pn2Ar2) with a succinctly different electronic structure are obtained. Electronically, the new complexes are best described as biradicaloids with antiferromagnetically coupled (via a π-bond) [Cp2TiIII]⋅+ and [Pn2Ar2]⋅- fragments. However, the biradical character of these systems is affected by the electronic features of the co-ligand and significantly decreases moving from PMe3/MeCN (σ-donors) to CNAd/CO (σ-donors/π-acceptors).

Nucleophilicity of 4-(Alkylthio)-3-imidazoline Derived Enamines.

Imidazolidine-4-thiones (ITOs) are cyclic, secondary amines that were considered as potential prebiotic organocatalysts for light-driven α-alkylations of aldehydes by bromoacetonitrile (BAN). Recent studies showed that the initially supplied ITOs represent the pre-catalyst because they undergo S-alkylation with BAN to give 4-(alkylthio)-3-imidazolines (TIMs). Given that the same reagent mix that undergoes light-driven α-alkylations is also effective in the dark, we synthesized ten ITO- or TIM-derived enamines of aldehydes and characterized their nucleophilic reactivities by kinetic studies in acetonitrile. The experimental second-order rate constants k2 for reactions of enamines with benzhydrylium ions (reference electrophiles) were evaluated by the Mayr-Patz equation, lg k2 (20 °C)=sN (N+E). The determined nucleophilicities N (and sN ) reveal the reactivity profiles of these enamines under prebiotically relevant conditions as well as their potential for use in organocatalytic synthesis.

Synthesis and Structure of the Small Superelectrophile [C2(OH)2Me2]2.

The acid-activation of 1,2-dicarbonyl compounds plays a key role in a variety of electrophilic reactions, some of which are only accessible in superacidic media when a superelectrophilic dication is formed. To obtain structural and electronic information about these elusive species, the vicinal dication [C2(OH)2Me2]2+ is synthesized and characterized by Raman spectroscopy and X-ray diffraction. Since this superelectrophile could not be stabilized in convenient superacids, the usage of liquid SO2 turned out to be crucial. The experimental data are discussed together with quantum-chemical calculations on the B3LYP/aug-cc-pVTZ level of theory. Natural Bond Orbital (NBO) analyses quantify the superelectrophilic interactions found in the solid state.

Central Ring Puckering Enhances the Stokes Shift of Xanthene Dyes.

Small-molecule dyes are generally designed based on well-understood electronic effects. However, steric hindrance can promote excited-state geometric relaxation, increasing the difference between the positions of absorption and emission bands (the Stokes shift). Accordingly, we hypothesized that sterically induced central ring puckering in xanthene dyes could be used to systematically increase their Stokes shift. Through a combined experimental/quantum-chemical approach, we screened a group of (9-acylimino)-pyronin dyes with a perturbed central ring geometry. Our results showed that an atom with sp3 hybridization in position 10 of (9-acylimino)-pyronins induces central ring puckering and facilitates excited-state geometric relaxation, thereby markedly enhancing their Stokes shifts (by up to ~2000 cm-1). Thus, we prepared fluorescent (9-acylimino)-pyronin pH sensors, which showed a Stokes shift disparity between acid and base forms of up to ~8700 cm-1. Moreover, the concept of ring puckering-enhanced Stokes shift can be applied to a wide range of xanthene analogues found in the literature. Therefore, central ring puckering may be reliably used as a strategy for enhancing Stokes shifts in the rational design of dyes.

The Perfluoro-o-phenylene-mercury Trimer [Hg(o-C6F4)]3 - a Textbook Example of Phase-Dependent Structural Differences.

The geometric and electronic structure of [Hg(o-C6F4)]3 (1) in the gas phase, i. e. free of intermolecular interactions, was determined by a synchronous gas-phase electron diffraction/mass spectrometry experiment (GED/MS), complemented by quantum chemical calculations. 1 is stable up to 498 K and the gas phase contains a single molecular form: the trimer [Hg(o-C6F4)]3. It has a planar structure of D3h symmetry with a Hg-C distance of 2.075(5) Šand a Hg-Hg distance of 3.614(7) Š(both rh1). Structural differences between the crystalline and gaseous state have been analyzed. Different DFT functional-basis combinations were tested, demonstrating the importance to consider the relativistic effects of the mercury atoms. The combination PBE0/MWB(Hg),cc-pVTZ(C,F) turned out to be the most appropriate for the geometry optimization of such organomercurials. The electronic structure of 1, the nature of the chemical bonding in C-Hg-C fragments and the nature of the Hg⋅⋅⋅Hg interactions have been analyzed in terms of the Natural Bond Orbital (NBO) and Quantum Theory of Atoms in Molecules (QTAIM) approaches. The influence of the nature of halogen substitution on the structure of the molecules in the series [Hg(o-C6H4)]3, [Hg(o-C6F4)]3, [Hg(o-C6Cl4)]3, [Hg(o-C6Br4)]3 was also analyzed.

Pyridyl-Substituted Nitronyl Nitroxides: Comprehensive Magnetochemical and Quantum Chemical Study.

A series of pyridyl-substituted nitronyl nitroxides was synthesized and structurally characterized. A comprehensive magnetochemical and quantum chemical study of extended raw of the nitroxides with different substituents R in the pyridine fragment was performed. It was shown, that temperature-dependent magnetic properties are determined by the short contacts between nitroxide groups of adjacent molecules as well as between nitroxide group and methyl substituents in the pseudo axial positions of imidazoline fragments. Quantum chemistry allows to select the appropriate model of exchange cluster for analysis of experimental magnetic data and evaluation of the exchange interaction parameters. For NN-PyCl the "order-disorder" transition was detected by means of low temperature XRD. The difference in the experimental and calculated exchange interaction energies may serve as an indicator of temperature-induced structural rearrangements. For instance, for methyl substituted nitronyl nitroxide NN-PyMe structural transformations and significant changes in exchange interaction energies were observed.

Photoinduced Dual C-F Bond Activation of Hexafluorobenzene Mediated by Boron Atom.

The reaction of laser-ablated boron atoms with hexafluorobenzene (C6 F6 ) was investigated in neon and argon matrices, and the products are identified by matrix isolation infrared spectroscopy and quantum-chemical calculations. The reaction is triggered by a boron atom insertion into one C-F bond of hexafluorobenzene on annealing, forming a fluoropentafluorophenyl boryl radical (A). UV-Vis light irradiation of fluoropentafluorophenyl boryl radical causes generation of a 2-difluoroboryl-tetrafluorophenyl radical (B) via a second C-F bond activation. A perfluoroborepinyl radical (C) is also observed upon deposition and under UV-Vis light irradiation. This finding reveals the new example of a dual C-F bond activation of hexafluorobenzene mediated by a nonmetal and provides a possible route for synthesis of new perfluorinated organo-boron compounds.

Redox Behaviour and Redox Potentials of Dyes in Aqueous Buffers and Protic Ionic Liquids.

Organic dyes hold promise as inexpensive electrochemically-active building blocks for new renewable energy technologies such as redox-flow batteries and dye-sensitised solar cells, especially if they display high oxidation and/or low reduction potentials in cheap, non-flammable solvents such as water or protic ionic liquids. Systematic computational and experimental characterisation of a representative selection of acidic and basic dyes in buffered aqueous solutions and propylammonium formate confirm that quinoid-type mechanisms impart electrochemical reversibility for the majority of systems investigated, including quinones, fused tricyclic heteroaromatics, indigo carmine and some aromatic nitrogenous species. Conversely, systems that generate long-lived radical intermediates -- arylmethanes, hydroquinones at high pH, azocyclic systems -- tend to display irreversible electrochemistry, likely undergoing ring-opening, dimerisation and/or disproportionation reactions.

Chromium(VI) Oxyfluoride Dianions, [Cr2 O4 F6 ]2- and [CrO2 F4 ]2- ; Syntheses and Structures of [XeF5 ]2 [Cr2 O4 F6 ], [XeF5 ]2 [Cr2 O4 F6 ] ⋠nX (X=HF, n=4; X=XeOF4 , n=2), and [XeF5 ][Xe2 F11 ][CrO2 F4 ].

The fluorobasic character of the strong oxidative fluorinator, XeF6 , and the oxidative resistance of the [XeF5 ]+ and [Xe2 F11 ]+ cations have been exploited for the syntheses of several novel Cr(VI) dianion salts. The reactions of XeF6 and CrO2 F2 in anhydrous HF and by direct fusion of the reactants in melts have yielded the first dinuclear Cr(VI) oxyfluoro-dianion salts, [XeF5 ]2 [Cr2 O4 F6 ], [XeF5 ]2 [Cr2 O4 F6 ] ⋅ 4HF, [XeF5 ]2 [Cr2 O4 F6 ] ⋅ 2XeOF4 , and mononuclear Cr(VI) oxyfluoro-dianion salt, [XeF5 ][Xe2 F11 ][CrO2 F4 ]. The salts were structurally characterized by low-temperature (LT) single-crystal X-ray diffraction (SCXRD) and LT Raman spectroscopy. The [CrO2 F4 ]2- and [Cr2 O4 F6 ]2- dianions have distorted octahedral cis-dioxo Cr(VI) coordination spheres in which two F-atoms are trans to one another and two F-atoms are trans to O-atoms, where the [Cr2 O4 F6 ]2- dianion is the fluorine-bridged dimer of the [CrO2 F3 ]- anion. Quantum-chemical calculations were used to obtain the energy-minimized, gas-phase geometries, and the calculated vibrational spectra of the gas-phase dianions and their ion-pairs, which were used to aid in the vibrational frequency assignments of the crystalline salts. NBO and MEPS analyses and SCXRD show these salts are comprised of intimate ion-pairs in which their cations and anions interact through primarily electrostatic Xe- - -F σ-hole bonds.

Quantum Chemistry and Pharmacy: Diagnostic Check of the Thermochemistry of Ibuprofen.

The thermodynamic data on ibuprofen available in the literature shows that the disarray of experimental results is unacceptable for this very important drug. The data on ibuprofens available in the literature were collected, combined with our complementary experimental results and evaluated. The enthalpies of combustion and formation of the crystalline RS-(±)- and S-(+)-ibuprofens were measured using high-precision combustion calorimetry. The temperature dependence of the vapour pressure of S-(+)-ibuprofen was measured using the transpiration method and the enthalpy of vaporization was derived from this measurement. The enthalpies of fusion of both compounds were measured using DSC. The G4 calculations have been carried out to determine the enthalpy of formation in the gaseous state of the most stable conformer. Thermochemical properties of the compounds studied were evaluated and tested for consistency with the "centerpiece approach". A set of reliable and consistent values of thermodynamic properties of ibuprofens at 298.15 K is recommended for thermochemical calculations of the pharmaceutical processes. The diagnostic protocol was developed to distinguish between the "sick" or "healthy" thermodynamic data. This diagnostic is also applicable to other drugs with a different structure than ibuprofen.

Primary photophysical and photochemical processes for cerium ammonium nitrate (CAN) in acetonitrile.

Cerium ammonium nitrate (CAN) is an important photolytic source of NO3• radicals in aqueous nitric acid solutions and in acetonitrile. In this work we performed the study of primary photochemical processes for CAN in acetonitrile by means of ultrafast TA spectroscopy and quantum chemical calculations. Photoexcitation of CAN is followed by ultrafast (< 100 fs) intersystem crossing; the vibrationally cooled triplet state decays to pentacoordinated Ce(III) intermediate and NO3• radical with the characteristic time of ca. 40 ps. Quantum chemical (QM) calculations satisfactorily describe the UV-vis spectrum of the triplet state. An important feature of CAN photochemistry in CH3CN is the partial stabilization of the radical complex (RC) [(NH4)2CeIII(NO3)5…NO3•], which lifetime is ca. 2 µs. The possibility of the RC stabilization is supported by the QM calculations.

Role of interaction mode of phenanthrene derivatives as selective PDE5 inhibitors using molecular dynamics simulations and quantum chemical calculations.

Phosphodiesterase type 5 (PDE5) inhibitors play a crucial role in blocking PDE5 to improve erectile dysfunction (ED). However, most PDE5 drugs revealed side effects including the loss of vision due to the PDE6 inhibition. Phenanthrene derivatives isolated from E. macrobulbon were previously reported as PDE5 inhibitors. Two phenanthrene derivatives (cpds 1-2) revealed better inhibition to PDE5 than PDE6 and cpd 1 is more selective to PDE5 than cpd 2. To elucidate why the phenanthrene derivatives could inhibit PDE5 and PDE6, their binding modes were investigated using molecular dynamics simulations and quantum chemical calculations, as compared to the PDE5 drugs. From the results, all four drugs and phenanthrene derivatives revealed similar π-π interactions to Phe820 in PDE5. Additional H-bond interaction to Gln817 in PDE5 resulted in better PDE5 inhibition of vardenafil and tadalafil. Moreover, cpds 1-2 were able to form the H-bond interaction with Asp764 in PDE5. In the case of the PDE6, the loss of π-π interaction to Phe776 and H-bond interaction to Gln773 indicated the important points for losing the PDE6 inhibition. In conclusion, to develop the new potent PDE5 inhibitors, not only the important interaction with PDE5 but also the interaction with PDE6 should be considered. In phenanthrene derivatives, the middle ring was significant to form π-π interactions to Phe820 in PDE5 and hydroxyl substituent was also the key part to form the H-bond interaction with Asp764 in PDE5. Principal component analysis (PCA) and free energy landscape (FEL) analysis indicated the stability of the system. The bioavailability, drug-likeness, and pharmacokinetics of phenanthrene derivatives were also predicted. These derivatives revealed good drug-likeness and GI absorption. The obtained results showed that phenanthrene derivatives could be interesting for the development of PDE5 inhibitors in the future.

Ganonorsterone A, a norsteroid from the medicinal fungus Ganoderma lingzhi.

Phytochemical investigation on the fruiting bodies of the medicinal fungus Ganoderma lingzhi led to the isolation of a new norsteroid, namely ganonorsterone A (1), together with one known steroid, cyathisterol (2). The structure and absolute configuration of compound 1 were assigned by extensive analysis of MS, NMR data, and quantum-chemical calculations including electronic circular dichroism (ECD) and calculated 13C NMR-DP4+ analysis. Bioassay results showed that compound 1 displayed moderate inhibition on NO production in RAW 264.7 macrophages.

Unveiling the Nature and Strength of Selenium-Centered Chalcogen Bonds in Binary Complexes of SeO2 with Oxygen-/Sulfur-Containing Lewis Bases: Insights from Theoretical Calculations.

Among various non-covalent interactions, selenium-centered chalcogen bonds (SeChBs) have garnered considerable attention in recent years as a result of their important contributions to crystal engineering, organocatalysis, molecular recognition, materials science, and biological systems. Herein, we systematically investigated π-hole-type Se∙∙∙O/S ChBs in the binary complexes of SeO2 with a series of O-/S-containing Lewis bases by means of high-level ab initio computations. The results demonstrate that there exists an attractive interaction between the Se atom of SeO2 and the O/S atom of Lewis bases. The interaction energies computed at the MP2/aug-cc-pVTZ level range from -4.68 kcal/mol to -10.83 kcal/mol for the Se∙∙∙O chalcogen-bonded complexes and vary between -3.53 kcal/mol and -13.77 kcal/mol for the Se∙∙∙S chalcogen-bonded complexes. The Se∙∙∙O/S ChBs exhibit a relatively short binding distance in comparison to the sum of the van der Waals radii of two chalcogen atoms. The Se∙∙∙O/S ChBs in all of the studied complexes show significant strength and a closed-shell nature, with a partially covalent character in most cases. Furthermore, the strength of these Se∙∙∙O/S ChBs generally surpasses that of the C/O-H∙∙∙O hydrogen bonds within the same complex. It should be noted that additional C/O-H∙∙∙O interactions have a large effect on the geometric structures and strength of Se∙∙∙O/S ChBs. Two subunits are connected together mainly via the orbital interaction between the lone pair of O/S atoms in the Lewis bases and the BD*(OSe) anti-bonding orbital of SeO2, except for the SeO2∙∙∙HCSOH complex. The electrostatic component emerges as the largest attractive contributor for stabilizing the examined complexes, with significant contributions from induction and dispersion components as well.

DFT Exploration of Metal Ion-Ligand Binding: Toward Rational Design of Chelating Agent in Semiconductor Manufacturing.

Chelating agents are commonly employed in microelectronic processes to prevent metal ion contamination. The ligand fragments of a chelating agent largely determine its binding strength to metal ions. Identification of ligands with suitable characteristics will facilitate the design of chelating agents to enhance the capture and removal of metal ions from the substrate in microelectronic processes. This study employed quantum chemical calculations to simulate the binding process between eleven ligands and the hydrated forms of Ni2+, Cu2+, Al3+, and Fe3+ ions. The binding strength between the metal ions and ligands was quantified using binding energy and binding enthalpy. Additionally, we explored the binding interaction mechanisms and explained the differences in binding abilities of the eleven ligands using frontier molecular orbitals, nucleophilic indexes, electrostatic potentials, and energy decomposition calculations based on molecular force fields. Based on our computational results, promising chelating agent structures are proposed, aiming to guide the design of new chelating agents to address metal ion contamination issues in integrated circuit processes.

Combining Experimental and Computational Methods to Produce Conjugates of Anticholinesterase and Antioxidant Pharmacophores with Linker Chemistries Affecting Biological Activities Related to Treatment of Alzheimer's Disease.

Effective therapeutics for Alzheimer's disease (AD) are in great demand worldwide. In our previous work, we responded to this need by synthesizing novel drug candidates consisting of 4-amino-2,3-polymethylenequinolines conjugated with butylated hydroxytoluene via fixed-length alkylimine or alkylamine linkers (spacers) and studying their bioactivities pertaining to AD treatment. Here, we report significant extensions of these studies, including the use of variable-length spacers and more detailed biological characterizations. Conjugates were potent inhibitors of acetylcholinesterase (AChE, the most active was 17d IC50 15.1 ± 0.2 nM) and butyrylcholinesterase (BChE, the most active was 18d: IC50 5.96 ± 0.58 nM), with weak inhibition of off-target carboxylesterase. Conjugates with alkylamine spacers were more effective cholinesterase inhibitors than alkylimine analogs. Optimal inhibition for AChE was exhibited by cyclohexaquinoline and for BChE by cycloheptaquinoline. Increasing spacer length elevated the potency against both cholinesterases. Structure-activity relationships agreed with docking results. Mixed-type reversible AChE inhibition, dual docking to catalytic and peripheral anionic sites, and propidium iodide displacement suggested the potential of hybrids to block AChE-induced ß-amyloid (Aß) aggregation. Hybrids also exhibited the inhibition of Aß self-aggregation in the thioflavin test; those with a hexaquinoline ring and C8 spacer were the most active. Conjugates demonstrated high antioxidant activity in ABTS and FRAP assays as well as the inhibition of luminol chemiluminescence and lipid peroxidation in mouse brain homogenates. Quantum-chemical calculations explained antioxidant results. Computed ADMET profiles indicated favorable blood-brain barrier permeability, suggesting the CNS activity potential. Thus, the conjugates could be considered promising multifunctional agents for the potential treatment of AD.