Synthetic and computational assessment of a chiral metal–organic framework catalyst for predictive asymmetric transformation

Understanding and controlling molecular recognition mechanisms at a chiral solid interface is a continuously addressed challenge in heterogeneous catalysis. Here, the molecular recognition of a chiral peptide-functionalized metal–organic framework (MOF) catalyst towards a pro-chiral substrate is evaluated experimentally and in silico. The MIL-101 metal–organic framework is used as a macroligand for hosting a Noyori-type chiral ruthenium molecular catalyst, namely (benzene)Ru@MIL-101-NH-Gly-Pro. Its catalytic perfomance toward the asymmetric transfer hydrogenation (ATH) of acetophenone into R- and S-phenylethanol are assessed. The excellent match between the experimentally obtained enantiomeric excesses and the computational outcomes provides a robust atomic-level rationale for the observed product selectivities. The unprecedented role of the MOF in confining the molecular Ru-catalyst and in determining the access of the prochiral substrate to the active site is revealed in terms of highly face-specific host–guest interactions. The predicted surface-specific face differentiation of the prochiral substrate is experimentally corroborated since a three-fold increase in enantiomeric excess is obtained with the heterogeneous MOF-based catalyst when compared to its homogeneous molecular counterpart.

Understanding and controlling molecular recognition mechanisms at a chiral solid interface has been addressed in metal–organic framework catalysts for the asymmetric transfer hydrogenation reaction.     

Comparing a selenium accumulator plant (Brassica juncea) to a nonaccumulator plant (Helianthus annuus) to investigate selenium-containing proteins

Selenoproteins have been identified in a diverse range of organisms, including bacteria and animals. Their occurrence and role in the plant kingdom are, however, less well-understood. This work investigated the water-soluble selenium-containing proteins extracted from a selenium-accumulating plant species (Brassica juncea) and a nonaccumulator species (Helianthus annuus) exposed to varying forms and concentrations of selenium. Firstly, protein extracts were analyzed by size exclusion chromatography coupled to inductively coupled plasma mass spectrometry; specific detection was achieved by monitoring characteristic isotopes. Then, proteolytic digests of the plant extracts were analyzed by reversed phase chromatography coupled to ICP–MS in order to investigate selenoamino acid and selenopeptide content. Selenomethionine was observed to be the primary constituent of the proteins of the nonaccumulator plant, while selenocystine and selenomethionine were found in the same proportion in the accumulator extract. One main selenium-containing species was present at higher levels in the root digests than in the leaf digests; levels were greater in the nonaccumulator than in the accumulator plant.     

Intrinsic Dynamic and Static Nature of Halogen Bonding in Neutral Polybromine Clusters,with the Structural Feature Elucidated by QTAIM Dual-Functional Analysis and MO Calculations

The intrinsic dynamic and static nature of noncovalent Br-∗-Br interactions in neutral polybromine clusters is elucidated for Br₄–Br₁₂, applying QTAIM dual-functional analysis (QTAIM-DFA). The asterisk (∗) emphasizes the existence of the bond critical point (BCP) on the interaction in question. Data from the fully optimized structures correspond to the static nature of the interactions. The intrinsic dynamic nature originates from those of the perturbed structures generated using the coordinates derived from the compliance constants for the interactions and the fully optimized structures. The noncovalent Br-∗-Br interactions in the L-shaped clusters of the C_s symmetry are predicted to have the typical hydrogen bond nature without covalency, although the first ones in the sequences have the vdW nature. The L-shaped clusters are stabilized by the n(Br)→σ*(Br–Br) interactions. The compliance constants for the corresponding noncovalent interactions are strongly correlated to the E(2) values based on NBO. Indeed, the MO energies seem not to contribute to stabilizing Br₄ (C_2h) and Br₄ (D_2d), but the core potentials stabilize them, relative to the case of 2Br₂; this is possibly due to the reduced nuclear–electron distances, on average, for the dimers.     

Effects of Ornamental Plant Density and Mineral/Plastic Media on the Removal of Domestic Wastewater Pollutants by Home Wetlands Technology

Wastewater treatment (WWT) is a priority around the world; conventional treatments are not widely used in rural areas owing to the high operating and maintenance costs. In Mexico, for instance, only 40% of wastewater is treated. One sustainable option for WWT is through the use of constructed wetlands (CWs) technology, which may remove pollutants using cells filled with porous material and vegetation that works as a natural filter. Knowing the optimal material and density of plants used per square meter in CWs would allow improving their WWT effect. In this study, the effect of material media (plastic/mineral) and plant density on the removal of organic/inorganic pollutants was evaluated. Low (three plants), medium (six plants) and high (nine plants) densities were compared in a surface area of 0.3 m² of ornamental plants (Alpinia purpurata, Canna hybrids and Hedychium coronarium) used in polycultures at the mesocosm level of household wetlands, planted on the two different substrates. Regarding the removal of contaminants, no significant differences were found between substrates (p ≥ 0.05), indicating the use of plastic residues (reusable) is an economical option compared to typical mineral materials. However, differences (p = 0.001) in removal of pollutants were found between different plant densities. For both substrates, the high density planted CWs were able to remove COD in a range of 86–90%, PO₄-P 22–33%, NH₄-N in 84–90%, NO₃-N 25–28% and NO₂-N 38–42%. At medium density, removals of 79–81%, 26–32, 80–82%, 24–26%, and 39–41%, were observed, whereas in CWs with low density, the detected removals were 65–68%, 20–26%, 79–80%, 24–26% and 31–40%, respectively. These results revealed that higher COD and ammonia were removed at high plant density than at medium or low densities. Other pollutants were removed similarly in all plant densities (22–42%), indicating the necessity of hybrid CWs to increase the elimination of PO₄-P, NO₃-N and NO₂-N. Moreover, high density favored 10 to 20% more the removal of pollutants than other plant densities. In addition, in cells with high density of plants and smaller planting distance, the development of new plant shoots was limited. Thus, it is suggested that the appropriate distance for this type of polyculture plants should be from 40 to 50 cm in expansion to real-scale systems in order to take advantage of the harvesting of species in these and allow species of greater foliage, favoring its growth and new shoots with the appropriate distance to compensate, in the short time, the removal of nutrients.     

Bioactive Molecules for Discriminating Robinia and Helianthus Honey: High-Performance Liquid Chromatography–Electron Spray Ionization–Mass Spectrometry Polyphenolic Profile and Physicochemical Determinations

Bioactive molecules from the class of polyphenols are secondary metabolites from plants. They are present in honey from nectar and pollen of flowers from where honeybees collect the “raw material” to produce honey. Robinia pseudoacacia and Helianthus annuus are important sources of nectar for production of two monofloral honeys with specific characteristics and important biological activity. A high-performance liquid chromatography–electro spray ionization–mass spectrometry (HPLC–ESI–MS) separation method was used to determine polyphenolic profile from the two types of Romanian unifloral honeys. Robinia and Helianthus honey showed a common flavonoid profile, where pinobanksin (1.61 and 1.94 mg/kg), pinocembrin (0.97 and 1.78 mg/kg) and chrysin (0.96 and 1.08 mg/kg) were identified in both honey types; a characteristic flavonoid profile in which acacetin (1.20 mg/kg), specific only for Robinia honey, was shown; and quercetin (1.85 mg/kg), luteolin (21.03 mg/kg), kaempferol (0.96 mg/kg) and galangin (1.89 mg/kg), specific for Helianthus honey, were shown. In addition, different phenolic acids were found in Robinia and Helianthus honey, while abscisic acid was found only in Robinia honey. Abscisic acid was correlated with geographical location; the samples collected from the south part of Romania had higher amounts, due to climatic conditions. Acacetin was proposed as a biochemical marker for Romanian Robinia honey and quercetin for Helianthus honey.     

Carbon support tuned electrocatalytic activity of a single-site metal–organic framework toward the oxygen reduction reaction

Metal–organic frameworks (MOFs) possess fantastic features such as structural diversity, tunable accessible pores and atomically dispersed active sites, holding tremendous potential as highly versatile platforms for fabricating single-site catalysts. The electrocatalytic activity of single-site MOFs can be improved and tuned via several approaches; however, the exploitation of different carbon supports to modulate the nature of single active sites in MOFs for electrocatalysis has not been reported. Here, we find that the electrocatalytic activity of single-site MOFs toward the oxygen reduction reaction (ORR) can be tuned by using carbon nanomaterials, i.e., carbon nanotubes and graphene, as supports through MOF–support interactions in the manner of geometric and electronic effects. The introduction of MOF–support interactions not only greatly improves the electrocatalytic performance of MOFs toward the ORR in terms of onset and half-wave potentials and current density, but also alters the reaction pathway of the ORR. This finding provides a new horizon for the design and synthesis of single-site MOFs for electrocatalysis.

MOF–support interactions are proposed for the first time for tuning the electrocatalytic activity of single-site MOFs in the manner of geometric and electronic effects.     

Synchrotron fourier transform infrared microspectroscopy: A new tool to monitor the fate of organic contaminants in plants

FTIR microspectroscopy, with synchrotron radiation as a source, was used for the first time to study changes in plant structure induced by organic contaminants. Sunflower (Helianthus annuus L.) plants were grown hydroponically in the presence of benzotriazole. Changes in the plant structure due to uptake, incorporation, and/or transformation of benzotriazole were observed. False color intensity maps of benzotriazole treated secondary root sections showed changes in plant structure, as well as the presence of aromatic CH peaks due to incorporation of benzotriazole within the plant. The presence of the characteristic benzotriazole CH out-of-plane bending mode suggests that the contaminant aromatic ring remains intact upon the uptake by the plant. Simultaneously, the changes in the lignin structure suggest that the plant suffered damage by the uptake of the benzotriazole. Spectral variations between the untreated and benzotriazole treated sunflowers were uncovered using principal components analysis (PCA). PCA also revealed clustering according to the different benzotriazole treatments.     

Backbonding contributions to small molecule chemisorption in a metal–organic framework with open copper(i) centers

Metal–organic frameworks are promising materials for applications such as gas capture, separation, and storage, due to their ability to selectively adsorb small molecules. The metal–organic framework Cu^I-MFU-4l, which contains coordinatively unsaturated copper(i) centers, can engage in backbonding interactions with various small molecule guests, motivating the design of frameworks that engage in backbonding and other electronic interactions for highly efficient and selective adsorption. Here, we examine several gases expected to bind to the open copper(i) sites in Cu^I-MFU-4l via different electronic interactions, including σ-donation, π-backbonding, and formal electron transfer. We show that in situ Cu L-edge near edge X-ray absorption fine structure (NEXAFS) spectroscopy can elucidate π-backbonding by directly probing excitations to unoccupied backbonding orbitals with Cu d-character, even for gases that participate in other dominant interactions, such as ligand-to-metal σ-donation. First-principles calculations based on density functional theory and time-dependent density functional theory additionally reveal the backbonding molecular orbitals associated with these spectroscopic transitions. The energies of the transitions correlate with the energy levels of the isolated small molecule adsorbates, and the transition intensities are proportional to the binding energies of the guest molecules within Cu^I-MFU-4l. By elucidating the molecular and electronic structure origins of backbonding interactions between electron rich metal centers in metal–organic frameworks and small molecule guests, it is possible to develop guidelines for further molecular-level design of solid-state adsorbents for energy-efficient separations of relevance to industry.

In situ near edge X-ray absorption fine structure spectroscopy directly probes unoccupied states associated with backbonding interactions between the open metal site in a metal–organic framework and various small molecule guests.     

Evaluation of sample preparation protocols for proteomic analysis of sunflower leaves

Six protocols for extraction of proteins from sunflower (Helianthus annuus L.) leaves were evaluated for their abilities in both removing interferents and attaining the best resolution in two-dimensional gel electrophoresis. “Classical” phenol extraction followed by precipitation with ammonium acetate in methanol displayed the most efficient protocol, which allowed the detection of 244 protein spots with ca. 485 μg of protein in gel electrophoresis. Tandem mass spectrometry was performed to identify proteins in 61 spots, and cross species identification was used for this task. Proteins from twenty two spots were identified, and 12 of these proteins are up to now not included into the ExPASy sunflower protein databank.     

Binding Free Energy (BFE) Calculations and Quantitative Structure–Activity Relationship (QSAR) Analysis of Schistosoma mansoni Histone Deacetylase 8 (smHDAC8) Inhibitors

Histone-modifying proteins have been identified as promising targets to treat several diseases including cancer and parasitic ailments. In silico methods have been incorporated within a variety of drug discovery programs to facilitate the identification and development of novel lead compounds. In this study, we explore the binding modes of a series of benzhydroxamates derivatives developed as histone deacetylase inhibitors of Schistosoma mansoni histone deacetylase (smHDAC) using molecular docking and binding free energy (BFE) calculations. The developed docking protocol was able to correctly reproduce the experimentally established binding modes of resolved smHDAC8–inhibitor complexes. However, as has been reported in former studies, the obtained docking scores weakly correlate with the experimentally determined activity of the studied inhibitors. Thus, the obtained docking poses were refined and rescored using the Amber software. From the computed protein–inhibitor BFE, different quantitative structure–activity relationship (QSAR) models could be developed and validated using several cross-validation techniques. Some of the generated QSAR models with good correlation could explain up to ~73% variance in activity within the studied training set molecules. The best performing models were subsequently tested on an external test set of newly designed and synthesized analogs. In vitro testing showed a good correlation between the predicted and experimentally observed IC₅₀ values. Thus, the generated models can be considered as interesting tools for the identification of novel smHDAC8 inhibitors.     

Red aqueous room-temperature phosphorescence modulated by anion–π and intermolecular electronic coupling interactions

Aqueous room temperature phosphorescence (aRTP) from purely organic materials has been intriguing but challenging. In this article, we demonstrated that the red aRTP emission of 2Br–NDI, a water-soluble 4,9-dibromonaphthalene diimide derivative as a chloride salt, could be modulated by anion–π and intermolecular electronic coupling interactions in water. Specifically, the rarely reported stabilization of anion–π interactions in water between Cl⁻ and the 2Br–NDI core was experimentally evidenced by an anion–π induced long-lived emission (λ_Anion–π) of 2Br–NDI, acting as a competitive decay pathway against the intrinsic red aRTP emission (λ_Phos) of 2Br–NDI. In the initial expectation of enhancing the aRTP of 2Br–NDI by inclusion complexation with macrocyclic cucurbit[n]urils (CB[n]s, n = 7, 8, 10), we surprisingly found that the exclusion complexation between CB[8] and 2Br–NDI unconventionally endowed the complex with the strongest and longest-lived aRTP due to the strong intermolecular electronic coupling between the nπ* orbit on the carbonyl rims of CB[8] and the ππ* orbit on 2Br–NDI in water. It is anticipated that these intriguing findings may inspire and expand the exploration of aqueous anion–π recognition and CB[n]-based aRTP materials.

The aqueous room temperature phosphorescence of 2Br–NDI is modulated by long-lived-emitting anion–π interactions and tremendously enhanced by intermolecular electronic coupling interactions with the ISC-boosting carbonyl rims of CB[8] host.     

Two New Aristolochic Acid Analogues from the Roots of Aristolochia contorta with Significant Cytotoxic Activity

Twelve compounds, including two new aristolochic acid analogues with a formyloxy moiety (9–10) and 10 known aristolochic acid derivates (1–8 and 11–12), were obtained from the roots of Aristolochia contorta. Their structures were elucidated using extensive spectroscopic methods. Their cytotoxic activity in human proximal tubular cells HK-2 was evaluated by the MTT method, which has been widely used to assess cell viability. Among these molecules, compounds 3 and 9 were found to be more cytotoxic. Furthermore, molecular modeling was used to evaluate, for the first time, the interactions of compounds 3 and 9 with the target protein organic anionic transporter 1 (OAT1) that plays a key role in mediating aristolochic acid nephropathy. Structure–activity relationships are briefly discussed.     

Synthesis and absolute configuration of annuionone A

Synthesis of both enantiomers of annuionone A (1), an allelopathic agent isolated from Helianthus annuus (sunflower), was accomplished. The absolute configuration of the naturally occurring 1 was determined to be 1S,5R,8R.     

Chemical Composition and Antimicrobial and Antioxidant Activities of Essential Oil of Sunflower (Helianthus annuus L.) Receptacle

Sunflower (Helianthus annuus L.) contains active ingredients, such as flavonoids, alkaloids and tannins. Nevertheless, few studies have focused on essential oil from the receptacle of sunflower (SEO). In this work, we investigated the chemical composition and antimicrobial and antioxidant activities of SEO. The yield of SEO was about 0.42% (v/w) by hydrodistillation. A total of 68 volatile components of SEO were putatively identified by gas chromatography–mass spectrometry (GC-MS). The main constituents of SEO were α-pinene (26.00%), verbenone (7.40%), terpinolene (1.69%) and α-terpineol (1.27%). The minimum inhibitory concentration (MIC) of SEO against P. aeruginosa and S. aureus was 0.2 mg/mL. The MIC of SEO against S. cerevisiae was 3.2 mg/mL. The MIC of SEO against E. coli and Candida albicans was 6.4 mg/mL. The results showed that SEO had high antibacterial and antifungal activities. Three different analytical assays (DPPH, ABTS and iron ion reducing ability) were used to determine the antioxidant activities. The results showed that SEO had antioxidant activities. To summarize, the results in this study demonstrate the possibility for the development and application of SEO in potential natural preservatives and medicines due to its excellent antimicrobial and antioxidant activities.     

An ab initio study of the electronic structure of SiH4, SiH3F and SiH2F2

Changes in molecular properties and in the electronic charge distribution of the molecules SiH₄, SiH₃F and SiH₂F₂ are studied within the framework of the ab initio Hartree—Fock SCF—LCAO—MO method. The ionisation potentials, calculated with the use of Koopmans' theorem, correlate well with the experimental vertical ionisation potentials. The combined s and p electronic populations of the Si atom are not substantially altered when adding Si 3d functions to the basis set.     

Glycan–protein cross-linking mass spectrometry reveals sialic acid-mediated protein networks on cell surfaces

A cross-linking method is developed to elucidate glycan-mediated interactions between membrane proteins through sialic acids. The method provides information on previously unknown extensive glycomic interactions on cell membranes. The vast majority of membrane proteins are glycosylated with complicated glycan structures attached to the polypeptide backbone. Glycan–protein interactions are fundamental elements in many cellular events. Although significant advances have been made to identify protein–protein interactions in living cells, only modest advances have been made on glycan–protein interactions. Mechanistic elucidation of glycan–protein interactions has thus far remained elusive. Therefore, we developed a cross-linking mass spectrometry (XL-MS) workflow to directly identify glycan–protein interactions on the cell membrane using liquid chromatography-mass spectrometry (LC-MS). This method involved incorporating azido groups on cell surface glycans through biosynthetic pathways, followed by treatment of cell cultures with a synthesized reagent, N-hydroxysuccinimide (NHS)–cyclooctyne, which allowed the cross-linking of the sialic acid azides on glycans with primary amines on polypeptide backbones. The coupled peptide–glycan–peptide pairs after cross-linking were identified using the latest techniques in glycoproteomic and glycomic analyses and bioinformatics software. With this approach, information on the site of glycosylation, the glycoform, the source protein, and the target protein of the cross-linked pair were obtained. Glycoprotein–protein interactions involving unique glycoforms on the PNT2 cell surface were identified using the optimized and validated method. We built the GPX network of the PNT2 cell line and further investigated the biological roles of different glycan structures within protein complexes. Furthermore, we were able to build glycoprotein–protein complex models for previously unexplored interactions. The method will advance our future understanding of the roles of glycans in protein complexes on the cell surface.

The cell surface glycocalyx is highly interactive defined by extensive covalent and non-covalent interactions. A method for cross-linking and characterizing glycan–peptide interactions in situ is developed.     

Thermodynamic consequences of Tyr to Trp mutations in the cation–π-mediated binding of trimethyllysine by the HP1 chromodomain

Evolution has converged on cation–π interactions for recognition of quaternary alkyl ammonium groups such as trimethyllysine (Kme3). While computational modelling indicates that Trp provides the strongest cation–π interaction of the native aromatic amino acids, there is limited corroborative data from measurements within proteins. Herein we investigate a Tyr to Trp mutation in the binding pocket of the HP1 chromodomain, a reader protein that recognizes Kme3. Binding studies demonstrate that the Trp-mediated cation–π interaction is about −5 kcal mol⁻¹ stronger, and the Y24W crystal structure shows that the mutation is not perturbing. Quantum mechanical calculations indicate that greater enthalpic binding is predominantly due to increased cation–π interactions. NMR studies indicate that differences in the unbound state of the Y24W mutation lead to enthalpy–entropy compensation. These results provide direct experimental quantification of Trp versus Tyr in a cation–π interaction and afford insight into the conservation of aromatic cage residues in Kme3 reader domains.

In this work, we experimentally validate that tryptophan provides the strongest cation–π binding interaction among aromatic amino acids and also lend insight into the importance of residue identity in trimethyllysine recognition by reader proteins.     

Phosphoryl- and phosphonium-bridged viologens as stable two- and three-electron acceptors for organic electrodes

Low molecular weight organic molecules that can accept multiple electrons at high reduction potentials are sought after as electrode materials for high-energy sustainable batteries. To date their synthesis has been difficult, and organic scaffolds for electron donors significantly outnumber electron acceptors. Herein, we report the synthesis and electronic properties of two highly electron-deficient phosphaviologen derivatives from a phosphorus-bridged 4,4''-bipyridine and characterize their electrochemical properties. Phosphaviologen sulfide (PVS) and P-methyl phosphaviologen (PVM) accept two and three electrons at high reduction potentials, respectively. PVM can reversibly accept three electrons between 3–3.6 V vs. Li/Li⁺ with an equivalent molecular weight of 102 g (mol⁻¹ e⁻) (262 mA h g⁻¹), making it a promising scaffold for sustainable organic electrode materials having high specific energy densities.

Two strongly electron-accepting viologens, including an intriguing tricationic species, are reported. The utility of the tricationic viologen for energy storage has been showcased via use as electrode in a proof-of-concept battery.     

The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations

The translocator protein (TSPO) is a 18kDa transmembrane protein, ubiquitously present in human mitochondria. It is overexpressed in tumor cells and at the sites of neuroinflammation, thus representing an important biomarker, as well as a promising drug target. In mammalian TSPO, there are cholesterol–binding motifs, as well as a binding cavity able to accommodate different chemical compounds. Given the lack of structural information for the human protein, we built a model of human (h) TSPO in the apo state and in complex with PK11195, a molecule routinely used in positron emission tomography (PET) for imaging of neuroinflammatory sites. To better understand the interactions of PK11195 and cholesterol with this pharmacologically relevant protein, we ran molecular dynamics simulations of the apo and holo proteins embedded in a model membrane. We found that: (i) PK11195 stabilizes hTSPO structural fold; (ii) PK11195 might enter in the binding site through transmembrane helices I and II of hTSPO; (iii) PK11195 reduces the frequency of cholesterol binding to the lower, N–terminal part of hTSPO in the inner membrane leaflet, while this impact is less pronounced for the upper, C–terminal part in the outer membrane leaflet, where the ligand binding site is located; (iv) very interestingly, cholesterol most frequently binds simultaneously to the so-called CRAC and CARC regions in TM V in the free form (residues L150–X–Y152–X(3)–R156 and R135–X(2)–Y138–X(2)–L141, respectively). However, when the protein is in complex with PK11195, cholesterol binds equally frequently to the CRAC–resembling motif that we observed in TM I (residues L17–X(2)–F20–X(3)–R24) and to CRAC in TM V. We expect that the CRAC–like motif in TM I will be of interest in future experimental investigations. Thus, our MD simulations provide insight into the structural features of hTSPO and the previously unknown interplay between PK11195 and cholesterol interactions with this pharmacologically relevant protein.     

Helivypolide G. A novel dimeric bioactive sesquiterpene lactone

In the course of our ongoing research for new allelochemicals from Helianthus annuus, a novel dimeric bioactive sesquiterpene lactone, helivypolide G has been isolated and characterized from the medium polar active fractions of the leaves of cultivar variety Stella. The monomers are connected through carbons C-15 of each unit and an oxygen bridge, forming an enolic oxane ring.