The rare-earth nanocrystals containing Er3+ emitters offer very promising tools for imaging applications, as they can not only exhibit up-conversion luminescence but also down-conversion luminescence in the second near-infrared window (NIR II). Doping non-lanthanide cations into host matrix was demonstrated to be an effective measure for improving the luminescence efficiency of Er3+ ions, while still awaiting in-depth investigations on the effects of dopants especially those with high valence states on the optical properties of lanthanide nanocrystals. To address this issue, tetravalent Zr4+ doped hexagonal NaGdF4:Yb,Er nanocrystals were prepared, and the enhancement effects of the Zr4+ doping level on both up-conversion luminescence in the visible window and down-conversion luminescence in NIR II window were investigated, with steady-state and transient luminescence spectroscopies. The key role of the local crystal field distortions around Er3+ emitters was elucidated in combination with the results based on both of Zr4+ and its lower valence counterparts, e.g., Sc3+, Mg2+, Mn2+. Univalent ions such as Li+ was utilized to substitute Na+ ion rather than Gd3+, and the synergistic effects of Zr4+ and Li+ ions by co-doping them into NaGdF4:Yb,Er nanocrystals were investigated toward optimal enhancement. Upon optimization, the up-conversion emission of co-doped NaGdF4:Yb,Er nanocrystals was enhanced by more than one order of magnitude compared with undoped nanocrystals. The current studies thus demonstrate that the local crystal field surrounding emitters is an effective parameter for manipulating the luminescence of lanthanide emitters.

HMF synthesis typically requires high temperature and is carried out in aqueous solutions. In this work, the low-temperature dehydration of fructose to HMF in different deep eutectic solvents (DES) was investigated. We found a very active and selective reaction system consisting of the DES tetraethyl ammonium chloride as hydrogen bond acceptor (HBA) and levulinic acid as hydrogen bond donor (HBD) in a molar ratio of 1:2 leading to a maximum HMF yield of 68% after 120 h at 323 K. The DES still contained a low amount of water at the initial reaction, and water was also produced during the reaction. Considering the DES properties, neither the molar ratio in the DES nor the reaction temperature had a significant influence on the overall performance of the reaction system. However, the nature of the HBA as well as the acidity of the HBD play an important role for the maximum achievable HMF yield. This was validated by measured yields in a DES with different combinations of HBD (levulinic acid and lactic acid) and HBA (choline chloride and tetra-n-alkyl ammonium chlorides). Moreover, addition of vanadium containing catalysts, especially the polyoxometalate HPA-5 (H8PV5Mo7O40) leads to drastically increased reaction kinetics. Using HPA-5 and the DES tetraethyl ammonium chloride-levulinic acid we could reach a maximum HMF yield of 57% after only 5 h reaction time without decreasing the very high product selectivity.

Severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 is a virus that belongs to the Coronaviridae family. This group of viruses commonly causes colds but possesses a tremendous pathogenic potential. In humans, an outbreak of SARS caused by the SARS-CoV virus was first reported in 2003, followed by 2012 when the Middle East respiratory syndrome coronavirus (MERS-CoV) led to an outbreak of Middle East respiratory syndrome (MERS). Moreover, COVID-19 represents a serious socioeconomic and global health problem that has already claimed more than four million lives. To date, there are only a handful of therapeutic options to combat this disease, and only a single direct-acting antiviral, the conditionally approved remdesivir. Since there is an urgent need for active drugs against SARS-CoV-2, the strategy of drug repurposing represents one of the fastest ways to achieve this goal. An in silico drug repurposing study using two methods was conducted. A structure-based virtual screening of the FDA-approved drug database on SARS-CoV-2 main protease was performed, and the 11 highest-scoring compounds with known 3CLpro activity were identified while the methodology was used to report further 11 potential and completely novel 3CLpro inhibitors. Then, inverse molecular docking was performed on the entire viral protein database as well as on the Coronaviridae family protein subset to examine the hit compounds in detail. Instead of target fishing, inverse docking fingerprints were generated for each hit compound as well as for the five most frequently reported and direct-acting repurposed drugs that served as controls. In this way, the target-hitting space was examined and compared and we can support the further biological evaluation of all 11 newly reported hits on SARS-CoV-2 3CLpro as well as recommend further in-depth studies on antihelminthic class member compounds. The authors acknowledge the general usefulness of this approach for a full-fledged inverse docking fingerprint screening in the future.

In a survey of novel interactions between an IgG1 antibody and different Fcγ receptors (FcγR), molecular dynamics simulations were performed of interactions of monoclonal antibody involved complexes with FcγRs. Free energy simulations were also performed of isolated wild-type and substituted Fc regions bound to FcγRs with the aim of assessing their relative binding affinities. Two different free energy calculation methods, Molecular Mechanical/Generalized Born Molecular Volume (MM/GBMV) and Bennett Acceptance Ratio (BAR), were used to evaluate the known effector substitution G236A that is known to selectively increase antibody dependent cellular phagocytosis. The obtained results for the MM/GBMV binding affinity between different FcγRs are in good agreement with previous experiments, and those obtained using the BAR method for the complete antibody and the Fc-FcγR simulations show increased affinity across all FcγRs when binding to the substituted antibody. The FcγRIIa, a key determinant of antibody agonistic efficacy, shows a 10-fold increase in binding affinity, which is also consistent with the published experimental results. Novel interactions between the Fab region of the antibody and the FcγRs were discovered with this in silico approach, and provide insights into the antibody-FcγR binding mechanism and show promise for future improvements of therapeutic antibodies for preclinical studies of biological drugs.

Cysteine protease enzymes are important for human physiology and catalyze key protein degradation pathways. These enzymes react via a nucleophilic reaction mechanism that involves a cysteine residue and the proton of a proximal histidine. Particularly efficient inhibitors of these enzymes are nitrile-based, however, the details of the catalytic reaction mechanism currently are poorly understood. To gain further insight into the inhibition of these molecules, we have performed a combined density functional theory and quantum mechanics/molecular mechanics study on the reaction of a nitrile-based inhibitor with the enzyme active site amino acids. We show here that small perturbations to the inhibitor structure can have dramatic effects on the catalysis and inhibition processes. Thus, we investigated a range of inhibitor templates and show that specific structural changes reduce the inhibitory efficiency by several orders of magnitude. Moreover, as the reaction takes place on a polar surface, we find strong differences between the DFT and QM/MM calculated energetics. In particular, the DFT model led to dramatic distortions from the starting structure and the convergence to a structure that would not fit the enzyme active site. In the subsequent QM/MM study we investigated the use of mechanical vs. electronic embedding on the kinetics, thermodynamics and geometries along the reaction mechanism. We find minor effects on the kinetics of the reaction but large geometric and thermodynamics differences as a result of inclusion of electronic embedding corrections. The work here highlights the importance of model choice in the investigation of this biochemical reaction mechanism.

Cancer stem cells (CSCs) are a small subset of cells that sit atop the hierarchical ladder in many cancer types. Liver CSCs have been associated with high chemoresistance and recurrence rates in hepatocellular carcinoma (HCC). However, as of yet, no satisfactorily effective liver CSC-targeted treatment is available, which drove us to design and investigate the efficacy of a liposome-based delivery system. Here, we introduce a redox-triggered dual-targeted liposome, CEP-LP@S/D, capable of co-delivering doxorubicin (Dox) and salinomycin (Sal) for the synergistic treatment of liver cancer. This system is based on the association of CD133- and EpCAM-targeted peptides to form Y-shaped CEP ligands that were anchored to the surface of the liposome and allowed the selective targeting of CD133+ EpCAM+ liver CSCs. After arriving to the CSCs, the CEP-LP@S/D liposome undergoes endocytosis to the cytoplasm, where a high concentration of glutathione (GSH) breaks its disulfide bonds, thereby degrading the liposome. This then induces a rapid release of Dox and Sal to synergistically inhibit tumor growth. Notably, this effect occurs through Dox-induced apoptosis and concurrent lysosomal iron sequestration by Sal. Interestingly, both in vitro and in vivo studies indicated that our GSH-responsive co-delivery system not only effectively enhanced CSC targeting but also eliminated the non-CSC faction, thereby exhibiting high antitumor efficacy. We believe that the smart liposome nanocarrier-based co-delivery system is a promising strategy to combat liver cancer, which may also lay the groundwork for more enhanced approaches to target other cancer types as well.

The steric shielding offered by sensitizers on semiconducting surfaces as a result of branching in the dyes used offers the less utilization of semiconducting substrate sites during device fabrication in dye-sensitized solar cells (DSSCs). This work proposes a strategy to increase the coverage through the utilization of small molecules which have the ability to penetrate into the sites. The small molecules play the dual role of vacancy filling and sensitization, which can be viewed as an alternative to co-sensitization also. Hence, we show for the first time ever that the co-adsorption of catechol with Z907 as a sensitizer enhances the electron density in the photo-anode by adsorbing on the vacant sites. Catechol was subsequently adsorbed on TiO2 after Z907 as it has a stronger interaction with TiO2 owing to its favorable thermodynamics. The reduced number of vacant sites, suppressed charge recombination, and enhanced spectral response are responsible for the improvement in the PCEs. Quantitatively, both organic and aqueous electrolytes were used and the co-sensitized DSSCs had PCE enhancements of 7.2 and 60%, respectively, compared to the control devices.

A μ-η1:η1-N2-bridged Mo dimer, {(η5-C5Me5)[N(Et)C(Ph)N(Et)]Mo}2(μ-N2), cleaves dinitrogen thermally resulting in a crystallographically characterized bis-μ-N-bridged dimer, {(η5-C5Me5)[N(Et)C(Ph)N(Et)]Mo}2(μ-N)2. A structurally related Mo dimer with a bulkier amidinate ligand, ([N(iPr)C(Me)N(iPr)]), is only capable of photochemical dinitrogen activation. These opposing reactivities were rationalized as steric switching between the thermally and photochemically active species. A computational analysis of the geometric and electronic structures of intermediates along the isomerization pathway from Mo2(μ-η1:η1-N2) to Mo2(μ-η2:η1-N2) and Mo2(μ-η2:η2-N2), and finally Mo2(μ-N)2, is presented here. The extent to which dispersion affects the thermodynamics of the isomers is evaluated, and it is found that dispersion interactions play a significant role in stabilizing the product and making the reaction exergonic. The concept of steric switching is further explored with theoretical models with sterically even less demanding ligands, indicating that systematic ligand modifications could be used to rationally design the N2 activation energy landscape. An analysis of electronic excitations in the computed UV-vis spectra of the two complexes shows that a particular type of asymmetric excitations is only present in the photoactive complex.

Deep Eutectic Solvents (DESs) are emerging as a promising medium for many chemical processes. They can be used to observe specific properties required for nanomaterials' applications. Controlled CO2 adsorption requires disaggregation of carbon nanotubes into smaller bundles which can be accomplished by dispersing them in aqueous DES system. In this study, response surface methodology (RSM) was adopted to examine the impacts of three important factors on the dispersion of single walled carbon nanotubes (SWNTs) in Choline Chloride-Glycerol (ChCl-Gly) DES; (i) ChCl-Gly (mass% in water), (ii) sonication energy input (J/mL), and (iii) SWNTs' concentration (mg/L). The net negative surface charge of ChCl-Gly, a "green solvent," provided superior dispersion of inherently negatively charged SWNTs in water via electrostatic repulsion. The impacts of the dispersion factors were quantified by the average aggregate diameter (nm) and polydispersity (polydispersity index, PDI) of SWNTs in aqueous-DES systems. Models were developed, experimentally verified, and statistically validated to map the impacts of these factors and to obtain optimized dispersions. The optimized dispersions, characterized by the small (<100 nm) and uniform (<0.1 PDI) SWNTs' aggregates, were achieved at lower sonication energy costs which can have promising implications across many nano-manufacturing fields. The dispersion/aggregation mechanism was proposed using COSMO-RS (based on equilibrium thermodynamics and quantum chemistry) modeling of ChCl-Gly and zeta potential measurements of SWNTs. This understanding will help create optimally sustainable and economically feasible DES-nanomaterial dispersions.

The most frequently diagnosed cancers in women are the estrogen receptor (ER)-positive breast cancer subtypes, which are characterized by estrogen dependency for their growth. The mainstay of clinical treatment for this tumor relies on the modulation of ERα action or on the suppression of estrogen biosynthesis via the administration of Selective ERα Modulators/Down-regulators (SERMs/SERDs) or aromatase inhibitors, respectively. Nevertheless, de novo and acquired resistance to these therapies frequently occurs and represents a major clinical concern for patient survival. Recently, somatic mutations affecting the hormone-binding domain of ERα (i.e., Y537S, Y537N, D538G) have been associated with endocrine resistance, disease relapse and increased mortality rates. Hence, devising novel therapies against these ERα isoforms represents a daunting challenge. Here, we identified five molecules active on recurrent Y537S ERα polymorphism by employing in silico virtual screening on commercial databases of molecules, complemented by ER-transactivation and MTT assays in MCF7 and MDA-MB-231 breast cancer cells expressing wild type or mutated ERα. Among them, one molecule selectively targets Y537S ERα without inducing any cytotoxicity in breast cell lines. Multi-microseconds (4.5 μs) of biased and unbiased molecular dynamics provided an atomic-level picture of the structural, thermodynamics (i.e., binding free energies) and the kinetic (i.e., dissociation free energy barriers) of these active ligands as compared to clinically used SERM/SERDs upon binding to wild type and distinct ERα variants (Y537S, Y537N, D538G). This study contributes to a dissection of the key molecular traits needed by drug-candidates to hamper the agonist (active)-like conformation of ERα, normally selected by those polymorphic variants. This information can be useful to discover mutant specific drug-candidates, enabling to move a step forward toward tailored approaches for breast cancer treatment.

Atrazine is one of the most common broad-leaf herbicides used in the world. However, due to extensive use for many years, atrazine often appears in surface and groundwater. Atrazine transport is inhibited by degradation or sorption to soil components, especially organic matter. Biochar is a charcoal-like material produced from pyrolysis of biomass. Due to the amount and type of functional groups found on biochar, this product has shown potential for sorption of atrazine from solution. There is an interest in developing best management practices utilizing biochar to filter atrazine from non-point drainage with pollution-control structures such as blind inlets. The objective of this study was to explore the kinetics and thermodynamics of atrazine sorption to biochar using two different approaches: flow-through sorption cells and isothermal titration calorimetry (ITC). Twenty-five milligrams of an oak (Quercus spp.)-derived biochar was suspended in water and titrated 25 times (0.01 mL per titration) with atrazine at three different concentrations, and by a single titration (0.25 mL), with heat of reaction directly measured with ITC. A benchtop atrazine sorption study that simulated the titration experiment was also conducted. A continuous flow-through system was used to quantify the impact of contact time on atrazine sorption to biochar. Atrazine sorption to biochar displayed both exothermic and endothermic signals within each titration, although the net reaction was exothermic and proportional to the degree of sorption. Net enthalpy was -4,231 ± 130 kJ mole-1 atrazine sorbed. The existence of both exotherms and endotherms within a single titration, plus observation of an initial fast reaction phase from 0 to 300 s followed by a slower phase, suggested multiple sorption mechanisms to biochar. Results of flow-through tests supported kinetics observations, with the 300 s contact time removing much more atrazine compared to 45 s, while 600 s improved little compared to 300 s. Based on flow-through results, annual atrazine removal goal of 50%, and typical Midwestern U.S. tile drainage conditions, a pollution-control structure implementing this biochar sample would require 32 and 4 Mg for a design utilizing a contact time of 45 and 300 s, respectively. Future work is necessary for estimating degradation of atrazine sorbed to biochar.

The lipid composition of the cellular membrane plays an important role in a number of biological processes including the binding of membrane-active peptides. Characterization of membrane binding remains challenging, due to the technical limitations associated with the use of standard biophysical techniques and available membrane models. Here, we investigate the lipid binding properties of two membrane-active peptides, VSTx1, a well characterized ion-channel inhibitor, identified from spider venom, that preferentially binds to anionic lipid mixtures, and AA139 an antimicrobial β-hairpin peptide with uncharacterised lipid binding properties, currently in pre-clinical development. The lipid binding properties of these peptides are elucidated using nanodiscs formed by both linear and circularized (sortase-mediated) forms of a membrane scaffold protein (MSP1D1ΔH5). We find that nanodiscs formed by circularized MSPs-in contrast to those formed by linear MSPs-are sufficiently stable under sample conditions typically used for biophysical measurements (including lipid composition, a range of buffers, temperatures and concentrations). Using these circularized nanodiscs, we are able to extract detailed thermodynamic data using isothermal titration calorimetry (ITC) as well as atomic resolution mapping of the lipid binding interfaces of our isotope labeled peptides using solution-state, heteronuclear, nuclear magnetic resonance (NMR) spectroscopy. This represents a novel and general approach for elucidating the thermodynamics and molecular interface of membrane-active peptides toward flat lipid bilayers of variable composition. Our approach is validated by first determining the thermodynamic parameters and binding interface of VSTx1 toward the lipid bilayer, which shows good agreement with previous studies using lipid micelles and liposomes. The method is then applied to AA139, where the membrane binding properties are unknown. This characterization, involved solving the high-resolution structure of AA139 in solution using NMR spectroscopy and the development of a suitable expression system for isotope labeling. AA139 was found to bind exclusively to anionic membranes with moderate affinity (K d~low μM), and was found to have a lipid binding interface involving the termini of the β-hairpin structure. The preference of AA139 for anionic lipids supports a role for membrane binding in the mode-of-action of this peptide, which is also consistent with its higher inhibitory activity against bacterial cells compared to mammalian cells. The described approach is a powerful method for investigation of the membrane binding properties of this important class of molecules.