Conformational Stability Research Articles

A hammerhead ribozyme selects mechanically stable conformations for catalysis against viral RNA

Ribozymes, widely found in prokaryotes and eukaryotes, target nucleic acids and can be engineered as biotechnical tools or for gene regulation or immune therapy. Among them, hammerhead is the smallest and best characterized ribozyme. However, the structure and biochemical data of ribozymes have been disagreed on, making the understanding of its catalysis mechanism a longstanding issue. Particularly, the role of conformational dynamics in ribozyme catalysis remains elusive. Here, we use single-molecule magnetic tweezers to reveal a concerted catalysis mechanism of mechanical conformational selection for a mini hammerhead ribozyme against a viral RNA sequence from the SARS-CoV-2. We identify a conformational set containing five mechanical conformers of the mini ribozyme, where magnesium ions select the active one. Our results are supported by molecular dynamics simulations. Our understanding of the RNA catalytic mechanism will be beneficial for ribozyme’s biotechnological applications and as potential therapeutics against RNA viruses.

Monitoring Dynamic Conformations of a Single Fluorescent Molecule Inside a Protein Cavity.

Fluorescence nanoscopy and single-molecule methods are entering the realm of structural biology, breaking new ground for dynamic structural measurements at room temperature and liquid environments. Here, single-molecule localization microscopy, polarization-dependent single-molecule excitation, and protein engineering are combined to determine the orientation of a fluorophore forming hydrogen bonds inside a protein cavity. The observed conformations are in good agreement with molecular dynamics simulations, enabling a new, more realistic interplay between experiments and simulations to identify stable conformations and the key interactions involved. Furthermore, jumps between conformations can be monitored with a precision of 3° and a time resolution of a few seconds, confirming the potential of this methodology for retrieving dynamic structural information of nanoscopic biological systems under physiologically compatible conditions.

Immobilization of snailase and β-glucosidase on L-aspartic acid-modified magnetic amorphous ZIF for efficiently and sustainably producing ginsenoside compound K.

Improving the catalytic efficiency and recyclability of immobilized enzyme remained a serious challenge in industrial applications. Enzyme immobilization in the amorphous zeolite imidazolate framework (aZIF) preserved high enzyme activity, but still faced separation difficulties and a low catalytic efficiency in practice. In this study, a one-pot co-precipitation method was used to form the enzyme-aZIF/magnetic nanoparticle (MNP) biocomposite by rapidly precipitating snailase (Sna) and β-glucosidase (β-G) with metal/ligand on MNP and modifying with L-aspartic acid (Asp). Thanks to Asp modification protecting the natural conformation of internal protein molecules and MNP stabilizing the conformation of active enzymes after immobilizing, Sna&β-G in the carrier had more stable conformations and higher catalytic efficiency than those in conventional ZIF-8, increasing the catalytic efficiency for converting ginsenoside Rb1 to rare ginsenoside compound K (CK) to 79.16%. Moreover, while improving the stability of Sna&β-G, owing to the magnetism imparted by MNP, the immobilized enzyme maintained high enzyme activity and recovery after 7cycles by rapid magnetic separation. The results provided guidance for developing immobilized Sna&β-G biocomposites with ideal catalytic efficiency and easy recovery to catalyze ginsenoside Rb1 to rare ginsenoside CK.

Semi-rational engineering of leucine dehydrogenase for enhanced L-tert-leucine production.

Leucine dehydrogenase (LeuDH) is a promising enzyme for the industrial production of L-tert-leucine (L-Tle), but its catalytic activity toward trimethylpyruvate (TMP) requires enhancement. In this study, we employed a semi-rational design approach involving homology modeling of LeuDH from Exiguobacterium sibiricum (EsiLeuDH) and molecular docking with TMP to predict potential mutation sites. These sites were tested using an alanine scanning strategy to assess their impact on enzymatic activity, followed by site-saturation mutagenesis and iterative saturation mutagenesis. The resulting mutant, EsiLeuDH-M3, exhibited a remarkable 306% increase in specific enzymatic activity (104.69U·mg-1), compared to the wild-type EsiLeuDH (WT). Molecular docking indicated that EsiLeuDH-M3 had an increased number of hydrogen bonds, improved stability, and an enlarged substrate-binding pocket. Moreover, molecular dynamics simulations suggested that EsiLeuDH-M3 possessed a more stable conformation but a more flexible pocket, allowing TMP to access the catalytic center more easily. Experiments examining the effects of different substrate concentrations on TMP bioconversion catalyzed by WT and EsiLeuDH-M3 indicated that EsiLeuDH-M3 tolerated higher TMP concentrations than the WT enzyme. Finally, L-Tle was produced using EsiLeuDH-M3 coupled with an NADH regeneration system, achieving a high conversion rate (91%) of TMP at a substrate concentration of 0.7M, which is expected to reduce production costs in the industrial application of L-Tle.

Synthesis and mechanistic studies of 4-aminoquinoline-Isatin molecular hybrids and Schiff's bases as promising antimicrobial agents.

In this investigation, to determine their potential as specific antibacterial agents, Schiff's bases (LT-SB1-23 and SB1-SB12) and novel quinoline-isatin hybrids were subjected to microbiological testing. The in-vitro screening against bacterial strains (Escherichia coli, Enterococcus faecalis, Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa, and Salmonella typhi) exhibited their antibacterial potential with many of the compounds showing inhibition range of 90-100% at 200μg/mL, against most of the tested strains. The MIC values of some of the compounds showed good antibacterial efficacy with values ranging from 32 to 128μg/mL. Their bacterial growth inhibitory potential was further supported by disk diffusion and growth curve assays. Interestingly, one of the Schiff's bases (LT-SB7) displayed strong synergistic activity against E. coli and S. typhi with 16-64 folds reduction in MIC values. Additionally, it exhibited up to 85% suppression of biofilm at ½MIC against AA209 environmental bacterial isolate and reduced the development of multidrug-resistant bacterial isolates. Promising compound LT-SB7 underwent 100 ns molecular dynamics simulations with biofilm-causing protein (PDB ID: 7C7U) to assess conformational changes and complex stability. Overall, this study identified compounds as effective antibacterial alternatives for the future.

Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics.

Potency optimization of macrocyclic peptides can include both modifying intermolecular interactions and modifying the conformational stability of the bioactive conformation. However, the number of possible modifications is vast. To identify modifications that enhance the stability of the binding conformations in a cost-effective manner, there is a need for a high-throughput in-silico method that scores the conformational stability of these modified molecules. For the common case where a binding conformation of a similar compound is known, the relative stability of this conformation for a series of compounds can theoretically be estimated by modeling the metastability of the bound state via conformational sampling techniques. Herein, we survey several sampling methods and report solution-state binding pose metadynamics as the most efficient of such sampling methods. In this manuscript, we compare both estimations of metastability from shorter solution-state sampling methods to both experimental affinities and more rigorous sampling methods to properly isolate the conformational effect on potency. In our benchmark calculations on macrocyclic peptide data sets where chemical modifications can be expected to influence the stability of the binding pose, our solution-state binding pose metadynamics workflow, which estimates conformational metastability of the bioactive state, agrees with more rigorous REST2 simulations while using significantly less computational resources. Further, for both the cases where REST2 simulations converge, as well as some others, the binding pose metadynamics metastability estimations correlated well with experimentally measured potencies, suggesting binding pose metadynamics may be an efficient method for quickly estimating the effect of binding pose metastability on potency.

3D-QSAR, design, molecular docking and dynamics simulation studies of novel 6-hydroxybenzothiazole-2-carboxamides as potentially potent and selective monoamine oxidase B inhibitors

Background6-hydroxybenzothiazole-2-carboxamide is a novel, potent and specific inhibitor of monoamine oxidase B (MAO-B), which can be used to study the molecular structure and develop new neuroprotective strategies.ObjectiveThe aim of this study was to create an effective predictive model from 6-hydroxybenzothiazole-2-carboxamide derivatives to provide a reliable predictive basis for the development of neuroprotective MAO-B inhibitors for the treatment of neurodegenerative diseases.MethodsFirst, the compounds were constructed and optimized using ChemDraw and Sybyl-X software. Subsequently, QSAR modeling was performed using the COMSIA method in Sybyl-X to predict the IC50 values of a set of novel 6-hydroxybenzothiazole-2-carboxamide derivatives. The ten most promising compounds were screened based on the IC50 values and tested for molecular docking. Finally, the binding stability and dynamic behavior of these compounds with MAO-B receptors were analyzed by molecular dynamics simulation (MD).ResultsThe 3D-QSAR model showed good predictive ability, with a q2 value of 0.569, r2 value of 0.915, SEE of 0.109 and F value of 52.714 for the COMSIA model. Based on the model, we designed a series of novel 6-HBC derivatives and predicted their IC50 values by the QSAR model. Among them, compound 31.j3 exhibited the highest predicted IC50 value and obtained the highest score in the molecular docking test. MD simulation results showed that compound 31.j3 was stable in binding to the MAO-B receptor, and the RMSD values fluctuated between 1.0 and 2.0 Å, indicating its conformational stability. In addition, energy decomposition analysis revealed the contribution of key amino acid residues to the binding energy, especially Van der Waals interactions and electrostatic interactions play an important role in stabilizing the complex.ConclusionIn this study, the potential of 6-hydroxybenzothiazole-2-carboxamide derivatives as MAO-B inhibitors was systematically investigated by 3D-QSAR, molecular docking and MD simulations. The successfully designed compound 31.j3 not only demonstrated efficient inhibitory activity, but also verified its stable binding to MAO-B receptor by MD simulation, which provides strong support for the development of novel therapeutic drugs for neurodegenerative diseases. These findings provide important theoretical basis and practical guidance for future drug design and experimental validation.

Accurate Spectroscopic Characterization and Formation Pathways of Ethane 1, 1 diol

With exceptions, the correlation between relative energies of isomers and their relative abundances in the interstellar medium (ISM) holds to an extent. Among the C2H6O2 isomers, ethylene glycol is the only known interstellar isomer but there is no report regarding the astronomical searches for ethane 1,1-ethanediol (the most stable isomer of the group) due to lack of spectroscopic and other parameters that would have warranted the search. In this article, the most energetically stable conformer of 1,1-ethanediol was investigated, its spectroscopic, and other parameters are obtained from high level ab initio quantum chemical methods. Accurate spectroscopic parameters are obtained at the CCSD(T) level. The proposed formation route of ethane 1,1-diol has a surmountable barrier considering the nature/abundance of the participating species and the energy sources in ISM. The astrophysical implications of these results are discussed and the astronomical searches of ethene 1, 1 diol are proposed.

Metabolic profiles and potential antioxidant mechanisms of hawk tea

Hawk tea has received increasing attention for its unique flavor and potential health benefits, with antioxidant function being one of its significant bioactivities. However, the metabolic profiles, potential antioxidant components, and action mechanisms of different types of hawk tea are still unclear. In this study, the chemical components of five hawk teas were determined using untargeted metabolomics. Then, the potential antioxidant metabolites and their possible action mechanisms were revealed by integrating network pharmacology and molecular docking. The results showed that the metabolic profiles of various hawk teas differed significantly, but the content of flavonoids was the highest in each group. Network pharmacology analyses suggested that 11 potential antioxidant metabolites—four of which were the same metabolites with high levels in the five types, and seven were differential metabolites—could be involved in several metabolic pathways in vivo. These pathways included the MAPK and PI3K/AKT signaling pathways, which may be closely related to antioxidant activity. Finally, molecular docking revealed potential antioxidant metabolites bound to 25 core antioxidant targets through hydrogen bonding and hydrophobic interactions. Among them, artemisinin, astragalin, isoquercetrin, isoquercitrin, kaempferol-3-glucuronide, and UDP-L-rhamnose exhibited low binding energies to core antioxidant targets such as AKT1, RELA, and MTOR, forming stable conformation. These insights lay the basis for further elucidating the antioxidant mechanism of hawk tea.

Exploring Biophysical and Chemoinformatics Approaches for Interactions of Ionic Liquids with Hemoglobin, DNA, BSA, and HSA.

This review paper provides an inclusive overview of the intricate interactions amid ionic liquids (ILs) and essential biomacromolecules, mainly Hemoglobin (Hb), Bovine Serum Albumin (BSA), Human Serum Albumin (HSA), and Calf Thymus-DNA (CT-DNA). ILs have recently become a topic of great attention because of their inimitable physicochemical properties and potential uses in different fields. The review systematically explores the binding mechanisms, thermodynamics, and structural changes induced by ILs on Hb, BSA, HSA, and CT-DNA using spectroscopic, thermodynamic, and computational techniques. The paper highlighted various experimental and computational methodologies to explore the interactions between ionic liquids (ILs) and biomacromolecules. It offers an in-depth analysis of the techniques employed to decode the intricate nature of these molecular associations and the influence of ILs along with their structural characteristics on the conformational stability, activity, and functionality of biomacromolecules. This foundational understanding is essential for advancing research and developing strategies that exploit the distinctive properties of ILs to foster innovative and sustainable applications within the biomedical field.

Molecular simulation of newly designed Mannich-based ciprofloxacin derivative as the promising scaffold for E. coli dihydropteroate synthase and DNA gyrase inhibitor

The increasing incidence of bacterial infections has led to rise in antimicrobial resistance (AMR), a significant concern in public health across the globe. Henceforth, there is an urgency to address the AMR catastrophe, including developing new antibiotics, promoting the appropriate use of existing antibiotics, and investing more in research and development. Development of potent antibiotic derivatives is the call of the day. Herein, we designed a novel series of ciprofloxacin derivatives joined with sulfa-drugs (CIS1-15) and screened them against E. coli Dihydropteroate synthase and DNA gyrase through molecular docking and molecular dynamics (MD) simulations. MD simulation displayed the dynamics stability of the top-ranked docked poses, while flexibility and low-energy conformational states of these complexes the dynamics stability of the top-ranked docked poses. In contrast, the flexibility and low-energy conformational states of these complexes were inferred using principal component analysis and free energy landscape analysis. The derivatives of CIS2, CIS3, CIS5, CIS6, CIS8 and CIS15 showed strong binding affinity against both the target receptors with retention of conformational stability during MD. Pre- and post-MD snapshots show the crucial role of Arg63, Arg1072, Gly1073, and Val71 residues in the recognition of ciprofloxacin derivatives. Our in-depth structural study advocates that CIS5 and CIS6 could effectively inhibit DNA gyrase and dihydropteroate synthase. Overall, our comprehensive computational approach employed in this study establishes a benchmark for the identification of physiologically significant small molecules against emerging drug targets to design drugs based on their structure and locating potent drug-like molecules with promise for antibacterial potential.

Binding of Homeodomain Proteins to DNA with Hoogsteen Base Pair.

In DNA double helices, Hoogsteen (HG) base pairing is an alternative mode of Watson-Crick (WC) base pairing. HG bp has a different hydrogen bonding pattern than WC bp. We investigate here the binding energy of homeodomain proteins with a HG-DNA duplex, where DNA adopts a HG bp in its sequence. We observe that the presence of the HG bp increases the binding energy of both the specific and nonspecific homeodomain proteins compared to WC-DNA bps. The neutral mutation in the N-terminal basic arm of the nonspecific protein significantly changes the binding energy between nonspecific protein and HG-DNA only, while the acidic mutation significantly changes the binding energy of both the specific and nonspecific proteins with HG-DNA. The significant variation in the binding energy of the homeodomains within distinct DNA-protein complexes can be ascribed to the differences in the number of intermolecular contacts between DNA bases and protein residues. Our conformational thermodynamics calculations based on the fluctuation of microscopic conformational variables at the interface show that with increasing conformational stability and order at the interface, the binding of the homeodomain protein gets stronger.

Antimicrobial Steroids from Poisonous Mushroom Gymnopilus orientispectabilis and Their Molecular Docking Studies

In this study, three fungal steroids (1–3) were isolated from the fruiting bodies of the poisonous mushroom Gymnopilus orientispectabilis, based on bioactivity-guided isolation methods. The chemical structures of the isolates (1–3) were determined using NMR spectroscopic methods. Compounds 1–3 exhibited inhibition activity against E. coli, and their interactions with several bacterial drug targets were studied via in silico molecular docking, where the lowest binding energies were observed for penicillin binding protein 3 (PBP3) (−62.89, −75.89 and −74.47 kcal/mol, for compounds 1, 2 and 3, respectively). An MD simulation was performed to examine the conformational stability, motion and flexibility of protein–ligand complexes. In conclusion, this study investigates fungal steroids from G. orientaspectabilis as potential sources for new antimicrobial agents, encouraging further research to develop novel therapies.

Computational Study on the Dynamics of a Bis(benzoxazole)-Based Overcrowded Alkene.

Understanding and controlling molecular motions is of pivotal importance for designing molecular machinery and functional molecular systems, capable of performing complex tasks. Herein, we report a comprehensive theoretical study to elucidate the dynamic behavior of a bis(benzoxazole)-based overcrowded alkene displaying several coupled and uncoupled molecular motions. The benzoxazole moieties give rise to 4 different stable conformers that interconvert through single-bond rotations. By performing excited- and ground-state molecular dynamics simulations, DFT calculations, and NMR studies, we found that the photochemical E-Z isomerization of the central double bond of each stable conformer is directional and leads to a mixture of metastable isomers. This transformation is analogous to the classical Feringa-type molecular motors, with the notable difference that, during the photochemical isomerization and the subsequent thermal helix inversion (THI) steps, multiple possible pathways take place that involve single-bond rotations that can be both coupled and uncoupled to the rotation of the naphthyl half of the molecule.

A comprehensive in silico analysis of structural and functional impacts of natural nonsynonymous SNPs in the ALDH2_HUMAN gene

BackgroundnsSNPs result in amino acid substitutions in coding regions that contribute significantly to the structural diversity of proteins in human populations and can affect protein function by altering solubility or stability. Mitochondrial aldehyde dehydrogenase 2 (ALDH2) is a key enzyme involved in the metabolism of acetaldehyde to acetate through a coenzyme-dependent mechanism. Acetaldehyde exhibits a toxic effect, highlighting the necessity of ALDH2’s proper functioning to protect against diseases associated with aldehyde toxicity. ALDH2 has three natural variants: E487K, E479K, and E320V. Consequently, it seems necessary to investigate the underlying molecular basis of the effect of each of these mutations on enzyme structure and function.ResultsEmploying molecular docking and scoring functions of NAD+ at the prosthetic site of ALDH2 indicate that only E487K significantly reduces binding affinity and has a higher inhibition constant. Furthermore, performing microsecond-timescale molecular dynamics simulations revealed that only the E487K mutation elevated the conformational instability and induced less compactness of the ALDH2. To compare the results, four distinct SNP predictors were employed. The outcomes generated by these tools were noteworthy and corroborated the results obtained from the molecular docking and dynamics simulations, indicating that only the E487K variant was identified as a deleterious mutation.ConclusionsThis study revealed that among three natural variants of ALDH2, only the E487K significantly reduces the interaction between NAD+ and ALDH2 due to structural instability in the enzyme, disrupting critical interactions with Cys302 and Glu268 required for enzyme activity. The exploration of the dynamic behavior of the dominant negative mutant in this investigation will contribute essential knowledge toward the potential restoration of its function.

Conformational Stability of α-Lactalbumin and Lysozyme in Ammonium-Based Ionic Liquids: A Comprehensive Insight into Structure–Activity Relationship

Conformational Stability of α-Lactalbumin and Lysozyme in Ammonium-Based Ionic Liquids: A Comprehensive Insight into Structure–Activity Relationship

The unique structure of the highly conserved PPLP region in HIV-1 Vif is critical for the formation of APOBEC3 recognition interfaces.

The human cellular cytidine deaminases APOBEC3s (A3s) inhibit virion infectivity factor (Vif)-deficient HIV-1 replication. However, virus-encoded Vifs abolish this defense system by specifically recruiting A3s to an E3 ubiquitin ligase complex to induce their degradation. The highly conserved Vif PPLP motif is critical for the Vif-mediated antagonism of A3s and is believed to be important for Vif multimerization. However, how the PPLP motif dictates the functions of Vif remains unclear. Here, we aimed to elucidate this mechanism using biochemical and structural biology approaches. First, we found that no stable Vif multimer complexes formed in our tandem coimmunoprecipitation assays. Next, a series of Vif truncation mutants were constructed, and the short α-helix α6 just downstream of PPLP was found to be the smallest fragment essential for efficient A3G degradation in cells. In silico structural analysis suggested that PPLP-α6 adopts a stable L-shaped conformation when complexed in Vif/CBF-β and contributes to the structural integrity of Vif. In vitro ubiquitination assays with recombinant proteins confirmed that PPLP-α6 is necessary to form the functional complex of the E3 ligase adaptor of Vif/CBF-β/elongin B/elongin C. Additionally, mutations of the highly conserved PPLP-α6 hydrophobic residues severely disrupted Vif function. In the Vif structure, PPLP-α6 is positioned behind α1-α2 that constitutes the A3-binding Vif interfaces. Therefore, both the PPLP motif and α6 play critical allosteric roles in maintaining the integrity of the A3 interaction interfaces. Our findings will also provide important data for the design of novel anti-HIV-1 compounds that disrupt the A3-binding Vif interfaces.IMPORTANCEThe APOBEC3 (A3) family enzymes potently block the replication of retroviruses, such as HIV-1. However, HIV-1 expresses Vif, a small multifaceted protein that binds and specifically eliminates A3s in infected cells via ubiquitination-proteasome degradation. Thus, A3-Vif interactions are attractive targets for anti-HIV-1 drug development. The Vif PPLP motif that is distal from these interfaces is necessary for A3 degradation; however, the mechanism by which PPLP participates in A3 degradation is unknown. In this study, we performed biochemical and structural biology analyses to elucidate the underlying mechanisms involved. We found that the PPLP motif, in addition to the short downstream fragment α6, forms a stable L-shaped conformation and acts as a scaffold for the A3 recognition interfaces. Importantly, mutations in α6 abolished Vif function to antagonize multiple A3 family enzymes. These findings provide important data for the development of novel HIV-1 inhibitors that utilize A3s as cellular defense enzymes.

Investigation into Alzheimer's-related amyloid-β conformational transformations and stability influenced by green iron oxide nanoparticles (GIONP).

Alzheimer's disease (AD) is popularly believed to be triggered by the aggregation of amyloid beta 1-42 (Aβ-42) peptides, eventually leading to neurodegeneration. Our study delves into the influential role played by Green Iron Oxide Nanoparticles (GIONP). GIONP are typically synthesized using a green chemistry approach, imposing curcumin as a biocompatible reducing and capping agent, leveraging its inherent antioxidant, anti-inflammatory, and neuroprotective attributes. Herein, our research particularly aims to decipher whether GIONP modulates the secondary structure of Aβ1-42 peptides with a close consideration to the surrounding physiological factors, as well as the membrane bilayer probable conformation changes. Raman spectroscopy was employed to investigate the interaction between GIONP and Aβ1-42 aggregates, demonstrating significant alterations in secondary structure dynamics of Aβ1-42 polypeptide. Fourier-transform infrared (FTIR) spectroscopy shed light on the chemical interactions between GIONP and curcumin, a capping agent. X-ray diffraction (XRD) analysis was performed to determine the crystalline structure and phase purity of the synthesized GIONP, providing insights into their stability and structural integrity. GIONP particle size distribution investigations and membrane architectures surrounding GIONP were carried out for their impact on membrane integrity and stability. The morphology of GIONP, membrane mimetic liposomal structures formation, and integrity were studied using transmission electron microscopy (TEM), accompanied with energy-dispersive X-ray spectroscopy (EDS), which displayed the elements distribution within each of the structures. The study uncovered that GIONP stabilizes the secondary structure of Aβ1-42, potentially offering modulation to the aggregation process. Furthermore, GIONP proved to have no negative impact on membrane integrity, implying that they could be safely employed as a therapeutic option for the modulation of peptide aggregation's pathological pathway of Alzheimer's disease. This study may contribute to broadening our understanding of nanoparticle-mediated therapies in modulating neurodegenerative disorders, highlighting their dual involvement in amyloid aggregation regulation and membrane structure maintenance.

Non covalent inhibitors of SARS-CoV-2 main protease, a rescaffolding attempt

Out of the results of the sole large-scale screening for inhibitors of SARS-CoV-1 main protease reported in 2013, attempts to improve the 3-pyridyl-bearing hits found have been conducted in research laboratories, either on this enzyme or more recently on the closely related SARS-CoV-2 main protease. From the resulting structural information reported, we sought to design analogues featuring some of the components providing an affinity for the active site of these proteases along with a different scaffold which would allow for further structure-activity relationship studies and/or pharmacological improvements. We describe here the introduction of a bridging component aiming at the stabilization of the ligand conformation adopted when bound to these proteases. Accordingly, this led us to prepare 3,3-disubtituted piperazin-2-ones from an array of ketones, via either a Bargellini reaction or a multistage condensation/cyclization/hydrolysis involving ethylene diamine and potassium cyanide. However, even the most elaborate and lipophilic biphenyl-bearing analog made, displayed only a weak effect in a bioluminescence-based SARS-CoV-2 main protease inhibition assay.

2,4-Dichlorophenoxyacetic Acid in the Gas and Crystal Phases and Its Intercalation in Montmorillonite-An Experimental and Theoretical Study.

Many properties of 2,4-dichlorophenoxyacetic acid (2,4-D) depend on its molecular environment, such as whether it is an isolated molecule, a dimer, or in a crystalline state. The molecular geometry, conformational analysis, and vibrational spectrum of 2,4-D were theoretically calculated using Density Functional Theory (DFT) methods. A new slightly more stable conformer was found, which is different to those previously reported. The most stable conformer shows a dimer by means of hydrogen bonds between the carboxylic groups of both molecules, which agrees with the experimental results. The crystal structure of 2,4-D was also calculated with 3D periodical boundary conditions at the DFT level. From the theoretical IR spectra, a vibrational analysis of this molecular species was accomplished, and the bands were reassigned. 1H and 13C NMR in the dissolution and solid states, respectively, showed intramolecular hydrogen bonds between carboxylic acid groups. The dimer is more stable than the isolated molecule. All these results indicated that the dimer can also exist in the solid state, which could explain the low solubility of this compound. In addition, the intercalation of 2,4-D into the confined interlayer space of montmorillonite was also calculated, and it was found that the adsorption is energetically favourable. This result was experimentally confirmed. These findings predicted that these natural clay minerals, which are found in the environment, can be excellent adsorbents for the 2,4-D pollutant.