One-Pot Transition-Metal-Free Synthesis of Alkynyl Amides.

Alkynyl amides play crucial roles in organic synthesis in the production of bioactive compounds and valuable heterocycles. Despite numerous studies on their synthesis, challenges persist due to the necessity of harsh or hazardous conditions and the use of costly or unstable reagents. Herein, we present a one-pot method for the synthesis of all three bonds of the alkyne under transition-metal free conditions. An important feature of this chemistry is the use of readily available feedstock chemicals, such as methyl esters and acetamides. This approach offers efficient access to a wide range of aryl and alkyl alkynyl amides and demonstrates excellent tolerance towards various functional groups in a sustainable and cost-effective manner.

Solvent Attenuation of London Dispersion in Polycyclic Aromatic Stacking.

Solvent competition for London dispersion attenuates its energetic significance in molecular recognition processes. By varying both the stacked contact area and the solvent, here we experimentally deconvolute solvent attenuation using molecular balances. Experimental stacking energies (phenyl to pyrene) correlated strongly with calculations only when dispersion was considered. Such calculations favoured stacking by up to -27 kJ mol-1 in the gas phase, but it was weakly disfavoured in our solution-phase experiments (+0.5 to +4.6 kJ mol-1). Nonetheless, the propensity for stacking increased with contact area and in solvents with lower bulk polarisabilities that compete less for dispersion. Experimental stacking energies ranged from -0.02 kJ mol-1 Å-2 in CS2, to -0.05 kJ mol-1 Å-2 in CD2Cl2, but were dwarfed by the calculated gas-phase energy of -0.6 kJ mol-1 Å-2. The results underscore the challenge facing the exploitation of dispersion in solution. Solvent competition strongly but imperfectly cancels dispersion at molecular recognition interfaces, making the energetic benefits difficult to realise.

High Rotational Barrier Atropisomers.

Atropisomers have attracted a great deal of attention lately due to their numerous applications in organic synthesis and to their employment in drug discovery. However, the synthetic arsenal at our disposal with which to access them remains limited. The research described herein is two-pronged; we both demonstrate the use of MCR chemistry as a synthetic strategy for the de novo synthesis of a class of atropisomers having high barriers to rotation with the simultaneous insertion of multiple chiral elements and we study these unprecedented molecular systems by employing a combination of crystallography, NMR and DFT calculations. By fully exploiting the synthetic capabilities of our chemistry, we have been able to monitor a range of different types of interaction, i. e. π-π, CH-π, heteroatom-π and CD-π, in order to conduct structure-property studies. The results could be applied both to atroposelective synthesis and in drug discovery.

Liquid-liquid phase separation of the prion protein is regulated by the octarepeat domain independently of histidines and copper.

Liquid-liquid phase separation (LLPS) of the mammalian prion protein is mainly driven by its intrinsically disordered N-terminal domain (N-PrP). However, the specific intermolecular interactions that promote LLPS remain largely unknown. Here, we used extensive mutagenesis and comparative analyses of evolutionarily distant PrP species to gain insight into the relationship between protein sequence and phase behavior. LLPS of mouse PrP is dependent on two polybasic motifs in N-PrP that are conserved in all tetrapods. A unique feature of mammalian N-PrP is the octarepeat domain with four histidines that mediate binding to copper ions. We now show that the octarepeat is critical for promoting LLPS and preventing the formation of PrP aggregates. Amphibian N-PrP, which contains the polybasic motifs but lacks a repeat domain and histidines, does not undergo LLPS and forms nondynamic protein assemblies indicative of aggregates. Insertion of the mouse octarepeat domain restored LLPS of amphibian N-PrP, supporting its essential role in regulating the phase transition of PrP. This activity of the octarepeat domain was neither dependent on the four highly conserved histidines nor on copper binding. Instead, the regularly spaced tryptophan residues were critical for regulating LLPS, presumably via cation-π interactions with the polybasic motifs. Our study reveals a novel role for the tryptophan residues in the octarepeat in controlling phase transition of PrP and indicates that the ability of mammalian PrP to undergo LLPS has evolved with the octarepeat in the intrinsically disordered domain but independently of the histidines.

Bayesian Inference for Model Analyses of Supramolecular Complexes: A Case Study with Nanocarbon Hosts.

A 126 π-electron nanobowl molecule, phenine tridehydrosumanene, was synthesized in 12 steps through the development of a polygon cyclization strategy that assembled the polygonal precursors by Ni-mediated macrocyclization. The bowl-shaped structure accommodated C70 as a guest at the concave site, and the ball-in-bowl structure was determined by X-ray crystallography. The host-guest equilibrium in solution was studied with titration experiments using isothermal calorimetry, which provided an interesting test case for studying the host-guest stoichiometry. Bayesian inference was introduced for stoichiometric analyses of the equilibrium, and a procedure to estimate the volume of prior probability in the parameter space was developed. The Bayesian procedure functioned as Occam's razor and provided quantitative support for a specific stoichiometry. The method was examined with five host-guest examples comprising nanocarbon hosts, which suggested the versatility of Bayesian inference for studies of supramolecular complexes.

Bioisoteres for carboxylic acids: From ionized isosteres to novel unionized replacements.

Carboxylic acids are key pharmacophoric elements in many molecules. They can be seen as a problem by some, due to perceived permeability challenges, potential for high plasma protein binding and the risk of forming reactive metabolites due to acyl-glucuronidation. By others they are viewed more favorably as they can decrease lipophilicity by adding an ionizable center which can be beneficial for solubility, and can add enthalpic interactions with the target protein. However, there are many instances where the replacement of a carboxylic acid with a bioisosteric group is required. This has led to the development of a number of ionizable groups which sufficiently mimic the carboxylic acid functionality whilst improving, for example, the metabolic profile of the molecule in question. An alternative strategy involves replacement of the carboxylate by neutral functional groups. This review initially details carefully selected examples whereby tetrazoles, acyl sulfonamides or isoxazolols have been beneficially utilized as carboxylic acid bioisosteres altering physicohemical properties, interactions with the target and metabolism and/or pharmacokinetics, before delving further into the binding mode of carboxylic acid derivatives with their target proteins. This analysis highlights new ways to consider the replacement of carboxylic acids by neutral bioisosteric groups which either rely on hydrogen bonds or cation-π interactions. It should serve as a useful guide for scientists working in drug discovery.

Biological importance of arginine: A comprehensive review of the roles in structure, disorder, and functionality of peptides and proteins.

Arginine shows Jekyll and Hyde behavior in several respects. It participates in protein folding via ionic and H-bonds and cation-pi interactions; the charge and hydrophobicity of its side chain make it a disorder-promoting amino acid. Its methylation in histones; RNA binding proteins; chaperones regulates several cellular processes. The arginine-centric modifications are important in oncogenesis and as biomarkers in several cardiovascular diseases. The cross-links involving arginine in collagen and cornea are involved in pathogenesis of tissues but have also been useful in tissue engineering and wound-dressing materials. Arginine is a part of active site of several enzymes such as GTPases, peroxidases, and sulfotransferases. Its metabolic importance is obvious as it is involved in production of urea, NO, ornithine and citrulline. It can form unusual functional structures such as molecular tweezers in vitro and sprockets which engage DNA chains as part of histones in vivo. It has been used in design of cell-penetrating peptides as drugs. Arginine has been used as an excipient in both solid and injectable drug formulations; its role in suppressing opalescence due to liquid-liquid phase separation is particularly very promising. It has been known as a suppressor of protein aggregation during protein refolding. It has proved its usefulness in protein bioseparation processes like ion-exchange, hydrophobic and affinity chromatographies. Arginine is an amino acid, whose importance in biological sciences and biotechnology continues to grow in diverse ways.

Collective Effects of Multiple Fluorine Atoms Causing π-philic Characteristic within a Caged Polyoxometalate Framework.

Perfluorination brings about distinctive properties arising from the unusual nature of the F element, which have been extensively developed in materials science and chemistry. Herein we report that the construction of F-rich inner space within a hollowed Mo132 O372 cage ([Mo132 O372 (OCOR)30 (H2 O)72 ]42- ) leads to the emergence of unique guest binding activities in encapsulation. Prominently, the trifluoroacetate-modified cage (R=CF3 , 2) having as many as 90 F groups inside favors trapping cyclopentadiene (Cp), which is hardly trapped by the non-fluorinated counterpart (R=CH3 , 1). Systematic studies using related hydrocarbons show that the amount of the encapsulated guest is correlated with the unsaturation degree of the guests, implying the involvement of the attractive interaction of the CF3 -modified interior wall with the guest π-electron clouds. Control experiments using the semi-fluorinated analogues (R=CF2 H, CFH2 ) reveal that the perfluorination is a critical factor to facilitate the Cp encapsulation by 2, indicating that collective effects of polar C-F bonds spreading over the interior surface, rather than the polarity of the individual C-F bonds, are responsible. We also provide a successful example of the physical molecular confinement within the cage through the "ship-in-a-bottle" Diels-Alder reaction between trapped diene and dienophile.

Graphene as a rational interface for enhanced adsorption of microcystin-LR from water.

Cyanotoxins such as microcystin-LR (MC-LR) represent a global environmental threat to ecosystems and drinking water supplies. The study investigated the direct use of graphene as a rational interface for removal of MC-LR via interactions with the aromatic ring of the ADDA1 chain of MC-LR and the sp2 hybridized carbon network of graphene. Intra-particle diffusion model fit indicated the high mesoporosity of graphene provided significant enhancements to both adsorption capacities and kinetics when benchmarked against microporous granular activated carbon (GAC). Graphene showed superior MC-LR adsorption capacity of 75.4 mg/g (Freundlich model) compared to 0.982 mg/g (Langmuir model) for GAC. Sorption kinetic studies showed graphene adsorbs 99% of MC-LR in 30 min, compared to zero removal for GAC after 24 hr using the same MC-LR concentration. Density functional theory (DFT), calculations showed that postulated π-based interactions align well with the NMR-based experimental work used to probe primary interactions between graphene and MC-LR adduct. This study proved that π-interactions between the aromatic ring on MC-LR and graphene sp2 orbitals are a dominant interaction. With rapid kinetics and adsorption capacities much higher than GAC, it is anticipated that graphene will offer a novel molecular approach for removal of toxins and emerging contaminants with aromatic systems.

Oxa-TriQuinoline: A New Entry to Aza-Oxa-Crown Architectures.

A new 15-membered-macrocyclic molecular entity, oxa-TriQuinoline (o-TQ), was designed and synthesized. In o-TQ, three oxygen atoms were joined onto three quinoline units at the 2- and 8-positions in a head-to-tail fashion by three-fold SN Ar reactions, giving rise to the characteristic N3 O3 aza-oxa-crown architecture. o-TQ can serve as a new tridentate nitrogen ligand to capture a CuI cation and adopt a bowl shape, before supramolecular complexation with corannulene and [12]cycloparaphenylene (CPP) occurs through π-π and CH-π interactions. In the presence of the CuI cation, the non-emissive o-TQ becomes a highly emissive material in the solid state, whereby the emission wavelengths depend on the ancillary ligand on the CuI cation. The o-TQ/CuI complex is able to promote carbene catalysis to provide a range of enamines with a gem-difluorinated terminus.

Investigation of the removal kinetics, thermodynamics and adsorption mechanism of anionic textile dye, Remazol Red RB, with powder pumice, a sustainable adsorbent from waste water.

Excessive growth and abnormal use of dyes and water in the textile industry cause serious environmental problems, especially with excessive pollution of water bodies. Adsorption is an attractive, feasible, low-cost, highly efficient and sustainable technique in terms of green chemistry for the removal of pollutants from water. This study aims to investigate the removal kinetics, thermodynamics and adsorption mechanism of Remazol Red RB, which was chosen as a representative anionic reactive dye, from synthetic wastewater using powdered pumice, taking into account various experimental parameters such as initial dye concentration, adsorption time, temperature and pH. Moreover, to support the proposed adsorption mechanism, before and after adsorption of the samples, the Fourier transform infrared spectrophotometer (FTIR) spectra, X-ray powder diffraction (XRD) diffractograms and High resolution transmission electron microscopy (HRTEM) images were also taken and used. The results show that powder pumice can be an efficient adsorbent for anionic dye removal with a relatively high adsorption capacity of 38.90 mg/g, and it is very effective in 30-60 min in mild conditions. The experimental data showed a high agreement with the pseudo-second-order kinetic model and the Freundlich adsorption isotherm equation. In addition, thermodynamically, the process exhibited exothermic nature and standard isosteric enthalpy and entropy changes of -4.93 kJ/mol and 16.11 J/mol. K were calculated. It was determined that the adsorption mechanism was predominantly based on T-shaped pi-pi interactions and had physical characteristics.

Rationalizing Aggregate Structures with Orbital Contributions to the Exchange-Repulsion Energy.

It is shown that repulsive interactions have a crucial influence on the structure of prototypical non-covalently bonded systems. To explain this, we propose a molecular orbital-based model for the exchange-repulsion contribution to the total interaction energy. As a central result, our model shows that energetically preferred aggregate structures frequently exhibit reduced exchange repulsion, which can be deduced from the nodal structure of certain occupied orbitals. This is used to explain key features of the intermolecular potentials of the Cl2 -He, benzene-benzene, and benzene-hexafluorobenzene aggregates, which are not correctly reproduced by commonly applied electrostatic models.

Balancing Attraction and Repulsion: The Influence of London Dispersion in [10]Cycloparaphenylene-Fullerene Complexes.

Herein we present a systematic study of the influence of different alkyl chains in malonyl ester fullerene adducts with [10]cycloparaphenylene ([10]CPP]) and a tert-butyl (tBu) ester-substituted [10]CPP analogue. The association constants between the nanoring hosts and the fullerene guests were determined by fluorescence quenching experiments. The trends in association were rationalized by an interplay of repulsion arising from an extended volume and London dispersion as an attractive counterpart.

Neutron Diffraction Study of Indole Solvation in Deep Eutectic Systems of Choline Chloride, Malic Acid, and Water.

Deep eutectic systems are currently under intense investigation to replace traditional organic solvents in a range of syntheses. Here, indole in choline chloride-malic acid deep eutectic solvent (DES) was studied as a function of water content, to identify solute interactions with the DES which affect heterocycle reactivity and selectivity, and as a proxy for biomolecule solvation. Empirical Potential Structure Refinement models of neutron diffraction data showed [Cholinium]+ cations associate strongly with the indole π-system due to electrostatics, whereas malic acid is only weakly associated. Trace water is sequestered into the DES and does not interact strongly with indole. When water is added to the DES, it does not interact with the indole π-system but is exclusively in-plane with the heterocyclic rings, forming strong H-bonds with the -NH group, and also weak H-bonds and thus prominent hydrophobic hydration of the indole aromatic region, which could direct selectivity in reactions.

Adsorption to the Surface of Hemozoin Crystals: Structure-Based Design and Synthesis of Amino-Phenoxazine ß-Hematin Inhibitors.

In silico adsorption of eight antimalarials that inhibit ß-hematin (synthetic hemozoin) formation identified a primary binding site on the (001) face, which accommodates inhibitors via formation of predominantly π-π interactions. A good correlation (r2 =0.64, P=0.017) between adsorption energies and the logarithm of ß-hematin inhibitory activity was found for this face. Of 53 monocyclic, bicyclic and tricyclic scaffolds, the latter yielded the most favorable adsorption energies. Five new amino-phenoxazine compounds were pursued as ß-hematin inhibitors based on adsorption behaviour. The 2-substituted phenoxazines show good to moderate ß-hematin inhibitory activity (<100 µM) and Plasmodium falciparum blood stage activity against the 3D7 strain. N1 ,N1 -diethyl-N4 -(10H-phenoxazin-2-yl)pentane-1,4-diamine (P2a) is the most promising hit with IC50 values of 4.7±0.6 and 0.64±0.05 µM, respectively. Adsorption energies are predictive of ß-hematin inhibitory activity, and thus the in silico approach is a beneficial tool for structure-based development of new non-quinoline inhibitors.

Sigma/pi Bonding Preferences of Solvated Alkali-Metal Cations to Ditopic Arylmethyl Anions.

Arylmethyl anions allow alkali-metals to bind in a σ-fashion to the lateral carbanionic centre or a π-fashion to the aryl ring or in between these extremities, with the trend towards π bonding increasing on descending group 1. Here we review known alkali metal structures of diphenylmethane, fluorene, 2-benzylpyridine and 4-benzylpyridine. Next, we synthesise Li, Na, K monomers of these diarylmethyls using polydentate donors PMDETA or Me6 TREN to remove competing oligomerizing interactions, studying the effect that two aromatic rings has on negative charge (de)localisation via NMR, X-ray crystallographic and DFT studies. Diphenylmethyl and fluorenyl anions maintain C(H)-M interactions regardless of alkali-metal, although the adjacent arene carbons engage in interactions with larger alkali-metals. Introducing a nitrogen atom into the ring (at the 2- or 4-position) encourages relocalisation of negative charge away from the deprotonated carbon and onto nitrogen. Phenyl(2-pyridyl)methyl moves from an enamide formation at one extremity (lithium) to an aza-allyl formation at the other extremity (potassium), while C- or N-coordination modes become energetically viable for Na and K phenyl(4-pyridyl)methyl complexes.

Structure and Photophysical Properties of 1,1,2,2-Tetra(1-anthryl)ethane: A C(sp3 )-C(sp3 ) Bond Substituted with Four Anthracene Units.

The title aromatic compound comprising four anthracene units was synthesized by the McMurry coupling of di(1-anthryl) ketone as a hydrogenated product in 65 % yield. The molecule forms a C2 symmetric structure with the ap conformation about the C(sp3 )-C(sp3 ) single bond, as revealed by X-ray analysis and DFT calculations. The UV/vis and fluorescence spectra of this compound were compared with those of anthracene, di(1-anthryl)methane, and 1,2-di(1-anthryl)ethane. The fluorescence spectrum showed a broad emission band at 450 nm having a long lifetime at 21 ns, which was assignable to an excimer-type emission, in contrast to the other reference compounds. The characteristic photophysical property is discussed in terms of the molecular structure with the aid of the noncovalent interaction plots and the conformational analysis.

1,2,3-Tri(9-anthryl)benzene: Photophysical Properties and Solid-State Intermolecular Interactions of Radially Arranged, Congested Aromatic π-Planes.

We report the Negishi coupling based synthesis of 1,2,3-tri(9-anthryl)benzene derivatives containing three radially arranged anthracenes in a π-cluster. In the crystalline state of the unsubstituted derivative, intermolecular π-π and CH-π interactions between the anthracene units drive the formation of the two-dimensional packing structure. Owing to though-space π-conjugation between anthracene units, the substances have unique electronic properties. The excited-state dynamic behavior occurring between the three anthracene moieties, such as exciton localization/delocalization, was elucidated by means of transient absorption measurements and quantum chemical calculations. Interestingly, even though the three anthracenes are closely oriented with approximately 3.0 Šbetween their C-9 positions, exciton localization on two anthracene units is energetically favorable because of the flexible nature of the radially arranged aromatic rings.

New Type of Aromatic π-Systems for Anion Recognition: Strong Anion-π and C-H⋠⋠⋠Anion Interactions Between Halides and Aromatic Ligands in Half-Sandwich Compounds.

Half-sandwich compounds of benzene, cyclopentadienyl, pentamethylcyclopentadienyl, and indenyl were studied as a new type of aromatic π-systems for interactions with halide anions. Although uncoordinated benzene forms only C-H⋅⋅⋅anion interactions, and hexafluorobenzene forms only anion-π interactions, aromatic ligands in half-sandwich compounds can form both types of interactions, because their entire electrostatic potential surface is positive. These aromatic ligands can form stronger anion-π interactions than organic aromatic molecules, as a consequence of more pronounced dispersion and induction energy components. Moreover, C-H⋅⋅⋅anion interactions of aromatic ligands are stronger than anion-π interactions, and significantly stronger than C-H⋅⋅⋅anion interactions of benzene. Our study shows that transition-metal coordination can make aromatic moieties suitable for strong interactions with anions, and gives insight into the design of new anion receptors.

A Molecular Compound for Highly Selective Purification of Ethylene.

Purification of C2 H4 from an C2 H4 /C2 H6 mixture is one of the most challenging separation processes, which is achieved mainly through energy-intensive, cryogenic distillation in industry. Sustainable, non-distillation methods are highly desired as alternatives. We discovered that the fluorinated bis(pyrazolyl)borate ligand supported copper(I) complex {[(CF3 )2 Bp]Cu}3 has features very desirable in an olefin-paraffin separation material. It binds ethylene exclusively over ethane generating [(CF3 )2 Bp]Cu(C2 H4 ). This molecular compound exhibits extremely high and record ideal adsorbed solution theory (IAST) C2 H4 /C2 H6 gas separation selectivity, affording high purity (>99.5 %) ethylene that can be readily desorbed from separation columns. In-situ PXRD provides a "live" picture of the reversible conversion between [(CF3 )2 Bp]Cu(C2 H4 ) and the ethylene-free sorbent in the solid-state, driven by the presence or removal of C2 H4 . Molecular structures of trinuclear {[(CF3 )2 Bp]Cu}3 and mononuclear [(CF3 )2 Bp]Cu(C2 H4 ) are also presented.