Search Results (25)

Small bifunctional molecules are attractive for use as models in different areas of knowledge. How can their functional groups interact in solids? This is important to know for the prediction of the physical and chemical properties of the materials based on them. In this study, two new hydrogen-bonded organic frameworks (HOFs) based on sterically demanding molecular compounds, bis(1-hydroxy-2-methylpropane-2-aminium) sulfate (1) and 2-methyl-4-oxopentan-2-aminium hydrogen ethanedioate hydrate (2), were synthesized and fully characterized by means of FTIR and NMR spectroscopies, as well as by X-ray powder diffraction and thermogravimetric analyses. Their molecular and crystal structures were established through single-crystal X-ray diffraction analysis. It was shown that both compounds have a layered structure due to the formation of a 2D hydrogen-bonding network, the layers being linked by systematically arranged Van der Waals contacts between the methyl groups of organic cations. To unveil some dependencies between the chemical nature of bifunctional molecules and their solid structure, Hirschfeld surface (HS) analysis was carried out for HOFs 1, 2, and their known congeners 1-hydroxy-2-methylpropan-2-aminium hemicarbonate (3) and 1-hydroxy-2-methylpropan-2-aminium (1-hydroxy-2-methylpropan-2-yl) carbamate (4). HS was performed to quantify and visualize the close intermolecular atomic contacts in the crystal structures. It is clearly seen that H–H contacts make the highest contributions to the amino alcohol based compounds 1, 3 and 4, with a maximal value of 65.2% for compound 3 having CO₃²⁻ as a counterion. A slightly lower contribution of H–H contacts (64.4%) was found for compound 4, in which the anionic part is represented by 1-hydroxy-2-methylpropan-2-yl carbamate. The significant contribution of the H–H contacts in the bifunctional moieties is due to the presence of a quaternary carbon atom with a short three-carbon chain. Full article

Although disubstituted imidazolium cation is sterically crowded, hundreds of ionic liquids based on this cation have been reported as electrolytes for energy storage devices. In contrast to disubstituted imidazolium, non-substituted imidazolium is uncrowded sterically and has not yet been investigated as an electrolyte, to the best of our knowledge. Hence, imidazolium hydrogen sulfate [Imi][HSO₄], in mixture with water, was studied as an electrolyte for PANI-based electrode materials. For comparison, pyrrolidinium with hydrogen sulfate or p-toluene sulfonate ([Pyrr][HSO₄] or [Pyrr][PTS]), in mixture with water, were also investigated as alternatives to the conventional electrolyte (i.e., aqueous H₂SO₄) for PANI electrodes. Walden plots of binary mixture ionic liquid–water weight ratios with the optimal ionic conductivity (i.e., [Imi][HSO₄]/water 48/52 wt% (195.1 mS/cm), [Pyrr][HSO₄]/water 41/59 wt% (186.6 mS/cm), and [Pyrr][PTS]/water 48/52 wt% (43.4 mS/cm) along with the electrochemical performances of PANI in these binary mixtures showed that [Pyrr][HSO₄]_aq or [Imi][HSO₄]_aq are convenient electrolytes for PANI/PIL, as opposed to [Pyrr][PTS]_aq. Furthermore, replacing the conventional aqueous electrolyte H₂SO₄ with [Imi][HSO₄] _aq increased the specific capacitance of PANI/PIL from 249.8 to 268.5 F/g at 15 mV/s. Moreover, PANI/PIL electrodes displayed a quasi-ideal capacitive behavior in [Imi][HSO₄]_aq (the correction factor of CPE₄ was 0.99). This primary study has shown that non-substituted imidazolium as an electrolyte could enhance the electrochemical performances of PANI electrodes and could be a good alternative to the conventional electrolyte. Full article

Conventional spherical nucleic acid enzymes (SNAzymes), made with gold nanoparticle (AuNPs) cores and DNA shells, are widely applied in bioanalysis owing to their excellent physicochemical properties. Albeit important, the crowded catalytic units (such as G-quadruplex, G4) on the limited AuNPs surface inevitably influence their catalytic activities. Herin, a hybridization chain reaction (HCR) is employed as a means to expand the quantity and spaces of G4 enzymes for their catalytic ability enhancement. Through systematic investigations, we found that when an incomplete G4 sequence was linked at the sticky ends of the hairpins with split modes (3:1 and 2:2), this would significantly decrease the HCR hybridization capability due to increased steric hindrance. In contrast, the HCR hybridization capability was remarkably enhanced after the complete G4 sequence was directly modified at the non-sticky end of the hairpins, ascribed to the steric hindrance avoided. Accordingly, the improved SNAzymes using HCR were applied for the determination of AFB1 in food samples as a proof-of-concept, which exhibited outstanding performance (detection limit, 0.08 ng/mL). Importantly, our strategy provided a new insight for the catalytic activity improvement in SNAzymes using G4 as a signaling molecule. Full article

According to Bader’s quantum theory of atoms in molecules (QTAIM), the simultaneous presence of a bond path and the corresponding bond critical point between any two atoms is both a necessary and sufficient condition for the atoms to be bonded to one another. In principle, this means that this pair of atoms should make a stabilizing contribution to the molecular system. However, the multitude of so-called counterintuitive bond paths strongly suggests that this statement is not necessarily true. Particularly ‘troublesome’ are endohedral complexes, in which encapsulation-enforced proximity between the trapped guest (e.g., an atom) and the host’s cage system usually ‘produces’ many counterintuitive bond paths. In the author’s opinion, the best evidence to demonstrate the repulsive nature of the intra-cage guest⋯host interaction is the use of some trapping systems containing small escape channels and then showing that the initially trapped entity spontaneously escapes outside the host’s cage during geometry optimization of the initially built guest@host endohedral complex. For this purpose, a group of 24 Ng@[3${}_n$]cyclophane (3$\le n\le$6) endohedral complexes is used. As a result, arguments are presented showing that Bader’s topological bond path does not necessarily indicate a stabilizing interaction. Full article

The binding affinity of trastuzumab and pertuzumab to HER2 has been studied using both experimental and in silico methods. The experiments were conducted using the antibodies in their complete IgG form, as used in clinical therapy, and the extracellular domain of the HER2 protein in solution. This approach provides a precise, reproducible, and reliable view of the interaction between them in physicochemical conditions similar to those found in the tumoral environment. Dynamic light scattering and size exclusion chromatography coupled with tetra detection were utilized to characterize the protein complexes, measure their concentrations, and calculate the equilibrium-free binding energy, ΔG_bind. In addition, PRODIGY, a QSAR-like model with excellent predictive ability, was employed to obtain in silico ΔG_bind estimations. The results obtained indicate that pertuzumab exhibits a slightly higher binding affinity to HER2 than trastuzumab. The difference in binding affinity was explained based on the contribution of the different interfacial contact (IC) descriptors to the ΔG_bind value estimated by the PRODIGY model. Furthermore, experiments revealed that the pertuzumab IgG antibody binds preferentially to two HER2 proteins, one per Fab fragment, while trastuzumab mainly forms a monovalent complex. This finding was interpreted based on a geometrical model that identified steric crowding in the trastuzumab–HER2 complex as compared with the pertuzumab–HER2 complex. Full article

Surface plasmon resonance (SPR) is a popular real-time technique for the measurement of binding affinity and kinetics, and bench-top instruments combine affordability and ease of use with other benefits of the technique. Biomolecular ligands labeled with the 6xHis tag can be immobilized onto sensing surfaces presenting the Ni²⁺-nitrilotriacetic acid (NTA) functional group. While Ni-NTA immobilization offers many advantages, including the ability to regenerate and reuse the sensors, its use can lead to signal variability between experimental replicates. We report here a study of factors contributing to this variability using the Nicoya OpenSPR as a model system and suggest ways to control for those factors, increasing the reproducibility and rigor of the data. Our model ligand/analyte pairs were two ovarian cancer biomarker proteins (MUC16 and HE4) and their corresponding monoclonal antibodies. We observed a broad range of non-specific binding across multiple NTA chips. Experiments run on the same chips had more consistent results in ligand immobilization and analyte binding than experiments run on different chips. Further assessment showed that different chips demonstrated different maximum immobilizations for the same concentration of injected protein. We also show a variety of relationships between ligand immobilization level and analyte response, which we attribute to steric crowding at high ligand concentrations. Using this calibration to inform experimental design, researchers can choose protein concentrations for immobilization corresponding to the linear range of analyte response. We are the first to demonstrate calibration and normalization as a strategy to increase reproducibility and data quality of these chips. Our study assesses a variety of factors affecting chip variability, addressing a gap in knowledge about commercially available sensor chips. Controlling for these factors in the process of experimental design will minimize variability in analyte signal when using these important sensing platforms. Full article

Weak polyelectrolytes (WPEs) are responsive materials used as active charge regulators in a variety of applications, including controlled release and drug delivery in crowded bio-related and synthetic environments. In these environments, high concentrations of solvated molecules, nanostructures, and molecular assemblies are ubiquitous. Here, we investigated the effect of high concentrations of non-adsorbing, short chains of poly(vinyl alcohol), PVA, and colloids dispersed by the very same polymers on charge regulation (CR) of poly(acrylic acid), PAA. PVA does not interact with PAA (throughout the full pH range) and thus can be used to examine the role of non-specific (entropic) interactions in polymer-rich environments. Titration experiments of PAA (mainly 100 kDa in dilute solutions, no added salt) were carried out in high concentrations of PVA (13–23 kDa, 5–15 wt%) and dispersions of carbon black (CB) decorated by the same PVA (CB-PVA, 0.2–1 wt%). The calculated equilibrium constant (and $p{K}_a$) was up-shifted in PVA solutions by up to ~0.9 units and down-shifted in CB-PVA dispersions by ~0.4 units. Thus, while solvated PVA chains increase the charging of the PAA chains, as compared to PAA in water, CB-PVA particles reduce PAA charging. To investigate the origins of the effect, we analyzed the mixtures using small-angle X-ray scattering (SAXS) and cryo-TEM imaging. The scattering experiments revealed re-organization of the PAA chains in the presence of the solvated PVA but not in the CB-PVA dispersions. These observations clearly indicate that the acid–base equilibrium and the degree of ionization of PAA in crowded liquid environments is affected by the concentration, size, and geometry of seemingly non-interacting additives, probably due to depletion and excluded volume interactions. Thus, entropic effects that do not depend on specific interactions should be taken into consideration when designing functional materials in complex fluid environments. Full article

The crowded interior of a living cell makes performing experiments on simpler in vitro systems attractive. Although these reveal interesting phenomena, their biological relevance can be questionable. A topical example is the phase separation of intrinsically disordered proteins into biomolecular condensates, which is proposed to underlie the membrane-less compartmentalization of many cellular functions. How a cell reliably controls biochemical reactions in compartments open to the compositionally-varying cytoplasm is an important question for understanding cellular homeostasis. Computer simulations are often used to study the phase behavior of model biomolecular condensates, but the number of relevant parameters increases as the number of protein components increases. It is unfeasible to exhaustively simulate such models for all parameter combinations, although interesting phenomena are almost certainly hidden in their high-dimensional parameter space. Here, we have studied the phase behavior of a model biomolecular condensate in the presence of a polymeric crowding agent. We used a novel compute framework to execute dozens of simultaneous simulations spanning the protein/crowder concentration space. We then combined the results into a graphical representation for human interpretation, which provided an efficient way to search the model’s high-dimensional parameter space. We found that steric repulsion from the crowder drives a near-critical system across the phase boundary, but the molecular arrangement within the resulting biomolecular condensate is rather insensitive to the crowder concentration and molecular weight. We propose that a cell may use the local cytoplasmic concentration to assist the formation of biomolecular condensates, while relying on the dense phase to reliably provide a stable, structured, fluid milieu for cellular biochemistry despite being open to its changing environment. Full article

The hydrogenation of N-(2-ethyl-6-methylphenyl)-1-methoxypropan-2-imine is the largest-scale asymmetric catalytic process for the industrial production of agrochemical (S)-metolachlor. The challenging hydrogenation across the sterically crowded carbon–nitrogen double bond was achieved using a mixture of [IrCl(COD)]₂, (R,S_Fc)-Xyliphos, NBu₄I and acetic acid. Acetic acid was critical in achieving excellent productivity and activity. Despite its industrial significance, a mechanism that explains how the sterically hindered bond in the imine is reduced has yet to be proposed. We propose a plausible proton-first, outer-sphere mechanism based on density functional theory calculations that is consistent with the experimentally observed activity and the enantioselectivity of the industrial process. Key findings include transition states involving acetate-assisted dihydrogen splitting, and a hydride transfer from a five-coordinate iridium trihydride directed by a C-H∙∙∙Ir interaction. This article was submitted to a Special Issue in honor of Professor Henri Kagan. Full article

In order to discover new ³¹P NMR markers for probing subtle pH changes (<0.2 pH unit) in biological environments, fifteen new conformationally constrained or sterically hindered α-aminophosphonates derived from diethyl(2-methylpyrrolidin-2-yl)phosphonate were synthesized and tested for their pH reporting and cytotoxic properties in vitro. All compounds showed near-neutral pK_as (ranging 6.28–6.97), chemical shifts not overlapping those of phosphorus metabolites, and spectroscopic sensitivities (i.e., chemical shifts variation Δδ_ab between the acidic and basic forms) ranging from 9.2–10.7 ppm, being fourfold larger than conventional endogenous markers such as inorganic phosphate. X-ray crystallographic studies combined with predictive empirical relationships and ab initio calculations addressed the inductive and stereochemical effects of substituents linked to the protonated amine function. Satisfactory correlations were established between pK_as and both the 2D structure and pyramidalization at phosphorus, showing that steric crowding around the phosphorus is crucial for modulating Δδ_ab. Finally, the hit ³¹P NMR pH probe 1b bearing an unsubstituted 1,3,2-dioxaphosphorinane ring, which is moderately lipophilic, nontoxic on A549 and NHLF cells, and showing pK_a = 6.45 with Δδ_ab = 10.64 ppm, allowed the first clear-cut evidence of trans-sarcolemmal pH gradients in normoxic Dictyostelium discoideum cells with an accuracy of <0.05 pH units. Full article

The rational design of small building block molecules and understanding their molecular assemblies are of fundamental importance in creating new stimuli-responsive organic architectures with desired shapes and functions. Based on the experimental results of light-induced conformational changes of four types of triangular azo dyes with different terminal functional groups, as well as absorption and fluorescence characteristics associated with their molecular assemblies, we report that aggregation-active emission enhancement (AIEE)-active compound (1) substituted with sterically crowded tert-butyl (t-Bu) groups showed approximately 35% light-induced molecular switching and had a strong tendency to assemble into highly stable hexagonal structures with AIEE characteristics. Their sizes were regulated from nanometer-scale hexagonal rods to micrometer-scale sticks depending on the concentration. This is in contrast to other triangular compounds with bromo (Br) and triphenylamine (TPA) substituents, which exhibited no photoisomerization and tended to form flexible fibrous structures. Moreover, non-contact exposure of the fluorescent hexagonal nanorods to ultraviolet (UV) light led to a dramatic hexagonal-to-amorphous structure transition. The resulting remarkable variations, such as in the contrast of microscopic images and fluorescence characteristics, were confirmed by various microscopic and spectroscopic measurements. Full article

A sterically crowded light-responsive host 1 was synthetized with a 93% yield by applying a post-functionalization protocol utilizing the double amidation of 4,4′-azodibenzoyl dichloride with a readily available 26-membered macrocyclic amine. X-ray structures of two hydrates of trans-1 demonstrate a very different alignment of the azobenzene linkage, which is involved in T-shape or parallel-displaced π⋯π stacking interactions with the pyridine-2,6-dicarboxamide moieties from the macrocyclic backbone. Despite the rigidity of the macrocyclic framework, which generates a large steric hindrance around the azobenzene chromophore, the host 1 retains the ability to undergo a reversible cis⟷trans isomerization upon irradiation with UVA (368 nm) and blue (410 nm) light. Moreover, thermal cis→trans back-isomerization (ΔG⁰ = 106.5 kJ∙mol⁻¹, t_½ = 141 h) is markedly slowed down as compared to the non-macrocyclic analog. ¹H NMR titration experiments in DMSO-d₆/0.5% water solution reveal that trans-1 exhibits a strong preference for dihydrogenphosphate (H₂PO₄⁻) over other anions (Cl⁻, MeCO₂⁻, and PhCO₂⁻), whereas the photogenerated metastable cis-1 shows lower affinity for the H₂PO₄⁻ anion. Full article

Fluorescent molecular assembly systems provide an exciting platform for creating stimuli-responsive nano- and microstructured materials with optical, electronic, and sensing functions. To understand the relationship between (i) the plausible molecular structures preferentially adopted depending on the solvent polarity (such as N,N-dimethylformamide [DMF], tetrahydrofuran [THF], and toluene), (ii) the resulting spectroscopic features, and (iii) self-assembled nano-, micro-, and macrostructures, we chose a sterically crowded triangular azo dye (3Bu) composed of a polar molecular core and three peripheral biphenyl wings. The chromophore changed the solution color from yellow to pink-red depending on the solvent polarity. In a yellow DMF solution, a considerable amount of the twisted azo form could be kept stable with the help of favorable intermolecular interactions with the solvent molecules. By varying the concentration of the DMF solution, the morphology of self-assembled structures was transformed from nanoparticles to micrometer-sized one-dimensional (1D) structures such as sticks and fibers. In a pink-red toluene solution, the periphery of the central ring became more planar. The resulting significant amount of the keto-hydrazone tautomer grew into micro- and millimeter-sized 1D structures. Interestingly, when THF-H₂O (1:1) mixtures were stored at a low temperature, elongated fibers were stacked sideways and eventually developed into anisotropic two-dimensional (2D) sheets. Notably, subsequent exposure of visible-light-irradiated sphere samples to solvent vapor resulted in reversible fluorescence off↔on switching accompanied by morphological restoration. These findings suggest that rational selection of organic dyes, solvents, and light is important for developing reusable fluorescent materials. Full article

Since the first preparation of triptycene, great progress has been made with respect to its synthesis and the understanding of its properties. Interest in triptycene-based systems is intense; in recent years, advances in the synthetic methodology and properties of new triptycenes have been reported by researchers from various fields of science. Here, an account of these new developments is given and placed in reference to earlier pivotal works that underpin the field. First, we discuss new approaches to the synthesis of new triptycenes. Progress in the regioselective synthesis of sterically demanding systems is discussed. The application of triptycenes in catalysis is also presented. Next, progress in the understanding of the relations between triptycene structures and their properties is discussed. The unique properties of triptycenes in the liquid and solid states are elaborated. Unique interactions, which involve triptycene molecular scaffolds, are presented. Molecular interactions within a triptycene unit, as well as between triptycenes or triptycenes and other molecules, are also evaluated. In particular, the summary of the synthesis and useful features will be helpful to researchers who are using triptycenes as building blocks in the chemical and materials sciences. Full article

Using a fairly structurally flexible and, therefore, very suitable for this type of research, superphane molecule, we demonstrate that the inclusion of a noble gas atom (Ng = He, Ne, Ar, and Kr) inside it and, thus, the formation of the Ng@superphane endohedral complex, leads to its ‘swelling’. Positive values of both the binding and strain energies prove that encapsulation and in turn ‘swelling’ of the superphane molecule is energetically unfavorable and that the Ng⋯C interactions in the interior of the cage are destabilizing, i.e., repulsive. Additionally, negative Mayer Bond Orders indicate the antibonding nature of Ng⋯C contacts. This result in combination with the observed Ng⋯C bond paths shows that the presence of a bond path in the molecular graph does not necessarily prove interatomic stabilization. It is shown that the obtained conclusions do not depend on the computational methodology, i.e., the method and the basis set used. However, on the contrary, the number of bond paths may depend on the methodology. This is yet another disadvantageous finding that does not favor the treatment of bond paths on molecular graphs as indicators of chemical bonds. The Kr@superphane endohedral complex features one of the longest C–C bonds ever reported (1.753 Å). Full article