Clustering of biphenyl oxamide ions by chiral recognition.

Gels created by self-assembly of small organic molecules are dynamic soft materials that have unique properties and demanding characterization. Four chiral gelators, with two valinol- or leucinoloxamido arms attached to the 2,2'-positions of the proatropisomeric biphenyl group were chosen to show that the electrospray ionization mass spectrometry (ESI-MS) could be used to differentiate the gelation feature of the chiral compounds 1-4 and also to shed light on the gelation processes. By inspecting the gelation of several solvents, we showed that 1 (R, R) proved to be the most efficient gelator, forming the largest observable assemblies in the gas phase. The strong intermolecular H-bonds hold single-charged assemblies consisting of up to five monomer units detectable by ESI MS. Enantiomer 1 (R, R) is a good gelator due to favorable intramolecular interactions that remain preserved in the gas phase. Compound 3 (meso) does not have gelator properties and detected signals of larger assemblies in the gas phase. So, the detected signals correlate with the conformations of the studied compounds. MS could be used to elucidate the preferential type of noncovalent interaction due to the chiral recognition. The study paves a novel way to investigate the influence of chirality on the molecular assembly and consequently macroscopic properties and functions of materials.

Advancing Flexible Sensors through On-Demand Regulation of Supramolecular Nanostructures.

The evolution of flexible sensors heavily relies on advances in soft-material design and sensing mechanisms. Supramolecular chemistry offers a powerful toolbox for manipulating nanoscale and molecular structures within soft materials, thus fostering recent advancements in flexible sensors and electronics. Supramolecular interactions have been utilized to nanoengineer functional sensing materials or construct chemical sensors with lower cost and broader targets. In this perspective, we will highlight the use of supramolecular interactions to regulate and optimize nanostructures within functional soft materials and illustrate their importance in expanding the nanocavities of bioreceptors for chemical sensing. Overall, a bridge between tissue-mimicking flexible sensors and cell-mimetic supramolecular chemistry has been built, which will further advance human healthcare innovation.

Temperature-Dependent Left- and Right-Twisted Conformational Changes in 1:1 Host-Guest Systems: Theoretical Modeling and Chiroptical Simulations.

An efficient strategy for high-performance chiral materials is to design and synthesize host molecules with left- and right- (M- and P-) twisted conformations and to control their twisted conformations. For this, a quantitative analysis is required to describe the chiroptical inversion, chiral transfer, and chiral recognition in the host-guest systems, which is generally performed using circular dichroism (CD) and/or proton nuclear magnetic resonance (1H-NMR) spectroscopies. However, the mass-balance model that considers the M- and P-twisted conformations has not yet been established. In this study, we derived the novel equations based on the mass-balance model for the 1:1 host-guest systems. Then, we further applied them to analyze the 1:1 host-guest systems for the achiral calixarene-based capsule molecule, achiral dimeric zinc porphyrin tweezer molecule, and chiral pillar[5]arene with the chiral and/or achiral guest molecules by using the data obtained from the CD titration, variable temperature CD (VT-CD), and 1H-NMR experiments. The thermodynamic parameters (ΔH and ΔS), equilibrium constants (K), and molar CD (Δε) in the 1:1 host-guest systems could be successfully determined by the theoretical analyses using the derived equations.

Naphthalene Diimide and Bis-heteroleptic Ru(II) Complex-Based Hybrid Molecule with 3-in-1 Functionalities.

Multipurpose applications of a newly developed homobimetallic Ru(II) complex, Ru-NDI[PF6]4, which incorporates 1,10-phenanthroline and triazole-pyridine ligands and linked via a (-CH2-)3 spacer to the reputed anion-π interacting NDI system, are described. Solution-state studies of the bimetallic complex, including EPR, PL, UV-vis, and NMR experiments, reveal two sequential one-electron transfers to the NDI unit, generating NDI·- and NDI2- in the presence of F- selectively. This process inhibits the primary electron transfer from Ru(II) to the NDI unit, thereby allowing the 3MLCT-based emission of the complex to be recovered, resulting in a corresponding ten-fold increase in luminescence intensity. DFT and TD-DFT computational studies further elucidate the experimentally observed absorption spectra of the complex. Secondly, CT-DNA binding studies with the complex are performed using various spectroscopic analyses such as UV-vis, PL, and CD. Comparative DNA binding studies employing EB and molecular docking reveal that the binding with CT-DNA occurs through both intercalative and groove binding modalities. Thirdly, the photocatalytic activities of the complex towards C-C, C-N, and C-O bond formation in organic cross-coupling reactions, including the amidation of α-keto acids to amines and the oxidation of alcohol to aldehydes, are also demonstrated.

Computational insights into the structure and decomposition behaviors of 2,4,6-triamino-5-nitropyrimidine-1,3-dioxide under high pressure up to 10 GPa.

CONTEXT: Inspired by the recent successful synthesis of the energetic compound 2,4,6-triamino-5-nitropyrimidine-1,3-dioxide (ICM-102), which displayed a good balance between high energy and sensitivity, the response of the structure and decomposition behaviors of ICM-102 to high pressure was systematically investigated using first principle calculations. ICM-102 exhibited a graphite-like layer structure, with the c-axis and the a-axis mainly contributing to the distance between the molecular planes. As the pressure increased from 1 atm to 10 GPa, this distance decreased from 3.166 to 2.689 Ǻ. The hydrogen bonds had the most contribution to the non-covalent interactions within the same molecular planes, resulting in the b-axis discontinuity. However, van der Waals interactions gradually appeared between molecular planes as the pressure increased to 2.5 GPa. Based on the analysis of crystal orbitals, the distribution of π bonds and the Laplacian bond order (LBO), it was determined that the generation mechanism of H2O molecules involved the cleavage of N-Oc (coordinated oxygen atoms), followed by intermolecular hydrogen transfer reactions, and ultimately the formation of H2O molecules through competition with H atoms in the amino groups within the same molecules. More importantly, the pressure dependence of LBO values for N-Oc revealed that high pressure could inhibit the ICM-102 decomposition process due to reinforcing hydrogen bonds and van der Waals interactions. This work will deepen our understanding of the stability of ICM-102 under high pressure and provide a helpful reference for its potential detonation applications. METHODS: All simulations, including geometry optimization and vibration analysis under quasi-hydrostatic pressure, were conducted using the CP2K code. The PBE function and the Goldk-Teter-Hutter (GTH) pseudopotential with the double-ζ-with-polarization (DZVP) basis set were employed. Additionally, the semiempirical dispersion correction D3 (BJ) was used to account for the intermolecular dispersion force. The simulations were performed under periodic boundary conditions, with a finest grid level cutoff set to 400 Ry for the Γ point. The Broyden-Flecher-Goldfarb-Shanno (BFGS) optimization method was used, with tighter convergence criteria applied for the subsequent calculations of infrared spectra. Finally, the wave-function analysis, such as non-covalent interaction and LBO, was conducted using the Multiwfn and VMD packages.

Transition State Stabilizing Effects of Oxygen and Sulfur Chalcogen Bond Interactions.

Non-covalent chalcogen bond (ChB) interactions have found utility in many fields, including catalysis, organic semiconductors, and crystal engineering. In this study, the kinetic effects of ChB interactions of oxygen and sulfur were experimentally measured using a series of molecular rotors. The rotors were designed to form ChB interactions in the bond rotation transition states. This enabled their kinetic influences to be assessed by monitoring changes in rotational barriers. Despite forming weaker ChB interactions, the smaller chalcogens were able to stabilize transition states and had measurable kinetic effects. Sulfur stabilized the bond rotation transition state by as much as -7.2 kcal/mol without electron-withdrawing groups. The key was to design a system where the sulfur ðœŽ-hole was aligned with the lone pairs of the chalcogen bond acceptor. Oxygen rotors also could form transition state stabilizing ChB interactions but required electron-withdrawing groups. For both oxygen and sulfur ChB interactions, a strong correlation was observed between transition state stabilizing abilities and electrostatic potential (ESP) of the chalcogen, providing a useful predictive parameter for the rational design of future ChB systems.

Low Valence Triel (I) Systems as Hydrogen Bond Acceptors and their Stability with Respect to Triel (III) Compounds.

A theoretical study of the complexes formed by carbene like Al(I), Ga(I), In(I) and Tl(I) compounds with hydrogen bond donors (HBD), XH (HCCH, HSH,HOH, HCN, HCl, HBr, HF, and HNC) have been carried out at MP2 computational level. The isolated triel(I) compounds show a negative region of the molecular electrostatic potential region associated with the triel atom suitable to interact with electron deficient groups. This region is associated to a lone pair based on the ELF analysis and to the location of the HOMO orbital. The complexes are similar to those found in nitrogen heterocyclic carbenes (NHC) with HBD. In addition, the oxidative addition reactions of those complexes to yield the corresponding valence III compounds have been characterized. The Al(III) compounds are much more stable than the corresponding Al(I) complexes. However, the stability of the triel(III) compounds decreases with the size of the triel atom and for the thallium derivatives, the Tl(I) complexes are more stable than the Tl(III) compounds in accordance with the number of the structures found in the CSD. The barrier of the TS connecting the triel(I) and triel(III) systems increases with the size of the triel atoms.

Beryllium as a Base: Complexes of Be(CO)3 with HX (X=F, Cl, Br, CN, NC, CCH, OH).

Beryllium chemistry is typically governed by its electron deficient character, but in some compounds it can act as a base. In order to understand better the unusual basicity of Be, we have systematically explored the complexes of one such compound, Be(CO)3, towards several hydrogen bond donors HX (X=F, Cl, Br, CN, NC, CCH, OH). For all complexes we find three different minima, two hydrogen bonded minima (to the Be or O atoms), and one weak beryllium bonded minimum. Further characterization of the interactions using a topological analysis of the electron density and Symmetry Adapted Perturbation Theory (SAPT) provide insight into the nature of these interactions. Overall these results highlight the capability of certain beryllium compounds to act as either a weak Lewis acid or, unconventionally, a Lewis base whose basicity towards hydrogen bonding is comparable to that of π systems.

DFT studies on N-(1-(2-bromobenzoyl)-4-cyano-1H-pyrazol-5-yl).

In this work, molecular descriptors of N-(1-(2-bromobenzoyl)-4-cyano-1H-pyrazol-5-yl) halogenated benzamides (1a-h) have been computed using a quantum chemical technique through DFT. Prior work involved the synthesis of compounds (1a-h) and the assessment of their anticancer activity on breast, colon, and liver tumors: MCF-7, HCT-116, and HepG-2 cell lines respectively. Since 1a, 1b, and 1d showed the most potential anticancer impact, their ability to inhibit EGFRWT was investigated. Based on the biological data, 1b inhibited EGFRWT the most. According to the docking evaluation, an H-bond with the threonine residue was one of the main non-covalent contacts between 1b and the EGFRWT active site residues. PES, MESP, HOMOs, LUMOs, energy band gap, global reactivity indices [electron affinity (A), ionization energies (I), electrophilicity index (ω), nucleophilicity index (ε), chemical potential (µ), electronegativity (χ), hardness (η), and softness (S)], condensed Fukui functions, NBO, and NCIs are the molecular descriptors of 1a-h that were computed using DFT technique. According to the theoretical investigation results, compounds (1a-h) might have anticancer effects; these findings are consistent with the biological findings from our previous research. Compound 1b had the lowest binding energy, according to an assessment of the binding energies between the threonine and the three most active compounds (1a, 1b, and 1d). This is consistent with the outcomes of the docking study and the biological examination of the influence of 1a, 1b, and 1d on EGFRWT.

Palladium-Catalyzed Remote C-H Functionalization: Non-Covalent Interactions and Reversibly Bound Templates.

Pd-catalysis has stood as a pivotal force in synthetic transformations for decades, maintaining its status as a paramount tool in the realm of C-H bond activation. While functionalization at proximal positions has become commonplace, achieving selective and sustainable access to distal positions continues to captivate scientific endeavors. Recently, a noteworthy trend has emerged, focusing on the utilization of non-covalent interactions to address the challenges associated with remote functionalization. The integration of these non-covalent interactions into palladium catalysis stands as a justified response to the demands of achieving selective transformations at distal positions. This review delves into the latest advancements and trends surrounding the incorporation of non-covalent interactions within the field of palladium catalysis. Furthermore, it is noteworthy to emphasize that multifunctional templates, particularly those harnessing hydrogen bonding, present an elegant and sophisticated approach to activate C-H bonds in a highly directed fashion. These templates showcase versatility and demonstrate potential applications across diverse contexts within the area of remote functionalization.

An Innovative Vortex-Assisted Liquid-Liquid Microextraction Approach Using Deep Eutectic Solvent: Application for the Spectrofluorometric Determination of Rhodamine B in Water, Food and Cosmetic Samples.

A new green and highly sensitive method for the determination of rhodamine B (RhB) by deep eutectic solvent-based vortex-assisted liquid-liquid microextraction with fluorescence detection (DES-VALLME-FLD) was developed. The extraction efficiency of conventional solvents and different deep eutectic solvent (DES) systems composed of tetrabutylammonium bromide (TBAB) and an alcohol (hexanol, octanol, or decanol) in different ratios were compared. DFT calculations of intermolecular electrostatic and non-covalent interactions of the most stable RhB forms with DES and water explain the experimental DESs' extraction efficiency. Semiempirical PM7 computations were used to obtain Hansen solubility parameters, which supported the good solubility of the monocationic RhB form in selected DESs. The dependence of the linear calibration of microextraction into 100 µL DES was observed in the RhB calibration range from 0.2 to 10.0 µg L-1 with a correlation coefficient of R2 = 0.9991. The LOD value was calculated to be 0.023 µg L-1. The accuracy and precision of the proposed method were verified over two days with RSD values of 2.9 to 4.1% and recovery of 94.6 to 103.7%. The developed method was applied to the determination of RhB in real samples (tap water, energy drink, and lipstick).

Chemistry and crystal engineering.

Recent studies published in the Chemistry and crystal engineering section of IUCrJ emphasize developments both in methodology and techniques as well as the diverse range of classes of compounds being studied and of problems being tackled.

Physicochemical Properties, Stability, and Functionality of Non-Covalent Ternary Complexes Fabricated with Pea Protein, Hyaluronic Acid and Chlorogenic Acid.

The aim of this study was to prepare and characterize stable non-covalent ternary complexes based on pea protein (PP, 0.5%), hyaluronic acid (HA, 0.125%), and chlorogenic acid (CA, 0~0.03%). The ternary complexes were comprehensively evaluated for physicochemical attributes, stability, emulsifying capacities, antioxidant properties, and antimicrobial efficacy. PP-HA binary complexes were first prepared at pH 7, and then CA was bound to the binary complexes, as verified by fluorescence quenching. Molecular docking elucidated that PP interacted with HA and CA through hydrogen bonding, hydrophobic and electrostatic interactions. The particle size of ternary complexes initially decreased, then increased with CA concentration, peaking at 0.025%. Ternary complexes demonstrated good stability against UV light and thermal treatment. Emulsifying activity of complexes initially decreased and then increased, with a turning point of 0.025%, while emulsion stability continued to increase. Complexes exhibited potent scavenging ability against free radicals and iron ions, intensifying with higher CA concentrations. Ternary complexes effectively inhibited Staphylococcus aureus and Escherichia coli, with inhibition up to 0.025%, then decreasing with CA concentration. Our study indicated that the prepared ternary complexes at pH 7 were stable and possessed good functionality, including emulsifying properties, antioxidant activity, and antibacterial properties under certain concentrations of CA. These findings may provide valuable insights for the targeted design and application of protein-polysaccharide-polyphenol complexes in beverages and dairy products.

The Role of Hydrogen Bonding in the Raman Spectral Signals of Caffeine in Aqueous Solution.

The identification and quantification of caffeine is a common need in the food and pharmaceutical industries and lately also in the field of environmental science. For that purpose, Raman spectroscopy has been used as an analytical technique, but the interpretation of the spectra requires reliable and accurate computational protocols, especially as regards the Resonance Raman (RR) variant. Herein, caffeine solutions are sampled using Molecular Dynamics simulations. Upon quantification of the strength of the non-covalent intermolecular interactions such as hydrogen bonding between caffeine and water, UV-Vis, Raman, and RR spectra are computed. The results provide general insights into the hydrogen bonding role in mediating the Raman spectral signals of caffeine in aqueous solution. Also, by analyzing the dependence of RR enhancement on the absorption spectrum of caffeine, it is proposed that the sensitivity of the RR technique could be exploited at excitation wavelengths moderately far from 266 nm, yet achieving very low detection limits in the quantification caffeine content.

Spirobipyridine Ligand Enabled Iridium-Catalyzed Site-Selective C-H Activation via Non-Covalent Interactions.

The selective borylation of specific C-H bonds in organic synthesis remains a formidable challenge. In this study, we present a novel spirobipyridine ligand that features a binaphthyl backbone. This ligand facilitates the iridium-catalyzed selective C-H borylation of benzene derivatives. The ligand is designed with "side-arm-wall" substituents that allow vicinal di- or multi-substituted benzene derivatives to approach metal center and effectively block other reactive sites by non-covalent interactions with substrates. The effectiveness of this strategy is demonstrated by the successful selective distal C-H activation of various alkaloids and its broad compatibility with functional groups.

Computational Design of Bidentate Hypervalent Iodine Catalysts in Halogen Bond-Mediated Organocatalysis.

In recent years, halogen bond-based organocatalysis has garnered significant attention as an alternative to hydrogen-based catalysis, capturing considerable interest within the scientific community. This transition has witnessed the evolution of catalytic scaffolds from monodentate to bidentate architectures, and from monovalent to hypervalent species. In this DFT-based study, we explored a bidentate hypervalent iodine(III)-based system that has already undergone experimental validation. Additionally, we explore various functionalisations (-CF$_3$, -CH$_3$, -tBu, -OH, -OMe, -NO$_2$, -CN) and scaffold modifications, such as sulfur oxidation, theoretically proposed for an indole-based Michael addition. The investigated systems favour bidentate O-type binding, underlining the importance of ligand coordination in catalytic activity. Electron-deficient scaffolds exhibited stronger binding and lower activation energies, indicating the pivotal role of electronic properties for $\sigma$-hole-based catalysis. Of these groups, Lewis-base-like moieties formed stabilising intramolecular interactions with hypervalent iodines when in the ortho-position. Furthermore, inductive electron withdrawal was deemed more effective than mesomeric withdrawal in enhancing catalytic efficacy for these systems. Lastly, increasing sulfur oxidation was theoretically proven to improve catalytic activity significantly.

Synthesis, crystal structure and Hirshfeld surface analysis of (3Z)-4-[(4-amino-1,2,5-oxa-diazol-3-yl)amino]-3-bromo-1,1,1-tri-fluoro-but-3-en-2-one.

In the title compound, C6H4BrF3N4O2, the oxa-diazole ring is essentially planar with a maximum deviation of 0.003 (2) Å. In the crystal, mol-ecular pairs are connected by N-H⋯N hydrogen bonds, forming dimers with an R 2 2(8) motif. The dimers are linked into layers parallel to the (10) plane by N-H⋯O hydrogen bonds. In addition, C-O⋯π and C-Br⋯π inter-actions connect the mol-ecules, forming a three-dimensional network. The F atoms of the tri-fluoro-methyl group are disordered over two sites in a 0.515 (6): 0.485 (6) ratio. The inter-molecular inter-actions in the crystal structure were investigated and qu-anti-fied using Hirshfeld surface analysis.

Ligand Isomerization Driven Electrocatalytic Switching.

The prevailing view about molecular catalysts is that the central metal ion is responsible for the reaction mechanism and selectivity, whereas the ligands mainly affect the reaction kinetics. Here, we question this paradigm and show that ligands have a dramatic influence on the selectivity of the product. We show how even a seemingly small change in ligand isomerization sharply alters the selectivity of the well-researched oxygen reduction reaction (ORR) Co phthalocyanine catalyst from an indirect 2e- to a direct 4e- pathway. Detailed analysis reveals that intramolecular hydrogen-bond interactions in the ligand activate the catalytic Co, directing the oxygen binding and thus deciding the final product. The resulting catalyst is the first example of a Co-based molecular catalyst catalyzing a direct 4e- ORR via ligand isomerization, for which it shows an activity close to the benchmark Pt in an actual H2-O2 fuel cell. The effect of the ligand isomerism is demonstrated with different central metal ions, thus highlighting the generalizability of the findings and their potential to open new possibilities in the design of molecular catalysts.

Bulk Photovoltaic Effect Induced by Non-Covalent Interactions in Bilayered Hybrid Perovskite for Efficient Passive X-Ray Detection.

Hydrogen bonding as a multifunctional tool has always influenced the structure of hybrid perovskites. Compared with the research on hydrogen bonding, the study of halogen-halogen interactions on the structure and properties of hybrid perovskites is still in its early stages. Herein, a polar bilayered hybrid perovskite (IEA)2FAPb2I7 (IEA+ is 2-iodoethyl-1-ammonium, FA is formamidinium) with iodine-substituted spacer is successfully constructed by changing the configuration of interlayer cations and regulating non-covalent interactions at the organic-inorganic interface, which shows a shorter interlayer spacing and higher density (ρ = 3.862 g cm-3). The generation of structure polarity in (IEA)2FAPb2I7 is caused by the synergistic effect of hydrogen bonding and halogen-halogen interactions. Especially, as the length of the carbon chain in organic cations decreases, the I---I interaction in the system gradually strengthens, which may be the main reason for the symmetry-breaking. Polarity-induced bulk photovoltaics (Voc = 1.0 V) and higher density endow the device based on (I-EA)2FAPb2I7 exhibit a high sensitivity of 175.6 µC Gy-1 cm-2 and an ultralow detection limit of 60.4 nGy s-1 at 0 V bias under X-ray irradiation. The results present a facile approach for designing polar multifunctional hybrid perovskites, also providing useful assistance for future research on halogen-halogen interactions.

An efficient method by combining different basis sets and SAPT levels.

In symmetry-adapted perturbation theory (SAPT), accurate calculations on non-covalent interaction (NCI) for large complexes with more than 50 atoms are time-consuming using large basis sets. More efficient ones with smaller basis sets usually result in poor prediction in terms of dispersion and overall energies. In this study, we propose two composite methods with baseline calculated at SAPT2/aug-cc-pVDZ and SAPT2/aug-cc-pVTZ with dispersion term corrected at SAPT2+ level using bond functions and smaller basis set with δ MP2 corrections respectively. Benchmark results on representative NCI data sets, such as S22, S66, and so forth, show significant improvements on the accuracy compared to the original SAPT Silver standard and comparable to SAPT Gold standard in some cases with much less computational cost.