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.

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.

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.

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.

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.

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.

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.

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.

Lone-Pair-π Bond Strength Unveiled by a Combined Experimental and Computational Study.

A series of naphthalene-diimide (NDI) and perylene-diimide (PDI) connected bis-N-heterocyclic carbene complexes of iridium(III) have been prepared and fully characterized. The analysis of their NMR spectroscopic features, together with their molecular structures show that these species display lone-pair-π interactions between the chloride ligands of the Ir(III) complex and the heterocycles of the NDI/PDI moieties. The detection of this type of interaction in solution is due to the formation of two atropisomers, which are formed as a result of the restricted rotation about the Ir-Ccarbene bond imposed by the (Cl)lp⋅⋅⋅π interaction. Variable-temperature 1H NMR analysis allowed the determination of the strength of this non-covalent interaction, which lies between ΔH=6.6 and 10 kcal/mol. The computational studies performed fully support the experimental findings.

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.

Adaptive Response to Solvation in Flexible Molecules: Oligo Hydrates of 4-Hydroxy-2-butanone.

Structural changes induced by water play a pivotal role in chemistry and biology but remain challenging to predict, measure, and control at molecular level. Here we explore size-governed gas-phase water aggregation in the flexible molecule 4-hydroxy-2-butanone, modeling the conformational adaptability of flexible substrates to host water scaffolds and the preference for sequential droplet growth. The experiment was conducted using broadband rotational spectroscopy, rationalized with quantum chemical calculations. Two different isomers were observed experimentally from the di- to the pentahydrates (4-hydroxy-2-butanone-(H2O)n=2-5), including the 18O isotopologues for the di- and trihydrates. Interestingly, to accommodate water molecules effectively, the heavy atom skeleton of 4-hydroxy-2-butanone reshapes in every observed isomer and does not correspond to the stable conformer of the free monomer. All solvates initiate from the alcohol group (proton donor) but retain the carbonyl group as secondary binding point. The water scaffolds closely resemble those found in the pure water clusters, balancing between the capability of 4-hydroxy-2-butanone for steering the orientation and position of the water molecules and the ability of water to modulate the monomer's conformation. The present work thus provides an accurate molecular description on how torsionally flexible molecules dynamically adapt to water along progressing solvation.

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.

Conformational Analysis of Conjugated Organic Materials: What Are My Heteroatoms Really Doing?

Organic semiconductor small molecules and polymers often incorporate heteroatoms into their chemical structures to affect the electronic properties of the material. A particular design philosophy has been to use these heteroatoms to influence torsional potentials, since the overlap of adjacent π-orbitals is most efficient in planar systems and is critical for charge delocalization in these systems. Since these design rules became popular, the messages from the earlier works have become lost in a sea of reports of "conformational locks", where the non-covalent interactions have relatively small contributions to planarizing torsional potentials. Greater influences can be found in the stabilization by extended conjugation, consideration of steric repulsion, and the interactions involving solubilizing chains and neighboring molecules or polymer chains in condensed phases.

Air-Stable and Eco-Friendly Symmetrical Imine with Thiadiazole Moieties in Neutral and Protonated form for Perovskite Photovoltaics.

This paper proposes molecular and supramolecular concepts for potential application in perovskite solar cells. New air-stable symmetrical imine, with thiadiazole moieties PPL2: (5E,6E)-N2,N5-bis(4-(diphenylamino)benzylidene)-1,3,4-thiadiazole-2,5-diamine), as a hole-transporting material was synthesised in a single-step reaction, starting with commercially available and relatively inexpensive reagents, resulting in a reduction in the cost of the final product compared to Spiro-OMeTAD. Moreover, camphorsulfonic acid (CSA) in both enantiomeric forms was used to change the HOMO-LUMO levels and electric properties of the investigated imine-forming complexes. Electric, optical, thermal, and structural studies of the imine and its complexes with CSA were carried out to characterise the new material. Imine and imine/CSA complexes were also characterised in depth by the proton Nuclear Magnetic Resonance 1H NMR method. The position of nitrogen in the thidiazole ring influences the basicity of donor centres, which results in protonation in the imine bond. Simple devices of ITO/imine (with or without CSA(-) or CSA(+))/Ag/ITO architecture were constructed, and a thermographic camera was used to find the defects in the created devices. Electric behaviour was also studied to demonstrate conductivity properties under the forward current. Finally, the electrical properties of imine and its protonated form with CSA were compared with Spiro-OMeTAD. In general, the analysis of thermal images showed a very similar response of the samples to the applied potential in terms of the homogeneity of the formed organic layer. The TGA analysis showed that the investigated imine exhibits good thermal stability in air and argon atmospheres.

Halogen Bond-Assisted Supramolecular Dimerization of Pyridinium-Fused 1,2,4-Selenadiazoles via Four-Center Se2N2 Chalcogen Bonding.

The synthesis and structural characterization of α-haloalkyl-substituted pyridinium-fused 1,2,4-selenadiazoles with various counterions is reported herein, demonstrating a strategy for directed supramolecular dimerization in the solid state. The compounds were obtained through a recently discovered 1,3-dipolar cycloaddition reaction between nitriles and bifunctional 2-pyridylselenyl reagents, and their structures were confirmed by the X-ray crystallography. α-Haloalkyl-substituted pyridinium-fused 1,2,4-selenadiazoles exclusively formed supramolecular dimers via four-center Se···N chalcogen bonding, supported by additional halogen bonding involving α-haloalkyl substituents. The introduction of halogens at the α-position of the substituent R in the selenadiazole core proved effective in promoting supramolecular dimerization, which was unaffected by variation of counterions. Additionally, the impact of cocrystallization with a classical halogen bond donor C6F3I3 on the supramolecular assembly was investigated. Non-covalent interactions were studied using density functional theory calculations and topological analysis of the electron density distribution, which indicated that all ChB, XB and HB interactions are purely non-covalent and attractive in nature. This study underscores the potential of halogen and chalcogen bonding in directing the self-assembly of functional supramolecular materials employing 1,2,4-selenadiazoles derived from recently discovered cycloaddition between nitriles and bifunctional 2-pyridylselenyl reagents.

Responsive Supramolecular Polymers for Diagnosis and Treatment.

Stimuli-responsive supramolecular polymers are ordered nanosized materials that are held together by non-covalent interactions (hydrogen-bonding, metal-ligand coordination, π-stacking and, host-guest interactions) and can reversibly undergo self-assembly. Their non-covalent nature endows supramolecular polymers with the ability to respond to external stimuli (temperature, light, ultrasound, electric/magnetic field) or environmental changes (temperature, pH, redox potential, enzyme activity), making them attractive candidates for a variety of biomedical applications. To date, supramolecular research has largely evolved in the development of smart water-soluble self-assemblies with the aim of mimicking the biological function of natural supramolecular systems. Indeed, there is a wide variety of synthetic biomaterials formulated with responsiveness to control and trigger, or not to trigger, aqueous self-assembly. The design of responsive supramolecular polymers ranges from the use of hydrophobic cores (i.e., benzene-1,3,5-tricarboxamide) to the introduction of macrocyclic hosts (i.e., cyclodextrins). In this review, we summarize the most relevant advances achieved in the design of stimuli-responsive supramolecular systems used to control transport and release of both diagnosis agents and therapeutic drugs in order to prevent, diagnose, and treat human diseases.

Aromatic-Carbonyl Interactions as an Emerging Type of Non-Covalent Interactions.

Aromatic-carbonyl (Ar···C═O) interactions, attractive interactions between the arene plane and the carbon atom of carbonyl, are in the infancy as one type of new supramolecular bonding forces. Here the study and functionalization of aromatic-carbonyl interactions in solution is reported. A combination of aromatic-carbonyl interactions and dynamic covalent chemistry provided a versatile avenue. The stabilizing role and mechanism of arene-aldehyde/imine interactions are elucidated through crystal structures, NMR studies, and computational evidence. The movement of imine exchange equilibria further allowed the quantification of the interplay between arene-aldehyde/imine interactions and dynamic imine chemistry, with solvent effects offering another handle and matching the electrostatic feature of the interactions. Moreover, arene-aldehyde/imine interactions enabled the reversal of kinetic and thermodynamic selectivity and sorting of dynamic covalent libraries. To show the functional utility diverse modulation of fluorescence signals is realized with arene-aldehyde/imine interactions. The results should find applications in many aspects, including molecular recognition, assemblies, catalysis, and intelligent materials.

Detection of paracetamol by a montmorillonite-modified carbon paste sensor: A study combining MC simulation, DFT computation and electrochemical investigations.

This study aims to develop a suitable electrochemical electrode through the incorporation of potassium montmorillonite (MMTK10)clay into the carbon matrix for the direct and sensitive determination of paracetamol (PAR) in pharmaceutical formulations. Electrochemical characterization of the electrodes involves the use of techniques such as cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and differential pulse voltammetry (DPV). The results reveal that the voltammetric response of PAR is linear over a wide concentration range (1.0-15 µM), with a low detection limit of 0.46 µM. Analytically, PAR recovery results were around 94%, indicating that the developed electrode is highly suitable for PAR detection in pharmaceutical formulation. Additionally, density functional theory (DFT) is employed to investigate the reactivity of PAR and explain the interaction process of PAR on the electrode surface at different pH values. A Monte Carlo simulations model is developed to provide a deeper understanding of the adsorption mechanism, particularly to comprehend molecular interactions and preferential orientations of PAR with MMT fractions at the electrode surface. Reduced Density Gradient is calculated and discussed using techniques such as Multiwfn and Visualization of Molecular Dynamics. The developed CPE-MMTK10 sensor provided a simple preparation method, rapid response, high sensitivity, reproducibility, strong selectivity, and extended stability. Moreover, there is a good correlation between most parameters calculated by DFT and experimental results, thereby reinforcing the validity of the theoretical approach in this study.

Automatic Determination of the Non-Covalent Stable Conformations of the NO2-Pyrene Cluster in Full Dimensionality (81D) Using the vdW-TSSCDS Approach.

We present the detailed topographical characterisation (stationary points and minimum energy paths connecting them) of the full dimensional (81D) intermolecular potential energy surface associated with the non-covalent interactions between the NO2 radical and the pyrene (C16H10) molecule. The whole procedure is (quasi) fully automated. We have used our recent algorithm vdW-TSSCDS as implemented on the freely-available AutoMekin software package. To this end, a series of inexpensive classical trajectories using forces from a low-level (semi-empirical) theory are used to sample the configuration space of the system in the search for candidates to first order saddle points. These guess structures are determined by means of a graph-theory based algorithm using the concept of adjacency matrix. Low-level optimizations are followed by re-optimizations at a final high-level of theory (DFT and CCSD(T)-F12 in our case.). The resulting set of stationary points and paths connecting them constitutes the so-called reaction network. In the case of NO2-pyrene, this network exhibits four major basins which can be characterized by their point-group symmetry. A central one, of global C2 symmetry, comprises the global minimum (as well as all other permutationally related conformers) together with the corresponding C2v saddle points connecting them. This central basin is connected to three others of lower C1 symmetry. The latter can be distinguished by the projection of the position of the NO2 nitrogen atom on the pyrene plane in combination with the relative orientation of the oxygen pair pointing either inwards, outwards, upwards or downwards.