Non-covalent interactions in the synthesis of coordination compounds: Recent advances

Natural Products from Herbal Medicine Self-Assemble into Advanced Bioactive Materials

Novel biomaterials are becoming more crucial in treating human diseases. However, many materials require complex artificial modifications and synthesis, leading to potential difficulties in preparation, side effects, and clinical translation. Recently, significant progress has been achieved in terms of direct self-assembly of natural products from herbal medicine (NPHM), an important source for novel medications, resulting in a wide range of bioactive supramolecular materials including gels, and nanoparticles. The NPHM-based supramolecular bioactive materials are produced from renewable resources, are simple to prepare, and have demonstrated multi-functionality including slow-release, smart-responsive release, and especially possess powerful biological effects to treat various diseases. In this review, NPHM-based supramolecular bioactive materials have been revealed as an emerging, revolutionary, and promising strategy. The development, advantages, and limitations of NPHM, as well as the advantageous position of NPHM-based materials, are first reviewed. Subsequently, a systematic and comprehensive analysis of the self-assembly strategies specific to seven major classes of NPHM is highlighted. Insights into the influence of NPHM structural features on the formation of supramolecular materials are also provided. Finally, the drivers and preparations are summarized, emphasizing the biomedical applications, future scientific challenges, and opportunities, with the hope of igniting inspiration for future research and applications.

Perhalogenated Anilines as Bifunctional Donors of Hydrogen and Halogen Bonds in Cocrystals with Ditopic Nitrogen-Containing Acceptors

In this study, we examine the experimental and theoretical capabilities of two perhalogenated anilines, 2,3,5,6-tetrafluoro-4-bromoaniline (btfa) and 2,3,5,6-tetrafluoro-4-iodoaniline (itfa) as hydrogen and halogen bond donors. A series of 11 cocrystals derived from the two anilines and selected ditopic nitrogen-containing acceptors (4,4'-bipyridine, 1,2-bis(4-pyridyl)ethane, and 1,4-diazabicyclo[2.2.2]octane) in 1:1 and 2:1 stoichiometries were prepared by liquid-assisted grinding and crystallization from solution. Crystallographic analysis revealed bifunctional donor properties in both anilines. The dominant supramolecular interaction in four cocrystals of btfa is the N-H···Nacceptor hydrogen bond between btfa and acceptor molecules, while in the one remaining cocrystal, donor and acceptor molecules are connected via the N-H···Nacceptor hydrogen bond and the Br···Nacceptor halogen bond. In two cocrystals of itfa, the dominant supramolecular interaction is the I···Nacceptor halogen bond between itfa and acceptor molecules, while in the remaining four cocrystals, donor and acceptor molecules are additionally connected by the N-H···Nacceptor hydrogen bond. Periodic density-functional theory (DFT) calculations have been conducted to assess the formation energies of these cocrystals and the strengths of the established halogen and hydrogen bonds. Molecular DFT calculations on btfa and itfa indicate that the differences in electrostatic potential between the competing sites on the molecules are 261.6 and 157.0 kJ mol-1 e-1, respectively. The findings suggest that itfa, with a smaller electrostatic potential difference between donor sites, is more predisposed to act as a bifunctional donor.

Long-range electrostatic effects from intramolecular Lewis acid binding influence the redox properties of cobalt-porphyrin complexes

A CoII-porphyrin complex (1) with an appended aza-crown ether for Lewis acid (LA) binding was synthesized and characterized. NMR spectroscopy and electrochemistry show that cationic group I and II LAs (i.e., Li+, Na+, K+, Ca2+, Sr2+, and Ba2+) bind to the aza-crown ether group of 1. The binding constant for Li+ is comparable to that observed for a free aza-crown ether. LA binding causes an anodic shift in the CoII/CoI couple of between 10 and 40 mV and also impacts the CoIII/CoII couple. The magnitude of the anodic shift of the CoII/CoI couple varies linearly with the strength of the LA as determined by the pKa of the corresponding metal-aqua complex, with dications giving larger shifts than monocations. The extent of the anodic shift of the CoII/CoI couple also increases as the ionic strength of the solution decreases. This is consistent with electric field effects being responsible for the changes in the redox properties of 1 upon LA binding and provides a novel method to tune the reduction potential. Density functional theory calculations indicate that the bound LA is 5.6 to 6.8 Å away from the CoII ion, demonstrating that long-range electrostatic effects, which do not involve changes to the primary coordination sphere, are responsible for the variations in redox chemistry. Compound 1 was investigated as a CO2 reduction electrocatalyst and shows high activity but rapid decomposition.

Self-indicating polymers: a pathway to intelligent materials

Self-indicating polymers have emerged as a promising class of smart materials that possess the unique ability to undergo detectable variations in their physical or chemical properties in response to various stimuli. This article presents an overview of the most important mechanisms through which these materials exhibit self-indication, including aggregation, phase transition, covalent and non-covalent bond cleavage, isomerization, charge transfer, and energy transfer. Aggregation is a prevalent mechanism observed in self-indicating polymers, where changes in the degree of molecular organization result in variations in optical or electrical properties. Phase transition-induced self-indication relies on the transformation between different phases, such as liquid-to-solid or crystalline-to-amorphous transitions, leading to observable changes in color or conductivity. Covalent bond cleavage-based self-indicating polymers undergo controlled degradation or fragmentation upon exposure to specific triggers, resulting in noticeable variations in their structural or mechanical properties. Isomerization is another crucial mechanism exploited in self-indicating polymers, where the reversible transformation between the different isomeric forms induces detectable changes in fluorescence or absorption spectra. Charge transfer-based self-indicating polymers rely on the modulation of electron or hole transfer within the polymer backbone, manifesting as changes in electrical conductivity or redox properties. Energy transfer is an essential mechanism utilized by certain self-indicating polymers, where energy transfer between chromophores or fluorophores leads to variations in the emission characteristics. Furthermore, this review article highlights the diverse range of applications for self-indicating polymers. These materials find particular use in sensing and monitoring applications, where their responsive nature enables them to act as sensors for specific analytes, environmental parameters, or mechanical stress. Self-indicating polymers have also been used in the development of smart materials, including stimuli-responsive coatings, drug delivery systems, food sensors, wearable devices, and molecular switches. The unique combination of tunable properties and responsiveness makes self-indicating polymers highly promising for future advancements in the fields of biotechnology, materials science, and electronics.

A synthetic approach towards drug modification: 2-hydroxy-1-naphthaldehyde based imine-zwitterion preparation, single-crystal study, Hirshfeld surface analysis, and computational investigation

The current work is about the modification of primary amine functionalized drugs, pyrimethamine and 4-amino-N-(2,3-dihydrothiazol-2-yl)benzenesulfonamide, via condensation reaction with 2-hydroxy-1-naphthaldehyde to produce new organic zwitterionic compounds (E)-1-(((4-(N-(2,3-dihydrothiazol-2-yl)sulfamoyl)phenyl)iminio)methyl)naphthalen-2-olate (DSPIN) and (E)-1-(((4-amino-5-(4-chlorophenyl)-6-ethylpyrimidin-2-yl)iminio)methyl)naphthalen-2-olate (ACPIN) in methanol as a solvent. The crystal structures of both compounds were confirmed to be imine-based zwitterionic products via single-crystal X-ray diffraction (SC-XRD) analysis which indicated that the stabilization of both crystalline compounds is achieved via various noncovalent interactions. The supramolecular assembly in terms of noncovalent interactions was explored by the Hirshfeld surface analysis. Void analysis was carried out to predict the crystal mechanical response. Compound geometries calculated in the DFT (Density Functional Theory) study showed reasonably good agreement with the experimentally determined structural parameters. Frontier molecular orbital (FMO) analysis showed that the DSPIN HOMO/LUMO gap is by 0.15 eV smaller than the ACPIN HOMO/LUMO gap due to some destabilization of the DSPIN HOMO and some stabilization of its LUMO. The results of the charge analysis implied formation of intramolecular hydrogen bonds and suggested formation of intermolecular hydrogen bonding and dipole-dipole and dispersion interactions.

Molecular Gas-Phase Conformational Ensembles

Accurately determining the global minima of a molecular structure is important in diverse scientific fields, including drug design, materials science, and chemical synthesis. Conformational search engines serve as valuable tools for exploring the extensive conformational space of molecules and for identifying energetically favorable conformations. In this study, we present a comparison of Auto3D, CREST, Balloon, and ETKDG (from RDKit), which are freely available conformational search engines, to evaluate their effectiveness in locating global minima. These engines employ distinct methodologies, including machine learning (ML) potential-based, semiempirical, and force field-based approaches. To validate these methods, we propose the use of collisional cross-section (CCS) values obtained from ion mobility-mass spectrometry studies. We hypothesize that experimental gas-phase CCS values can provide experimental evidence that we likely have the global minimum for a given molecule. To facilitate this effort, we used our gas-phase conformation library (GPCL) which currently consists of the full ensembles of 20 small molecules and can be used by the community to validate any conformational search engine. Further members of the GPCL can be readily created for any molecule of interest using our standard workflow used to compute CCS values, expanding the ability of the GPCL in validation exercises. These innovative validation techniques enhance our understanding of the conformational landscape and provide valuable insights into the performance of conformational generation engines. Our findings shed light on the strengths and limitations of each search engine, enabling informed decisions for their utilization in various scientific fields, where accurate molecular structure determination is crucial for understanding biological activity and designing targeted interventions. By facilitating the identification of reliable conformations, this study significantly contributes to enhancing the efficiency and accuracy of molecular structure determination, with particular focus on metabolite structure elucidation. The findings of this research also provide valuable insights for developing effective workflows for predicting the structures of unknown compounds with high precision.

Regioselective Thiol-yne Reaction of Thiol with ((Methyl-d3)sulfonyl)ethyne: Synthesis of (2-((Methyl-d3)sulfonyl)vinyl)sulfides

Herein, we have developed a new method for the synthesis of ((methyl-d3)sulfonyl)ethyne, which is cost-effective and environmentally friendly and can be synthesized at the gram level. As an ideal thiol-yne reagent, it can be reacted with various types of thiols to afford (Z)- and (E)-type vinyl sulfides under different conditions with high selectivity. In addition, it can complete the conformational transition from Z- to E-type products under suitable conditions, and can also carry out further derivatization smoothly. The deuterium content of all products was greater than 99%. The preliminary mechanistic studies support the visible light-mediated radical course, and herein provide a novel and efficient synthetic strategy for the direct introduction of deuterated methyl groups, enriching the methods for the construction of C-S bond-containing compounds.

Shape memory hydrogels with remodelable permanent shapes and programmable cold-induced shape recovery behavior

Most shape memory polymers apply glass transition or crystallization of domains to fix temporary shapes and shape recovery is induced by heating, which hinders their application under heat-intolerant conditions. Moreover, the permanent shapes of polymers normally cannot be altered arbitrarily after fabrication. Herein, we present a novel shape memory hydrogel with a remodelable permanent shape and programmable cold-induced shape recovery behavior. Poly(acrylic acid) (PAA) hydrogel is prepared in the presence of diethylenetriamine (DETA) and subsequently treated with calcium acetate (Ca(Ac)2). The charge-assisted hydrogen bonding between PAA and DETA imparts the hydrogel with remodelability, while the heat-induced hydrophobic aggregation of polymer chains and acetate groups results in shape fixation by heating and shape recovery by cooling. Afterwards, programmable deformable devices are obtained by assembling hydrogel blocks with different concentrations of Ca(Ac)2. This design strategy promotes the development of shape memory polymers with diverse potential applications.

The Decay of Dispersion Interaction and Its Remarkable Effects on the Kinetics of Activation Reactions Involving Alkyl Chains

The importance of dispersion interactions in many chemical processes is well recognized. It is known that the dispersion strength would decay with the increasing separation between the interacting groups; however, its effects on chemical reactivity have not been well understood. Here we reveal the decay law of dispersion interactions along the n-alkyl chain, its effective interaction ranges for common functional groups, and their remarkable effects on the kinetics of activation reactions involving alkyl chains. This is achieved by DLPNO-CCSD(T) calculations and the local energy decomposition analysis and is supported by experimental findings. In particular, our calculations indicate that the lifetime of alkyl-substituted cis-azobenzenes increases with the alkyl chain length but reaches a steady value when alkyl chains are longer than butyl groups, which is in satisfactory accordance with experimental measurements. We also propose a concise expression to describe the dispersion decay, which shows excellent agreement with our computed results.

Revisiting conventional noncovalent interactions towards a complete understanding: from tetrel to pnicogen, chalcogen, and halogen bond

Typical noncovalent interactions, including tetrel (TtB), pnicogen (PniB), chalcogen (ChalB), and halogen bonds (HalB), were systematically re-investigated by modeling the N⋯Z interactions (Z = Si, P, S, Cl) between NH3 - as a nucleophilic, and SiF4, PF3, SF2, and ClF - as electrophilic components, employing highly reliable ab initio methods. The characteristics of N⋯Z interactions when Z goes from Si to Cl, were examined through their changes in stability, vibrational spectroscopy, electron density, and natural orbital analyses. The binding energies of these complexes at CCSD(T)/CBS indicate that NH3 tends to hold tightly most with ClF (-34.7 kJ mol-1) and SiF4 (-23.7 kJ mol-1) to form N⋯Cl HalB and N⋯Si TtB, respectively. Remarkably, the interaction energies obtained from various approaches imply that the strength of these noncovalent interactions follows the order: N⋯Si TtB > N⋯Cl HalB > N⋯S ChalB > N⋯P PniB, that differs the order of their corresponding complex stability. The conventional N⋯Z noncovalent interactions are characterized by the local vibrational frequencies of 351, 126, 167, and 261 cm-1 for TtB, PniB, ChalB, and HalB, respectively. The SAPT2+(3)dMP2 calculations demonstrate that the primary force controlling their strength retains the electrostatic term. Accompanied by the stronger strength of N⋯Si TtB and N⋯Cl HalB, the AIM and NBO results state that they are partly covalent in nature with amounts of 18.57% and 27.53%, respectively. Among various analysis approaches, the force constant of the local N⋯Z stretching vibration is shown to be most accurate in describing the noncovalent interactions.

Halogen Bonding Involving Isomeric Isocyanide/Nitrile Groups

2,3,5,6-Tetramethyl-1,4-diisocyanobenzene (1), 1,4-diisocyanobenzene (2), and 1,4-dicyanobenzene (3) were co-crystallized with 1,3,5-triiodotrifluorobenzene (1,3,5-FIB) to give three cocrystals, 1·1,3,5-FIB, 2·2(1,3,5-FIB), and 3·2(1,3,5-FIB), which were studied by X-ray diffraction. A common feature of the three structures is the presence of I···Cisocyanide or I···Nnitrile halogen bonds (HaBs), which occurs between an iodine σ-hole and the isocyanide C-(or the nitrile N-) atom. The diisocyanide and dinitrile cocrystals 2·2(1,3,5-FIB) and 3·2(1,3,5-FIB) are isostructural, thus providing a basis for accurate comparison of the two types of noncovalent linkages of C≡N/N≡C groups in the composition of structurally similar entities and in one crystal environment. The bonding situation was studied by a set of theoretical methods. Diisocyanides are more nucleophilic than the dinitrile and they exhibit stronger binding to 1,3,5-FIB. In all structures, the HaBs are mostly determined by the electrostatic interactions, but the dispersion and induction components also provide a noticeable contribution and make the HaBs attractive. Charge transfer has a small contribution (<5%) to the HaB and it is higher for the diisocyanide than for the dinitrile systems. At the same time, diisocyanide and dinitrile structures exhibit typical electron-donor and π-acceptor properties in relation to the HaB donor.

Guiding Principles for the Rational Design of Hybrid Materials: Use of DFT Methodology for Evaluating Non-Covalent Interactions in a Uranyl Tetrahalide Model System

Together with the synthesis and experimental characterization of 14 hybrid materials containing [UO2 X4 ]2- (X=Cl- and Br- ) and organic cations, we report on novel methods for determining correlation trends in their formation enthalpy (ΔHf ) and observed vibrational signatures. ΔHf values were analyzed through isothermal acid calorimetry and a Density Functional Theory+Thermodynamics (DFT+T) approach with results showing good agreement between theory and experiment. Three factors (packing efficiency, cation protonation enthalpy, and hydrogen bonding energy [E H , norm total ${{E}_{H,{\rm { norm}}}^{{\rm { total}}}}$ ]) were assessed as descriptors for trends in ΔHf . Results demonstrated a strong correlation betweenE H , norm total ${E_{{\rm{H}},{\rm{norm}}}^{{\rm{total}}} }$ and ΔHf , highlighting the importance of hydrogen bonding networks in determining the relative stability of solid-state hybrid materials. Lastly, we investigate how hydrogen bonding networks affect the vibrational characteristics of uranyl solid-state materials using experimental Raman and IR spectroscopy and theoretical bond orders and find that hydrogen bonding can red-shift U≡O stretching modes. Overall, the tightly integrated experimental and theoretical studies presented here bridge the trends in macroscopic thermodynamic energies and spectroscopic features with molecular-level details of the geometry and electronic structure. This modeling framework forms a basis for exploring 3D hydrogen bonding as a tunable design feature in the pursuit of supramolecular materials by rational design.

Chalcogen bonding in copper(II)-mediated synthesis

The chalcogen bond (ChB) is a noncovalent attraction between an electrophilic chalcogen atom and a nucleophilic (Nu) region in the same (intramolecular) or another (intermolecular) molecular entity: R-Ch⋯Nu (Ch = O, S, Se or Te; R = substituents; Nu = nucleophile). ChB is comparable to the hydrogen and halogen bonds both in terms of strengths and directionality. However, in contrast to the monovalent halogen atoms, usually the divalent or tetravalent chalcogen atoms are able to display more than one electrophilic centre (on account of the existence of two or three species bonded to the chalcogen atom), which provides an additional opportunity in the use of this type of noncovalent binding in synthetic operations. In this work, the role of ChB at the secondary coordination sphere of metal complexes through copper(II)-mediated activation of dioxygen or of one nitrile group of a 1,2,5-selenadiazole-3,4-dicarbonitrile ligand to form a carbimidate or an imino-carboxylic acid is demonstrated. DFT calculations allowed evaluation of the strength of the ChBs and proved their relevant structure directing role in the solid state architectures. The effect of metal-coordination on the σ-hole opposite to the coordinated SeO bond has been analysed using molecular electrostatic potential (MEP) surfaces and explains the greater ability of the coordinated selenoxide derivatives to form strong ChBs.

l-Isoleucine-Schiff Base Copper(II) Coordination Polymers: Crystal Structure, Spectroscopic, Hirshfeld Surface, and DFT Analyses

A new copper(II) coordination polymer was synthesized from the l-isoleucine-Schiff base and characterized by elemental analysis, Fourier transform infrared (FT-IR) spectroscopy, ultraviolet-visible (UV-vis) spectroscopy, single-crystal X-ray diffraction (XRD) analysis, electronic paramagnetic resonance, and thermogravimetric analysis. XRD analysis confirmed the square planar coordination geometry of metallic centers and a zipper-like polymer structure. Vibrational, electronic, and paramagnetic spectroscopies and thermal analysis were consistent with the crystal structure. A Hirshfeld surface (HS) and density functional theory (DFT) analyses were employed to gain additional insight into interactions responsible for complex packing. The quantitative examination of two-dimensional (2D) fingerprint plots revealed, among other van der Waals forces, the dominating participation of H···H and H···Cl interactions in the molecular packing. The use of computational methods provided great help in detailing the supramolecular interactions occurring in the crystal, which were mainly van der Waals attractions. The electronic transition analysis helped corroborate the electronic transitions observed experimentally in the absorption spectrum. The frequency and vibrational mode analysis gave a deeper insight into the characterization of the CuL_CL complex.

Reconsideration of the ESIPT off mechanism for fluorescent probe MNC in aqueous solution

Fluorescent probes with excited state intramolecular proton transfer (ESIPT) properties play a significant role in the research of life science and material science. Guo et al. designed 3-hydroxy-2-(6-Methoxynaphthalen-2-yl)-4H-chromen-4-one (MNC) as a control to achieve the dual-color fluorescence imaging of lipid droplets and endoplasmic reticulum (ER). They deemed that the ESIPT process would be turned off in ER with high water content [J. Am. Chem. Soc. 2021, 143, 3169-3179]. However, contrary to the conventional ESIPT off case, the enol* state fluorescence intensity that should have been enhanced was severely quenched in water. Here, combined with ultrafast spectrum, steady-state fluorescence spectrum and potential energy surface, the mechanism of ESIPT process of MNC turned off in water is revised. Furthermore, the formation of aggregated states in water is responsible for the quenching of MNC fluorescence. This work is expected to provide broader ideas for the design of hydrophobic fluorescent probes.

Automated and Efficient Generation of General Molecular Aggregate Structures

Modeling intermolecular interactions of complex non-covalent structures is important in many areas of chemistry. To facilitate the generation of reasonable dimer, oligomer, and general aggregate geometries, we introduce an automated computational interaction site screening (aISS) workflow. This easy-to-use tool combines a genetic algorithm employing the intermolecular force-field xTB-IFF for initial search steps with the general force-field GFN-FF and the semi-empirical GFN2-xTB method for geometry optimizations. Compared with the alternative CREST program, aISS yields similar results but with computer time savings of 1-3 orders of magnitude. This allows for the treatment of systems with thousands of atoms composed of elements up to radon, e.g., metal-organic complexes, or even polyhedra and zeolite cut-outs which were not accessible before. Moreover, aISS can identify reactive sites and provides options like site-directed (user-guided) screening.

Dative B←N bonds based crystalline organic framework with permanent porosity for acetylene storage and separation

The utilization of dative B←N bonds for the creation of crystalline organic framework (BNOF) has increasingly received intensive interest; however, the shortage of permanent porosity is an obstacle that must be overcome to guarantee their application as porous materials. Here, we report the first microporous crystalline framework, BNOF-1, that is assembled through sole monomers, which can be scalably synthesized by the cheap 4-pyridine boronic acid. The 2D networks of BNOF-1 were stacked in parallel to generate a highly porous supramolecular open framework, which possessed not only the highest BET surface area of 1345 m² g^-1 amongst all of the BNOFs but also features a record-high uptake of C₂H₂ and CO₂ in covalent organic framework (COF) materials to date. Dynamic breakthrough experiments demonstrated that BNOF-1 material can efficiently separate C₂H₂/CO₂ mixtures. In addition, the network can be regenerated in organic solvents with no loss in performance, making its solution processable. We believe that BNOF-1 would greatly diversify the reticular chemistry and open new avenues for the application of BNOFs.

Halogen Bonding Involving Gold Nucleophiles in Different Oxidation States

A single-crystal X-ray diffraction (XRD) study of diaryliodonium tetrachloroaurates (or, in the recent terminology, tetrachloridoaurates), [(p-XC₆H₄)₂I][AuCl₄] (X = Cl, 1; Br, 2), was performed for 1 (the structure is denoted as 1a to show similarity with the isomorphic structure 2a) and two polymorphs─2a (obtained from MeOH) and 2b (from 1,2-C₂H₄Cl₂). Examination of the XRD data for these three structures revealed 2-center C-X···Au^III (X = Cl and Br) and 3-center bifurcated C-Br···(Cl-Au) halogen bonding (abbreviated as XB) between the p-Cl or p-Br atoms of the diaryliodonium cations and the gold(III) atom of [AuCl₄]^-. The noncovalent nature of Au^III-involving interactions, the nucleophilicity of the gold(III) atoms, and the electrophilic role of p-X atoms of the diaryliodonium cations in the XBs were studied by a set of complementary computational methods. Combined experimental and theoretical studies allowed the recognition of the d-nucleophilicity of the [d⁸Au^III] atom which, regardless of its rather substantial formal 3+ charge, can function as a d-nucleophilic partner of XB. This conclusion was also supported by theoretical calculations performed for the structures' refcodes BINXOM and ICSD 62511; the obtained data verified the nucleophilicity of Au^III toward a K⁺ ions or a σ-(Cl)-hole, respectively. All our results, together with consideration of relevant literature, indicate that gold atoms in the three oxidation states (0, I, and even III) exhibit nucleophilicity in XBs.

Heteroleptic Zn(II)–Pentaiodobenzoate Complexes: Structures and Features of Halogen–Halogen Non-Covalent Interactions in Solid State

Reactions between Zn(II) nitrate, pentaiodobenzoic acid (HPIBA) and different pyridines in dimethylformamide (DMF) result in the formation of the heteroleptic neutral complexes [Zn(3,5-MePy)2PIBA2] (1) and [Zn(DMF)3(NO3)PIBA] (2). Both compounds were isolated in pure form, as shown by the PXRD data. The features of specific non-covalent interactions involving halogen atoms (halogen bonding) were examined by means of DFT calculations (QTAIM analysis and the estimation of corresponding energies).

Water: new aspect of hydrogen bonding in the solid state

All water-water contacts in the crystal structures from the Cambridge Structural Database with d _OO ≤ 4.0 Å have been found. These contacts were analysed on the basis of their geometries and interaction energies from CCSD(T)/CBS calculations. The results show 6729 attractive water-water contacts, of which 4717 are classical hydrogen bonds (d _OH ≤ 3.0 Å and α ≥ 120°) with most being stronger than -3.3 kcal mol^-1. Beyond the region of these hydrogen bonds, there is a large number of attractive interactions (2062). The majority are antiparallel dipolar interactions, where the O-H bonds of two water molecules lying in parallel planes are oriented antiparallel to each other. Developing geometric criteria for these antiparallel dipoles (β₁, β₂ ≥ 160°, 80 ≤ α ≤ 140° and T _HOHO > 40°) yielded 1282 attractive contacts. The interaction energies of these antiparallel oriented water molecules are up to -4.7 kcal mol^-1, while most of the contacts have interaction energies in the range -0.9 to -2.1 kcal mol^-1. This study suggests that the geometric criteria for defining attractive water-water interactions should be broader than the classical hydrogen-bonding criteria, a change that may reveal undiscovered and unappreciated interactions controlling molecular structure and chemistry.

Estimations of OH·N hydrogen bond length from positions and intensities of IR bands

In this computational work applicability of IR spectral parameters for evaluations of OH···N hydrogen bond length is discussed. For a set of 124 complexes with OH···N hydrogen bond formed by combinations of methanol/acetic acid and pyridine (and their fluorine substituted versions) geometries, energies and IR parameters were calculated at MP2/def2-TZVP level of theory. For a number of IR parameters (the shift of proton donor group stretching vibration Δν_s, increase of its intensity I, the low-frequency hydrogen bond stretching vibration ν_σ, bending in-plane δ and out-of-plane γ vibrations) equations linking them with interatomic distances are proposed, the robustness and accuracy of such equations are discussed. The enthalpy of OH···N hydrogen bond formation ΔH was also linked with electron density parameters in (3; -1) critical point.

Towards Anion Recognition and Precipitation with Water-Soluble 1,2,4-Selenodiazolium Salts: Combined Structural and Theoretical Study

The synthesis and structural characterization of a series of supramolecular complexes of bicyclic cationic pyridine-fused 1,2,4-selenodiazoles with various anions is reported. The binding of trifluoroacetate, tetrachloroaurate, tetraphenylborate, perrhenate, and pertechnetate anions in the solid state is regarded. All the anions interact with selenodiazolium cations exclusively via a pair of “chelating” Se⋯O and H⋯O non-covalent interactions, which make them an attractive, novel, non-classical supramolecular recognition unit or a synthon. Trifluoroacetate salts were conveniently generated via novel oxidation reaction of 2,2′-dipyridyl diselenide with bis(trifluoroacetoxy)iodo)benzene in the presence of corresponding nitriles. Isolation and structural characterization of transient 2-pyridylselenyl trifluoroacetate was achieved. X-ray analysis has demonstrated that the latter forms dimers in the solid state featuring very short and strong Se⋯O and Se⋯N ChB contacts. 1,2,4-Selenodiazolium trifluoroacetates or halides show good solubility in water. In contrast, (AuCl₄)⁻, (ReO₄)⁻, or (TcO₄)⁻ derivatives immediately precipitate from aqueous solutions. Structural features of these supramolecular complexes in the solid state are discussed. The nature and energies of the non-covalent interactions in novel assembles were studied by the theoretical methods. To the best of our knowledge, this is the first study that regards perrhenate and pertechnetate as acceptors in ChB interactions. The results presented here will be useful for further developments in anion recognition and precipitation involving cationic 1,2,4-selenodiazoles.

Synthesis, Crystal Structure, and Hirshfeld Surface Analysis of Hexachloroplatinate and Tetraclorouranylate of 3-Carboxypyridinium—Halogen Bonds and π-Interactions vs. Hydrogen Bonds

This work aimed to synthesize new platinum and uranium compounds with nicotinic acid. In this article we describe the synthesis of two new anionic complexes (HNic)2[PtCl6] and (HNic)2[UO2Cl4] using wet chemistry methods. The structure of the obtained single crystals was established by single-crystal X-ray diffraction. The Hirshfeld surface analysis of the obtained complexes and their analogue (HNic)2[SiF6] was carried out for the analysis of intermolecular interactions. Hydrogen bonds (H···Hal/Hal···H and O···H/H···O) make the main contribution to intermolecular interactions in all compounds. Other important contacts in cations in all compounds are H···H, C···H/H···C and C···Hal/Hal···C; in anions H···Hal/Hal···H. The Pt-containing complex has a halogen-π interaction and halogen bonds, but Si-containing complex has a π–π staking interaction; these types of interactions are not observed in the U-containing compound.

Synthesis, spectroscopic findings and crystal engineering of Pb(ii)-Salen coordination polymers, and supramolecular architectures engineered by σ-hole/spodium/tetrel bonds: a combined experimental and theoretical investigation

Spontaneous self-assembly is one of the available synthetic routes to achieve structurally versatile and unique crystal complexes with selected metal-ligand combinations in the spirit of pseudohalides. In this endeavour, we designed a novel 1D coordination polymer (CP), [(Cd)(Pb)(L)(η¹-NCS)(η¹-SCN)] _n (1), using a compartmental Salen ligand (H₃L) in the presence of NaSCN. The characterization of the CP was accomplished using several spectroscopic techniques: MALDI-TOF, PXRD, SEM, EDX mapping, and single-crystal X-ray crystallography. The CP crystallizes in the monoclinic space group P2₁/c with Z = 4. SCXRD reveals Cd(ii) and Pb(ii) metal ions fulfilled distorted square pyramidal and hemi-directed coordination spheres. Cd(ii) is placed in the inner N₂O₂ and heavier Pb(ii) in the outer O₄ compartments of the de-protonated form of the ligand [L]^2-. Supramolecular interactions in the intricate crystal structure produced attractive molecular architectures of the compound. The flexible aliphatic -OH pendent group coordinates with the Pb(ii) ions. This unique binding further elevates the supramolecular crystal topographies. The supramolecular interactions were authenticated by Hirshfeld surface analysis (HSA). The observation of the recurring unconventional tetrel bonds was rationalized by DFT calculations and surface plots of molecular electrostatic potential (MEP). In the 1D polymeric chain in the complex, the O-atom of the -OH groups shows a tetrel bonding interaction with the Pb atom. We have found that the combination of QTAIM/NCI and QTAIM/ELF plots helps reveal the nature of these contacts. Moreover, the QTAIM/ELF plot determines the donor-acceptor interaction between the O-atom and the Pb atom, establishing the σ-hole. Agreeably, the σ-hole interaction also helps Pb(ii) serve as a Lewis acid in the complex. Finally, spodium and tetrel bonds are formed, possible thanks to a hemi-directional coordination sphere of the Pb atoms in the polymer described.

Molecular Assemblies Offering Hydrogen-Bonding Cavities: Influence of Macrocyclic Cavity and Hydrogen Bonding on Dye Adsorption

This work presents a set of Hg macrocycles of amide-phosphine-based ligands offering H-bonding cavities of different dimensions. Such macrocycles are shown to selectively adsorb anionic dyes followed by neutral dyes as well as Prontosil, a biologically relevant antibiotic, within their cavities with the aid of H-bonding-assisted encapsulation. Kinetic experiments supported by spectroscopic and docking studies illustrate the importance of the cavity structure as well as H-bonds for the selective adsorption of dyes.

π-π Stacking Interaction of Metal Phenoxyl Radical Complexes

π-π stacking interaction is well-known to be one of the weak interactions. Its importance in the stabilization of protein structures and functionalization has been reported for various systems. We have focused on a single copper oxidase, galactose oxidase, which has the π-π stacking interaction of the alkylthio-substituted phenoxyl radical with the indole ring of the proximal tryptophan residue and catalyzes primary alcohol oxidation to give the corresponding aldehyde. This stacking interaction has been considered to stabilize the alkylthio-phenoxyl radical, but further details of the interaction are still unclear. In this review, we discuss the effect of the π-π stacking interaction of the alkylthio-substituted phenoxyl radical with an indole ring.

Rotational Spectra of 2-Ethynylpyridine and Its Monohydrate: Influence of the Ortho-Substitution on Ring Geometry and Intermolecular Hydrogen Bonds

Rotational spectra of the 2-ethynylpyridine monomer and its monohydrate have been characterized by pulsed jet Fourier transform microwave spectroscopy complemented with quantum chemical calculations. The measurements of rotational transitions of the 2-ethynylpyridine monomer and its eight monosubstituted isotopologues (¹⁵N and ¹³C) in natural abundances allow an accurate structural description of the skeleton of 2-ethynylpyridine. For the monohydrate, only the most stable isomer, stabilized by an O-H···N and a secondary C-H···O hydrogen bonds, has been observed in the supersonic jet. Johnson's noncovalent interaction and quantum theory of atoms in molecules analyses have been performed and compared with results for several ortho-substituted pyridine derivatives to elucidate the general trend in their binding energies.

Exploring Supramolecular Assembly Space of Cationic 1,2,4-Selenodiazoles: Effect of the Substituent at the Carbon Atom and Anions

Chalcogenodiazoles have been intensively studied in recent years in the context of their supramolecular chemistry. In contrast, the newly discovered cationic 1,2,4-selenodiazole supramolecular building blocks, which can be obtained via coupling between 2-pyridylselenyl halides and nitriles, are virtually unexplored. A significant advantage of the latter is their facile structural tunability via the variation of nitriles, which could allow a fine tuning of their self-assembly in the solid state. Here, we explore the influence of the substituent (which derives from the nitrile) and counterions on the supramolecular assembly of cationic 1,2,4-selenodiazoles via chalcogen bonding.

Insight into non-covalent interactions in a [Cu(N3)4]2- bridged hetero-pentanuclear copper(II)/sodium complex with special emphasis on the strong CH···π[Cu(N3)4] interactions

The swastika-shaped anion, [Cu(N3)4]2- in the pentanuclear hetero-metallic copper(II)-Sodium complex, [(CuLNa)2(µ-N3)2Cu(N3)2] (1), where H2L = N,N'-bis(3-ethoxysalicylidene)-2,2-dimethylpropane-1,3-diamine (N2O4 donor compartmental Schiff base) is nearly planar and provides a π-basic surface adequate...

Heterovalent chalcogen bonding: supramolecular assembly driven by the occurrence of a tellurium(ii)⋯Ch(i) (Ch = S, Se, Te) linkage

The revealed heterovalent TeII⋯ChI (Ch = S, Se, Te) chalcogen bonding was used for targeted noncovalent integration of two Ch centers in different oxidation states.

Structural topologies involving energetically significant antiparallel π-stacking and unconventional N(nitrile)⋯π(fumarate) contacts in dinuclear Zn(ii) and polymeric Mn(ii) compounds: antiproliferative evaluation and theoretical studies

Anticancer activities considering cell viability, apoptosis and molecular docking have been explored in dinuclear Zn(ii) and polymeric Mn(ii) compounds involving energetically significant unconventional N(nitrile)⋯π(fum) contacts.

Chameleonic Metal-bound Isocyanides: π-Donating CuI-center Imparts a Nucleophilicity to the Isocyanide Carbon toward Halogen Bonding

In the structures of the isostructural cocrystals [CuI3(CNXyl)3]·CHX3 (X = Br, I), two adjacent CuI-bound isocyanide groups, whose carbon lone pairs are blocked by the ligation, exhibit nucleophilic properties induced...

Halogen bonding in cadmium(II) MOFs: its influence on the structure and on the nitroaldol reaction in aqueous medium

A solvothermal reaction of Cd(II) with the dicarboxyl-functionalized arylhydrazone pro-ligands, 5-(2-(2,4,6-trioxotetrahydro-pyrimidin-5(2H)-ylidene)hydrazineyl)isophthalic acid (H₅L¹) and 5-(2-(2,4-dioxopentan-3-ylidene)hydrazineyl)isophthalic acid (H₃L²), or their halogen bond donor centre(s) decorated analogs 2,4,6-triiodo-5-(2-(2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene)hydrazineyl)isophthalic acid (H₅L³) and 5-(2-(2,4-dioxopentan-3-ylidene)hydrazineyl)-2,4,6-triiodoisophthalic acid (H₃L⁴), leads to the formation of known [Cd(H₃L¹)(H₂O)₂]_n (1) and new {[Cd(HL²)(H₂O)₂(DMF)]·H₂O}_n (2), [Cd(H₃L³)]_n (3) and {[Cd₂(μ-H₂O)₂(μ-H₂L⁴)₂(H₂L⁴)₂]·2H₂O}_n (4) coordination compounds, respectively. The aggregation of mononuclear units via Cd-OC and Cd-OH₂ coordination and C_Ar-I⋯I types of intramolecular halogen bonds lead to a dinuclear tecton 4. Both C_Ar-I⋯O and C_Ar-I⋯I types of intermolecular halogen bonds play a fundamental role in the supramolecular architectures of the obtained metal-organic frameworks 3 and 4. Theoretical (DFT) calculations confirmed the presence of the C_Ar-I⋯O and C_Ar-I⋯I halogen bonds in 3 and 4 and allowed their characterisation. The formation of intermolecular noncovalent interactions between the attached iodine substituents to the hydrazone ligands and polar solvent (water or methanol) molecules promoted, at least in part, the solubility of the corresponding complexes (3 and 4), which act as homogeneous catalyst precursors in the Henry reaction between aldehydes and nitroethane. The corresponding β-nitroalkanol products were obtained in good yields (66-79%) and with good diastereoselectivity (threo/erythro ca. 72 : 28) in water at room temperature.

Remote Amino Acid Recognition Enables Effective Hydrogen Peroxide Activation at a Manganese Oxidation Catalyst

Precise delivery of a proton plays a key role in O₂ activation at iron oxygenases, enabling the crucial O−O cleavage step that generates the oxidizing high‐valent metal–oxo species. Such a proton is delivered by acidic residues that may either directly bind the iron center or lie in its second coordination sphere. Herein, a supramolecular strategy for enzyme‐like H₂O₂ activation at a biologically inspired manganese catalyst, with a nearly stoichiometric amount (1–1.5 equiv) of a carboxylic acid is disclosed. Key for this strategy is the incorporation of an α,ω‐amino acid in the second coordination sphere of a chiral catalyst via remote ammonium‐crown ether recognition. The properly positioned carboxylic acid function enables effective activation of hydrogen peroxide, leading to catalytic asymmetric epoxidation. Modulation of both amino acid and catalyst structure can tune the efficiency and the enantioselectivity of the reaction, and a study on the oxidative degradation pathway of the system is presented.