Anticooperativity and Competition in Some Cocrystals Featuring Iodine-Nitrogen Halogen Bonds

Phenomena such as anticooperativity and competition among non-covalent bond donors and acceptors are key considerations when exploring the polymorphic and stoichiomorphic landscapes of binary and higher-order cocrystalline architectures. We describe the preparation of four cocrystals of 1,3,5-trifluoro-2,4,6-triiodobenzene with N-heterocyclic compounds, namely acridine, 3-aminopyridine, 4-methylaminopyridine, and 1,2-di(4-pyridyl)ethane. The cocrystals, which are characterized by single-crystal and powder X-ray diffraction experiments, all show moderately strong and directional iodine⋅⋅⋅nitrogen halogen bonds with reduced distance parameters ranging from 0.79 to 0.92 and carbon-iodine⋅⋅⋅nitrogen bond angles ranging from 165.4(3) to 175.31(7)°. The cocrystal comprising 1,3,5-trifluoro-2,4,6-triiodobenzene and acridine provides a relatively rare example where all three halogen bond donor sites form halogen bonds with three acceptor molecules, overcoming an anticooperative effect. This effect manifests itself through the lengthening of non-halogen-bonded C-I bonds, weakening their potential to form halogen bonds. The effect is only observed once two halogen bonds have been formed to 1,3,5-trifluoro-2,4,6-triiodobenzene; one such bond does not appear to be adequate. Among the four cocrystals studied, competition between the pyridyl nitrogen atoms and the amine nitrogen atoms suggests that the former are the preferred halogen bond acceptors. Analysis by Hirshfeld fingerprint plots and ¹³ C and ¹⁹ F magic-angle spinning solid-state nuclear magnetic resonance (NMR) spectroscopy provides additional insights into the prevalence of various short contacts in the crystal structures and into the spectral response to halogen-bond-induced cocrystallization.

Near-IR Absorbers Based on Pt(II)-Dithiolene Donor–Acceptor Charge-Transfer (CT) Systems: A Structural Analysis to Highlight DA Interactions

The packing interactions of a series of electron donor (D) and electron acceptor (A) charge transfer (CT) near-IR absorbers based on platinum-dithiolene complexes are reinvestigated here as a case study also by using the Hirshfeld surface analysis. This analysis on systems, which exhibit the 1:1, 2:1 and 2:2 columnar stacking patterns between D and A, allows us to point out that several interactions of atoms and fragments are involved in the stacking interactions but also that only a limited fraction of these interactions, limited to the 1:1 D/A columnar stacking case, can be relatable to the absorption features of this class of compounds.

Synthesis, Structure, Hirshfeld Surface Analysis, Non-Covalent Interaction, and In Silico Studies of 4-Hydroxy-1-[(4-Nitrophenyl)Sulfonyl]Pyrrolidine-2-Carboxyllic Acid

The new compound 4-hydroxy-1-[(4-nitrophenyl)sulfonyl]pyrrolidine-2-carboxyllic acid was obtained by the reaction of 4-hydroxyproline with 4-nitrobenzenesulfonyl chloride. The compound was characterized using single crystal X-ray diffraction studies. Spectroscopic methods including NMR, FTIR, ES-MS, and UV were employed for further structural analysis of the synthesized compound. The title compound was found to have crystallized in an orthorhombic crystal system with space group P212121. The S1-N1 bond length of 1.628 (2) Å was a strong indication of the formation of the title compound. The absence of characteristic downfield 1H NMR peak of pyrrolidine ring and the presence of S-N stretching vibration at 857.82 cm-1 on the FTIR are strong indications for the formation of the sulfonamide. The experimental study was complemented with computations at the B3LYP/6-311G +  + (d,p) level of theory to gain more understanding of interactions in the compound at the molecular level. Noncovalent interaction, Hirsfeld surface analysis and interaction energy calculations were employed in the analysis of the supramolecular architecture of the compound. Predicted ADMET parameters, awarded suitable bioavailability credentials, while the molecular docking study indicated that the compound enchants promising inhibition prospects against dihydropteroate synthase, DNA topoisomerase, and SARS-CoV-2 spike.

Graphical Abstract

Herein we present the solid state structure, noncovalent interaction and spectroscopic analysis of a prospective bioactive compound 4-hydroxy-1-[(4-nitrophenyl)sulphonyl]pyrrolidine-2-carboxyllic acid.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10870-023-00978-0.

Structural and Biological Properties of Heteroligand Copper Complexes with Diethylnicotinamide and Various Fenamates: Preparation, Structure, Spectral Properties and Hirshfeld Surface Analysis

Herein, we discuss the synthesis, structural and spectroscopic characterization, and biological activity of five heteroligand copper(II) complexes with diethylnicotinamide and various fenamates, as follows: flufenamate (fluf), niflumate (nifl), tolfenamate (tolf), clonixinate (clon), mefenamate (mef) and N, N-diethylnicotinamide (dena). The complexes of composition: [Cu(fluf)2(dena)2(H2O)2] (1), [Cu(nifl)2(dena)2] (2), [Cu(tolf)2(dena)2(H2O)2] (3), [Cu(clon)2(dena)2] (4) and [Cu(mef)2(dena)2(H2O)2] (5), were synthesized, structurally (single-crystal X-ray diffraction) and spectroscopically characterized (IR, EA, UV-Vis and EPR). The studied complexes are monomeric, forming a distorted tetragonal bipyramidal stereochemistry around the central copper ion. The crystal structures of all five complexes were determined and refined with an aspheric model using the Hirshfeld atom refinement method. Hirshfeld surface analysis and fingerprint plots were used to investigate the intermolecular interactions in the crystalline state. The redox properties of the complexes were studied and evaluated via cyclic voltammetry. The complexes exhibited good superoxide scavenging activity as determined by an NBT assay along with a copper-based redox-cycling mechanism, resulting in the formation of ROS, which, in turn, predisposed the studied complexes for their anticancer activity. The ability of complexes 1–4 to interact with calf thymus DNA was investigated using absorption titrations, viscosity measurements and an ethidium-bromide-displacement-fluorescence-based method, suggesting mainly the intercalative binding of the complexes to DNA. The affinity of complexes 1–4 for bovine serum albumin was determined via fluorescence emission spectroscopy and was quantitatively characterized with the corresponding binding constants. The cytotoxic properties of complexes 1–4 were studied using the cancer cell lines A549, MCF-7 and U-118MG, as well as healthy MRC-5 cells. Complex 4 exhibited moderate anticancer activity on the MCF-7 cancer cells with IC50 = 57 μM.

Luminescence Enhancement and Temperature Sensing Properties of Hybrid Bismuth Halides Achieved via Tuning Organic Cations

Bismuth-halide-based inorganic-organic hybrid materials (Bi-IOHMs) are desirable in luminescence-related applications due to their advantages such as low toxicity and chemical stability. Herein, two Bi-IOHMs of [Bpy][BiCl₄(Phen)] (1, Bpy = N-butylpyridinium, Phen = 1,10-phenanthroline) and [PP14][BiCl₄(Phen)]·0.25H₂O (2, PP14 = N-butyl-N-methylpiperidinium), containing different ionic liquid cations and same anionic units, have been synthesized and characterized. Single-crystal X-ray diffraction reveals that compounds 1 and 2 crystallize in the monoclinic space group of P2₁/c and P2₁, respectively. They both possess zero-dimensional ionic structures and exhibit phosphorescence at room temperature upon excitation of UV light (375 nm for 1, 390 nm for 2), with microsecond lifetime (24.13 μs for 1 and 95.37 μs for 2). Hirshfeld surface analysis has been utilized to visually exhibit the different packing motifs and intermolecular interactions in 1 and 2. The variation in ionic liquids makes compound 2 have a more rigid supramolecular structure than 1, resulting in a significant enhancement in photoluminescence quantum yield (PLQY), that is, 0.68% for 1 and 33.24% for 2. In addition, the ratio of the emission intensities for compounds 1 and 2 shows a correlation with temperature. This work provides new insight into luminescence enhancement and temperature sensing applications involving Bi-IOHMs.

Synthesis, Empirical and Theoretical Investigations on New Histaminium Bis(Trioxonitrate) Compound

In this paper, a novel hybrid material, entitled histaminium bis(trioxonitrate), with the general chemical formula (C₅H₁₁N₃)(NO₃)₂, denoted by HTN was presented. Single-crystal X-ray diffraction was used to determine the structural characteristics of this compound after it was made using a slow evaporation method at room temperature. This compound was elaborated and crystallized to the monoclinic system with space group P2₁/c, and the lattice parameters obtained were: a = 10.4807 (16)Å, b = 11.8747 (15)Å, c = 16.194 (2)Å, β = 95.095 (6)°, V = 2007.4 (5)ų and Z = 8. The title compound's atomic structure couldbe modeled as a three-dimensional network. Organic cations and nitrate anions were connected via N-H...O and C-H...O hydrogen bonds in the HTN structure. The intermolecular interactions responsible for the formation of crystal packing were evaluated using Hirshfeld surfaces and two-dimensional fingerprint plots. The compound's infrared spectrum, which ranged from 4000 to 400 cm^-1, confirmed the presence of the principal bands attributed to the internal modes of the organic cation and nitrate anions. Additionally, spectrofluorimetry and the ultraviolet-visible spectrum was used to investigate this compound. DFT calculations were used to evaluate the composition and properties of HTN. The energy gap, chemical reactivity and crystal stability of HTN were quantified by performing HOMO-LUMO frontier orbitals analysis. Topological analysis (AIM), Reduced Density Gradient (RDG), molecular electrostatic potential surface (MEPS) and Mulliken population were processed to determine the types of non-covalent interactions, atomic charges and molecular polarity in detail.

The Selection of the Best Derivatization Reagents for the Determination of Polyamines in Home-Made Wine Samples

The procedures of putrescine, spermine, spermidine, and cadaverine derivatization using 2-chloro-1,3-dinitro-5-(trifluoromethyl)benzene, 1-fluoro-2-nitro-4-(trifluoromethyl) benzene, and 3,5-bis-(trifluoromethyl)phenyl isothiocyanate for chromatographic determination in home-made wine samples are compared in the present study. The procedures discussed were compared regarding simplicity, linearity, precision, and accuracy. The polyamines derivatives were isolated and characterized by X-ray crystallography and ¹H, ¹³C, and ¹⁹F NMR spectroscopy. The obtained structures of aliphatic amines showed that all amino groups, four in spermine, two in putrescine and cadaverine, and three in spermidine, regardless of the applied reagent, were substituted. The applicability of the described procedures was tested during the chromatographic analysis of the compounds' content in home-made wines. For this purpose, a simple and environmentally friendly sample preparation procedure was developed. The obtained results present the derivatization of polyamines with 1-fluoro-2-nitro-4-(trifluoromethyl)benzene as a better choice for the determination of these compounds in food samples.

Piperonal chalcone derivative incorporating the pyrazolo[3,4-b]pyridine moiety; crystal structure, spectroscopic characterization and quantum chemical investigations

A single crystal of a piperonal chalcone derivative was obtained, fully characterized, and crystallized by a slow evaporation technique. The synthesized compound was characterized by UV-Visible, FT-IR, HRMS, ¹H NMR, and ¹³C NMR spectroscopic studies and X-ray crystallography, revealing that the crystal belongs to a triclinic crystal system with a P1̄ space group, Z = 2. In the present work, we focus on molecular modeling studies such as Hirshfeld surface analysis, energy framework calculations, frontier molecular orbital analysis, natural bond orbital analysis, and NLO properties of a π-conjugate system combining the chalcone and the pyrazole[3,4-b]pyridine scaffolds to describe the in-depth structural analysis thereof. Good agreement was found between the calculated results and experimental data. In addition, Hirshfeld surface analysis of the crystal structure showed that the intermolecular stabilization in the crystal packing comes mainly from H⋯H bond interactions. The chalcone crystal exhibits significant NLO properties suggesting that it could be considered a potential candidate for application in nonlinear optical devices.

Structural and theoretical investigations, Hirshfeld surface analysis and anti-SARS CoV-2 of nickel (II) coordination complex

A nickel(II) Schiff base complex, [Ni(L)(DMF)](1), was synthesized by treating NiCl₂.6H₂O with an ONS-donor Schiff base ligand(H₂L) derived from the condensation 3,5-Dichlorosalicylaldehyde and 4,4-Dimethyl-3-thiosemicarbazide in DMF. The geometry around the center metal ion in [Ni(L)(DMF)](1) was square planar as revealed by the data collection from diffraction studies. DFT calculations were performed on the complex to get a structure-property relationship. Hirshfeld surface analysis was also carried out in the crystal structure of nickel (II) Schiff base complex. Additionally, inspiring from recent developments to find a potential inhibitor for SARS-CoV-2 virus, we have also performed molecular docking study of [Ni(L)(DMF)](1) to see if our novel complex show affinity for main protease (M^pro) of SARS-CoV-2 M^pro (PDB ID: 6LZE). Interestingly, the results are found quite encouraging where the binding affinity and inhibition constant was found to be -6.6 kcal/mol and 2.358 µM, respectively, for the best docked confirmation of complex [Ni(L)(DMF)](1) with M^pro protein. This binding affinity is reasonably well as compared to recently known antiviral drugs. For instance, the binding affinity of complex [Ni(L)(DMF)](1) is found to be better than that of recently docking results of anti-SARS-CoV-2 drugs like chloroquine (-6.293 kcal/mol), hydroxychloroquine (-5.573 kcal/mol) and remdesivir (-6.352 kcal/mol) when targeted to the active-site of SARS-CoV-2 M^pro. Besides this, molecular docking against G25K GTP-nucleotide binding protein (PDB ID: 1A4R) was also studied. We believe that current results can intrigue not only for the biomedical community but also for the materials chemists who are engaged to explore the application coordination complexes. Communicated by Ramaswamy H. Sarma.

A data-driven interpretation of the stability of organic molecular crystals

Due to the subtle balance of intermolecular interactions that govern structure-property relations, predicting the stability of crystal structures formed from molecular building blocks is a highly non-trivial scientific problem. A particularly active and fruitful approach involves classifying the different combinations of interacting chemical moieties, as understanding the relative energetics of different interactions enables the design of molecular crystals and fine-tuning of their stabilities. While this is usually performed based on the empirical observation of the most commonly encountered motifs in known crystal structures, we propose to apply a combination of supervised and unsupervised machine-learning techniques to automate the construction of an extensive library of molecular building blocks. We introduce a structural descriptor tailored to the prediction of the binding (lattice) energy and apply it to a curated dataset of organic crystals, exploiting its atom-centered nature to obtain a data-driven assessment of the contribution of different chemical groups to the lattice energy of the crystal. We then interpret this library using a low-dimensional representation of the structure-energy landscape and discuss selected examples of the insights into crystal engineering that can be extracted from this analysis, providing a complete database to guide the design of molecular materials.

Bridging the crystal and solution structure of a series of lipid-inspired ionic liquids

A series of 1,2-dimethylimidazolium ionic liquids bearing a hexadecyl alkyl chain are thoroughly examined via X-ray crystallography. The crystal structures reveal several key variations in the non-covalent interactions in the lipid-like salts. Specifically, distinct cation-cation π interactions are observed when comparing the bromide and iodide structures. Changing the anion to bis(trifluoromethane)sulfonimide (Tf₂N^-) changes these cation-cation π interactions with anion⋯π interactions. Additionally, several well-defined geometries of the cations are noted based on torsion and core-plane angles of the alkyl chains. Hirshfeld surface analysis is used to distinguish the interactions and geometries in the solid state, helping to reveal characteristic structural fingerprints for the compounds. The solid-state structures of the ionic liquids are correlated with the solution-state structures through UV-vis spectroscopic studies, further emphasizing the importance of the π interactions in the formation of aggregates. Finally, we investigated the thermal properties of the ionic liquids, revealing complex phase transitions for the iodide-containing species. These phase transitions are further rationalized via the analysis of the data gathered from the structures of the other crystallized salts.

Synthesis, crystal structure and dielectric properties of a hybrid dihydrogen arsenate salt: (C9H11N4)H2AsO4

The use of the organic aromatic amine molecule 5-amino-3-methyl-1-phenyl-1H-1,2,4-triazole to synthesize a dihydrogen arsenate hybrid salt leads to a supramolecular structure type. Single crystals of (C9H11N4)H2AsO4 were grown through slow evaporation in solution. The synthesized compound crystallizes in the monoclinic system with the non-centrosymmetric P21 space group according to the following parameters; a = 9.655 (3) Å, b = 4.7090 (15) Å, c = 14.022 (4) Å, β = 108.147 (5)° and Z = 4. The mineral part building from dihydrogen arsenate anions [H2AsO4]− is linked together and to the organic cations [C9H11N4]+ by hydrogen bonds only. The results of Hirshfeld’s analysis show that in all possible molecular contacts, the hydrogen–hydrogen and the oxygen–hydrogen are the most important interaction in the crystal (37.5 and 31.9%, respectively). The Fourier transform infrared (FT-IR) confirms the existence of vibrational modes corresponding to the organic amine molecule and mineral arsenate tetrahedron. The optimized molecular structure and the vibrational spectra were calculated by the density functional theory DFT methods and the semi-empirical PM3 calculations. Dielectric study of this compound has been measured in order to determine the electrical conductivity type giving rise to an activation energy of ΔEσ = 0.17 eV.

Unraveling the Nature of Hydrogen Bonds of "Proton Sponges" Based on Car-Parrinello and Metadynamics Approaches

The nature of intra- and intermolecular non-covalent interactions was studied in four naphthalene derivatives commonly referred to as "proton sponges". Special attention was paid to an intramolecular hydrogen bond present in the protonated form of the compounds. The unsubstituted "proton sponge" served as a reference structure to study the substituent influence on the hydrogen bond (HB) properties. We selected three compounds substituted by methoxy, amino, and nitro groups. The presence of the substituents either retained the parent symmetry or rendered the compounds asymmetric. In order to reveal the non-covalent interaction properties, the Hirshfeld surface (HS) was computed for the crystal structures of the studied compounds. Next, quantum-chemical simulations were performed in vacuo and in the crystalline phase. Car-Parrinello molecular dynamics (CPMD), Path Integral Molecular Dynamics (PIMD), and metadynamics were employed to investigate the time-evolution changes of metric parameters and free energy profile in both phases. Additionally, for selected snapshots obtained from the CPMD trajectories, non-covalent interactions and electronic structure were studied. Quantum theory of atoms in molecules (QTAIM) and the Density Overlap Regions Indicator (DORI) were applied for this purpose. It was found based on Hirshfeld surfaces that, besides intramolecular hydrogen bonds, other non-covalent interactions are present and have a strong impact on the crystal structure organization. The CPMD results obtained in both phases showed frequent proton transfer phenomena. The proton was strongly delocalized in the applied time-scale and temperature, especially in the PIMD framework. The use of metadynamics allowed for tracing the free energy profiles and confirming that the hydrogen bonds present in "proton sponges" are Low-Barrier Hydrogen Bonds (LBHBs). The electronic and topological analysis quantitatively described the temperature dependence and time-evolution changes of the electronic structure. The covalency of the hydrogen bonds was estimated based on QTAIM analysis. It was found that strong hydrogen bonds show greater covalency, which is additionally determined by the proton position in the hydrogen bridge.

Structural Diversity, XAS and Magnetism of Copper(II)-Nickel(II) Heterometallic Complexes Based on the [Ni(NCS)6]4- Unit

The new heterometallic compounds, [{Cu(pn)₂}₂Ni(NCS)₆]_n·2nH₂O (1), [{Cu^II(trien)}₂Ni(NCS)₆Cu^I(NCS)]_n (2) and [Cu(tren)(NCS)]₄[Ni(NCS)₆] (3) (pn = 1,2-diaminopropane, trien = triethylenetetramine and tren = tris(2-aminoethylo)amine), were obtained and characterized by X-ray analysis, IR spectra, XAS and magnetic measurements. Compounds 1, 2 and 3 show the structural diversity of 2D, 1D and 0D compounds, respectively. Depending on the polyamine used, different coordination polyhedron for Cu(II) was found, i.e., distorted octahedral (1), square pyramidal (2) and trigonal bipyramidal (3), whereas coordination polyhedron for nickel(II) was always octahedral. It provides an approach for tailoring magnetic properties by proper selection of auxiliary ligands determining the topology. In 1, thiocyanate ligands form bridges between the copper and nickel ions, creating 2D layers of sql topology with weak ferromagnetic interactions. Compound 2 is a mixed-valence copper coordination polymer and shows the rare ladder topology of 1D chains decorated with [Cu^II(tren)]²⁺ antennas as the side chains attached to nickel(II). The ladder rails are formed by alternately arranged Ni(II) and Cu(I) ions connected by N2 thiocyanate anions and rungs made by N3 thiocyanate. For the Cu(I) ions, the tetrahedral thiocyanate environment mixed N/S donor atoms was found, confirming significant coordination spheres rearrangement occurring at the copper precursor together with the reduction in some Cu(II) to Cu(I). Such topology enables significant simplification of the magnetic properties modeling by assuming magnetic coupling inside {Ni^IICu^II₂} trinuclear units separated by diamagnetic [Cu(NCS)(SCN)₃]^3- linkers. Compound 3 shows three discrete mononuclear units connected by N-H…N and N-H…S hydrogen bonds. Analysis of XAS proves that the average ligand character and the covalency of the unoccupied metal d-based orbitals for copper(II) and nickel(II) increase in the following order: 1 → 2 → 3. In 1 and 2, a weak ferromagnetic coupling between copper(II) and nickel(II) was found, but in 2, additional and stronger antiferromagnetic interaction between copper(II) ions prevailed. Compound 3, as an ionic pair, shows, as expected, a spin-only magnetic moment.

Selective Low-Level Detection of a Perilous Nitroaromatic Compound Using Tailor-Made Cd(II)-Based Coordination Polymers: Study of Photophysical Properties and Effect of Functional Groups

Three coordination polymers (CPs 1-3) are prepared based on diverse electron-donating properties and coordination arrangements of conjugated ligands. Interestingly, this is also reflected in their photophysical properties. The distinguishable high emissive nature of the luminescent coordination polymer shows its potentiality toward the detection of the perilous substance 2,4,6-trinitrophenol (TNP) or picric acid (PA). TNP has a higher propensity among explosive nitroaromatic compounds (epNACs) due to its significant π···π interaction with the free benzene moieties present in the CPs. Among CPs 1-3, 2 exhibits the highest sensitivity and selectivity toward TNP because of the most favorable π-π stacking with the conjugated organic linker. The calculated limit of detection (LOD) and corresponding quenching constant (K_SV) from the Stern-Volmer (SV) plot for 1, 2, and 3 are found to be 0.68 μM and 7.49 × 10⁴ M^-1, 0.41 μM and 8.01 × 10⁴ M^-1, and 1.18 μM and 8.1 × 10⁴ M^-1, respectively. The fluorescence quenching mechanism is also highly influenced by their structure and coordination arrangement.

Halogen-Bonding-Mediated Radical Reactions: The Unexpected Behavior of Piperazine-Based Dithiooxamide Ligands in the Presence of Diiodine

N,N'-Dialkylpiperazine-2,3-dithiones (R₂pipdt) were recognized as a class of hexa-atomic cyclic dithiooxamide ligands with peculiar charge-transfer donor properties toward soft electron-acceptors such as noble metal cations and diiodine. The latter interaction is nowadays better described as halogen bonding. In the reaction with diiodine, R₂pipdt unexpectedly provides the corresponding triiodide salts, differently from the other dithiooxamides, which instead typically achieve ligand·nI₂ halogen-bonded adducts. In this paper, we report a combined experimental and theoretical study that allows elucidation of the nature of the cited products and the reasons behind the unpredictable behavior of these ligands. Specifically, low-temperature single-crystal X-ray diffraction measurements on a series of synthetically obtained R₂pipdt (R = Me, ⁱPr, Bz)/I₃ salts, complemented by neutron diffraction experiments, were able to experimentally highlight the formation of [R₂pipdtH]⁺ cations with a -S-H bond on the dithionic moiety. Differently, with R = Ph, a benzothiazolylium cation, resulting from an intramolecular condensation reaction of the ligand, is obtained. Based on density functional theory (DFT) calculations, a reasonable reaction mechanism where diiodine plays the fundamental role of promoting a halogen-bonding-mediated radical reaction has been proposed. In addition, the comparison of combined experimental and computational results with the corresponding reactions of N,N'-dialkylperhydrodiazepine-2,3-dithione (R₂dazdt, a hepta-atomic cyclic dithiooxamide), which provide neutral halogen-bonded adducts, pointed out that the difference in the torsion angle of the free ligands represents the structural key factor in determining the different reactivities of the two systems.