Cl Halogen Bonds Research Articles

Hydrogen bonding, halogen bonding and C–H…π interactions governing the supramolecular architecture of 1-(4-(4-bromophenyl)piperazin-1-yl)-2-chloroethan-1-one: Insights from X-ray crystallography, DFT calculations and urease inhibitory assessment

The use of organic ligands for the generation of supramolecular architectures exhibiting interesting structural properties in crystal engineering have garnered significant attention. In this context, the current work highlights the use of 1-(4-(4-bromophenyl)piperazin-1-yl)-2-chloroethan-1-one (3) as a valuable synthon for evaluating the conspicuous role of several types of noncovalent interactions governing the formation of supramolecular assemblies. Compound 3 was successfully synthesized in good yield using a facile two-step approach and characterized through spectroscopic and X-ray crystallographic methods. Noncovalent interactions including C—H…O, C—H…Cl, C—H…π as well as C—Br…Cl halogen bonds were found as the key contacts in the crystal packing of compound 3. DFT calculations were employed to identify and assess the impact of the C—Br…Cl halogen bond, utilizing MEP, QTAIM, and NBO analyses. These studies confirmed that the Br atom acts as the halogen bond donor and the Cl atom as the halogen bond acceptor. Assessment of urease inhibitory efficacy revealed that the tested compound exhibits a 16-folds superior inhibition than thiourea. Computational modeling analysis augmented the in vitro results by exhibiting numerous favorable binding interactions between compound 3 and active site residues such as TYR32, LYS709, PHE712, ASP730, VAL744 and MET746. The pharmacokinetic evaluation classified the investigated piperazine derivative into a druggable compound.

Exploring the effect of substituents on the supramolecular assemblies built by non-covalent interactions in three closely related 1,3,4-oxadiazole-2(3H)-thione derivatives: An evaluation of antimicrobial and anti-proliferative activities

Three closely related 1,3,4-oxadiazole-2(3H)-thione N-Mannich bases were synthesized and characterized by spectroscopic and single crystal X-ray diffraction methods. X-ray analysis reveals that the title molecules adopt l-shaped conformation, and a slight structural deviation around substituent groups is noted. The Hirshfeld surface and 2D fingerprint plots demonstrate the effect of substituents (piperidine, morpholine, and thiomorpholine) on the intermolecular interactions. The CLP-PIXEL energy analysis identified the most significant interactions in the molecular dimers (that characterize the crystal packing) with respect to the total intermolecular interaction energies. These dimers are held together by various non-covalent interactions including C–H⋅⋅⋅S/N/O/Cl/π interactions in addition to unconventional lone pair⋅⋅⋅π interactions. A molecule with thiomorpholine substituent is favoured by two σ-hole interactions (Cl⋅⋅⋅Cl halogen bond and S⋅⋅⋅N chalcogen bond) in the solid state. Furthermore, the molecular electrostatic potential (MEP) surfaces and deformation electron density help to describe the existence of σ-hole on the Cl and thione S atoms. Noncovalent interaction index (NCI) and quantum theory of atoms in molecules (QTAIM) methods are used to delineate the nature of observed noncovalent interactions in the molecular dimers. In vitro data of antibacterial and anti-proliferative activities indicate that compound with morpholine substituent showed a moderate antibacterial activity against all tested Gram-positive bacterial strains. However, molecules with piperidine and thiomorpholine showed notable effectiveness against the HepG-2 cell line. Molecular docking analysis was performed with two liver cancer targets, VEGFR2 and RET, in order to understand the interactions between the ligand and the active site residues of these targets.

One-pot cocrystallization of 1D linear and zigzag cobalt(II) polymers assembled by triclopyr and 4,4′-bipyridine: Structural comparison, conformational analysis, non-covalent interactions as well as the magnetic property of the latter

A pair of cobalt(II) compounds with formulas of [Co(3,5,6-tcpa)2(4,4′-bipy)(EtOH)]n (1A) and [Co(3,5,6-tcpa)2(4,4′-bipy)(EtOH)2]n (1B), have been cosynthesized through the solvothermal reaction of cobalt chloride hexahydrate with triclopyr (systematic name 2-((3,5,6-trichloropyridin-2-yl) oxy)acetic acid, abbreviation 3,5,6-Htcpa) and 4,4′-bipyridine (4,4′-bipy) coligands. Single-crystal X-ray diffraction analysis indicated that complex 1A has orthorhombic system, space group Aea 2 (no. 41), while 1B showed monoclinic system, space group I2/a (no. 15). Compound 1A displays a 1D linear chain but 1B presents a zigzag chain, and 3,5,6-tcpa anion are both unidentate between them. The non-covalent interactions of CH···O/CH···Cl hydrogen bonds and Cl···O/ Cl···Cl halogen bonds undertake a significant role in their 3D molecule packing, which have been further verified by the careful Hirshfeld surface analyses. Based on the deeply structural comparisons, it was supposed that conformational flexibility of 3,5,6-tcpa might be responsible for the cocrystallization of 1A and 1B. Besides, the magnetic determinations revealed weak antiferromagnetic interactions for intrachain cobalt(II) ions in 1B.

One-pot cocrystallization of mononuclear and 1D cobalt(II) complexes based on flexible triclopyr and 2,2′-bipyridine coligands: Structural analyses, conformation comparison, non-covalent interactions and magnetic properties

A pair of cobalt(II) complexes with formulas of [Co(3,5,6-tcpa)(2,2′-bpy)Cl] (1A) and [Co(3,5,6-tcpa)2(2,2′-bpy)]n (1B) have been cocrystallized by the solvothermal reaction of cobalt chloride hexahydrate with triclopyr (systematic name 2-((3,5,6-trichloropyridin-2-yl) oxy)acetic acid, abbreviation 3,5,6-Htcpa) and 2,2′-bipyridine (2,2′-bpy). Single-crystal X-ray diffraction analysis indicated that both 1A and 1B crystallized in triclinic system, space group P1¯ (no. 2). Compound 1A is mononuclear and 3,5,6-tcpa anion in it is a bidentate chelate ligand. In contrast, 1B is a 1D double-stranded chain structure in which 3,5,6-tcpa are bidentate bridging-μ2 linkers. The non-covalent interactions of Cl···Cl halogen bonds, C–H···O/Cl hydrogen bonds as well as π···π stacking interactions play an important part in their crystal packing, which have been confirmed by the careful Hirshfeld surface analyses. After deeply structural analyses, it was proposed that flexible conformation alteration of 3,5,6-tcpa might be in charge of the cocrystallization phenomenon of 1A and 1B. In addition, the magnetic characterizations suggested antiferromagnetic coupling between neighbouring cobalt(II) centers in 1B.

A new copper(II) complex containing triclopyr: one-pot crystallization, structure, conformation and Hirshfeld surface analyses

Abstract A new copper(II) complex [Cu(3,5,6-tcpa)(2,2′-bipy)Cl] (1) has been obtained through the one-pot hydrothermal reaction of copper chloride dihydrate with triclopyr (systematic name 2-((3,5,6-trichloropyridin-2-yl)oxy)acetic acid, abbreviation 3,5,6-Htcpa) and 2,2′-bipyridine (2,2′-bipy) coligands. 1 has crystallized in triclinic crystal system, P 1 ‾ $\overline{1}$ space group. The central copper(II) ion displayed a distorted square–pyramidal geometry and was connected by one chlorido co-ligand (Clˉ), one 3,5,6-tcpa anionic chelator and one chelating 2,2’-bipy ligand to afford a mononuclear structure. 1 is further extended into a 3D network by the non-covalent interactions of H⋯Cl, H⋯O hydrogen bonds, aromatic π⋯π stacking together with Cl⋯Cl halogen bond interactions. The co-crystallization process, the crystal structure of 1 as well as the Hirshfeld surface analysis for 1 have been analyzed and described. In addition, the flexible conformation of phenoxy methylene group among 1, triclopyr acid and its previously reported co-crystallized compound also have been carefully compared and discussed.

A combined crystallographic and theoretical investigation of noncovalent interactions in 1,3,4-oxadiazole-2-thione-N-Mannich derivatives: in vitro bioactivity and molecular docking.

Two 1,3,4-oxadiazole-2-thione-N-Mannich derivatives, specifically 5-(4-chlorophenyl)-3-[(2-trifluoromethylphenylamino)methyl]-1,3,4-oxadiazole-2(3H)-thione (1) and 5-(4-chlorophenyl)-3-[(2,5-difluorophenylamino)methyl]-1,3,4-oxadiazole-2(3H)-thione (2), were synthesized and then characterized by elemental analysis and NMR (1H and 13C) spectroscopy and the single crystal X-ray diffraction method. The formed weak intermolecular interactions in the solid-state structures of these derivatives were thoroughly investigated utilizing a variety of theoretical tools such as Hirshfeld surface analysis and quantum theory of atoms in molecules (QTAIM). Furthermore, the CLP-PIXEL and density functional theory calculations were used to study the energetics of molecular dimers. Numerous weak intermolecular interactions such as C-H⋯S/Cl/F/π interactions, a directional C-Cl⋯Cl halogen bond, π-stacking, type C-F⋯F-C contact and a short F⋯O interaction, help to stabilize the crystal structure of 1. Crystal structure 2 also stabilizes with several weak intermolecular contacts, including N-H⋯S, C-H⋯N//Cl/F interactions, a highly directional C1-Cl1⋯C(π) halogen bond and C(π)⋯C(π) interaction. In vitro antimicrobial potency of compounds 1 and 2 was assessed against various Gram-positive and Gram-negative bacterial strains and the pathogenic yeast-like Candida albicans. Both compounds showed marked activity against all tested Gram-positive bacteria and weak activity against Escherichia coli and lacked inhibitory activity against Pseudomonas aeruginosa. In addition, compounds 1 and 2 displayed good in vitro anti-proliferative activity against hepatocellular carcinoma (HepG-2) and mammary gland breast cancer (MCF-7) cancer cell lines. Molecular docking studies revealed the binding modes of title compounds at the active sites of prospective therapeutic targets.

Activation of metal-involved halogen bonds and classical halogen bonds in gold(I) catalysis.

In gold(I) catalysis, the activation of Au(I) chloride catalysts via chloride abstraction and noncovalent interactions has become a research focus in organometallic catalysis. In this work, taking halogen bond donors (C4H2INO2, C6F5I, C8H9O2I) as activators for a Au(I) chloride catalyst (Ph3PAuCl), the mechanism of the cyclization reaction of propargylic amide was investigated. It was found that there are two activation modes as design principles to obtain the catalytically active species Ph3PAu+: the halogen bond donors activate the Cl atoms of Ph3PAuCl to form X-I⋯Cl (X = C, N) classical halogen bonds and activate the Au atoms of Ph3PAuCl to form X-I⋯Au (X = C, N) metal-involved halogen bonds. For the two activation modes, the mechanism of the cyclization reaction of propargylic amide has pathways: the chloride abstraction process of the first step and the 5-exo/6-endo cyclization process of the second step. Both activation modes show good activity for the cyclization reaction with the activation ability of classical halogen bonds being slightly stronger than that of the metal-involved halogen bonds, which is consistent with the strength of the X-I⋯Cl halogen bonds being slightly stronger than that of the X-I⋯Au halogen bonds. Therefore, both metal-involved halogen bonds and classical halogen bonds have important development prospects for the activation of catalysts in gold(I) catalysis.

The synthesis, crystal structure and conformation analysis of triclopyr ethyl ester

Abstract Triclopyr ethyl ester (1) has been co-synthesized through one-pot solvothermal reaction and the crystal structure has been determined by single crystal X-ray structure analysis. The compound C18H16Cl6N2O6 crystallizes in the monoclinic crystal system, P21/c space group with unit-cell parameters: a = 4.9615(2) Å, b = 30.9297(14) Å, c = 15.9155(10) Å, β = 91.466(4)° and Z = 4. Each unit cell is composed of two discrete, similar but reversely arranged triclopyr ethyl ester organic molecules. In the 3D packing plot, 1 is further assembled into a network structure via rich Cl⋯Cl halogen bond interactions. In addition, the crystal structure, the flexible conformation of phenoxy methylene group of 1 has been carefully compared and discussed with those of triclopyr acid.

Role of Cl• • •Cl halogen bonds in tuning the crystals of Uranyl-Dicholorothiophene carboxylate based hybrid cluster materials through N-donor counter ions

• Eight new uranyl complexes containing 2,5-Dichlorothiophene-3-carboxylic acid with differently sized N-donor ligands were utilized to assemble under hydrothermal conditions. • The crystal structures of these uranyl complexes display the propensity of CTDC ligand and its capability of partaking in Cl•••Cl interactions and the Cl•••Cl interactions are confirmed through QTAIM analysis as well. • Photocatalytic behavior under UV light irradiation, shows remarkable advantages in the degradation of organic dyes. Hydrothermal synthesis has afforded eight uranyl bearing hybrid materials with various ancillary ligands such as 2,5-Dichlorothiophene-3-carboxylate (CTDC) as the main ligand and 4,4’-bipyridine (4BPY), 4,4′-Trimethylenedipyridine (4TBY), trans-1-(2-pyridyl)-2-(4-pyridyl)ethylene (TTPY), 1,10-Phenanthroline (PHEN), or 2,2′-Dipyridylamine (2DPY). These uranyl complexes; (UO 2 ) 0.5 (CTDC)(4BPY) 0.5 ( I ), UO 2 (CTDC) 2 (4BPY) 0.5 , ( II ); [(UO 2 ) 4 (μ 3 -O) 2 (μ 2 -OH) 2 (CTDC) 4 (4TBY) 2 ].(H 2 4TBY).2H 2 O ( III ); [(UO 2 ) 2 (μ3-O)(CTDC) 3 ].(HTTPY).H 2 O ( IV ); [(UO 2 )(CTDC) 2 (PHEN)] 2 ( V ); [(UO 2 )(μ 2 -OH)(CTDC)(PHEN)] ( VI ); [UO 2 (CTDC) 3 ] 2 (H2DPY) 2 ( VII ); [UO 2 (CTDC) 3 ] 2 (H4TBY) 2 ( VIII ) were characterized by single-crystal X-ray diffraction, powder X-ray diffraction, elemental analysis, FT-IR spectroscopy, thermogravimetric analysis and by their uranyl emission spectra. The complexes ( I ) and ( II ) are the first examples of uranyl complexes with aromatic carboxylates formed in the presence of a coordinated 4,4’-bipyridine ligand. Here, the complexes ( V ) and ( VI ) were concomitant polymorphs while ( II ) and ( VIII ) are polymorphs of ( I ) and ( III ) respectively and were obtained by varying the pH in synthetic procedures. Halogen bonding (Cl···Cl) interactions were found to play a strong role in expanding their dimensionality into 3D and defining their crystal packing patterns. To gain insights into the Cl···Cl interactions, a detailed QTAIM study is taken up. The photocatalytic properties of ( I - VIII ) for degradation of various organic dyes under Hg-lamp irradiation were performed. Interestingly, complexes ( I, II, V ) which are mononuclear uranyl clusters possess the highest efficiency in degradation of organic dyes than the tetranuclear uranyl clusters ( III, IV ). Thus, this work sheds light on the structural features of these uranyl complexes to extend our knowledge and understanding of uranyl chemistry.

One-pot solvothermal synthesis of mononuclear and oxalate-bridged binuclear nickel compounds: Structural analyses, conformation alteration and magnetic properties

Two new discrete compounds with the formula [Ni(3,5,6-tcpa)(2,2′-bipy)Cl] (1) and [Ni2(3,5,6-tcpa)2(2,2′-bipy)2(ox)]·2EtOH (2) (3,5,6-Htcpa = 2-((3,5,6-trichloro pyridin-2-yl)oxy)acetic acid, 2,2′-bipy = 2,2′-bipyridine, ox = oxalate dianion) have been co-synthesized under solvothermal conditions in the same medium. Single-crystal X-ray diffraction analysis shows that both 1 and 2 have crystallized in triclinic system, space group P1¯ and the central NiII ions are both in deformed square–pyramids. The NiII ion in 1 was bonded by one chloride ion (Cl-), one bidentate chelate 3,5,6-tcpa anion and one 2,2′-bipy to give a mononuclear complex 1. While for 2, the NiII ion was coodinated with one monodentate 3,5,6-tcpa, one oxalate anion and one 2,2′-bipy. The oxalate anion linked two equivalent NiII ions to form the binuclear cluster 2. The Cl···Cl halogen bonds, π···π stacking interactions and/or OH···O hydrogen bonds play an important part in the crystal packing for 1 and 2. Their deeply structural analyses revealed that the similar structure features and conformation alteration of 3,5,6-tcpa may be responsible for the cocrystallization phenomenon of 1 and 2. The magnetic measurements indicated the presence of intramolecular weak ferromagnetic coupling with J = 1.02 cm−1 in 2.

Nonconventional C(sp3)⋯Cl halogen bond in complexes of alkyl carbanions

Based on NBO analysis, Bader's theory, and decomposition of the interaction energy, the unique properties of the C(sp3)⋯Cl halogen bond in carbanionic complexes were revealed. In contrast to “electrostatic” complexes of hydroxyl and halide anions, in complexes of alkyl carbanions, charge transfer makes the main contribution to the binding energy. The C(sp3)⋯Cl interaction is partially covalent, and the interaction energy grows very slowly with an increase in the electron density at BCP of the intermolecular contact. The nature of the halogen bonds involving the C(sp3) atom of alkyl carbanions is determined by the high energy of the carbon lone pair.

Doubly mononuclear cocrystal and oxalato-bridged binuclear copper compounds containing flexible 2-((3,5,6-trichloropyridin-2-yl)oxy)acetate tectons: Synthesis, crystal analysis and magnetic properties

Two new copper compounds, namely [Cu(3,5,6-tcpa)2(H2O)4]·[Cu(3,5,6-tcpa)2(H2O)2] (1) and [Cu2(3,5,6-tcpa)2(2,2′-bipy)2(oxa)]·2EtOH (2) (3,5,6-Htcpa = 2-((3,5,6-trichloro pyridin-2-yl)oxy)acetic acid, 2,2′-bipy = 2,2′-bipyridine, oxa = oxalate dianion), have been synthesized by solvothermal method and systematically characterized. Single-crystal X-ray diffraction analysis show that 1 is an interesting double mononuclear cocrystal and consists of two discrete and stereochemically different complexes: one octahedral, the other tetrahedral about the copper centres. While for 2, two equivalent copper ions are in square pyramidal geometry and linked by oxalate anion forming a novel binuclear cluster. The OH···O hydrogen bonds, Cl···Cl halogen bonds and/or π···π stacking interactions play an important part in construction of the 3D networks for 1 and 2. The magnetic measurements indicate that there is weak antiferromagnetic coupling between two copper ions in 1 and 2. Notably, compound 2 also can be obtained in a higher yield with 1 as one of the starting material and the driving force for this transition process have been carefully discussed.

The first 3, 5, 6-trichloropyridine-2-oxyacetate bridged manganese coordination polymer with features of π⋯π stacking and halogen⋯halogen interactions: Synthesis, crystal analysis and magnetic properties

A new coordination polymer [Mn(3, 5, 6-tcpa)2(2, 2′-bipy)]n (1) has been synthesized by the hydrothermal reaction of manganese sulfate hydrate with 3, 5, 6-trichloropyridine-2-oxyacetic acid (3, 5, 6-Htcpa) and 2, 2′-bipyridine (2, 2′-bipy) coligands. The X-ray single-crystal diffraction analysis shows that the MnII center is in deformed octahedral geometry bonded by two pyridyl nitrogen atoms of 2, 2′-bipy molecule and four carboxy oxygen atoms of four different 3, 5, 6-tcpa− ligands. The 3, 5, 6-tcpa− anions play as bidentate bridging-μ2 linkers and connect neighbouring MnII ions together to form the 1D double-stranded chain structure of 1, which displays interesting chair form [Mn2(COO)2] eight-membered rings. 1 is further assembled into 3D network by the co-effects of π⋯π stacking and Cl⋯Cl halogen bonds interactions. In addition, the magnetic characterizations indicated weak antiferromagnetic coupling between MnII centers for 1.

A Binuclear Cadmium(II) Cluster Based on π···π Stacking and Halogen···Halogen Interactions: Synthesis, Crystal Analysis and Fluorescent Properties

An interseting binuclear complex [Cd2(tcpa)4(bipy)2] (1) has been hydrothermally synthesized with 3, 5, 6-trichloropyridine phenoxy acetatic acid (Htcpa) and 2, 2′-bipyridine (bipy) coligands. The X-ray single-crystal diffraction analysis shows that the CdII center is situated on unusual triangular prismatic geometry formed by two pyridyl nitrogen atoms of a bipy molecule and four carboxyl oxygen atoms of four different tcpa− ligands. The four tcpa− anions play as bis-monodentate linkers and connect two CdII ions together to form the dimer structure of 1. 1 is further assembled into a 2D layer by the co-effects of π···π stacking and Cl···Cl halogen bonds interactions. Moreover, 1 exhibits intense solid-state luminescence emissions centered at 442 nm at room temperature, which mainly originates from the intraligand π → π* transitions of tcpa−. The CCDC number of 1 is 1,935,091.

Melting point, molecular symmetry and aggregation of tetrachlorobenzene isomers: the role of halogen bonding.

Tetrachlorobenzenes represent one of the best known, but not yet fully understood, group of isomers of the structure-melting point relationship. The differences in melting temperatures of these structurally related compounds were rationalized in terms of the hierarchy and nature of formed noncovalent interactions, and the molecular aggregation that is influenced by molecular symmetry. The highest melting point is associated with the highly symmetric 1,2,4,5-tetrachlorobenzene isomer. The structures of less symmetrical 1,2,3,4-tetrachlorobenzene and 1,2,3,5-tetrachlorobenzene, determined at 270 and 90 K, show a distinct pattern of halogen bonds, characterized by the different numbers and types of interactions. The evolution of Cl...Cl/H distances with temperature indicates the attractive character of intermolecular interactions and their importance to the structural and thermodynamic parameters of isomeric compounds. The favoured Cl...Cl halogen bonds were found to play a decisive role in differentiating the melting temperatures of tetrachlorobenzene isomers. It was also found that, besides the molecular symmetry and ability to form specific intermolecular interactions, both the type and the distribution of interactions are the important factors responsible for the melting behaviour of the studied isomers. The observed preferences, in tetrachlorobenzenes, for the formation of specific noncovalent interactions correspond to the distribution of calculated partial atomic charges and to the magnitudes of electrostatic potential on the molecular surfaces as well as correlate with the enthalpy of melting parameters.

Cl...Cl halogen bonds and N-oxide...N-oxide interactions in the crystal structure of pentachloropyridine N-oxide

Cl...Cl halogen bonds and <i>N</i>-oxide...<i>N</i>-oxide interactions in the crystal structure of pentachloropyridine <i>N</i>-oxide

Design of two series of 1:1 cocrystals involving 4-amino-5-chloro-2,6-dimethylpyrimidine and carboxylic acids.

Two series of a total of ten cocrystals involving 4-amino-5-chloro-2,6-dimethylpyrimidine with various carboxylic acids have been prepared and characterized by single-crystal X-ray diffraction. The pyrimidine unit used for the cocrystals offers two ring N atoms (positions N1 and N3) as proton-accepting sites. Depending upon the site of protonation, two types of cations are possible [Rajam et al. (2017). Acta Cryst. C73, 862-868]. In a parallel arrangement, two series of cocrystals are possible depending upon the hydrogen bonding of the carboxyl group with position N1 or N3. In one series of cocrystals, i.e. 4-amino-5-chloro-2,6-dimethylpyrimidine-3-bromothiophene-2-carboxylic acid (1/1), 1, 4-amino-5-chloro-2,6-dimethylpyrimidine-5-chlorothiophene-2-carboxylic acid (1/1), 2, 4-amino-5-chloro-2,6-dimethylpyrimidine-2,4-dichlorobenzoic acid (1/1), 3, and 4-amino-5-chloro-2,6-dimethylpyrimidine-2-aminobenzoic acid (1/1), 4, the carboxyl hydroxy group (-OH) is hydrogen bonded to position N1 (O-H...N1) of the corresponding pyrimidine unit (single point supramolecular synthon). The inversion-related stacked pyrimidines are doubly bridged by the carboxyl groups via N-H...O and O-H...N hydrogen bonds to form a large cage-like tetrameric unit with an R42(20) graph-set ring motif. These tetrameric units are further connected via base pairing through a pair of N-H...N hydrogen bonds, generating R22(8) motifs (supramolecular homosynthon). In the other series of cocrystals, i.e. 4-amino-5-chloro-2,6-dimethylpyrimidine-5-methylthiophene-2-carboxylic acid (1/1), 5, 4-amino-5-chloro-2,6-dimethylpyrimidine-benzoic acid (1/1), 6, 4-amino-5-chloro-2,6-dimethylpyrimidine-2-methylbenzoic acid (1/1), 7, 4-amino-5-chloro-2,6-dimethylpyrimidine-3-methylbenzoic acid (1/1), 8, 4-amino-5-chloro-2,6-dimethylpyrimidine-4-methylbenzoic acid (1/1), 9, and 4-amino-5-chloro-2,6-dimethylpyrimidine-4-aminobenzoic acid (1/1), 10, the carboxyl group interacts with position N3 and the adjacent 4-amino group of the corresponding pyrimidine ring via O-H...N and N-H...O hydrogen bonds to generate the robust R22(8) supramolecular heterosynthon. These heterosynthons are further connected by N-H...N hydrogen-bond interactions in a linear fashion to form a chain-like arrangement. In cocrystal 1, a Br...Br halogen bond is present, in cocrystals 2 and 3, Cl...Cl halogen bonds are present, and in cocrystals 5, 6 and 7, Cl...O halogen bonds are present. In all of the ten cocrystals, π-π stacking interactions are observed.

Using protonation to change a Cl⋯N halogen bond in N-Base:ClOH complexes to a Cl⋯O halogen bond

Ab initio MP2/aug′-cc-pVTZ calculations demonstrate that protonation of N-Base:ClOH complexes at O leads to complexes (N-Base-Cl)+:OH2, as a traditional N⋯Cl halogen bond is replaced by a chlorine-transferred Cl⋯O bond. For a fixed base, the binding energies of the latter complexes are more than an order of magnitude greater than the former. As a function of the ClN distance, EOM-CCSD ClN coupling constants show the evolution of the traditional halogen bond in the N-Base:ClOH complexes, to a chlorine-shared halogen bond in N2:ClOH2+, to a covalent bond in (N-Base-Cl)+:OH2. 1J(ClN) values for these complexes resemble 1J(ClN) for the ions (N-Base-Cl)+.

Crystal structure and Hirshfeld surface analysis of (E)-3-[(2,3-di-chloro-benzyl-idene)amino]-5-phenyl-thia-zolidin-2-iminium bromide.

In the cation of the title salt, C16H14Cl2N3S+·Br-, the central thia-zolidine ring adopts an envelope conformation. The phenyl ring is disordered over two sites with a refined occupancy ratio of 0.541 (9):0.459 (9). In the crystal, C-H⋯Br and N-H⋯Br hydrogen bonds link the components into a three-dimensional network with the cations and anions stacked along the b-axis direction. Weak C-H⋯π inter-actions, which only involve the minor disorder component of the ring, also contribute to the mol-ecular packing. In addition, there are also inversion-related Cl⋯Cl halogen bonds and C-Cl⋯π (ring) contacts. A Hirshfeld surface analysis was conducted to verify the contributions of the different inter-molecular inter-actions.

4-Chloronaphthalen-1-yl 4-methylbenzenesulfonate

In the title compound, C17H13ClO3S, the naphthalene ring system and the benzene ring of the tosylate substituent are inclined to one another by 55.32 (5)°. The crystal structure features weak intermolecular C—H...O hydrogen bonds, one of which forms inversion dimers. Additional C—H...O hydrogen bonds and weak Cl...Cl halogen bonds stack the molecules along the b-axis direction.