Intermolecular Cl Research Articles

Crystal structures and Hirshfeld surface analyses of methyl 4-{2,2-dichloro-1-[(E)-phenyldiazenyl]ethenyl}benzoate, methyl 4-{2,2-dichloro-1-[(E)-(4-methylphenyl)diazenyl]ethenyl}benzoate and methyl 4-{2,2-dichloro-1-[(E)-(3,4-dimethylphenyl)diazenyl]ethenyl}benzoate

The crystal structures and Hirshfeld surface analyses of three similar azo compounds are reported. Methyl 4-{2,2-dichloro-1-[(E)-phenyldiazenyl]ethenyl}benzoate, C16H12Cl2N2O2, (I), and methyl 4-{2,2-dichloro-1-[(E)-(4-methylphenyl)diazenyl]ethenyl}benzoate, C17H14Cl2N2O2, (II), crystallize in the space group P21/c with Z = 4, and methyl 4-{2,2-dichloro-1-[(E)-(3,4-dimethylphenyl)diazenyl]ethenyl}benzoate, C18H16Cl2N2O2, (III), in the space group P\overline{1} with Z = 2. In the crystal of (I), molecules are linked by C—H...N hydrogen bonds, forming chains with C(6) motifs parallel to the b axis. Short intermolecular Cl...O contacts of 2.8421 (16) Å and weak van der Waals interactions between these chains stabilize the crystal structure. In (II), molecules are linked by C—H...O hydrogen bonds and C—Cl...π interactions, forming layers parallel to (010). Weak van der Waals interactions between these layers consolidate the molecular packing. In (III), molecules are linked by C—H...π and C—Cl...π interactions forming chains parallel to [011]. Furthermore, these chains are connected by C—Cl...π interactions parallel to the a axis, forming (0\overline{1}1) layers. The stability of the molecular packing is ensured by van der Waals forces between these layers.

Ten-Membered Cyclodecatetraene Derivatives Including Two Gallium Atoms: Experimental and Theoretical Studies on Synthesis, Structures, and Their Transformations to Nine- and Five-Membered Gallacycles

The chemistry of medium-sized ring compounds, including group 13 elements, has scarcely been investigated. Herein, we report that 5,10-digallacyclodeca-1,3,6,8-tetraene derivatives Cl2Ga2C8R8 (R = Me (5a), Et (5b)) can be obtained by the reaction of GaCl3 and zirconacyclopentadiene Cp2ZrC4R4 (R = Me (2a), Et (2b), Cp: η5-C5H5) in toluene. X-ray crystal structure analysis revealed that compound 5b has a 10-membered cyclodecatetraene structure composed of two butadiene skeletons and two GaCl fragments. X-ray crystal structure analysis and IR measurement confirmed that compound 5b forms Ga2Cl2 four-membered rings via intermolecular Cl to Ga donor–acceptor interactions, which result in the formation of oligomeric chain structures in the solid state and toluene solution. The treatment of compound 5b with 2 equivalents of 4-(dimethylamino)pyridine (DMAP) proceeded via the coordination of DMAP to the Ga center and the ring contraction to give DMAP-coordinated five-membered gallole Cl(DMAP)GaC4Et4 (4bDMAP). The reaction of compound 5a with 2 equivalents of MesLi (Mes: 2,4,6-Me3C6H2) in toluene to form a 9,10-digallabicyclo[4.3.1]decatriene derivative (MesGaC8Me8)GaMes (6a) caused ring contraction. Theoretical investigation revealed that the 10-membered ring derivative, Cl2Ga2C8H8 (GaH-10), is formed by the dimerization of two gallole molecules, ClGaC4H4 (GaH-5), via the addition of two Ga–C bonds without an energy barrier. The immediate formation of GaH-10 was attributed to the transannular electronic interaction between the expanded empty p-orbital on the Ga atom and the electron-rich sp2 carbons of the C═C double bond in GaH-5. Moreover, GaH-10 and one of the isomer, nine-membered ring derivative (ClGaC8H8)GaCl, were found to be thermodynamically more stable, as compared to GaH-5.

Crystal structure and Hirshfeld surface analysis of (3aR,4S,7S,7aS)-4,5,6,7,8,8-hexa-chloro-2-{6-[(3aR,4R,7R,7aS)-4,5,6,7,8,8-hexa-chloro-1,3-dioxo-1,3,3a,4,7,7a-hexa-hydro-2H-4,7-methano-isoindol-2-yl]hex-yl}-3a,4,7,7a-tetra-hydro-1H-4,7-methano-iso-indole-1,3(2H)-dione.

The mol-ecule of the title compound, C24H16Cl12N2O4, is generated by a crystallographic inversion centre at the midpoint of the central C-C bond. A kink in the mol-ecule is defined by a torsion angle of -169.86 (15)° about this central bond of the alkyl bridge. The pyrrolidine ring is essentially planar [max. deviation = 0.014 (1) Å]. The cyclo-hexane ring has a boat conformation, while both cyclo-pentane rings adopt an envelope conformation. In the crystal structure, mol-ecules are linked by inter-molecular C-H⋯O, C-H⋯Cl and C-Cl⋯π inter-actions, and short inter-molecular Cl⋯O and Cl⋯Cl contacts, forming a three-dimensional network.

Dinuclear Organotin Building Blocks and their Conversion into a Tetranuclear Macrocycle Containing Sn−O−Sn Linkages

AbstractSix dinuclear organotin building blocks of general composition RR′R′′SnCH2Si(CH3)2−biphenyl−Si(CH3)2CH2SnR′′R′R, in which the tin atoms are separated by a p,p′‐biphenylene bridge and carry different substituents [BD1 with R, R′=CH2Si(CH3)3, R′′=Ph; BD2 with R, R′=CH2Si(CH3)3, R′′=Cl; BD3, with R, R′=CH2Si(CH3)3, R′′=I; BD4 with R=CH2Si(CH3)2(C5H4FeCp), R′, R′′=Ph; BD5 with R=CH2Si(CH3)2(C5H4FeCp), R′=Ph, R”=Cl; BD6 with R=CH2Si(CH3)2(C5H4FeCp), R′=Ph, R′′=I], were synthesized and characterized by spectroscopic and spectrometric methods. Furthermore, the crystal and molecular structures of BD2 were determined by single‐crystal X‐ray diffraction (SCXRD) analysis, revealing the formation of molecular strands through intermolecular Cl→Sn contacts. The 1D coordination polymer [BD2]n comprises macrocyclic rings of composition [BD2]2 that motivated the generation of a related molecular macrocyclic structure by reaction of BD2 with silver (I) oxide in a 2 : 2 stoichiometry. The [2+2] macrocyclization yielded the 30‐membered tetra‐nuclear ring structure M1, viz., {[R2SnCH2Si(CH3)2−biphenyl−(CH3)2SiCH2SnR2](μ‐O)}2, in which two BD2 dinuclear building blocks are linked through two covalent Sn−O−Sn moieties. Examination by DFT calculations at the B3LYP/def2svp and B3LYP/6‐31G*(C,H,O,Si)/LanL2DZ(Sn) levels of theory gave energy minima for molecular conformers of M1 carrying the Sn−O−Sn and p,p′‐biphenylene bridges in syn‐ or anti‐orientation.

4-(2,3-Di-chloro-phen-yl)piperazin-1-ium picrate.

The title compound, C6H2N3O7 -·C10H13Cl2N2 +, crystallizes with one 1-(2,3-di-chloro-phen-yl)piperazine (DP) cation and one picrate (PA) anion in the asymmetric unit. In the crystal structure, the DP cation and PA anion are inter-connected via several N-H⋯O and C-H⋯O hydrogen bonds. The DP cation and PA anion are further connected through C-Cl⋯π [3.8201 (4), 3.7785 (4) Å] and N-O⋯π [3.7814 (4) Å] inter-actions. The DP cations are further inter-connected via a weak inter-molecular Cl⋯Cl [3.2613 (4) Å] halogen-halogen inter-action. The combination of these supra-molecular inter-actions leads to a herringbone like supra-molecular architecture.

Mechanisms of the Reactions of B‐Substituted Amine Boranes with THF·BH3

The reactions of NH3BH2R (R = Me, Ph and Cl) with THFBH3 have been investigated and it was found that different substituents on the B atom help to proceed the reactions in different ways. The expected doubly‐bridged B‐substituted aminodiborane products, similar to aminodiborane (ADB, BH2(µ‐H)(µ‐NH2)BH2) via the reaction of ammonia borane (AB, NH3BH3) and tetrahydrofuran borane (THFBH3), are not obtained. Two competitive reactions occurred with the change of R = Me or Ph. When R is a Me group, an “open“ version of B‐substituted µ‐aminodiborane, THFBH(Me)(µ‐NH2)BH3, is formed as a major product; when R is a Ph group, AB and THFBH2Ph are formed as main products via the intermolecular NH3–THF exchange reaction. However, if R is Cl, then NH3BH2Cl reacts with THFBH3 through reversible intermolecular Cl–H exchange mechanism. Furthermore, DFT calculations are performed to elucidate the formation mechanism of THFBH(Me)(µ‐NH2)BH3 via the reaction of NH3BH2Me and THFBH3 as well as the exchange mechanism of Cl–H in the reaction of NH3BH2Cl and THFBH3.

Crystal structure, spectroscopic characterization, DFT computations and molecular docking study of a synthesized Zn(II) complex

The Zn(II) complex, dichloro[N-hydroxy-1,1-di(2-pyridinyl)methanimine]zinc(II), was synthesized from the reaction between ZnCl2 and di-2-pyridylketone oxime. The structural and spectral characterizations were performed by using single crystal X-ray diffraction, FT-IR, Laser-Raman, NMR and UV–Vis spectroscopic techniques. To support experimental evidences, computational results were obtained with the DFT/B3LYP method using the 6-311++G(d,p)+LanL2DZ mixed basis set. Theoretical analyses of some structural and spectroscopic results of effects of intermolecular Cl···H interactions in the crystal packing of the Zn(II) complex were investigated with the mentioned computational level. The non-bonding interactions in the experimental crystal packing of the complex were examined by Hirshfeld surface analysis. The HOMO and LUMO analyses were used for investigation of electronic transitions obtained with UV–Vis spectroscopy. NBO analyses were used to investigate the hyperconjugation interactions between donor and acceptor groups, coordination environment, electronic configuration and electron numbers of the Zn(II) metal ion and the natural atomic charges of the complex. The nucleophilic and electrophilic reactive sites of the complex were studied by MEP surface analysis. The static polarizabilities (α) and static hyperpolarizabilities (β) were analyzed theoretically to characterize NLO profile of the complex. The interaction with A-DNA (PDB ID: 1ZF6) of the Zn(II) complex was investigated with a molecular docking study.

A heuristic approach to evaluate peri interactions versus intermolecular interactions in an overcrowded naphthalene.

Octachloronaphthalene (OCN), a serious environmental pollutant, has been investigated by charge density analysis to unravel several unexplored factors responsible for steric overcrowding. The topological features of the enigmatic peri interactions contributing to steric overcrowding are qualified and quantified from experimental and theoretical charge-density studies. A new facet in the fundamental understanding of peri interactions is revealed by NCI (non-covalent interaction) analysis. The potential role of these interactions in deforming the molecular geometry and subsequent effect on aromaticity are substantiated from NICS (Nuclear Independent Chemical Shift) and QTAIM (Quantum Theory of Atoms in Molecules) calculations. The eye-catching dissimilarity in the out-of-plane twisting of OCN renders the molecule in an asymmetric geometry in the crystalline phase compared with symmetric geometry in the optimized solvated phase. This is uniquely characterized by their molecular electrostatic potential (MESP), respectively, and is explained in terms of conflict between two opposing forces - peri interactions, and symbiotic intermolecular Cl⋯Cl and Cl⋯π contacts.

Vibrational spectra and molecular structure of isomeric 1-(adamantan-1-ylcarbonyl)-3-(dichlorophenyl)thioureas

1-(adamantan-1-ylcarbonyl)-3-(2,3-dichlorophenyl)thiourea, 1, and 1-(adamantan-1-ylcarbonyl)-3-(2,5-dichlorophenyl)thiourea, 2, were synthesized in reasonable yields from admanantyl-1-carbonyl chloride and ammonium thiocyanate followed by treatment of the resulting adamantane-1-carbonylisothiocyanate with the 2,3- and 2,5-dichloroanilines. A complete vibrational analysis was performed on the basis of FTIR and Raman spectra. The formation of intramolecular NH⋯O and intermolecular NH⋯S hydrogen bonds in the solids affect vibrational modes, with low frequency values observed for the ν(CO) and ν(CS) stretching modes. Structural data obtained by single-crystal X-ray diffraction at low temperature confirm this picture. Compound 1 crystallizes in the triclinic system and compound 2 crystallizes with two unique molecules in the asymmetric unit of the orthorhombic unit cell. The molecular structures reveal that the carbonylthiourea units in 1 and both molecules of 2 are planar due in part to the formation of intramolecular NH⋯OC hydrogen bonds that generate S (6) rings. Moreover, the crystal structures are stabilized by an extensive series of classical and non-classical hydrogen bonds and, in the case of 1 by an intermolecular Cl⋯Cl halogen bond.

Trigonal Bipyramid Ni3Cl3O2 Cluster Showing the High-Spin S = 3 Ground State with Uniaxial Magnetic Anisotropy

Abstract We have prepared a novel nickel(II) trinuclear compound [Ni3(tmen)3(µ2-Cl)3(µ3-OMe)(µ3-OH)](BPh4)·0.5MeOH·0.5CH2Cl2 (1; tmen: N,N,N′,N′-tetramethylethylenediamine) with a trigonal bipyramid molecular structure, where the basal plane consists of Ni3(µ2-Cl)3 atoms. Two known compounds [Ni3(tmen)3X4(OH)]X (X = Cl (2), Br (3)) were also investigated. Magnetic study clarified the ground high-spin (S = 3) state, and the intramolecular exchange coupling parameters were determined as 2J/kB = 18.0 ± 0.2, 27.2 ± 0.2, and 19.6 ± 0.2 K for 1, 2, and 3, respectively. Crystallographic analysis clarified the unique geometry of 1. The molecular axes are aligned almost parallel in the crystallographic b axis. Relatively short intermolecular Cl···Cl distances (3.725(1) and 3.847(2) Å) are found among linearly arrayed complex ions. A single-crystal magnetic study gave a zero-field-splitting parameter DS=3/kB = −2.2 ± 0.1 K. An intermolecular exchange coupling parameter was determined as 2j/kB = −0.15 ± 0.01 K from simulation. A pulsed-field magnetization study at 0.5 K for 1 showed a jump around 1.2 T, which is explained in terms of intermolecular interaction. Alternating current magnetic susceptibility measurements revealed the Arrhenius behavior with Ea = 10.1 ± 0.8 K at zero bias field. Therefore, the magnetic properties of 1 can be understood as an antiferromagnetic chain made of potential single-molecule magnets.

Crystal structure of ethyl 2-amino-4-(4-chloro-phen-yl)-4H-1-benzothieno[3,2-b]pyran-3-carboxyl-ate.

The title compound, C20H16ClNO3S, is built up from three fused rings, one five- and two six-membered rings, linked to a 3-eth­oxy­carbonyl group and to a 4-chloro­phenyl ring. The hydropyran ring has a flattened envelope conformation, with the C atom substituted by the 4-chloro­phenyl ring as the flap (displaced by 0.077 (2) Å from the plane through the other atoms). The fused three-ring system is quasi-planar (r.m.s. deviation = 0.057 Å), with the largest deviation from the mean plane being 0.106 (1) Å for the C atom substituted by the 4-chloro­phenyl ring. The 4-chloro­phenyl ring is approximately perpendicular to the mean plane of the fused ring system, as indicated by the dihedral angle of 77.32 (6)° between their mean planes. There is an intra­molecular N—H⋯O hydrogen bond forming an S(6) ring motif. In the crystal, mol­ecules are linked by pairs of N—H⋯O hydrogen bonds, forming inversion dimers with an R 2 2(12) ring motif. There are also short inter­molecular Cl⋯O inter­actions present [3.1226 (12) Å] between neighbouring mol­ecules.

"Hummingbird" behaviour of N-heterocyclic carbenes stabilises out-of-plane bonding of AuCl and CuCl units.

An N-heterocyclic carbene substituted by two expanded 9-ethyl-9-fluorenyl groups was shown to bind an AuCl unit in an unusual manner, namely with the AuX rod sitting out of the plane defined by the heterocyclic carbene unit. As shown by X-ray studies and DFT calculations, the observed large pitch angle (21°) arises from an easy displacement of the gold(I) atom away from the carbene lone-pair axis, combined with the stabilisation provided by weak CH⋅⋅⋅Au interactions involving aliphatic and aromatic H atoms of the NHC wingtips. Weak, intermolecular Cl⋅⋅⋅H bonds are likely to cooperate with the H⋅⋅⋅Au interactions to stabilise the out-of-plane conformation. A general belief until now was that tilt angles in NHC complexes arise mainly from steric effects within the first coordination sphere.

Nitrile-Halogen Interactions in Some Bridge-Flipped Isomeric Benzylideneanilines

We designate as "bridge-flipped isomers" those pairs of molecules that differ only in the orientation of a bridge of atoms linking two major molecular fragments: in benzylideneanilines, Ar-CH=N-Ar' vs. Ar-N=CH-Ar'; in phenylhydrazones, Ar-NH-N=CH-Ar' vs. Ar-CH=N-NH-Ar' (Ar = aryl). We use them as a context in which to evaluate the roles of molecular conformation, hydrogen bonding, space-filling requirements, and supramolecular synthons in establishing crystalline isomorphism or non-isomorphism. To examine nitrile-halogen and halogen-halogen interactions in solid isomeric benzylideneanilines, we have determined the structures of 2-cyanobenzylidene-2'-iodoaniline (I), 2-iodobenzylidene-2'-cyanoaniline (II), 2-cyanobenzylidene-2'-bromoaniline (III), 2-cyanobenzylidene-2'-chloroaniline (IV), and 2-chlorobenzylidene-2'-cyanoaniline (V) by single-crystal X-ray diffraction. I/II and IV/V are bridge-flipped isomeric pairs. I, III, and IV are isomorphous; the I/II and IV/V pairs are not. In I, III, and IV, translationally related molecules are linked into chains by C≡N···X contacts; no close X···X contacts occur. Although C≡N···X contacts between translationally related molecules define chains in II similar to those in I, III, and IV, and although II likewise lacks close X···X contacts, the molecular packing arrangements differ (monoclinic for I, III, and IV vs. triclinic for II). V in contrast assumes an orthorhombic structure from which the C≡N···X interaction is absent and which is isomorphous with 2-chlorobenzylidene-2'-chloroaniline (VI), the nitrile group of V exchanged for the aniline-side chlorine of VI, that chlorine atom in VI not involved in a close intermolecular Cl···Cl contact. Although neither C≡N···X nor X···X contacts result in isomorphous bridge-flipped isomers in the cases of I/II and IV/V, the C≡N···X contacts apparently play a major structure-defining role and supersede any potential X···X contacts in I-IV.

Crystal structure of triclopyr.

In the title compound {systematic name: 2-[(3,5,6-tri­chloro­pyridin-2-yl)­oxy]acetic acid}, the herbicide triclopyr, C7H4Cl3NO3, the asymmetric unit comprises two independent mol­ecules in which the dihedral angles between the mean plane of the carb­oxy­lic acid group and the pyridyl ring plane are 79.3 (6) and 83.8 (5)°. In the crystal, pairs of inter­molecular O—H⋯O hydrogen bonds form dimers through an R 2 2(8) ring motif and are extended into chains along [100] by weak π–π inter­actions [ring centroid separations = 3.799 (4) and 3.810 (4) Å]. In addition, short inter­molecular Cl⋯Cl contacts [3.458 (2) Å] connect the chains, yielding a two-dimensional architecture extending parallel to (020). The crystal studied was found to be non-merohedrally twinned with the minor component being 0.175 (4).

Chlorine aggregation in the supramolecular structure of chlorobenzene-o-chlorotoluene solutions

An analysis of the concentration dependences of the molecular light scattering parameters in chlorobenzene-o-chlorotoluene solutions shows that the entire concentration range can be split into three intervals with different structural features: 0–0.2 ppm, 0.2–0.9 ppm, and 0.9–1 ppm chlorobenzene. The features are manifest in physicochemical properties such as sound velocity and excess molar volume, adiabatic compressibility, and molar refraction. Experimental data are compared with those obtained by molecular dynamics simulation. It is concluded that the chlorobenzene structure is determined by Cl…Cl interactions while the structuring of liquid o-chlorotoluene and its solutions is largely determined by intermolecular Cl…Me interactions.

4-Chloro-3-ethylphenol

The title compound, C8H9ClO, packs with two independent mol­ecules in the asymmetric unit, without significant differences in corresponding bond lengths and angles, with the ethyl group in each oriented nearly perpendicular to the aromatic ring having ring-to-side chain torsion angles of 81.14 (18) and −81.06 (19)°. In the crystal, mol­ecules form an O—H⋯O hydrogen-bonded chain extending along the b-axis direction, through the phenol groups in which the H atoms are disordered. These chains pack together in the solid state, giving a sheet lying parallel to (001), via an offset face-to-face π-stacking inter­action characterized by a centroid–centroid distance of 3.580 (1) Å, together with a short inter­molecular Cl⋯Cl contact [3.412 (1) Å].

Synthesis, crystal structure and spectroscopic characterization of a new organic bismuthate (III) [C9H28N4][Bi2Cl10].H2O

The chemical preparation, crystal structure and spectroscopic characterization of [C9H28N4][Bi2Cl10].H2O have been reported. This compound crystallizes in the monoclinic system in space group P21/c and cell parameters a = 12.2385 (6), b = 17.3062 (7), c = 13.0772 (6) Å, β = 104.475 (5)°, Z = 4 and V = 2681.9 (2) Å3. Its crystal structure has been determined and refined to R = 0.049, using 5848 independent reflections. The atomic arrangement can be described by an alternation of organic and inorganic layers. The inorganic layer built up of [Bi2Cl10]4– bioctahedra arranged in sandwich between the organic layer. The organic groups are interconnected by the water molecules through N-H…O(W) hydrogen bonds to form infinite zig-zag chains spreading along the b-axis. These Chains are themselves interconnected by means of the N–H…Cl hydrogen bonds originating from [Bi2Cl10]4– anions, to form a three-dimensional network. Intermolecular Cl…Cl interactions between adjacent dimeric [Bi2Cl10]4– anions have been observed. The compound was also characterized by FT-IR and Raman spectrscopies.

Bis(2,3-di-chloro-phen-yl) di-sulfide.

The title compound, C12H6Cl4S2, features an S—S bond [2.0252 (8) Å] that bridges two 2,3-di­chloro­phenyl rings with a C—S—S—C torsion angle of 88.35 (11)°. The benzene rings are normal one to the other with a dihedral angle of 89.83 (11)°. The crystal structure features inter­molecular Cl⋯Cl [3.4763 (11) Å] and π–π stacking inter­actions [centroid–centroid distances = 3.696 (1) and 3.641 (2) Å]. Intra­molecular C—H⋯S inter­actions are also observed.

2-[(E)-(4-Bromo-phenyl)imino-methyl]-4-chloro-phenol.

In the title compound, C13H9BrClNO, the dihedral angle between the substituted benzene rings is 44.25 (11)°. There are strong intra­molecular O—H⋯N hydrogen bonds, which generate S(6) rings, and also inter­molecular Cl⋯Cl [3.431 (3) Å] and Br⋯ Br [3.846 (1) Å] contacts. The crystal packing a C—H⋯O and C—H⋯π inter­actions.

Cl···Cl Interactions in Molecular Crystals: Insights from the Theoretical Charge Density Analysis

The structure, IR harmonic frequencies and intensities of normal vibrations of 20 molecular crystals with the X-Cl···Cl-X contacts of different types, where X = C, Cl, and F and the Cl···Cl distance varying from ~3.0 to ~4.0 Å, are computed using the solid-state DFT method. The obtained crystalline wave functions have been further used to define and describe quantitatively the Cl···Cl interactions via the electron-density features at the Cl···Cl bond critical points. We found that the electron-density at the bond critical point is almost independent of the particular type of the contact or hybridization of the ipso carbon atom. The energy of Cl···Cl interactions, E(int), is evaluated from the linking E(int) and local electronic kinetic energy density at the Cl···Cl bond critical points. E(int) varies from 2 to 12 kJ/mol. The applicability of the geometrical criterion for the detection of the Cl···Cl interactions in crystals with two or more intermolecular Cl···Cl contacts for the unique chlorine atom is not straightforward. The detection of these interactions in such crystals may be done by the quantum-topological analysis of the periodic electron density.