Short Intermolecular Contacts Research Articles

Bonds or not bonds? Pancake bonding in 1,2,3,5-dithiadiazolyl and 1,2,3,5-diselenadiazolyl radical dimers and their derivatives

Unusually long bonds or short intermolecular contacts occur in the title compounds reminiscent of pancake bonding. Pancake bonding interactions seem analogous to π-stacking interactions, but they display much shorter contact distances than normally seen in van der Waals (vdW) dimers. The interpretation of these SN and SeN containing structures has been an outstanding challenge for some time. The antibonding (π*) singly occupied molecular orbital (SOMO) of the radical is the source of two-electron multicenter bonding (2e/mc). Preferred conformations thus can be traced back to SOMO-SOMO overlap. We used several computational methods to understand the nature of pancake bonding in the title compounds including four wave function methods (WFT) and a dozen density functional theories (DFT) including empirical dispersion corrections. We used experimental data and high level CCSD(T)/6-311++G(d,p) and MRPT2/6-311++G(d,p) calculations for comparison. The analysis provided the interpretation a wealth of experimental data including conformational preferences of these SN and SeN containing radical dimers leading to a better overall understanding of pancake bonding. Analysis of the various components of the inter-radical interactions showed that SOMO-SOMO bonding interaction and dispersion interaction contribute to the binding energy and neither of these interactions alone is sufficient to bind the dimer. The dimer is predicted to show weak diradical character.

4-Allyl-2-methoxyphenyl 3,4-dichlorobenzenesulfonate

The title compound, C16H14Cl2O4S, was obtained by the reaction of eugenol (4-allyl-2-meth­oxy­phenol) and 3,4-dichloro­benzene­sulfonyl chloride. The dihedral angle between the benzene rings in the mol­ecule is 40.53 (4)°. No significantly short inter­molecular contacts are observed in the crystal structure.

Synthesis, spectroscopic and structural characterization of novel interaction product of 5-trifluoromethyl-pyridine-2-thione with iodine

Abstract The behavior of 5-trifluoromethyl-pyridine-2-thione, which is a potential antithyroid drug, toward molecular iodine was investigated. The formation of the n–σ* complex of 5-trifluoromethyl-pyridine-2-thione with molecular iodine of the composition C6H4F3NS·I2 in dilute chloroform solutions was studied by UV-spectroscopy. The crystal structure of the new salt bis(5-trifluoromethyl-pyridine-2-ylthio)iodonium triiodide determined by X-ray diffraction and consists of separated, perfectly linear, centrosymmetrical anions I 3 - and cationic moieties (C6H3F3NS)2I+ containing the almost linear S–I+–S linker. Iodonium cations are linked to dimers through the I(4)–I(5)–I(4′) anion by means of N-H⋯I, C–H⋯I hydrogen bonds (N(1)–H(1А)⋯I(4) 3.11 A, N(2)–H(2B)⋯I(4) 2.99 A, C(5)–H(5A)⋯I(5) 3.05 A), interatomic distance I(1)⋯I(4) 4.2040(7) A. These dimers are linked into layers parallel to the ab0 plane by short intermolecular contacts I(1 M)⋯S(1) 3.850(2) A, I(1)⋯I(1 M) 3.9326(8) A.

Synthesis, Structure, and Magnetic Properties of Three 1D Chain Complexes Based on High-Spin Metal–Cyanide Clusters: [MnIII6MIII] (M = Cr, Fe, Co)

On the basis of high-spin metal-cyanide clusters of Mn(III)(6)M(III) (M = Cr, Fe, Co), three one-dimensional (1D) chain complexes, [Mn(salen)](6)[Cr(CN)(6)](2)·6CH(3)OH·H(2)O (1), [Mn(5-CH(3))salen)](6)[Fe(CN)(6)](2)·2CH(3)CN·10H(2)O (2), and [Mn(5-CH(3))salen)](6)[Co(CN)(6)](2)·2CH(3)CN·10H(2)O (3) [salen = N,N'-ethylenebis(salicylideneiminato) dianion], have been synthesized and characterized structurally as well as magnetically. Complexes 2 and 3 are isomorphic but slightly different from complex 1. All three complexes contain a 1D chain structure which is comprised of alternating high-spin metal-cyanide clusters of [Mn(6)M](3+) and a bridging group [M(CN)(6)](3-) in the trans mode. Furthermore, the three complexes all exhibit extended 3D supramolecular networks originating from short intermolecular contacts. Magnetic investigation indicates that the coupling mechanisms are intrachain antiferromagnetic interactions for 1 and ferromagnetic interactions for 2, respectively. Complex 3 is a magnetic dilute system due to the diamagnetic nature of Co(III). Further magnetic investigations show that complexes 1 and 2 are dominated by the 3D antiferromagnetic ordering with T(N) = 7.2 K for 1 and 9.5 K for 2. It is worth noting that the weak frequency-dependent phenomenon of AC susceptibilities was observed in the low-temperature region in both 1 and 2, suggesting the presence of slow magnetic relaxations.

2-Methyl-5-nitro-1H-benzimidazole monohydrate

In the title compound, C8H7N3O2·H2O, the 2-methyl-5-nitro-1H-benzimidazole mol­ecule, excluding the methyl H atoms, is approximately planar, with a maximum deviation of 0.137 (1) Å. The crystal structure is stabilized by water mol­ecules via N—H⋯O(water), O(water)—H⋯O and O(water)—H⋯N hydrogen bonds, forming sheets parallel to the (100) plane. A short inter­molecular contact between the benzene and imidazole rings, with a centroid–centroid distance of 3.6419 (10) Å, indicates a π–π inter­action.

Synthesis and Structures of 1′,2′,3′,4′,5′-Pentamethylazaferrocene Complexes with Lewis Acidic Boranes

The syntheses, X-ray crystal structures, and electrochemistry of BH3 (2) and BF3 (3) adducts of 1′,2′,3′,4′,5′-pentamethylazaferrocene (1) are reported, together with an improved synthesis, an X-ray crystal structure and the electrochemistry of the known compound, 1. 13C NMR data reveal a similiar dependence of chemical shift on nitrogen lone-pair coordination to that seen for heteroarene analogs. X-ray structural data for 1−3 reveal subtle changes in the binding of the pyrrolyl ring to iron in the Lewis Acid adducts, and intersting short intermolecular contacts in the case of 1 and 3. In cyclic voltammetry studies, 1 displays a reversible metal-based oxidation allowing estimation of the effect of N for −CH− substitution in the oxidation potential of azaferrocenes as compared to ferrocenes. 2 and 3 do not show reversible electrochemistry.

Enantiomeric crystallization of (±)-trans-1,2-diaminocyclohexane under pressure

The isothermal and isochoric crystallizations of (±)-trans-1,2-diaminocyclohexane, C6H10(NH2)2, (±)-DACH, yield enantiomeric conglomerates of orthorhombic symmetry, space groupP21212, the same as obtained by isobaric crystallization. Despite the compression to 73% of ambient pressure volume, no racemic compound of DACH was formed. This contradicts for this compound the possibility of reverse causality between density and preferred enantiomorphic/racemic crystallization in Wallach's rule. The crystal structures have been determined at 0.36, 0.52, 0.65, 1.19 and 2.04 GPa at 296 K by single-crystal X-ray diffraction. It has been established that the enantiomeric-conglomerate crystallization of DACH at ambient pressure is mainly due to the molecular arrangement, governed by the close-packing rule in the crystal. High pressure enhances the close packing, and it does not change the course of crystallization of (±)-DACH. The shortest intermolecular contacts, NH⋯N and CH⋯N, become most compressed between 0.36 and 2.04 GPa, indicating that such weak hydrogen bonds are enhanced by pressure. The phase diagram of (±)-DACH has been outlined to 2.04 GPa.

Complete and incomplete spin transitions in 1D chain iron(ii) compounds

The synthesis and characterisation of two new octahedral iron(II) SCO coordination polymers [FeL1(bimm)] (1) and [FeL2(bppa)](MeOH)0.5 (2) (L1 = [3,3′]-[1,2-phenylenebis(iminomethylidyne)bis(4-phenyl-2,4-butanedionato)(2-)-N,N′,O2,O2′], L2 = [E,E]-[{diethyl 2,2′-1,2-phenylenebis(iminomethylidyne)bis(3-oxo-3-phenylpropanato)}(2-)-N,N′,O3,O3′], bimm = bis(1H-imidazol-1-yl)methane and bppa = 1,3-bis(pyridine-4-yl)propane) is presented. Results from X-ray structure analysis at different temperatures revealed in the case of 1 that the transition from a gradual to a cooperative SCO with a 5 K wide hysteresis is due to an increase of the short intermolecular contacts, which exceed a certain threshold for the cooperative effect. In the case of compound 2 an incomplete spin transition with a 4 K wide hysteresis was observed. The low temperature χMT product remains constant at a value typical for a mixed HS/LS state in stepwise spin transitions. A quantitative correlation between the cooperative effects of 12 monomer and polymer iron(II) SCO complexes and their structural properties derived from X-ray structure analysis, the so-called crystal contact index, CCI, is introduced.

2,9-Bis(3,5-dimethyl-1H-pyrazol-1-yl-κN2)-1,10-phenanthroline-κ2N,N′]bis(thiocyanato-κN)cadmium(II)

In the title complex, [Cd(NCS)2(C22H20N6)], the CdII ion is in a CdN6 coordination geometry which is inter­mediate between octa­hedral and trigonal–prismatic. The dihedral angles formed between the mean planes of the pyrazole rings and the phenanthroline system are 15.74 (15) and 16.30 (13)°. In the crystal, there is a π–π stacking inter­action involving two symmetry-related pyrazole rings, with a centroid–centroid distance of 3.664 (3) Å. In addition, there is a relatively short inter­molecular contact between C atoms [C⋯C = 3.399 (6) Å] involving symmetry-related pyridine rings along the a axis.

Very strong centrosymmetric [O...H...O]+ and asymmetric [O-H...O]+ hydrogen bonds in a new POM-Based hybrid material

A specific assembly process, driven by coexisting X-H...O hydrogen bonding and X...O short intermolecular contacts (X = C, N, O) is described, in which the pseudo-Keggin polyoxoanion and two types of molecule...cation pairs (with C1 and Ci symmetries) were assembled to the programmed supramolecular architecture. Cooperation of the positive-charge, resonance effect and the O=C...Oterminal intermolecular contact led to the short and strong symmetrical [O...H...O]+ hydrogen bond (O...O = 2.449(13) A) in one of the molecule...cation pairs [C4H9NO...H...ONC4H9]+ with the H-bonded proton in the center of inversion. The other [C4H9NOH...ONC4H9]+ molecule...cation pair (non-centrosymmetric) was formed through a very strong asymmetric [O.H.O]+ hydrogen bond of 2.431(13) A in length which was created via the synergistic effect between the minor N-H...O secondary interaction, +CAHB (positive-charge-assisted hydrogen bond) and RAHB (resonance assisted hydrogen bond) mechanisms.

ChemInform Abstract: X-Ray Diffraction Study of the Electronic Ground State of (meso- Tetraphenylporphinato)iron(II).

The charge distribution in crystalline (meso-tetraphenylporphinato)iron(II) has been derived from 10,154 intensity data measured at 120 (5) K. Crystal data are a = 14.992 (2), {angstrom}, c = 13.778 {angstrom}, Z = 4, space group I{bar 4}2d. The data have been analyzed with the aspherical-atom multipole formalism including anharmonic thermal parameters for the iron atom. The deformation density maps indicate preferential occupancy of the d{sub z}2 and d{sub xy} orbitals of the iron atom, a conclusion confirmed by the d-orbital populations derived from the aspherical-atom multipole refinement. The results are in agreement with an SCF-CI calculation by Rohmer and an INDO-CI calculation by Edwards, Weiner, and Zerner and supports the {sup 3}H{sub 2g} state as the leading contributor to the ground state of the complex. The ground-state assignment is in contrast to results on the intermediate spin complex iron(II) phthalocyanine, for which the electron density indicates a {sup 3}E{sub g} ground state. The difference is attributed to the effect of short intermolecular Fe-N contacts in crystalline iron(II) phthalocyanine on the relative order of closely spaced energy levels.

1-[2-(3,5-Difluorobenzyloxy)phenyl]ethanone

In the title compound, C15H12F2O2, the dihedral angle between the aromatic rings is 70.43 (4)°. The crystal packing exhibits no significantly short inter­molecular contacts.

Ethyl 2-{3-[(2-chloro-1,3-thiazol-5-yl)methyl]-4-nitroimino-1,3,5-triazinan-1-yl}acetate

In the title compound, C11H15ClN6O4S, which belongs to the neonicotinoid class of insecticidally active heterocyclic compounds, the six-membered triazine ring adopts an opened envolope conformation. The planar nitro imine group [dihedral angle between nitro and imine groups = 1.07 (7)°] and the thia­zole ring are oriented at a dihedral angle of 69.62 (8)°. A classical intra­molecular N—H⋯O hydrogen bond is found in the mol­ecular structure. Moreover, one classical inter­molecular N—H⋯N and four non-classical C—H⋯O and C—H⋯N hydrogen bonds are also present in the crystal structure. Besides inter­molecular hydrogen bonds, the Cl atom forms an inter­molecular short contact [3.020 (2) Å] with one of the nitro O atoms.

Using the nitro group to induce π-stacking in terthiophenes

A new synthetic route to mononitrated oligothiophenes is described, as well as the preparation of halogenated derivatives (Br, I) thereof. An unusual deep red colour is observed and explained, with the aid of DFT calculations, as arising from a significant quinoidal contribution to the molecular structure. The crystal structures of two compounds, H(C4H2S)3NO2 and Br(C4H2S)3NO2, are presented. Both compounds have planar sheets held together by intermolecular short contacts (hydrogen bonds and, for the latter, NO2···Br interactions); the sheets do not directly superimpose, so the effect of the π-stacking is not maximized. Solid-state fluorescence and extended-Hückel band-structure calculations are also presented for these materials.

Helicene and Double Helicene

A high-yield synthesis of three ­novel helicene compounds (3, 5 and 6) was developed. X-ray single-crystal structure analysis revealed multiple intermolecular short contacts and UV/Vis spectra indicate significant π-delocalization in double helicene 6, indicating potential in organic functional materials.

Selected AChE reactivators in different crystalline environment: salts and enzyme

The investigation of relationships between the molecular structure of the compounds capable to reactivate acetylcholinesterase (AChE) inhibited by organophosphorus toxins, such as nerve agents and pesticides, is an important step toward synthesis of more efficient antidota. In the present article, we describe the crystal structures of two new AChE reactivators, which are bromides of (E)-1,4-bis(4-hydroxyiminomethylpyridinium)-but-2-ene (K075) and of 4,4′-bis(hydroxyiminomethyl)-1,1′-(1,4-phenylenedimethyl)-bispyridinium (K114). Their molecular geometry and intermolecular interactions in the crystalline state are compared to those in the crystal structures of the well-known AChE reactivators, obidoxime, and TMB-4. Inspection of hydrogen bonds and other short intermolecular contacts in the crystalline AChE–obidoxime complex revealed their similarity to those observed in the crystal structures of K075 and K114.

1-[4-(3-Chloropropoxy)-2-hydroxyphenyl]ethanone

The title compound, C11H13ClO3, has been obtained in the reaction of 2, 4-dihydroxy­lacetonephenone, potassium carbonate and 1-bromo-3-chloro-hexane. The hydr­oxy group is involved in an intra­molecular O—H⋯O hydrogen bond. The crystal packing exhibits no significantly short inter­molecular contacts

(1R,3S)-Methyl 2-benzyl-6,7-dimethoxy-1-phenyl-1,2,3,4-tetrahydroisoquinoline-3-carboxylate

In the title compound, C26H27NO4, a precursor to novel chiral catalysts, the N-containing six-membered ring assumes a half-boat conformation. Various C—H⋯π interactions and intermolecular short contacts (C⋯H = 2.81–2.90 Å) link the mol­ecules together in the crystal structure.

(3R*)-Methyl 3-[(2S*)-4,6-dimethoxy-2-(4-methoxyphenyl)-3-oxo-2,3-dihydro-1-benzofuran-2-yl]-2-methoxycarbonyl-3-phenylpropionate

The title compound, C29H28O9, was isolated from the reaction of 4,6-dimeth­oxy-2-(4-methoxy­phen­yl)-3-benzofuran and α-methoxy­carbonyl­cinnaminate. The two aromatic rings form a dihedral angle of 22.7 (1)°. One methoxy­carbonyl group is disordered between two orientations in a 0.612 (4):0.388 (4) ratio. The crystal structure exhibits no significantly short inter­molecular contacts.

Bis[(18-crown-6-κ6O)sodium] (18-crown-6-1κ6O)-μ-thiocyanato-1:2κ2S:N-pentathiocyanato-2κ5N-indate(III)sodium 1,2-dichloroethane sesquisolvate

The title complex, [Na(C12H24O6)]2[InNa(NCS)6(C12H24O6)]·1.5C2H4Cl2, has been synthesized by the reaction of 18-crown-6 with InCl3 and NaSCN. The In atom has a six-coordinate octa­hedral environment, being bonded to the N atoms of six thio­cyanate groups. The bond lengths and angles show normal values. The crystal packing exhibits no significantly short inter­molecular contacts.