Short Intermolecular Contacts Research Articles

Syntheses, Crystal Structures, and Magnetic Properties of Four New Cyano-Bridged Bimetallic Complexes Based on the mer-[FeIII(qcq)(CN)3]− Building Block

Four new cyano-bridged bimetallic complexes, [{Mn(III)(salen)}2{Fe(III)(qcq)(CN)3}2]n·3nCH3CN·nH2O (1) [salen = N,N'-ethylenebis(salicylideneiminato) dianion; qcq(-) = 8-(2-quinoline-2-carboxamido)quinoline anion], [{Mn(III)(salpn)}2{Fe(III)(qcq)(CN)3}2]n·4nH2O (2) [salpn = N,N'-1,2-propylenebis(salicylideneiminato)dianion], [{Mn(II)(bipy)(CH3OH)}{Fe(III)(qcq)(CN)3}2]2·2H2O·2CH3OH (3) (bipy = 2,2'-bipyridine), and [{Mn(II)(phen)2}{Fe(III)(qcq)(CN)3}2]·CH3CN·2H2O (4) (phen = 1,10-phenanthroline) have been synthesized and characterized both structurally and magnetically. The structures of 1 and 2 are both unique 1-D linear branch chains with additional structural units of {Mn(III)(salen/salpn)}{Fe(III)(qcq)(CN)3} dangling on the sides. In contrast, 3 and 4 are cyano-bridged bimetallic hexanuclear and trinuclear clusters, respectively. The intermolecular short contacts such as π-π interactions and hydrogen bonds extend 1-4 into high dimensional supermolecular networks. Magnetic investigation reveals the dominant intramolecular antiferromagnetic interactions in 1, 3, and 4, while ferromagnetic and antiferromagnetic interactions coexist in 2. Alternating current measurement at low temperature indicates the existence of slow magnetic relaxation in 1 and 2, which should be due to the single ion anisotropy of Mn(III).

1,4-Bis(hexyloxy)benzene

The asymmetric unit of the title compound, C18H30O2, contains one half-mol­ecule situated on an inversion center. The alkyl chain adopts a fully extended all-trans conformation. The C atoms of the alkyl chain are almost coplanar, with a maximum deviation of 0.042 (6) Å from the mean plane,which is inclined to the central benzene ring by 6.80 (9)°. The crystal packing exhibits no short inter­molecular contacts.

Hirshfeld surface analysis of new organotin(IV)-phosphoramide complexes

Hirshfeld surfaces and two-dimensional fingerprint plots are used to study short intermolecular contacts in new organotin(IV)-phosphoramide complexes, (L1)2Cl2Me2Sn (1), (L2)Cl2Me2Sn (2) and (L3)2Cl2Me2Sn (3) [L1 = (C5H9NH)3PO, L2 = [(CH3)3CNH][C6H5CH2N(CH3)]2PO and L3 = (3-F-C6H4C(O)NH)(N(CH3)C6H11)2PO]. The previously reported structure L3 is also analyzed for a comparison with the related complex, 3. While 2 and 3, respectively, contain one independent molecule and one-half of a molecule, the asymmetric unit of 1 is composed of three independent molecules with different conformations of ligands around the tin center but with very similar Hirshfeld surfaces and fingerprint plots. The SnIV coordination geometries are octahedral for 1 and 3 with cis-phosphoramides in each independent molecule of 1 and trans-phosphoramides in 3. For 2, the SnIV adopts a distorted trigonal bipyramidal environment with the axial positions occupied by the ligand phosphoramide and one Cl atom. Two-dimensional fingerprint plots of 1 and 2 show pairs of spikes attributed to the intermolecular H⋯Cl contacts including N–H⋯Cl hydrogen bonds. Two spikes found in 3 are much shorter comparing with 1 and 2 due to absence of the intermolecular N–H⋯Cl hydrogen bond and lower contribution of C–H⋯Cl contacts. In the ligand L3 the presence of N–H⋯OP hydrogen bond is reflected as a deep-red area of Hirshfeld surfaces. Moreover, in fingerprint plot of L3 two intense spikes are observed related to the intermolecular H⋯O contacts including N–H⋯OP hydrogen bond. The more shallow red spots on the Hirshfeld surface of 3 with respect to L3 are caused by absence of N–H⋯O hydrogen bond and the lower contribution of H⋯O contacts.

C6H4S2AsCl: description and interpretation of an incommensurately modulated molecular crystal structure

Crystals of 2-chloro-benzo-1,3,2-dithiarsole have a strongly modulated structure that can be solved and refined with relative ease in a P(1), Z' = 17 approximate supercell but that is better described as incommensurate. Two conventional refinements (different superstructure approximations that differ in the placement of their crystallographic inversion centers) and a (3 + 1)-dimensional superspace refinement are all nearly equally successful, at least as measured by the usual agreement factors; the data integration, however, shows that the incommensurate description is preferable. The overall packing is determined by the stacking of the aromatic rings and probably by the segregation of As and Cl atoms to give short As...Cl contacts. A refinement of the average (Z' = 1) structure shows that there are two basic orientations of the C6S2 plane, but that those orientations must be correlated in several directions to avoid impossibly short intermolecular contacts. Along the modulation vector q the orientation of the C6S2 plane varies smoothly, but q is not a direction in which the molecules are in contact. Along the directions in which the molecules are in contact the orientation of the C6S2 plane alternates; there are also positional shifts. The single modulation q relieves packing problems in several different directions well enough that crystals that diffract well can be grown.

Advances in Charge Carrier Mobilities of Semiconducting Polymers Used in Organic Transistors

In this review, we describe and discuss recent advances in the performance of polymeric semiconductors in organic field effect transistors (OFETs). Design concepts such as short intermolecular contacts, low conformational disorder, side chain optimization, and noncovalent interactions have all been successfully employed to improve the charge carrier mobility of polymer thin films. The relationship between the molecular design, thin film microstructure, and electrical performance has been exemplified by a range of thiophene, bridged and fused ring, diketopyrrolopyrrole (DPP), and isoindigo containing polymers which are reviewed and discussed.

Charge density distribution and the electrostatic moments of CTPB in the active site of p300 enzyme: A DFT and charge density study

A molecular docking and charge density analysis have been carried out to understand the conformational change, charge distribution and electrostatic properties of N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-6-pentadecyl-benzamide (CTPB) in the active site of p300. The nearest neighbors, shortest intermolecular contacts between CTPB-p300 and the lowest binding energy of CTPB have been analyzed from the docking analysis. Further, a charge density analysis has been carried out for the molecule in gas phase and for the corresponding molecule lifted from the active site of p300. Due to the intermolecular interaction between CTPB and the amino acids of active site, the conformation of the CTPB has been significantly altered (particularly the pentadecyl chain). CTPB forms strong interaction with the amino acid residues Tyr1397 and Trp1436 at the distance 2.12 and 2.72Å, respectively. However, the long pentadecyl alkyl chain of CTPB produces a barrier and reducing the chance of forming hydrogen bonding with p300. The electron density ρbcp(r) of the polar bonds (C–O, C–N, C–F and C–Cl) of CTPB are increased when it present in the active site. The dipole moment of CTPB in the active site is significantly less (5.73D) when compared with the gas phase (8.16D) form. In the gas phase structure, a large region of negative electrostatic potential (ESP) is found at the vicinity of O(2) and CF3 group, which is less around the O(1) atom. Whereas, in the active site, the negative ESP around the CF3 group is decreased and increased at the O(1) and O(2)-atoms. The ESP modifications of CTPB in the active site are mainly attributed to the effect of intermolecular interaction. The gas phase and active site study insights the molecular flexibility and the electrostatic properties of CTPB in the active site.

Hirshfeld surface analysis of new phosphoramidates

Hirshfeld surfaces and two-dimensional fingerprint plots are used to visualize and analyze intermolecular interactions in six new phosphoramidate structures, [2,6-F2-C6H3C(O)NH]P(O)[X]2 {X = N(C2H5)2 (1), [X]2 = NHCH2C(CH3)2CH2NH and with one CH3OH solvated molecule (2)}, [C6H5O]2P(O)Y [Y = NC4H8O (3), NHC6H4(3-Br) (4)] and [Z]2P(O)OP(O)[Z]2 [Z = N(CH3)(CH2C6H5) (5), NHC6H4(4-CH3) (6)]. Study of the short intermolecular contacts in structures (1)-(6) by Hirshfeld surfaces demonstrate that the O atom of P=O is a better H-atom acceptor than the O atom of C=O for (1) and (2), and also relative to the O atom of the C6H5O group for (3) and (4), and relative to the bridge O atom of the P(O)OP(O) segment for (5) and (6). The results confirm that the crystal packing is related to the kind of substituent linked to the P atom. Compounds (1), (2), (4) and (6), with characteristic N-H···O hydrogen bonds, show a pair of intense spikes (including the intermolecular H···O contacts) in the fingerprint plots, summarizing the major features of each structure in the related two-dimensional plot. For (3) and (5), without any N-H unit, the two short spikes are observed for (3) but are absent for (5). The upper d(e) and d(i) values (distances to the Hirshfeld surfaces for the nearest atoms outside and inside) in the fingerprint plots are more compact in (3) than in (4), and in (5) than in (6), reflecting the more efficient packing in (3) and (5). The tertiary N atoms of (3) and (5) do not take part in any intermolecular contacts involving H atoms. Moreover, structures (3)-(6) show greater contribution from C···H contacts relative to O···H contacts. Finally, Hirshfeld surfaces and fingerprint plots are employed for a comparison of the two independent molecules in the asymmetric unit of (1) and also, for a comparison of (6), in the orthorhombic crystal system, with the previously reported monoclinic polymorph (Pourayoubi, Fadaei et al., 2012).

1,2-Bis{2-[(4-methoxybenzylidene)amino]phenyl}disulfane

The asymmetric unit of the title compound, C28H24N2O2S2, contains one-half mol­ecule, which is completed by twofold rotation symmetry with the twofold axis passing through the mid-point of the central S—S bond. The planes of the two benzene rings linked by the di­sulfide chain form a dihedral angle of 76.1 (1)°, while the planes of the two benzene rings in the benzyl­ideneaniline fragment form a dihedral angle of 48.9 (1)°. The crystal packing exhibits no significantly short inter­molecular contacts.

Molecular flexibility and the electrostatic moments of curcumin and its derivatives in the active site of p300: A theoretical charge density study

A molecular docking analysis and quantum chemical calculation coupled with the charge density analysis have been carried out to understand the conformational change, charge density distribution and the electrostatic properties of HAT inhibitors curcumin and its derivatives (cinnamoyl compounds) in the active site of p300. The nearest neighbours, the shortest intermolecular contacts between the inhibitors and receptor p300; their binding energies were calculated from molecular docking analysis. A high level quantum chemical calculations were performed using density functional theory (DFT-B3LYP) with the basis set 6-311G∗∗ combined with the theory of atoms in molecules (AIM) for the inhibitors in gas phase and in the active site of p300. It is observed that, when the molecules present in the active site of p300, relatively, their geometrical, bond topological and the electrostatic properties are significantly altered. The comparative study on the geometrical and electrostatic properties of these three inhibitors in gas phase and amino acid environment gives an insight on the molecular flexibility and the exact modification of electrostatic interaction of the inhibitor in the active site of p300. These fine details at electronic level allow to understand the exact drug–receptor interaction.

(1S,3R,8R,9S,11R)-2,2-Dibromo-10,10-dichloro-3,7,7,11-tetramethyltetracyclo[6.5.0.01,3.09,11]tridecane

The title compound, C17H24Br2Cl2, was synthesized from β-himachalene (3,5,5,9-tetra­methyl-2,4a,5,6,7,8-hexa­hydro-1H-benzo­cyclo­heptene), which was isolated from the essential oil of the Atlas cedar (Cedrus Atlantica). The mol­ecule contains fused six-, seven- and two three-membered rings. The six-membered ring has a half-chair conformation, while the seven-membered ring displays a boat conformation. The absolute structure was unambiguously established from anomalous dispersion effects. The crystal packing exhibits no short inter­molecular contacts.

(Z)-3β-(2-Chloroanilino)-17(20)-pregnene

In the pregnene fragment of the title compound, C27H38ClN, the three six-membered rings exhibit chair conformations and the five-membered ring has a distorted envelope form with the fused C atom not bearing a methyl group as the flap atom. The amino group is involved in the formation of an intra­molecular N—H⋯Cl hydrogen bond. The crystal packing exhibits no short inter­molecular contacts.

Structure of Dibenzoylbrowniine

The C19-norditerpenoid alkaloid 14-benzoylbrowniine that was isolated from Delphinium biternatum is known to exhibit valuable pharmacological properties [1]. It can be obtained from browniine (an alkaloid of the plants D. biternatum, D. corymbosum, D. iliense, D. rotundifolium, etc.) by benzoylation with benzoylchloride. In addition to it as the main product, the dibenzoyl derivative of browniine can also be produced. The structure 8,14-O,O -dibenzoylbrowniine was proposed based on PMR and mass spectra [2]. According to the chemical structure of browniine, the benzoylation reaction could occur at three positions of the carbon framework, which has a secondary and two tertiary hydroxyls. The question of which positions (C7, C8, or C14) were benzoylated was answered by us (in favor of C7 and C14) by performing an x-ray crystal structure analysis (XSA) of the reaction product. The C8 hydroxyl remained unaffected as a result of the reaction. The chemical formula and molecular structure of the alkaloid from the XSA are shown below (Fig. 1). All stereochemical issues of the synthesized molecule were resolved by the XSA. Figure 1 shows the established absolute configuration of the carbon skeleton. The hydroxymethyl group in the C1 position and the benzoyl group in the C14 position had the -orientation. The other hydroxyls in the C6, C7, C8, and C16 positions and the methoxymethyl in the C4 position had the -orientation. The hydroxyl O atom on C8 in dibenzoylbrowniine was simultaneously close to three O atoms, i.e., the carbonyl O of the C7 benzoyl group (distance O6...O5 3.018 A° ), the C6 methoxyl O (distance O6...O3 2.703 A° ), and the ester O of the second benzoyl group on C14 (distance O6...O7 2.898 A° ). The position of the H atom that was found experimentally indicated that a bidentate intramolecular H-bond of this proton and the C6 methoxyl O atoms (distance H...O3 2.30 A° , angle O6–H...O3 128°) and the C7 benzoyl carbonyl O atom (distance H...O5 2.51 A° , angle O6–H...O5 129°) could form. Apparently, this was responsible for the formation of dibenzoylbrowniine with benzoyl groups on C14 and C7. The molecules in the crystal were situated within van-der-Waals distances. Short intermolecular contacts were not observed.

1-[(2-Methylpiperidin-1-yl)(phenyl)methyl]naphthalen-2-ol

In the title compound, C23H25NO, an intra­molecular O—H⋯N hydrogen bond defines the mol­ecular conformation; the naphthol mean plane and the benzene ring form a dihedral angle of 75.8 (2)°. The piperidine ring adopts a chair conformation. The crystal packing exhibits no short inter­molecular contacts.

Density Functional Theory as a tool to identify the dominant magnetic interactions in the [Cu(hfac)2(N3TEMPO)]n chain

Density Functional Theory (DFT) was employed to investigate the dominant magnetic interactions in the [Cu(hfac) 2 N 3 TEMPO] n chain (hfac = hexafluoroacetylacetonate and N 3 TEMPO = 4-azido-2,2,6,6-tetramethylpiperidine-1-oxyl). This compound crystallizes with two copper(II) sites bridged coordinated in the axial positions by N 3 TEMPO radicals originating a chain. Short intermolecular contacts between nitroxide groups belonging to adjacent chains result in an effective pathway to magnetic interactions. DFT calculations show that intrachain magnetic interactions between the Cu2 center and the N 3 TEMPO radical are considerably weaker than intermolecular magnetic interactions between two N 3 TEMPO radicals. This result agrees with experimental data which show that the pathway for magnetic interaction does not coincide with the covalent skeleton, being indeed due to intermolecular contacts. DFT calculations were performed to determine the dominant magnetic pathway in the [Cu(hfac)2N3TEMPO]n chain showing the relevance of intermolecular short contacts to the magnetic behavior. ► The magnetic chain does not coincide with the covalent skeleton. ► DFT calculations are able to identify the magnetic interaction pathway. ► The interchain magnetic interaction occurs mediated by methyl groups.

3-(3-Methoxyphenyl)benzo[d]thiazolo[3,2-a]imidazol-9-ium hydrogen sulfate

In the title mol­ecular salt, C16H13N2OS+·HSO4 −, the thia­zolo[3,2-a]benzimidazolium ring system is roughly planar [maximum deviation = 0.046 (3) Å] and makes a dihedral angle of 58.22 (11)° with the benzene ring. The meth­oxy group is almost coplanar with its attached benzene ring [Cmeth­yl—O—C—C = −1.6 (5)°]. In the crystal, the cation is linked to the anion by a bifurcated N—H⋯(O,O) hydrogen bond, generating an R 1 2(4) ring motif. The ion pairs are then connected by a C—H⋯O hydrogen bond into inversion dimers and these dimers are further linked by O—H⋯O hydrogen bonds into an infinite tape along [100]. A π–π stacking inter­action [centroid-to-centroid distance = 3.5738 (18) Å] and a short inter­molecular contact [S⋯O = 2.830 (3) Å] are also observed.

4-Bromoacetyl-3-phenylsydnone

In the title compound (systematic name: 4-bromoacetyl-1,2,3-oxadiazol-3-ylium-5-olate), C10H7BrN2O3, the 1,2,3-oxadiazole ring and bromo­acetyl group are essentially planar [maximum deviation = 0.010 (4) and 0.013 (3) Å respectively] and form dihedral angles of 59.31 (19) and 67.96 (11)°, respectively, with the phenyl ring. The 1,2,3-oxadiazole ring is twisted slightly from the mean plane of the bromo­acetyl group, forming a dihedral angle of 9.16 (24)°. In the crystal, mol­ecules are linked by pairs of weak C—H⋯O hydrogen bonds into inversion dimers with R 2 2(12) ring motifs. The dimers are further connected by weak C—H⋯O hydrogen bonds into an infinite tape parallel to the b axis. In addition, π–π stacking inter­actions [centroid–centroid distance = 3.6569 (19) Å] and short inter­molecular contacts [O⋯O = 2.827 (3) and C⋯C = 3.088 (5) Å] are observed.

Close Encounters of the 3D Kind – Exploiting High Dimensionality in Molecular Semiconductors

AbstractIn this Research News article we discuss the significance of dimensionality on the charge‐transport properties of organic semiconductors. Dimensionality is defined in two ways: as a function of (i) the π‐conjugated framework within the molecular structure, and (ii) the degree and direction of intermolecular close‐contacts between molecules in the bulk. In terms of dimensionality, silicon is a good role model for organic semiconductors, since it demonstrates 3D architecture in the bulk through covalent bonding. Achieving this for organics is challenging and requires not only a 3D molecular structure, but also a network of intermolecular short contacts in three dimensions. This review identifies the limitations of low dimensional materials and summarizes the challenges faced in progressing towards fully 3D organic semiconductors.

Magnetic properties of spacer-armed dinuclear copper(II) complexes

The results of static magnetic susceptibility studies of spacer-armed dinuclear copper(II) complexes with dicarboxylic acid acylhydrazones are described. Weak exchange coupling between paramagnetic centers has been detected with an exchange parameter value of −2J ∼ 1–7 cm−1. Short intermolecular contacts give rise to additional weak antiferromagnetic exchange coupling between copper cations comparable in terms of energy with superexchange inside the dinuclear complex (−zJ′ ∼ 0.6–5.0 cm−1).

Spin‐Crossover Behaviors Based on Intermolecular Interactions for Cobalt(II) Complexes with Long Alkyl Chains

AbstractA new family of terpyridine (terpy)‐based spin‐crossover cobalt(II) complexes, [Co(HO–Cn‐terpy)2](BF4)2 [n = 6 (1), 8 (2), 10 (3), 12 (4), and 14 (5)] that possesses a hydroxy‐appended long alkyl chain present on the terpyridine skeleton was synthesized and characterized by X‐ray structure analysis and temperature‐dependent magnetic susceptibility. In the solid state, the compounds 1·H2O, 4, and 5·H2O were crystallized in the triclinic P$\bar {1}$ space groups, and their central cobalt(II) ion was coordinated by six nitrogen atoms from two terpyridine units to form a pseudo‐octahedral symmetry. In the case of 1·H2O, one of the terminal hydroxy substituents was involved in hydrogen bonding with a water molecule. For compound 4, on the other hand, both of terminal hydroxy units form a short intermolecular contact with the BF4– anion. The temperature‐dependent magnetic behavior of 1 and 2 showed a gradual spin crossover, whereas 3 and 4 revealed an abrupt spin transition with a wide thermal hysteresis loop (ΔT = 21 K, T1/2↑ = 316 K, and T1/2↓ = 295 K for 3; ΔT = 40 K, T1/2↑ = 348 K, and T1/2↓ = 308 K for 4), and 5 exhibits “reverse spin transition” (ΔT = 17 K, T1/2↑ = 214 K, andT1/2↓ = 231 K). It has been suggested that compounds 3 and 4 form stronger intermolecular interactions through the fastener effect and hydrogen bonding than 1 and 2. On the basis of a comparison of the resulting magnetic behaviors of the compounds that contain long alkyl chains with a hydroxy group at the end, it was found that the long alkyl chains with the terminal hydroxy group could induce stronger intermolecular interactions between molecules. However, there are many short contacts through the counteranions for 5·H2O, but thermal motion of the long alkyl chains can be expected. Compound 5 exhibits “reverse spin transition” induced by a structural phase transition.

Low-melting molecular complexes. Halogen bonds in molecular complexes of bromoform

Single crystals of three new low-melting molecular complexes of bromoform have been grown in situ, their crystal structures characterized by X-ray crystallography and compared with those of their chloroform analogues. The calculations of pair-wise energies of intermolecular interactions in these structures reveal that in some cases the strongest interactions exist between the molecules which are not linked by any short direction-specific intermolecular contacts. A high versatility of bonding modes of bromoform in comparison to chloroform is demonstrated and the relative role of various intermolecular interactions (including halogen bonds) in studied molecular complexes is discussed.