Short Intermolecular Contacts Research Articles

A study on interwoven hydrogen bonding interactions in new zidovudine-picric acid (1:1) cocrystal through single crystal XRD, spectral and computational methods

High throughput of cocrystals furnishes information on the proximity of an Active Pharmaceutical Ingredient (API) and coformer. In this paper, the mechanochemical synthesis of 1:1 cocrystal of anti-HIV drug Zidovudine (AZT), with Picric acid (PA) is presented. The single-crystal X-ray diffraction confirms that cocrystal is crystallized in the monoclinic crystal system (space group P21) with one molecule of AZT and a molecule of PA in the asymmetric unit. The molecular interactions in the crystal structure were analyzed by considering short contacts and intermolecular contacts using quantum topological atoms in molecules (QTAIM) and Hirshfeld surface methods. In the crystal structure of AZT-PA, intermolecular hydrogen bonds (N–H⋯O, O–H⋯O, C–H⋯O, and C–H⋯N) and intermolecular interactions (C–O···π, N–O···π and C–H···π) were involved in the formation of supramolecular assembly. The major inter contacts O⋯H and N⋯H contribute 38.4% and 11.1% respectively as resulted from Hirshfeld Surfaces. The cocrystal models were illustrated using density functional theory and the quantum topology. The experimental and theoretical FTIR spectrum of the cocrystal was compared and analyzed. Also, the crystal packing was analyzed using molecular dynamics (supercell model). Additionally, Thermoanalytical methods (DSC/TGA) indicated that the crystallinity of AZT-PA was preserved up to 129 °C.

Ethanol coordinated zinc trimethoxyphenylporphyrin: Structure, theoretical studies and formation of isoporphyrin

An axial ethanol bound zinc porphyrin, [Zn(TMPP)(C2H5OH)]·2CH2Cl21 (TMPP = 5,10, 15,20-tetrakis(3,4,5-trimethoxyphenyl)porphyrin) was synthesized and characterised using single crystal X-ray diffraction method. The complex 1 is a penta co-ordinated zinc porphyrin via the Zn–O(ethanol) bond and shows one - dimensional chain network through O-atom of axially bound ethanol to peripheral meta-methoxy group of a consecutive porphyrin unit. The hydroxy-isoporphyrin of complex 1 was synthesized on reaction with ceric ammonium nitrate (CAN) as oxidizing agent. The partial molecular energy diagram of selected frontier orbitals and the electronic transitions were determined for compound 1 using Gaussian 09 software. The Hirshfeld surface analysis and 2D fingerprint plots were also performed to understand the origin of H-bonding and other intermolecular short contacts present in the crystal lattice of compound 1. The electrochemical and luminescence properties of the complex 1 was studied and compared with its hydroxy isoporphyrin analogue.

Crystal structure and Hirshfeld surface analysis of a bromo-chalcone: (E)-1-(3-bromo-phen-yl)-3-(2,6-di-chloro-phen-yl)prop-2-en-1-one.

In the title chalcone derivative, C15H9BrCl2O, the aryl rings are inclined to each by 14.49 (17)°, and the configuration about the C=C bond is E. There is a short intra-molecular C-H⋯Cl contact present resulting in the formation of an S(6) ring motif. In the crystal, the shortest inter-molecular contacts are Cl⋯O contacts [3.173 (3) Å] that link the mol-ecules to form a 21 helix propagating along the b-axis direction. The helices stack up the short crystallographic a axis, and are linked by offset π-π inter-actions [inter-centroid distance = 3.983 (1) Å], forming layers lying parallel to the ab plane. A qu-anti-fication of the inter-molecular contacts in the crystal were estimated using Hirshfeld surface analysis and two-dimensional fingerprint plots.

LiTFSI/TBP-free hole transport materials with nonlinear π-conjugation for efficient inverted perovskite solar cells

We have synthesized two non-linear molecules with Y-shaped (XSln847) and X-shaped (XSln1453) structures via a facile synthetic route. Comparable to an X-shaped structure, the Y-shaped structural backbone of XSln847 enables a tight molecular stacking arrangement through multiple intermolecular short contacts, which affords a nest-layer in molecules. As a result, the pristine, Y-shaped XSln847 gives higher hole-mobility and more effective photoluminescence quenching than does XSln1453. Additionally, a decreased charge recombination occurs in the XSln847-fabricated inverted perovskite solar cells. As a consequence, the device based on XSln847 affords a higher power conversion efficiency of 15.02% than does that of XSln1453 (12.65%) under standard global AM 1.5 illumination. The efficiency is further improved to 17.16% when using XSln847 doping with 2, 3, 5, 6-tetrafluoro- 7, 7, 8, 8-tetracyanoquinodimethane, which is much higher than that of the widely-used PEDOT:PSS (11.95%) when measured under the same condition. These results demonstrate that the molecular engineering of hole transport materials with non-linear structure is a promising strategy for designing efficient molecules for inverted perovskite solar cells.

An approach to fluorinated phthalonitriles containing a nitronyl nitroxide or iminonitroxide moiety

A 4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-3-oxide-1-oxyl lithium derivative was found to react with perfluorophthalonitrile with formation of 2-(3,4-dicyano-2,5,6-trifluorophenyl)- (1) and 2-(2-amino-4,5-dicyano-3,6-difluorophenyl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazol-3-oxide-1-oxyl (2). The yields of 1 were near 15% independently of reaction time (from 2 to 6 h), whereas the yields of 2 considerably increased from a trace amount to 20%. Both nitronyl nitroxides were reduced to the corresponding iminonitroxides in the presence of NaNO2/AcOH with yields 80–95%. Molecular and crystal structures of the obtained nitroxides were solved by monocrystal X-ray diffraction analysis, and the nature of the radical was ascertained by electron spin spectroscopy (ESR) and SQUID magnetometry. Static magnetochemical measurements of 1 revealed domination of the ferromagnetic exchange interactions between the odd electrons of the paramagnetic centres. The exchange interactions probably proceed via short intermolecular contacts (3.021(3) and 3.05(2) Å) between the nitroxide O atoms and cyanide C atoms. Structural characteristics of the prepared nitroxides make them valuable precursors for the synthesis of paramagnetic macrocycles, which may serve as building blocks in the field of molecular magnetism.

Synthesis, characterization, crystal structures, Hirshfeld surface analysis and theoretical calculations of some new bisphosphoramidate derivatives and novel binuclear triorganotin(IV) complexes with diphosphoryl ligand

A series of new bisphosphoramidate and (thio)phosphoramidate derivatives with the general formula R1R2P(X)–Y–P(X)R1R2 have been synthesized and characterized by IR and NMR spectroscopies (L1–L12). The crystal structure of compound 1,4-[(C2H5O)2P(S)(CH2)3NH]2C4H8N2 (L4) is also investigated by X-ray diffraction analysis. Two novel organotin(IV) complexes μ-{1,4-[(C6H5)2P(O)(CH2)3NH]2C4H8N2}[SnR3Cl]2, R3SnCl (R = phenyl/butyl), C1 and C2, respectively, are prepared by the reaction of new diphosphoryl ligand L1 and R3SnCl under different conditions. C1 and C2 are characterized by IR and NMR spectroscopies and X-ray crystallography diffraction analysis. X-ray analysis illustrates that both complexes have similar structures containing binuclear triorganotin(IV) skeletons and ligand coordinates in a bridging mode through two phosphoryl groups. Sn(IV) coordination geometries are distorted trigonal bipyramidal (TBP) for C1, and C2 structures contained binuclear arrangement with two SnPh3Cl/SnBu3Cl groups linked via the bridging diphosphoryl ligand. The organization of the crystal structures and the intermolecular interactions are discussed. Hirshfeld surfaces and two-dimensional fingerprint plots are used to study short intermolecular contacts in C1, C2, and L4. Finally, the influence of chain length and the effects of various substituents on P=O and P=S bond strength in synthesized ligands (L1–L12) and optimized ligands (L13–L17) are theoretically investigated by NBO analysis to survey the character of mentioned bonds in these ligands. The AIM analysis is also used to determine the nature of the P=O bond in L1 and also P=O and O⋯Sn4+ bonds in C1 and C2. Results show ionic character for O⋯Sn4+ interaction in both complexes and mostly electrostatic character for P=O bond in the free ligand, but with a little shift to the covalent character after the complexation.

Tetrathiafulvalene Dimer Merged with a Binuclear Ring of Sn and Sb: Synthesis and Molecular Structures Induced by Heteroatoms

In this study, we describe the synthesis and characterization of dimeric tetrathiafulvalene (TTF) derivatives that are doubly bridged by Sn (1) and Sb (2a) atoms as a new class of organic‐inorganic hybrid compounds able to provide enhanced dimensionality in the solid state. The antimony heterocyclic framework was constructed by a simple Sn–Sb metal exchange reaction of a 1,4‐distannine moiety with p‐tolyl antimony dichloride (p‐tolSbCl2). Compound 2a was obtained in cis and trans forms as a stable configurational isomer. From X‐ray crystallographic analysis, there were three conformational isomers in which the tolyl rings were directed in the endo or exo direction. Crystal packing revealed a supramolecular three‐dimensional network through intermolecular short contacts of Sb···S and Sb···π. These packing forces gave a trans‐2aexo–exo conformation in the crystal, although the theoretical calculations predict its instability compared with other conformers. Cyclic voltammetry (CV) measurements of 1 and cis/trans‐2a revealed two pairs of reversible redox processes corresponding to the formation of TTF/TTF·+ and TTF·+/TTF2+. Furthermore, CV of cis/trans‐2a also revealed the reduction waves derived from the reduction of SbIII. Dicationic and tetracationic species were prepared by chemical oxidation, and their electronic structures were also investigated by electronic spectroscopy.

Solid-phase transitions of polymorphs of 4-(4-N,N-dialkylaminophenyl)azobiphenyl-2,3’,4’-tricarbonitriles and their analogues

A new series of push–pull azo-dyes containing tricyanodiphenyl electron-withdrowing block, namely (4-N,N-dialkylaminophenyl)azobiphenyl-2,3’,4’-tricarbonitriles, was proposed and synthesized. The azo-dyes possess high temperature stability and are prone to form polymorph modifications. DSC measurements indicated solid-phase transitions of these polymorphs. X-ray diffraction (XRD) analysis revealed that in all solved structures, there is a network of short intermolecular contacts between HArom atoms and N atoms of cyano groups. The supramolecular structure of these contacts depends on the alkyl chain length in the aniline moiety, and changes after temperature induced phase transitions.

Crystal Structure of Liguzinediol, 2,5-Dimethylol-3,6-dimethylpyrazine

The 2,5-dimethylol-3,6-dimethylpyrazine, C8H12N2O2, liguzinediol, has been recently discovered as a potential agent for the treatment of heart failure with low safety risk. The crystal structure of liguzinediol, which has been determined by single-crystal X-ray diffraction analysis, is reported for the first time. The liguzinediol crystal may be obtained from 50% ethanol or ethyl acetate. The compound crystallizes in the monoclinic system with the sp. gr. P21/n and the unit cell parameters a = 4.0560(8) A, b = 12.280(3) A, c = 8.5370(17) A, β = 96.93(3)°, Z = 2. The molecule forms S2-symmetric conformation in the crystal. The hydroxyl H atom forms short intermolecular contacts with the neighbouring pyrazine N atom, which forms the weak hydrogen bonds in the crystal.

A Crystallographic Study of a Novel Tetrazolyl-Substituted Nitronyl Nitroxide Radical

Spin-labelled compounds are widely used in chemistry, physics, biology, and material sciences, but the directed synthesis of some functionalized organic radicals is still a challenge. We succeeded in the preparation of a tetrazolyl-substituted nitronyl nitroxide radical in pure crystalline form. According to the single-crystal X-ray data, intra- (NH…O, 2.43 Å) and inter-molecular hydrogen bonds (NH…O, 1.91 Å) are formed between NH groups of the tetrazole cycles and O atoms of the paramagnetic moieties. The intermolecular H-bonds connect the molecules forming chains along the a-axis. Moreover, there are short intermolecular contacts between the O atoms (3.096 Å) and between the O and C atoms (3.096 Å) of the nitronyl nitroxide moieties within the chain. The spin-unrestricted broken-symmetry calculations performed at the BS-UB3LYP/def2-TZVP level of theory predicted a sufficient ferromagnetic interaction (J ≈ 20 cm–1) between the adjacent radicals inside the chain, but a weak antiferromagnetic interaction (−J ≤0.2 cm−1) between the nearest radicals belonging to the different chains. Thus, a rare case when stable radicals, the tetrazolyl-substituted nitronyl nitroxides, are ordered into ferromagnetic chains was revealed; an investigation of the magneto-structural correlations inherent in the nitroxide radical will demand a special experiment in the sub-Kelvin regime.

Synthesis, crystal structure, magnetic properties and DFT calculations of a mononuclear copper(II) complex: Relevance of halogen bonding for magnetic interaction

The synthesis, crystal structure, magnetic properties and DFT calculations of a new mononuclear copper(II) complex containing a pyrazole-based ligand are reported. In the crystal structure of the [CuCl2L2] complex (L = Ethyl 5-amino-1-(4-methoxyphenyl)-1H-pyrazole-4-carboxylate), a network of hydrogen bonds connects the molecular units in the crystal packing. The magnetic studies revealed predominant antiferromagnetic interactions among molecular units. Since there are multiple intermolecular contacts that can act as pathway for magnetic interactions, DFT calculations revealed the fundamental role of N–H⋯Cl short intermolecular contacts in magnetic behavior. Supported by DFT calculation, the magnetic data above 7.0 K was modeled as a regular Heisenberg chain (H=-2J∑i=1n-1S→Ai·S→Ai+1) resulting in a weak magnetic coupling constant (J) of −2.6 cm−1. Below this temperature, an unusual magnetic behavior for mononuclear copper(II) complexes was observed: divergence between zero-field cooled (ZFC) and field cooled (FC) magnetic susceptibilities and magnetic hysteresis cycles at low temperatures attributed to spin canting along the chain.

Presence of Short Intermolecular Contacts Screens for Kinetic Stability in Packing Polymorphs.

Polymorphism is pervasive in molecular solids. While computational predictions of the molecular polymorphic landscape have improved significantly, identifying which polymorphs are preferentially accessed and experimentally stable remains a challenge. We report a framework that correlates short intermolecular contacts with polymorphic stability. The presence of short contacts between neighboring molecules prevents structural rearrangement and stabilizes the packing arrangement, even when the stabilized polymorph is not enthalpically favored. In the absence of such intermolecular short contacts, the molecules have added degrees of freedom for structural rearrangement, and solid-solid polymorphic transformations occur readily. Starting with a series of core-halogenated naphthalene tetracarboxylic diimides, we establish this framework with the packing polymorphs of more than 20 compounds, ranging from molecular semiconductors to pharmaceutics and biological building blocks. This framework, widely applicable across molecular solids, can help refine computational predictions by identifying the polymorphs that are kinetically stable.

Highly Nonplanar Macrocyclic Ring Conformation in the Crystal Structures of Ni(II) And Cu(II) Octaphenylporphyrins

Crystal structures of solvated highly nonplanar nickel(II) and copper(II) complexes of 2,3,5,10,12,13,15,20- octaphenylporphyrin are determined by single crystal XRD analysis. The macrocycles in these systems exhibit mainly ruffled and saddled conformations. The average displacement of the pyrrole carbon atom ΔCb from the mean plane of the porphyrin ring is as high as ±0.70 A. The Hirshfeld surface analysis of both structures reveals mainly H…H (57-59%) intermolecular short contacts with a smaller contribution from C…H (16-22%) and H…Cl (11-19%) interactions. The present work suggests that the nonplanarity of the macrocycle in NiTPP(Ph)4 is largely due to the core Ni(II) ion and less influenced by intermolecular interactions/crystal packing forces, whereas the opposite is true in the case of the nonplanar CuTPP(Ph)4 structure.

Highly nonplanar macrocyclic ring conformation in the crystal structures of Ni(II) and Cu(II) octaphenylporphyrins

Crystal structures of solvated highly nonplanar nickel(II) and copper(II) complexes of 2,3,5,10,12,13,15,20-octaphenylporphyrin are determined by single crystal XRD analysis. The macrocycles in these systems exhibit mainly ruffled and saddled conformations. The average displacement of the pyrrole carbon atom ΔCb from the mean plane of the porphyrin ring is as high as ±0.70 Å. The Hirshfeld surface analysis of both structures reveals mainly H…H (57—59 %) intermolecular short contacts with a smaller contribution from C…H (16—22 %) and H…Cl (11—19 %) interactions. The present work suggests that the nonplanarity of the macrocycle in NiTPP(Ph)4 is largely due to the core Ni(II) ion and less influenced by intermolecular interactions/crystal packing forces, whereas the opposite is true in the case of the nonplanar CuTPP(Ph)4 structure.

Loose crystals engineered by mismatched halogen bonds in hexachloroethane

The shortest intermolecular contacts in the engineered loose crystal of hexachloroethane are longer than the sum of van der Waals radii, reached only at the pressure of 1.2 GPa.

Adiponitrile at 100 K.

Adiponitrile, C6H8N2, is a key intermediate in the synthesis of the polyamide Nylon 66 and is produced industrially on a large scale. We have determined the crystal and molecular structure of adiponitrile by single-crystal X-ray analysis at 100 K, a suitable crystal (m.p. 275 K) having been grown from the melt at low temperature. The compound crystallizes in the monoclinic space group P21/c with Z = 2. In the crystal structure, the molecule adopts an exact Ci-symmetric gauche-anti-gauche conformation of the C-C-C-C skeleton about an inversion centre. The molecules are densely packed, with short intermolecular contacts between the α-H and nitrile N atoms.

2,2-Difluoro-3-(4-fluorophenyl)-2H-benzo[e][1,3,2]oxazaborinin-3-ium-2-uide

There is one independent molecule in the asymmetric unit of the title compound, C13H9BF3NO, which crystallizes in the non-centrosymmetric space groupCc. In the molecular structure, the BF2-carrying ring is distorted from planarity and its mean plane makes a dihedral angle of 42.3 (1)° with the 4-fluorophenyl ring. F atoms are involved in all of the short intermolecular contacts of the crystal structure, which link molecules to form chains along [001] and [010].

Synthesis, structural elucidation, antioxidant, CT-DNA binding and molecular docking studies of novel chloroquinoline derivatives: Promising antioxidant and anti-diabetic agents

The synthesized novel chloroquinoline derivatives 1-(2-chloro-4-phenylquinolin-3-yl)ethanone (CPQE), 1-(2,6-dichloro-4-phenylquinolin-3-yl)ethanone (DCPQE), methyl 2,6-dichloro-4-phenylquinoline-3-carboxylate (MDCPQC),methyl 2-chloro-4-methylquinoline-3-carboxylate (MCMQC) were subjected to the elementary analysis like FT-IR, NMR and Mass spectra using GCMS. Also, single crystal X-ray diffraction study was executed for the compound MDCPQC. The crystal packing is stabilized by C–H…π and π–π interactions and also Chlorine–Chlorine short intermolecular contacts generating a three-dimensional supramolecular network. The antioxidant activity reduces high glucose level in the human body and hence the synthesized compounds were subjected for the estimation of antioxidant activity using DPPH method which exhibited good percentage of inhibition in comparison with ascorbic acid, a well-known anti-oxidant. The binding interaction of the chloroquinoline derivatives with calf thymus DNA (CT-DNA) has been explored by fluorescence quenching studies and molecular docking analysis has been employed to confirm the nature of binding. The prediction of pharmacological properties such as drug-likeness, molecular properties like absorption, distribution, metabolism, excretion and toxicity (ADMET) was carried out by computational studies to compare chloroquinoline derivatives with standard drug. Owing to the various potential biological activities of the quinoline compounds, molecular docking studies were also further carried out for the chloroquinoline derivatives, showing that they may act as effective anti-diabetic agents by inhibiting Glycogen Phosphorylase a protein.

Photophysical Study of DPPTT‐T/PC70BM Blends and Solar Devices as a Function of Fullerene Loading: An Insight into EQE Limitations of DPP‐Based Polymers

Diketopyrrolopyrrole (DPP)‐based polymers have been consistently used for the fabrication of solar cell devices and transistors due to the existence of intermolecular short contacts, resulting in high electron and hole mobilities. However, they also often show limited external quantum efficiencies (EQEs). In this contribution, the authors analyze the limitations on EQE by a combined study of exciton dissociation efficiency, charge separation, and recombination kinetics in thin films and solar devices of a DPP‐based donor polymer, DPPTT‐T (thieno[3,2‐b]thiophene‐diketopyrrolopyrrole copolymer) blended with varying weight fractions of the fullerene acceptor PC70BM. From the correlations between photoluminescence quenching, transient absorption studies, and EQE measurements, it is concluded that the main limitation of photon‐to‐charge conversion in DPPTT‐T/PC70BM devices is poor exciton dissociation. This exciton quenching limit is related not only to the low affinity/miscibility of the materials, as confirmed by wide angle X‐ray diffraction diffraction and transmission electron microscopy data, but also to the relatively short DPPTT‐T singlet exciton lifetime, possibly associated with high nonradiative losses. A further strategy to improve EQE in this class of polymers without sacrificing the good extraction properties in optimized blends is therefore to limit those nonradiative decay processes.

Synthesis, physicochemical analysis of two new hemilabile ether-phosphine ligands and their first stable bis-ether-phosphine/cobalt(II) tetrahedral complexes

New tridentate ether-phosphine {P, 2O} and ether-phosphine oxide {OP, 2O} ligands with P and O donor-atoms have been synthesized starting from ClCH2CH(OCH3)2. The oxidation process of Ph2PCH2CH(OCH3)2 to its oxide derivative Ph2P(O)CH2CH(OCH3)2 was monitored by 31P NMR for the first time. The desired ligands and their Co(II) complexes structures were deduced from IR, EA, MS, NMR, UV–Vis., TG/DTG and XRD physical measurements. The tridentate chelating coordination behavior of the ether-phosphine wasn't detected leading only to the mono-dentate coordination mode through the phosphorous atoms to set up a X2Co[η1-Ph2PCH2CH(OCH3)2]2 as final isomer formula (X = Cl or Br). The Cl2Co[η1-Ph2PCH2CH(OCH3)2]2 isomer belongs to complex 1 was supported by single crystal measurement. Polar/non-polar intermolecular short contacts were detected by XRD and Hirshfeld surface theoretical analysis.