Evaluation of N—H…S and N—H…π interactions in O,O′‐diethyl N‐(2,4,6‐trimethylphenyl)thiophosphate: a combination of X‐ray crystallographic and theoretical studies

In the crystal structure of O,O′‐diethyl N‐(2,4,6‐trimethylphenyl)thiophosphate, C₁₃H₂₂NO₂PS, two symmetrically independent thiophosphoramide molecules are linked through N—H…S and N—H…π hydrogen bonds to form a noncentrosymmetric dimer, with Z′ = 2. The strengths of the hydrogen bonds were evaluated using density functional theory (DFT) at the M06‐2X level within the 6‐311++G(d,p) basis set, and by considering the quantum theory of atoms in molecules (QTAIM). It was found that the N—H…S hydrogen bond is slightly stronger than the N—H…π hydrogen bond. This is reflected in differences between the calculated N—H stretching frequencies of the isolated molecules and the frequencies of the same N—H units involved in the different hydrogen bonds of the hydrogen‐bonded dimer. For these hydrogen bonds, the corresponding charge transfers, i.e. lp (or π)→σ*, were studied, according to the second‐order perturbation theory in natural bond orbital (NBO) methodology. Hirshfeld surface analysis was applied for a detailed investigation of all the contacts participating in the crystal packing.     

A combined computational and experimental approach for investigating a hydrogen‐bonded supermolecular compound comprising benzimidazole and malonic acid

A hydrogen‐bonded tetramer supramolecular motif of 2:2 benzimidazole (BIZ) and malonic acid (MLA) has been synthesized and characterized by elemental analysis, infrared (IR), and X‐ray single crystal diffraction. Thermal stability analyses demonstrate that this supramolecular adduct is a new material and it is not the ordinary superposition of the original monomers. Density function theory (DFT) calculations for the models of dimers, trimers, and tetramer comprising BIZ and MLA have been carried out at B3LYP/6‐31G* and PBE1PBE/6‐31G* levels of theory, respectively. By comparing the calculated results with the experiments (single crystal structure, IR spectra, and thermal analysis) and based on the statistic thermodymnamic calculations, it is concluded that the dimers cannot exist at room temperature and the tetramer can simulate the title supramolecular complex better than the two trimers. Further studies on the model of tetramer indicate that the hydrogen bond of N···H? O is stronger than that of O···H? N. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Crystal structure and solid state computational (DFT/Hirshfeld surface) study for probing a new efficient and recyclable oxidation reagent, 1,2-ethandiylbis(triphenylphosphonium) peroxodisulfate dihydrate

A new, efficient and recyclable reagent, 1,2-Ethandiylbis(triphenylphosphonium) peroxodisulfate dihydrate, for the oxidation of benzylic alcohols has been synthesized and characterized by IR, NMR spectroscopy, and single crystal X-ray crystallography. Using the title compound, the results indicate that the oxidation reactions are rapid, take place under mild reaction conditions, easily to work-up and high yielding. The Hirshfeld surface and associated finger print plots were derived from the X-ray structure to visualize the significant nonclassical C-H ??? O/π interactions in the crystal packing. The geometry, vibrational spectroscopy and electronic properties of the bis(triphenylphosphonium) dication have also been investigated by various DFT computational methods.     

Crystal structure of a new polyoxometalate (POM) compound with a high level of crystallographic disorder

The crystal structure, Hirshfeld surface analysis and spectroscopic analysis of a new polyoxometalate (POM) compound, namely, nonakis(2‐methoxyaniline) bis(diphosphopentamolybdate) trihydrate, (C₇H₉NO)₉[P₂Mo₅O₂₃]₂·3H₂O, is reported. The title compound was synthesized using the solution method and was structurally characterized by single‐crystal X‐ray diffraction, which revealed P symmetry. A study of the intermolecular interactions using Hirshfeld surface analysis confirmed that the hydrogen‐bonding interactions play the dominant role in the stability of the crystal structure. The refinement was complicated by extensive disorder affecting 11 of the 16 ions and molecules in the asymmetric unit. IR and UV–Vis spectroscopic techniques were used to identify the vibrational modes and to classify this compound as an insulator.     

Synthesis,experimental and in silico studies of N‐fluorenylmethoxycarbonyl‐O‐tert‐butyl‐N‐methyltyrosine,coupled with CSD data: a survey of interactions in the crystal structures of Fmoc–amino acids

Recently, fluorenylmethoxycarbonyl (Fmoc) amino acids (e.g. Fmoc–tyrosine or Fmoc–phenylalanine) have attracted growing interest in biomedical research and industry, with special emphasis directed towards the design and development of novel effective hydrogelators, biomaterials or therapeutics. With this in mind, a systematic knowledge of the structural and supramolecular features in recognition of those properties is essential. This work is the first comprehensive summary of noncovalent interactions combined with a library of supramolecular synthon patterns in all crystal structures of amino acids with the Fmoc moiety reported so far. Moreover, a new Fmoc‐protected amino acid, namely, 2‐{[(9H‐fluoren‐9‐ylmethoxy)carbonyl](methyl)amino}‐3‐{4‐[(2‐hydroxypropan‐2‐yl)oxy]phenyl}propanoic acid or N‐fluorenylmethoxycarbonyl‐O‐tert‐butyl‐N‐methyltyrosine, Fmoc‐N‐Me‐Tyr(t‐Bu)‐OH, C₂₉H₃₁NO₅, was successfully synthesized and the structure of its unsolvated form was determined by single‐crystal X‐ray diffraction. The structural, conformational and energy landscape was investigated in detail by combined experimental and in silico approaches, and further compared to N‐Fmoc‐phenylalanine [Draper et al. (2015). CrystEngComm, 42 , 8047–8057]. Geometries were optimized by the density functional theory (DFT) method either in vacuo or in solutio. The polarizable conductor calculation model was exploited for the evaluation of the hydration effect. Hirshfeld surface analysis revealed that H…H, C…H/H…C and O…H/H…O interactions constitute the major contributions to the total Hirshfeld surface area in all the investigated systems. The molecular electrostatic potentials mapped over the surfaces identified the electrostatic complementarities in the crystal packing. The prediction of weak hydrogen‐bonded patterns via Full Interaction Maps was computed. Supramolecular motifs formed via C—H…O, C—H…π, (fluorenyl)C—H…Cl(I), C—Br…π(fluorenyl) and C—I…π(fluorenyl) interactions are observed. Basic synthons, in combination with the Long‐Range Synthon Aufbau Modules, further supported by energy‐framework calculations, are discussed. Furthermore, the relevance of Fmoc‐based supramolecular hydrogen‐bonding patterns in biocomplexes are emphasized, for the first time.     

Synthesis,structural characterization,density functional theory calculations and biological evaluation of a new organotin(IV) complex containing N‐isonicotinyl‐N',N″‐diaryl phosphorictriamide as N‐donor ligand

A new diorganotin(IV) complex with the formula SnCl₂(CH₃)₂L₂ ( C_1a ), L = 4‐NC₅H₄CONHPO(NCH₃CH₂C₆H₅)₂, was synthesized and characterized using ¹H NMR, ¹³C NMR, ³¹P NMR, ¹¹⁹Sn NMR and infrared spectroscopies. The molecular structure of C_1a was determined using X‐ray crystallography, revealing that C_1a contains hexa‐coordinated Sn(IV) centres with trans‐configuration of donor atoms around them. Each Sn(IV) atom is positioned in the centre of inversion of an octahedron. C_1a forms one‐dimensional chains via two equal intermolecular P?O…H? N hydrogen bonds. These hydrogen bonds produce centrosymmetric rings as a supramolecular hydrogen‐bonded pattern. In order to compare the relative stability of C_1a (with N‐ligated configuration) and its possible O‐ligated isomer, C_1b , density functional theory calculations were performed, the results showing a preference of C_1a over C_1b from an energy point of view. Also, natural bond orbital analysis was carried out to obtain detailed information on the electronic features of the optimized structures. The theoretical results show that intermolecular hydrogen bonding in the crystal structure has a significant role in the stabilization of C_1a , and Sn(IV) interacts more strongly with the N_py atom than the P?O functional group. Furthermore, the free ligand and its complex were tested against three human cancer cell lines, i.e. human cervical carcinoma (HeLa), human prostate cancer (PC‐3) and human breast adenocarcinoma cancer (MCF‐7). C_1a displays moderate to good cytotoxicity towards all three cancer cell lines. Moreover, antibacterial tests were carried out using the disc‐diffusion method, in which C_1a shows high activity against selected Gram‐negative and Gram‐positive bacteria. Copyright © 2015 John Wiley & Sons, Ltd.     

Crystallographic report: Di(o‐chlorobenzyl)tin(IV) bis(N‐methylpiperazinyldithiocarbamate)

The tin atom in {(2‐Cl‐C₆H₄CH₂)₂Sn[S₂CN(CH₂CH₂)₂NCH₃]₂}₂ is in a skew‐trapezoidal bipyramidal geometry defined by a C₂S₄ set with C? Sn? C 150.61(19)°. Centrosymmetric pairs associated via weak Sn·S to form a dimer. Copyright © 2005 John Wiley & Sons, Ltd.     

Crystallographic report: Bis[tri(o‐chlorobenzyl)tin(IV)] terephthalate

The centrosymmetric structure of (o‐ClC₆H₄)₃SnO₂CC₆H₄CO₂Sn(C₆H₄Cl‐o)₃ features an unsymmetrically chelating carboxylate group, so that a distorted trigonal bipyramidal cis‐C₃O₂ coordination geometry for tin results. Copyright © 2004 John Wiley & Sons, Ltd.     

Crystallographic report: Bis[tri(o‐chlorobenzyl)tin(IV)] piperazinylbisdithiocarbamate

The centrosymmetric structure of (o‐C₆H₄CH₂)₃SnS₂CN(CH₂CH₂)₂NCS₂Sn(CH₂C₆H₄‐o)₃ features chelating dithiocarbamate ligands, so that a trigonal bipyramidal C₃S₂ coordination geometry for tin results. Copyright © 2004 John Wiley & Sons, Ltd.     

Catalyst‐ and solvent‐free synthesis of 2‐fluoro‐N‐(3‐methylsulfanyl‐1H‐1,2,4‐triazol‐5‐yl)benzamide through a microwave‐assisted Fries rearrangement: X‐ray structural and theoretical studies

An efficient approach for the regioselective synthesis of (5‐amino‐3‐methylsulfanyl‐1H‐1,2,4‐triazol‐1‐yl)(2‐fluorophenyl)methanone, C₁₀H₉FN₄OS, (3), from the N‐acylation of 3‐amino‐5‐methylsulfanyl‐1H‐1,2,4‐triazole, (1), with 2‐fluorobenzoyl chloride has been developed. Heterocyclic amide (3) was used successfully as a strategic intermediate for the preparation of 2‐fluoro‐N‐(3‐methylsulfanyl‐1H‐1,2,4‐triazol‐5‐yl)benzamide, C₁₀H₉FN₄OS, (4), through a microwave‐assisted Fries rearrangement under catalyst‐ and solvent‐free conditions. Theoretical studies of the prototropy process of (1) and the Fries rearrangement of (3) to provide (4), involving the formation of an intimate ion pair as the key step, were carried out by density functional theory (DFT) calculations. The crystallographic analysis of the intermolecular interactions and the energy frameworks based on the effects of the different molecular conformations of (3) and (4) are described.     

An enantiomerically pure P‐stereogenic bisphosphine: (S,S)‐ethylenebis[(2‐methylphenyl)phenylphosphine] (o‐tolyl‐DiPAMP)

In connection with a research program involving the synthesis, structure determination, reactivity and ability to coordinate to metal centres of chiral bisphosphine ligands, we have synthesized and structurally characterized, by means of single‐crystal X‐ray diffraction analysis, the title compound {systematic name: (S,S)‐(ethane‐1,2‐diyl)bis[(2‐methylphenyl)phenylphosphane], abbreviated as o‐tolyl‐DiPAMP}, C₂₈H₂₈P₂. So far, neither the free bisphosphine (DiPAMP) nor analogues that incorporate the ethylenebisphosphine frame have had their crystal structures reported. The investigated compound forms crystals which are isostructural with the bisphosphine dioxide analogue [King et al. (2007). Acta Cryst. E 63 , o3278], despite the involvement of the dioxide in C—H...O(=P) hydrogen bonds and the lack of similar hydrogen bonds in the investigated crystal structure. In both molecules, the P—C—C—P chain is in a trans conformation, extended further at both ends by one of the two P—C_ipso bonds. The planes of the phenyl and o‐tolyl rings attached to the same P atom are nearly perpendicular to one another. Both crystal structures are mainly stabilized by dispersive interactions.     

Synthesis,structural elucidation,characterization and theoretical DFT study of 1‐(o‐tolyl)biguanidium chloride

The structure of the new salt 1‐(o‐tolyl)biguanidium chloride, C₉H₁₄N₅⁺·Cl^?, has been determined by single‐crystal X‐ray diffraction. The salt crystallizes in the monoclinic space group C2/c. In this structure, the chloride and biguanidium hydrophilic ions are mostly connected to each other via N—H…N and N—H…Cl hydrogen bonds to form layers parallel to the ab plane around y = and y = . The 2‐methylbenzyl groups form layers between these layers around y = 0 and y = , with the methyl group forming C—H…π interactions with the aromatic ring. Intermolecular interactions on the Hirshfeld surface were investigated in terms of contact enrichment and electrostatic energy, and confirm the role of strong hydrogen bonds along with hydrophobic interactions. A correlation between electrostatic energy and contact enrichment is found only for the strongly attractive (N—H…Cl^?) and repulsive contacts. Electrostatic energies between ions reveal that the interacting biguanidium cation pairs are repulsive and that the crystal is maintained by attractive cation…Cl^? dimers. The vibrational absorption bands were identified by IR spectroscopy.     

Hydrogen bonding in two benzene‐1,2‐diaminium pyridine‐2‐carboxylate salts and a cocrystal of benzene‐1,2‐diamine and benzoic acid

The isostructural salts benzene‐1,2‐diaminium bis(pyridine‐2‐carboxylate), 0.5C₆H₁₀N₂²⁺·C₆H₄NO₂^?, (1), and 4,5‐dimethylbenzene‐1,2‐diaminium bis(pyridine‐2‐carboxylate), 0.5C₈H₁₄N₂²⁺·C₆H₄NO₂^?, (2), and the 1:2 benzene‐1,2‐diamine–benzoic acid cocrystal, 0.5C₆H₈N₂·C₇H₆O₂, (3), are reported. All of the compounds exhibit extensive N—H…O hydrogen bonding that results in interconnected rings. O—H…N hydrogen bonding is observed in (3). Additional π–π and C—H…π interactions are found in each compound. Hirshfeld and fingerprint plot analyses reveal the primary intermolecular interactions and density functional theory was used to calculate their strengths. Salt formation by (1) and (2), and cocrystallization by (3) are rationalized by examining pK_a differences. The R₂²(9) hydrogen‐bonding motif is common to each of these structures.     

Structural studies of bis(histidinato)nickel(II): Combined experimental and computational studies

A distorted octahedral nickel(II) complex, [Ni(2-amino-3-(1H-imidazol-4-yl)propanoic acid)₂] (1), has been synthesized by a solvothermal method and characterized by single-crystal X-ray diffraction. Geometry optimization in the gas phase and pyridine together with Hirshfeld surface and reduced density gradient analyses reveal that this complex shows different distortions from octahedral in the gas, liquid, and solid phases. The reason seems to be because of the presence of two intramolecular NH⋯O weak interactions in the gas phase and two sets of rather strong intermolecular NH⋯O and CH⋯O interactions in the solid phase. Time-dependent density functional theory (TD-DFT) calculations suggest that these different distortions result in different electronic absorption spectra.     

Synthesis,crystal structure and studies on the interaction with albumin of a new silver(I) complex based on 2‐(4‐nitrobenzenesulfonamido)benzoic acid

In the present work, the two‐dimensional (2D) polymer poly[[μ₄‐2‐(4‐nitrobenzenesulfonamido)benzoato‐κ⁴O¹:O¹:O^1′:N⁶]silver(I)] (AgL), [Ag(C₁₃H₉N₂O₆S)]_n, was obtained from 2‐(4‐nitrobenzenesulfonamido)benzoic acid (HL), C₁₃H₁₀N₂O₆S. FT–IR, ¹H and ¹³C{¹H} NMR spectroscopic analyses were used to characterize both compounds. The crystal structures of HL and AgL were determined by single‐crystal X‐ray diffraction. In the structure of HL, O—H…O hydrogen bonds between neighbouring molecules result in the formation of dimers, while the silver(I) complex shows polymerization associated with the O atoms of three distinct deprotonated ligands (L^?). Thus, the structure of the Ag complex can be considered as a coordination polymer consisting of a one‐dimensional linear chain, constructed by carboxylate bridging groups, running parallel to the b axis. Neighbouring polymeric chains are further bridged by Ag—C monohapto contacts, resulting in a 2D framework. Fingerprint analysis of the Hirshfeld surfaces show that O…H/H…O hydrogen bonds are responsible for the most significant contacts in the crystal packing of HL and AgL, followed by the H…H and O…C/C…O interactions. The Ag…Ag, Ag…O/O…Ag and Ag…C/C…Ag interactions in the Hirshfeld surface represent 12.1% of the total interactions in the crystal packing. Studies of the interactions of the compounds with human serum albumin (HSA) indicated that both HL and AgL interact with HSA.     

Two dinuclear copper (II) and nickel (II) complexes based on 4‐(diethylamino)salicylaldehyde: X‐ray structures,spectroscopic, electrochemical,antibacterial, Hirshfeld surfaces analyses,and time‐dependent density functional theory calculations

The quinazoline‐type ligand 2‐(4‐diethylamino‐2‐hydroxyphenyl)‐4‐methyl‐1,2‐dihydroquinazoline 3‐oxide ( HL ¹ ; H is the deprotonatable hydrogen) was prepared. Two 2‐D supramolecular complexes [Cu₂( L ² )₂(NO₃)₂] ( 1 ) and [Ni₂( L ² )₂(CH₃COO)₂] ( 2 ) ( L ² = 1‐(2‐{[(E)‐(4‐diethylamino‐2‐hydroxybenzylidene]amino} phenyl)ethanone oxime) were synthesized using HL ¹ and characterized by elemental analysis, spectroscopic methods, and single‐crystal X‐ray diffraction studies. It revealed that 1 had coordinated two nitrate ions whereas 2 had acetate ions. In the crystal structures, six‐coordinated Cu (II) complex 1 formed an infinite 2‐D and X‐shaped 3‐D supramolecular frameworks. Simultaneously, Ni (II) complex 2 assembled into wavy 2‐D networks. Furthermore, electrochemical properties and antimicrobial activities of all compounds were as well investigated. Afterwards, the electrophilic and nucleophilic attack sites identified by electrostatic potential (ESP) calculations confirmed that hydrogen bonds were observed in the optimized structure of the crystal, and the closest contact between the active atoms of both complexes was confirmed through Hirshfeld surface analysis and time‐dependent density functional theory (TD‐DFT) calculations.     

Water‐mediated intermolecular interactions in 1,2‐O‐cyclohexylidene‐myo‐inositol: a quantitative analysis

The syntheses of new myo‐inositol derivatives have received much attention due to their important biological activities. 1,2‐O‐Cyclohexylidene‐myo‐inositol is an important intermediate formed during the syntheses of certain myo‐inositol derivatives. We report herein the crystal structure of 1,2‐O‐cyclohexylidene‐myo‐inositol dihydrate, C₁₂H₂₀O₆·2H₂O, which is an intermediate formed during the syntheses of myo‐inositol phosphate derivatives, to demonstrate the participation of water molecules and hydroxy groups in the formation of several intermolecular O—H…O interactions, and to determine a low‐energy conformation. The title myo‐inositol derivative crystallizes with two water molecules in the asymmetric unit in the space group C 2/c , with Z = 8. The water molecules facilitate the formation of an extensive O—H…O hydrogen‐bonding network that assists in the formation of a dense crystal packing. Furthermore, geometrical optimization and frequency analysis was carried out using density functional theory (DFT) calculations with B3LYP hybrid functionals and 6‐31G(d), 6‐31G(d,p) and 6‐311G(d,p) basis sets. The theoretical and experimental structures were found to be very similar, with only slight deviations. The intermolecular interactions were quantitatively analysed using Hirshfeld surface analysis and 2D (two‐dimensional) fingerplot plots, and the total lattice energy was calculated.     

The Theoretical and Experimental Investigation of the Fluorinated Palladium β-Diketonate Derivatives: Structure and Physicochemical Properties

To search for new suitable Pd precursors for MOCVD/ALD processes, the extended series of fluorinated palladium complexes [Pd(CH₃CXCHCO(R))₂] with β-diketone [tfa−1,1,1-trifluoro-2,4-pentanedionato (1); pfpa−5,5,6,6,6-pentafluoro-2,4-hexanedionato (3); hfba−5,5,6,6,7,7,7-heptafluoro-2,4-heptanedionato (5)] and β-iminoketone [i-tfa−1,1,1-trifluoro-2-imino-4-pentanonato (2); i-pfpa−5,5,6,6,6-pentafluoro-2-imino-4-hexanonato (4); i-hfba-5,5,6,6,7,7,7-heptafluoro-2-imino-4-heptanonato (6)] ligands were synthesized with 70–80% yields and characterized by a set of experimental (SXRD, XRD, IR, NMR spectroscopy, TG) and theoretical (DFT, Hirshfeld surface analysis) methods. Solutions of Pd β-diketonates contained both cis and trans isomers, while only trans isomers were detected in the solutions of Pd β-iminoketonates. The molecules 2–6 and new polymorphs of complexes 3 and 5 were arranged preferentially in stacks, and the distance between molecules in the stack generally increased with elongation of the fluorine chain in ligands. The H…F contacts were the main ones involved in the formation of packages of molecules 1–2, and C…F, F…F, NH…F contacts appeared in the structures of complexes 4–6. The stability of complexes and their polymorphs in the crystal phases were estimated from DFT calculations. The TG data showed that the volatility differences between Pd β-iminoketonates and Pd β-diketonates were minimized with the elongation of the fluorine chain in the ligands.     

Crystal structures,packing features,Hirshfeld surface analyses and DFT calculations of hydrogen‐bond energy of two homologous 8a‐aryl‐2,3,4,7,8,8a‐hexahydropyrrolo[1,2‐a]pyrimidin‐6(1H)‐ones

The crystal structures and packing features of two homologous Meyer's bicyclic lactams with fused pyrrolidone and medium‐sized perhydropyrimidine rings, namely, 8a‐phenyl‐2,3,4,7,8,8a‐hexahydropyrrolo[1,2‐a]pyrimidin‐6(1H)‐one, C₁₃H₁₆N₂O ( 1 ), and 8a‐(4‐methylphenyl)‐2,3,4,7,8,8a‐hexahydropyrrolo[1,2‐a]pyrimidin‐6(1H)‐one, C₁₄H₁₈N₂O ( 2 ), were elucidated, and Hirshfeld surface plots were calculated and drawn for visualization and a deeper analysis of the intermolecular noncovalent interactions. Molecules of 1 and 2 are weakly linked by intermolecular C=O…H—N hydrogen bonds into chains, which are in turn weakly linked by other C=O…H—C_ar interactions. The steric volume of the substituent significantly affects the crystal packing pattern.