Hydrogen-bonded supramolecular motifs in crystal structures of trimethoprim barbiturate monohydrate (I) and 2-amino-4,6-dimethylpyrimidinium barbiturate trihydrate (II)

In the present study, we report the crystal structures of two organic salts, namely 2,4-diamino-5-(3′,4′,5′-trimethoxybenzyl)pyrimidinium (TMP) barbiturate monohydrate (TMPBAR) (I), 2-amino-4,6-dimethylpyrimidinium (AMPY) barbiturate trihydrate (AMPYBAR) (II). In both complexes, one ring nitrogen of TMP and AMPY are protonated as a result of proton transfer from the−CH₂ group of barbituric acid. In compound (I), the TMP cation and barbiturate anion are paired through twoN−H···O and one N−H···N hydrogen bonds. This pair further self-organizes through N−H···O hydrogen bonds to generate an array of six hydrogen bonds. These arrays are further cross-linked by N−H···O hydrogen bonds forming a sheet-like structure. The water molecule is also embedded in the sheet via O−H···O and C−H···O hydrogen bonds, forming a rosette-like supramolecular motif. TMP cations are also bridged by alternating water molecules via C−H···O and O−H···N hydrogen bonds. In compound (II), the symmetrical barbiturate anions self-organize on both sides through N−H···O hydrogen bonds generating a supramolecular chain. These chains are cross-linked by the three water molecules. A pair of barbiturate anions and two water molecules constitute an array of four hydrogen bonds (DADA quadruple array). These arrays are cross-linked by another water molecule. 2-Amino-4,6-dimethylpyrimidine cations are paired through N−H···N hydrogen bonds. These pairs are bridged by three water molecules generating a supramolecular ribbon. The barbiturate chains and base pairs are arranged in an alternate manner via N−H···O and O−H···O hydrogen bonds to generate a 3-D network.     

The effect of methyl group on the cooperativity between three types of hydrogen bond: O?H···O,C?H···O,and O?H···π

The effect of the methyl group on the cooperativity between three types of hydrogen bond (O H···O, C H···O, and O H···π) in cyclic complex involving an acetylene and two waters has been studied on the basis of high-level ab initio calculations. The total interaction energy of three hydrogen bonds increases as the number of methyl group in the complex increases. The binding distances of O H···π and O H···O hydrogen bonds shorten, while that of C H···O hydrogen bond elongates with increasing methyl group. This indicates that addition of methyl group leads to enhancement of O H···π and O H···O hydrogen bonds, and weakening of C H···O hydrogen bond, as also shown in frequency shift, chemical shifts, charge populations, and stabilization energies of orbital interactions. Although the presence of methyl group has a complicated effect on different type of hydrogen bond, the cooperativity of three hydrogen bonds increases in general with the addition of methyl group. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Cellulose Iβ investigated by IR-spectroscopy at low temperatures

Highly crystalline oriented Halocynthia roretzi cellulose Iβ films were investigated by IR-spectroscopy between ?180 and +10 °C. Changes in the IR-spectra induced by temperature were compared to published changes induced by mechanical stretching. This made it possible to conclude that frequency shifts in the O–H stretching region of the IR-spectra due to temperature were not predominantly an indirect effect of thermal expansion leading to greater O–O distances, but were due directly to the effect of temperature on the O–H···O hydrogen bonds. Temperature induced frequency shifts of C–H stretching bands were consistent with the presence of weak inter-sheet C–H···O bonds. Furthermore, no phase transition in cellulose Iβ was found between ?180 and +10 °C.     

Two-dimensional sheet based on C–H···N hydrogen bonds within an organic cocrystal: a crystallographic,spectroscopic and theoretical study

The cocrystal containing 1,2,4,5-tetracyanobenzene (TCNB) and trans-1,2-bis(4-pyridyl)ethylene (4,4′-BPE) has been realised (TCNB)·(4,4′-BPE) 1. Compound 1 produces a two-dimensional sheet based on two different types of C–H···N hydrogen bonds. Each molecule within the cocrystal functions as both a donor and an acceptor of hydrogen bonds. Weak hydrogen bonds such as these, acting as the driving force to produce a polymeric assembly, are not investigated as frequently as stronger and more traditional O–H···O and O–H···N hydrogen bonds within multicomponent cocrystals. The existence of the different types of C–H···N hydrogen bonds was confirmed by single-crystal X-ray diffraction as well as infrared spectroscopy. The overall interaction energies for both types of hydrogen bonds were determined by computational calculations at various levels of theory.     

Unraveling weak interactions in aniline-pyrrole dimer clusters

Weak intermolecular interactions in aniline-pyrrole dimer clusters have been studied by the dispersion-corrected density functional theory(DFT) calculations. Two distinct types of hydrogen bonds are demonstrated with optimized geometric structures and largest interaction energy moduli. Comprehensive spectroscopic analysis is also addressed revealing the orientation-dependent interactions by noting the altered red-shifts of the infrared and Raman activities. Then we employ natural bond orbital(NBO)analysis and atom in molecules(AIM) theory to have determined the origin and relative energetic contributions of the weak interactions in these systems. NBO and AIM calculations confirm the V-shaped dimer cluster is dominated by N.H···N and C.H···π hydrogen bonds, while the J-aggregated isomer is stabilized by N.H···π, n→π* and weak π···π* stacking interactions.The noncovalent interactions are also demonstrated via energy decomposition analysis associated with electrostatic and dispersion contributions.     

Structure-based evaluation of the regioselectivity in bifurcated hydrogen bonds

Unsymmetrical phenolic (thio)urea molecules are investigated and compared to evaluate the regioselectivity of the bifurcated hydrogen bonds. The supramolecular aggregation can feature self-sorting homomeric α-networks through recognition between N–H···O(S) and O–H···O intermolecular hydrogen bonds. The regioselectivity of bifurcated hydrogen bond was investigated using single crystal X-ray diffraction studies, DFT calculations and Cambridge Structural Database analysis. The influence of several key variables on the fidelity of regioselectivity was described.     

Synthesis,structure, and character of two rare earth carboxylic acid complexes

Two rare earth carboxylic acid complexes, [Sm(MeBA)₃(2,2′-bipy)]₂·2(2,2′-bipy) (MeBA = 3-methylbenzoic acid; 2,2′-bipy = 2,2′-bipyridine) (1) and [Pr(MeBA)₃(H₂O)₂]_n?n(4,4′-bipy) (4,4′-bipy = 4,4′-bipyridine) (2), have been synthesized under hydrothermal conditions and structurally determined by single-crystal X-ray diffraction. Compound 1 is a dimer and further assembles into an infinite chain, two-dimensional net and three-dimensional supramolecular structure via weak π–π and C–H···π interactions. Some 2,2′-bipy coordinates with Sm and some exist by non-covalent C–H···π interactions. Compound 2 is a 1D infinite chain structure, with adjacent 1D chains connected into a 2D layer structure by O–H···N hydrogen bonds. The two complexes were characterized by elemental analyses, IR, photoluminescence, and TGA. In order to illustrate subtle structural characteristics of intermolecular interactions and magnetic sensitivity of the complex, 2D-IR correlation spectra (2D-IR COS) under magnetic perturbation for 1 were performed.     

A new imidazophenanthroline derivative and its Hg(II) complex: structures,photophysical properties,and DFT calculations

A new ligand (L) and its mercury(II) complex have been synthesized under mild conditions. X-ray single-crystal structural analyses reveal 1-D, 2-D, and 3-D supermolecular structure of L and HgLI₂. Solvent molecules and various weak interactions, including hydrogen bonds (N–H···N, O–H···O, and O–H···N) and π–π interactions play signi?cant roles in the ?nal supermolecular structures. Detailed investigation on ¹H NMR spectra of L and HgLI₂ are presented. Their photophysical properties were investigated both experimentally and theoretically.     

A polarizable dipole–dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen‐bonded complexes

In this article, a polarizable dipole–dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen‐bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N? H, C?O, and C? H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole–dipole interaction model to a series of hydrogen‐bonded complexes containing the N? H···O?C and C? H···O?C hydrogen bonds, such as simple amide‐amide dimers, base‐base dimers, peptide‐base dimers, and β‐sheet models. We find that a simple two‐term function, only containing the permanent dipole–dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6‐31G(d) method, whereas the high‐quality counterpoise‐corrected (CP‐corrected) MP2/aug‐cc‐pVTZ interaction energies for the hydrogen‐bonded complexes can be well‐reproduced by a four‐term function which involves the permanent dipole–dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole–dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen‐bonded complexes are further discussed. © 2013 Wiley Periodicals, Inc.     

Synthesis and Crystal Structure of a [Mo8O26]4– Cluster Derivative with 4‐MePyH+. First β‐Octamolybdate Derivative with π–π Stacking

Dioxobis(pyridine‐2‐thiolate‐N, S)molybdenum(VI) (MoO₂(Py‐S)₂), reacts with of 4‐methylpyridine (4‐MePy) in acetonitrile, by slow diffusion, to afford the title compound. This has been characterized by elemental analysis, IR and ¹H NMR spectroscopy. The X‐ray single crystal structure of the complex is described. Structural studies reveal that the molecular structure consists of a β‐Mo₈O₂₆ polyanion with eight MoO₆ distorted edge‐shared octahedra with short terminal Mo–O bonds (1.692–1.714 Å), bonds of intermediate length (1.887–1.999 Å) and long bonds (2.150–2.473 Å). Two different types of hydrogen bonds have been found: N–H···O (2.800–3.075 Å) and C–H···O (3.095–3.316 Å). The presence of π–π stacking interactions and strong hydrogen bonds are presumably responsible for the special disposition of the pyridinic rings around the polyanion cluster.     

Synthesis and crystal structure of 2-{5-[2-(2,6-dichlorophenylamino)benzyl]-4-p-tolyl-4H-1,2,4-triazol-3-ylthio}acetate

The compound 2-{5-[2-(2,6-dichlorophenylamino)benzyl]-4-p-tolyl-4H-1,2,4-triazol-3-ylthio}acetate has been prepared and characterized by IR, ¹H NMR, ¹³C NMR and mass spectra. The crystal and molecular structure were further confirmed using single crystal X-ray diffraction. The crystal structure has been found to be stabilized by intermolecular C–H···O interaction generating bifurcated hydrogen bonds whereas the C–H···N interactions generate chain of molecules. The intramolecular N–H···N hydrogen bond forms a ring with S(7) graph-set motif.     

Intramolecular S···O chalcogen bond in thioindirubin

Results of X-ray diffraction study and quantum-chemical calculations revealed that molecular conformation of thioindirubin molecule creates suitable conditions for formation of intramolecular C–H···O and S···O interactions. Analysis of molecular electrostatic potential (MEP) demonstrates existence of two areas of positive MEP (σ-holes) in the outermost part of the sulfur atom on the continuation of the lines of the C–S bonds. One of these σ-holes is oriented toward region of negative MEP around the oxygen atom of carbonyl group. Such situation corresponds to formation of σ-hole or chalcogen bond. Existence of both types of bonding interactions is confirmed by topological analysis of electron density distribution using “Atoms in Molecules” (AIM) theory. Energies of the C–H···O hydrogen bond and the S···O σ-hole bond derived from AIM and NBO theories are very close.     

A DFT investigation on hydrogen- and halogen-bonding interactions in dichloroacetic acid: application of NMR-GIAO and Bader theories

A quantum chemistry investigation was carried out to examine hydrogen- and halogen-bonds properties in crystalline dichloroacetic acid (DCAA). We reported a systematic density functional theory study of the ¹⁷O, ³⁵Cl, and ¹H nuclear magnetic resonance (NMR) parameters in DCAA. Our results indicated that for those nuclei participated in the hydrogen- and halogen-bonding interactions; NMR parameters exhibit considerable changes on going from the isolated molecule model to the crystalline DCAA. Of course, the magnitude of these changes at each nucleus depends directly on its amount of contribution to the interactions. The topology of the electron density of O–H···O, C–H···O, Cl···Cl, and Cl···O interactions in solid DCAA was characterized using quantum theory of atoms in molecules (QTAIM). Based on QTAIM results, a partial covalent character is attributed to the O–H···O hydrogen bonds in DCAA, whereas all C–H···O, Cl···O, and Cl···Cl intermolecular contacts are weak and basically electrostatic in nature. Moreover, an approximate linear relationship seems to exist for each of the proton chemical shifts and anisotropies as a function of ρ_BCP.     

Molecular dynamics of 6‐methyl‐2‐phenyl‐2,3‐dihydro‐4H‐chromen‐4‐one and 6‐methyl‐2‐(4‐nitrophenyl)‐2,3‐dihydro‐4H‐chromen‐4‐one (flavanone) derivatives in a solution studied by NMR spectroscopy

Molecular dynamics of benzoxazepin, oxime, pyrazole, and thiosemicarbazone derivatives of some flavanones have been investigated in a solution using NMR. The results confirm the formation of different O–H···O, O–H···N, N···H–N type intramolecular hydrogen bonds in the pyrazole and oxime molecules. The rotational barrier energy and energy of intramolecular hydrogen bonds have been determined. Copyright © 2013 John Wiley & Sons, Ltd.     

A novel 1:2 cucurbit[8]uril inclusion complex with N-phenylpiperazine hydrochloride

A new 1:2 inclusion complex of cucurbit[8]uril (CB[8]) and protonated N-phenylpiperazine was synthesized and characterized by ¹H NMR and X-ray crystallography. The crystal structure showed that the phenyl rings of the two equivalents of guest encapsulated in the cavity of CB[8] are parallel to one another with a mean plane separation of 3.899 Å. In contrast, the piperazinyl phenyl ammonium moieties slightly protrude from the ureidyl carbonyl lined portals in order to accommodate the ion–dipole interaction between host and guest which provides a substantial driving force for the assembly. The oxygen atoms of the carbonyl groups form hydrogen bonds with the hydrogen atoms in both bridging methylene groups of CB[8] and water molecules. There are also hydrogen bonds formed among CB[8], water, and the protonated piperazinyl rings. These hydrogen bonds are formed between the ureidyl C=O groups and hydrogens in methylenes of piperazinyl rings; through hydrogen bonding N⁺–H···O(H)–H···O=C. The protonated piperazinyl rings connect the carbonyl groups with the bridging water molecules.     

Azabicyclo[3.3.1]nonanone: a case when weak interactions are preferred over strong hydrogen bonds

Derivatives of azabicyclo[3.3.1]nonanone tend to prefer for weak interactions in the crystal over strong N–H···O hydrogen bonds. The main stabilizing forces in the investigated azatricyclo[7.3.1.0^2,7]trideca-trienone derivatives are C–H···O, N–H···π and C–H···π interactions, leading to interesting structural patterns. The azabicyclo[3.3.1]nonanone ring adopts chair-envelope conformation having exo-C2,C4-aromatic substituents. Amino NH is in trigonal pyramidal configuration. The interesting stereochemistry of azabicyclo[3.3.1]nonanone, driving exceptional preference for weaker interactions over strong hydrogen bonds serves a useful example toward engineering and design strategy, and structure prediction methodologies.     

Synthesis and crystal structure of mercury(II) chloride–ferron (7-iodo-8-hydroxyquinoline-5-sulfonic acid) adduct

A mercury(II) chloride adduct of ferron (7-iodo-8-hydroxyquinoline-5-sulfonic acid), [HgCl₂ (C₉H₆INO₄)·H₂O] has been synthesized and characterized by X-ray diffraction analysis and spectroscopic studies. The compound crystallizes in P2₁/c space group, a?=?8.919(3), b?=?23.216(3), c?=?7.714(3)?Å, β?=?95.79(3)°. The coordination geometry around mercury is distorted square planar [(2+2) coordination] with two short Hg–Cl bonds [2.308(2) and 2.309(18)?Å] and two long Hg–O(sulfonate) [2.738(4)?Å] and Hg–O(water) [2.889(4)?Å] bonds. The sulfonic group is deprotonated, the proton having migrated to the quinoline N atom that forms intermolecular hydrogen bonds. The inversion related organic ligands are stacked over one another. The crystal structure is further stabilized by a C–H···O, O–H···O and N–H···O hydrogen bonds.     

Hirshfeld surface analysis and spectroscopic and DFT studies of p-acetotoluidide and p-thioacetotoluidide

The Hirshfeld surface analysis, theoretical calculation, and IR and Raman spectra of p-acetotoluidide and p-thioacetotoluidide were reported. Hirshfeld surfaces and fingerprint plot have been used for visualizing, exploring, and quantifying intermolecular interactions in the crystal lattice of the title compounds. The packing of the molecules in the crystal structure of p-acetotoluidide and p-thioacetotoluidide forms the chains of N–H···O and N–H···S hydrogen bonds, respectively. The close contacts are also dominated by H···H and H···C/C···H interactions. The analysis of Hirshfeld surface has been well correlated with the spectroscopic studies. Theoretical calculations of the title compounds’ isolated molecule have been carried out using DFT at the B3LYP level.     

Polysulfonylamine. CLXXVIII Onium‐Salze des Benzol‐1,2‐di(sulfonyl)amins (HZ): Eine zweite Kristallform des Ammonium‐Salzes NH4Z·H2O und Kristallstruktur des Bis(triphenylphosphoranyliden)ammonium‐Salzes [Ph3PNPPh3]Z

Polysulfonylamines. CLXXVIII. Onium Salts of Benzene‐1,2‐di(sulfonyl)amine (HZ): A Second Crystal Form of the Ammonium Salt NH₄Z·H₂O and Crystal Structure of the Bis(triphenylphosphoranylidene)ammonium Salt [Ph₃PNPPh₃]Z A dimorphic form of NH₄Z·H₂O, where Z^? is N‐deprotonated ortho‐benzenedisulfonimide, has been obtained and structurally characterized (previously known form 1A : monoclinic, P2₁/c, Z′ = 1; new polymorph 1B : monoclinic, P2₁/n, Z′ = 1). Both structures are dominated by an abundance of classical hydrogen bonds N⁺–H/O–H···O=S/OH₂, whereby the anionic N^? function does not act as an acceptor. The major difference between the dimorphs arises from the topology of the hydrogen bond network, which is two‐dimensional in 1A , leading to a packing of discrete lamellar layers, but three‐dimensional in 1B . Moreover, the latter network is reinforced by a set of weak C–H··O/N hydrogen bonds, whereas the layered structure of 1A displays only one independent C–H···O bond, providing a link between adjacent layers. The compound [Ph₃PNPPh₃]Z ( 2 , monoclinic, P2₁/c, Z′ = 1) is the first structurally authenticated example of an ionic Z^? derivative in which the cation contains neither metal bonding sites nor strong hydrogen bond donors. This structure exhibits columns of anions, surrounded by four parallel columns of cations, giving a square array. The large cations are associated into a three‐dimensional framework via weak C–H···C(π) interactions and an offset face‐to‐face phenyl interaction, while the anions occupy tunnels in this framework and are extensively bonded to the surrounding cations by C–H···O/N^? hydrogen bonds and C–H···C(π) interactions.     

Synthesis and Structure of Tetraphenylphosphonium Carboxylates

Hydrates of tetraphenylphosphonium carboxylates were synthesized by the reaction of equimolar amounts of pentaphenylphosphorus with 2-methoxybenzoic, 2-nitrobenzoic, and maleic acids in benzene. The product of the pentaphenylphosphorus reaction with tetrafluorophthalic acid (mole ratio 2: 1) is bis- (tetraphenylphosphonium) tetrafluorophthalate hydrate. According to the X-ray analysis data, crystals of tetraphenylphosphonim carboxylates are formed by tetraphenylphosphonim tetrahedral cations and single- or double-charged carboxylate anions. Structural organization of the crystals is determined by C–H···O weak hydrogen bonds formed with the participation of carboxylate groups and water molecules or manifold C–H···F interactions between cations and anions.