Hydrogen bonding of formo- and thioformohydroxamic acid with methanethiol and methaneselenol as amino acid side chain groups

Hydrogen (H-) bonding ability of most stable keto and enol tautomers of formo- and thioformohydroxamic acids has been investigated by optimizing their 1:1 aggregates with MeSH and MeSeH as model molecules for sulfur and selenium containing amino acid side chains. Although enol is the most stable conformer of thioformohydroxamic acid, yet the most stable aggregate in both hydroxamic acids (HAs) being formed with keto conformer suggests that H-bonding can influence specific conformational dominance. In the aggregates, HAs preferably act as H-bond donor and S/Se of MeSH and MeSeH act as H-bond acceptor. The S···H and Se···H H-bonds although disfavored by electrostatics yet are favored by significant charge transfer. H-bonding preference and strength of interaction of HAs with MeSH and MeSeH is remarkably similar but markedly different from MeOH. AIM and NBO analysis have been employed to understand the role of electron delocalization, bond polarizations, charge transfer etc. as contributors to stabilization energy.     

Crystallographic and conformational analysis of two novel trans-azo benzene compounds

The molecular and crystal structure of (E)-2-Acetyl-4-(2-bromophenyldiazenyl)phenol (1) and (E)-2-Methyl-4-(o-tolyldiazenyl)phenol (2) were characterized and determined by single crystal X-ray diffraction method besides spectroscopic means. The periodic organization of 1 is stabilized by C–H···O type weak H-bond and Br···O type weak halogen bonding and thus, a two dimensional puckered network is established almost parallel to () the plane. Molecules of 2 are linked into C(7) chains generated by translation along the [1 0 1] direction with the aid of O–H···N type H-bonds, and these chains are strengthened by C–H···π interactions involving o-tolylphenol ring. Quantum chemical studies at B3LYP/6-311 ++G(d,p) level reveal that potential barrier of the compounds around Ar–N torsions is of double minimum character unless it is defected by the presence of o-substituent groups in the vicinity of the azo bridge. The results from crystallographic and quantum chemical studies suggest that azo benzene compounds may adapt non-planar geometry apart from the most stable planar conformation, which is located on the secondary minima of double potential barrier regarding rotational motion around Ar–N bonds.     

Synthesis,crystal structure and other properties of the complexes of Er(III), Yb(III) and Lu(III) with 4,4′-bipyridine and dichloroacetates

A novel mixed-ligand complexes of Er(III), Yb(III) and Lu(III) with title ligands were prepared and characterized by chemical and elemental analysis and IR spectroscopy, conductivity (in methanol, dimethyloformamide and dimethylsulphoxide). The thermal properties of complexes in the solid state were studied. The mode of metal–ligand coordination was discussed. The title compounds are isomorphic and isostructural in solid state. All atoms in studied compounds lie in general positions but occurrence of inversion on the midpoint of the bond linking two pyridine rings leads to existence in asymmetric unit one complex molecule and half of outer coordination sphere 4-bpy molecule. All chelating carboxylate groups are symmetrically bonded to the metal cations. The molecules of studied compounds are connected to the three dimensional network via O–H···O and O–H···N intermolecular hydrogen bonds. In the structures also exist C–H···O, C–H···Cl weak hydrogen bonds and π····π stacking interactions.     

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.     

Self-assembly of a [2]Pseudorotaxane Composed of Cucurbit[6]uril into Linear Pseudopolyrotaxanes by N–H···O, C–H···O and π···π Interactions

The [2]pseudorotaxane of cucurbit[6]uril (Q6) with 1,6-bis(imidazol-1-yl)hexane dihydrobromide was synthesized and its crystal structure was described. The structure of [2]pseudorotaxane was mainly stablized by host–guest C–H···O interactions. Self-assembly of the [2]pseudorotaxane produces infinite one-dimensional chains with intermolecular N–H···O, C–H···O, and π···π interactions; thus, a linear non-covalent pseudopolyrotaxane is formed.     

Combined DFT with NBO and QTAIM studies on the hydrogen bonds in (CH<Subscript>3</Subscript>OH)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 2–8) clusters

The (CH₃OH) _n (n = 2–8) clusters formed via hydrogen bond (H-bonds) interactions have been studied systemically by density functional theory (DFT). The relevant geometries, energies, and IR characteristics of the intermolecular OH···O H-bonds have been investigated. The quantum theory of atoms in molecule (QTAIM) and natural bond orbital (NBO) analysis have also been applied to understand the nature of the hydrogen bonding interactions in clusters. The results show that both the strength of H-bonds and the deformation are important factors for the stability of (CH₃OH) _n clusters. The weakest H-bond was found in the dimer. The strengths of H-bonds in clusters increase from n = 2 to 8, moreover, the strengths of H-bonds in (CH₃OH) _n (n = 4–8) clusters are remarkably stronger than those in (CH₃OH) _n (n = 2, 3) clusters. The small differences of the strengths of H-bonds among (CH₃OH) _n (n = 6–8) clusters indicate that a partial covalent character is attributed to the H-bonds in these clusters. The linear relationships between the electron density of BCP (ρ_b) and the H···O bond length of H-bonds as well as the second-perturbation energies E(2) have also been investigated and used to study the nature of H-bonds, respectively.     

Syntheses,weak interactions, 3D network structures and magnetic properties of two salts based on bis(maleonitriledithiolate)copper(II) anion and substituted triphenylphosphonium cation

Two new salts, [BzTPP]₂[Cu(mnt)₂] (1) and [4NO₂BzTPP]₂[Cu(mnt)₂] (2) (BzTPP⁺ = benzyltriphenylphosphonium and mnt²⁻ = maleonitriledithiolate) have been prepared and characterized by elemental analyses, UV, IR, molar conductivity and single-crystal X-ray diffraction. The single-crystal structure analysis shows that 1 crystallizes in the monoclinic space group P2₁/n, while 2 crystallizes in the triclinic space group P−1. The effects of weak intramolecular interactions such as C–H···O, C–H···S, C–H···N, C–H···Cu hydrogen bonds and p···π, π···π stacking interactions in the solids generate a 3D network structure. It is noted that the change in the molecular topology of the counteraction when the 4-substituted group in the benzyl ring is changed from H to NO₂ results in differences in the crystal system, space group, weak interactions and the stacking mode of the cations and anions of 1 and 2. The magnetic susceptibilities of these salts measured in the temperature range 2.0 to 300 K show weak ferromagnetic coupling features with θ = 2.05 × 10⁻² K for 1 and 5.13 × 10⁻³ K for 2.     

Electron-density studies on hydrogen bonding in chromone derivatives. Part II: comparative study

The experimental electron density of a chromone derivative was determined from a multipole refinement of 100 K X-ray synchrotron data and complemented by theoretical calculations with experimental and optimized geometry. Atomic and topological properties were obtained using the Quantum Theory of Atoms in Molecules approach. The examination of topological parameters unambiguously showed π-delocalization within the H-bonded ring. The application of source function analysis confirmed the intramolecular N–H···O hydrogen bond to be a resonance-assisted hydrogen bond. The topological study confirmed the covalent nature of N–H···O interaction and the electrostatic nature of weak C–H···O interactions.     

Self-assembled cobalt(II) Schiff base complex: synthesis, structure, and magnetic properties

Abstract  

A mononuclear complex [CoL₂Cl₂]·3.5H₂O (L = 2-[(2,2-diphenylethylimino)methyl]pyridine-1-oxide) has been synthesized and characterized by X-ray structure analysis. The crystal structure confirms the formation of an interesting porous framework with channel diameters of about 8 ? through weak C–H···π and C–H···Cl interactions. The magnetic properties of this complex have also been studied, and the susceptibility and magnetization data were analyzed in terms of the spin Hamiltonian formalism. They confirm substantial zero-field splitting, D/hc = 75 cm⁻¹.     

Hydrogen-bonding interaction in a complex of amino acid with urea studied by DFT calculations

Theoretical studies on hydrogen-bonded complexes between amino acids (glycine, alanine, and leucine) and urea in gas phase have been carried out using density functional theory (DFT) and ab initio methods at the B3LYP/6-311++g** and MP2/6-311++g** theory levels. The structures, binding energy, Chelpg (charges from electrostatic potentials using a grid-based method) charge distribution, and bond characteristics of the mentioned complexes were calculated. Urea is a good H-bond donor and an excellent receptor for highly electronegative atoms like O and N, through the formation of two or more hydrogen bonds. The NH₂ and COOH groups of amino acids can form several different types of H-bonds with urea molecular, as well as C^αH and alkyl side chains. The calculated high binding energy also suggests multiple H-bonds formed in one complex. The OH···O contact is the strongest hydrogen bond interaction with H···O separation around 1.65 Å and its relevant angle close to 176°. The closely linear amide H-bonds NH···O and OH···N strongly stabilize the amino acid–urea complex with H···O separation between 1.89 and 2.38 Å. The weaker CH···O/N H-bonds are also discussed as significant interaction in biological systems involving amino acids.     

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.     

Syntheses,molecular structures and magnetic properties of two hybrid organic–inorganic salts of bis(maleonitriledithiolato)copper(II) and substituted benzyl-4-dimethylaminopyridinium cations

Two new hybrid organic–inorganic salts, [BzDMAP]₂[Cu(mnt)₂](1) and [NO₂BzDMAP]₂[Cu(mnt)₂] (2) ([BzDMAP]⁺ = 1-benzyl-4′-dimethylaminopyridinium, [NO₂BzDMAP]⁺ = 1-(4′-nitrobenzyl)-4′-dimethylaminopyridinium, and mnt²⁻ = maleonitriledithiolate) have been characterized structurally and magnetically. The [BzDMAP]⁺ or [NO₂BzDMAP]⁺ cations (C) and the [Cu(mnt)₂]²⁻ anions (A) in 1 and 2 stack into a 1D alternating CC-A-CC-A-CC column. The Cu···N, π···π, C–H···N, C–H···O, and C–H···S weak interactions play important roles in the molecular stacking and generate a 2D or 3D structure of 1 and 2. The magnetic susceptibilities of these salts measured in the temperature range 2.0–300 K show weak antiferromagnetic coupling features with θ = −2.370 K for 1 and −0.222 K for 2.     

Four complexes with a bulky carboxylate ligand: syntheses,crystal structures,and luminescent properties

Abstract  

Four complexes of 3,3-diphenylpropanoate (L) and 4,4′-bipyridine as auxiliary bridging ligands were synthesized and characterized, namely [Zn(L)₂(4bpy)(EtOH)₂]_∞ (1), [Co(L)₂(4bpy)(EtOH)₂]_∞ (2), [Ni(L)₂(4bpy)(EtOH)₂]_∞ (3), and [Cu(L)₂(4bpy)(H₂O)]_∞ (4) (4bpy = 4,4′-bipyridine). X-ray single-crystal diffraction analyses show that complexes 1–4 all take one-dimensional (1D) fishbone-like structures incorporating bridging 4bpy ligands. The complexes show different supramolecular frameworks interlinked via intermolecular hydrogen bonds, π···π stacking, and/or C–H···π supramolecular interactions. Complex 3 only has a simple one-dimensional fishbone-like chain, whereas complexes 1 and 2 show two-dimensional supramolecular structures by interchain C–H···O hydrogen bonds. Complex 4 is assembled into two-dimensional layers and then an overall three-dimensional framework by a combination of interchain O–H···O hydrogen bonds and C–H···π supramolecular interactions. The luminescent properties of the ligands and their complexes were investigated.     

Synthesis of some cyclopentenones and crystal structure of 4-hydroxy-3,4-bis(4-methoxyphenyl)-5,5-dimethyl-2-cyclopenten-1-one

Abstract  

Sodium-hydroxide-catalyzed condensation of di-p-methyl- and di-p-methoxybenzil with acetone derivatives was investigated in methanol. Di- and trisubstituted products were obtained as cyclopentenones, while tetraaryl-substituted systems were isolated as cyclopentadienones. The structures of the products were identified by elemental analysis, infrared (IR), nuclear magnetic resonance (¹H NMR), and mass spectroscopy. The solid-state structure of 4-hydroxy-3,4-bis(4-methoxyphenyl)-5,5-dimethyl-2-cyclopenten-1-one was further studied by single-crystal X-ray diffraction analysis. The title compound crystallizes in an orthorhombic space group and intermolecular O–H···O and C–H···O hydrogen bonds stabilize the crystal lattice.     

X-ray crystal structures of <Emphasis Type="Italic">p</Emphasis>-halogenated 6,6-diphenylfulvenes

Crystal structures of a series of p-halogenated 6,6-diphenylfulvenes 2–5 are reported and comparatively discussed including the known structure of the non-halogenate parent compound 1. The molecular structures show twisted conformations of the plane aryl and fulvene subunits against each other, rather unaffected by the different halogen substituents. The packing structures exclusively involve C–H···X (X = F, Cl, π) contacts while Hal···Hal and π-stacking interactions do not occur.     

Density functional theory and topological analysis on the hydrogen bonds in cysteine–propanoic acid complexes

The complexes formed via hydrogen bonding interactions between cysteine and propanoic acid have been studied at the density three-parameter hybrid functional DFT-B3LYP/6-311++G(d,p) level regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis was employed to elucidate the interaction characteristics in cysteine–propanoic acid (Cys–Prop) complexes. More than 10 kinds of hydrogen bonds (H-bonds) including intra- and inter-molecular H-bonds have been found in Cys–Prop complexes. The results show that both the strength of H-bonds and the deformation are important factors for the stability of Cys–Prop complexes. The strongest H-bonds (O2H^A···O1^B and O2H^A···O1^B) exist in the most stable Cys–Prop complex. The stronger H-bonds formed between hydroxyl and O (or N) atom usually stronger than those involve C (or S) atom. Relationships between the electron density (ρ) of BCP and H-bond length as well as the Fock matrix element (F _ij) has also been investigated and used to study the nature of H-bonds. Moreover, the results show that the change of the bond length linearly correlates with the corresponding frequency shift.     

Two manganese(II) complexes based on anthracene-9-carboxylate: Syntheses,crystal structures,and magnetic properties

Abstract  To explore the influence of the anthracene ring skeleton, with a large conjugated π-system, on the structures and properties of its complexes, two Mn^II complexes with anthracene-9-carboxylate ligand were synthesized and structurally characterized: {[Mn(L)₂(H₂O)₂](H₂O)}_∞ (1) and [Mn₂(L)₄(phen)₂(μ-H₂O)](CH₃OH) (2) (L = anthracene-9-carboxylate and phen = 1,10-phenanthroline). Complex (1) has a one-dimensional (1D) chain structure that is further assembled to form a two-dimensional (2D) sheet, and then an overall three-dimensional (3D) network by π···π stacking and/or C–H···π interactions. Complex (2) makes a dinuclear structure by incorporating the chelating phen ligand, which is further interlinked via inter-molecular π···π stacking and C–H···π interactions to generate a higher-dimensional supramolecular network along the different crystallographic directions. The results reveal that the bulky anthracene ring skeleton in L, by virtue of intra- and/or inter-molecular π···π stacking and C–H···π interactions, plays an important role in the formation of complexes (1) and (2). The magnetic properties of (1) and (2) were further investigated. As expected, the very long inter-metallic separations result in weak magnetic coupling, with the corresponding coupling constant values of J = −10 cm⁻¹ for (1) and J = −2.46 cm⁻¹ for (2). Graphical abstract  The constructions of two new Mn^II complexes comprising 1D chain (1) and dinuclear subunit (2) structures have been successfully achieved by using a bulky anthracene-9-carboxylic acid (HL), together with incorporating the chelating 1,10-phenanthroline as a co-ligand for (2). The result reveals that the bulky anthracene ring skeleton of HL, by virtue of intra- and/or inter-molecular π···π stacking and C–H···π interactions, plays an important role in the formation of the supramolecular architectures of (1) and (2). Moreover, magnetic properties of the complexes have been investigated.      

Structural and aromatic aspects for tautomerism of (Z)-6-((4-bromophenylamino)methylene)-2,3-dihydroxycyclohexa-2,4-dienone

The molecular and crystal structure of (Z)-6-((4-bromophenylamino)methylene)-2,3-dihydroxycyclohexa-2,4-dienone were determined by single crystal X-ray diffraction and spectroscopic methods. Molecules of the compound can be regarded as a resonance hybrid of cis-keto tautomer and zwitterionic form. Pairs of molecules of the compound generate pseudocyclic centrosymmetric R₂² (10) R_{2}^{2} (10) supramolecular synthons with the aid of O–H···O type intermolecular H-bonds. Stacking of R₂² (10) R_{2}^{2} (10) synthons along b-axis is stabilized by π···π interactions. Changes in both covalent topology and molecular geometry of the compound accompanying proton transfer were monitored by a relaxed PES scan with respect to hydroxyl bond length used as redundant internal coordinate. Quantum chemical studies at 6-311 + G(d,p) level reveal that bond lengths which are indicative to tautomerization process cannot reach their expected values even if proton transfer occurs in gas phase and pseudo-aromatic chelate ring formation has primary effect on the stabilization of NH tautomer. Resonance-assisted intramolecular H-bond affects the electronic state of its neighboring aromatic fragments.     

Studies on mono- and dinuclear bisoxime copper complexes with different coordination geometries

Two new mono- and dinuclear Cu(II) complexes, namely [CuL¹]·0.5H₂O (1) and [(Cu₂(L²)₂)(DMF)]·0.5DMF (2) (H₂L¹ = 1,2-bis{[(Z)-(3-methyl-5-oxo-1-phenyl-1H-pyrazolidin-4(4H)-yl)(phenyl)]methylene-aminooxy}ethane; H₂L² = 1,3-bis{[(Z)-(3-methyl-5-oxo-1-phenyl-1H-pyrazolidin-4(4H)-yl)(phenyl)] methyleneaminooxy}propane), have been synthesized and characterized by X-ray crystallography. The unit cell of complex 1 contains two crystallographically independent but chemically identical [CuL¹] molecules and one crystalline water molecule, showing a slightly distorted square-planar coordination geometry and forming a wave-like pattern running along the a-axis via hydrogen bonding and π···π stacking interactions. Complex 2 has a dinuclear structure, comprising two Cu(II) atoms, two completely deprotonated phenolate bisoxime (L²)²⁻ moieties (in the form of enol), and both coordinated and hemi-crystalline DMF molecules. Complex 2 has square-planar and square-pyramidal geometries around the two copper centers, whose basic coordination planes are almost perpendicular and form an infinite three-dimensional supramolecular network structure involving intermolecular C–H···N, C–H···O, and C–H···π(Ph) hydrogen bonding and π···π stacking interactions of neighboring pyrazole rings.     

Crystallographic and theoretical studies of 4,4′-dimethyl-7,7′-bi([1,2,5]thiadiazolo[3,4-b]pyridylidene)–chloranilic acid (1/1) with intermolecular O–H···N hydrogen bonds and S···O heteroatom interactions

Abstract  The molecular and crystal structure of a 1:1 co-crystal of 4,4′-dimethyl-7,7′-bi([1,2,5]thiadiazolo[3,4-b]pyridylidene)–chloranilic acid, (1), has been determined by X-ray diffraction at the monoclinic space group P2₁/c with cell parameters of a = 8.422(6), b = 7.343(4), c = 16.112(7) ?, β = 104.988(8)°, V = 962.5(10) ?³ and Z = 2. In the crystal structure, two components connect via the intermolecular O–H···N hydrogen bonds [2.804(4) ?] and S···O heteroatom interaction [2.945(3) ?] with R ₂ ²(7) couplings to form a unique and infinite one-dimensional supramolecular tape structure. The calculations of (1) at the HF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels can almost reproduce X-ray geometry. In addition, the distances of the intermolecular O–H···N and S···O interactions by MP2/6-31G(d) and B3LYP/6-31G(d) levels agree well with those in the crystal. The calculated binding energies corrected BSSE and ZPE are −4.487 (HF), −7.473 (MP2), and −5.640 (B3LYP) kcal/mol. The results suggest that the complex (1) is very stable and the dispersion interaction is significantly important for the attractive intermolecular interaction in (1). The NBO analysis has revealed that the n(N) → σ*(O–H) interaction gives the strongest stabilization to the system and the major interaction for the intermolecular S···O contact is n(O) → σ*(S–N). Index Abstract  In the crystal structure of the title compound, the molecules are linked by intermolecular O–H···N hydrogen bonds and short S···O heteroatom interactions with R ₂ ²(7) couplings to construct a unique and infinite one-dimensional supramolecular tape structure.