Weak hydrogen-, halogen- and stacking ππ bonding in crystalline 5-chloro-1-indanone. An analysis by using X-ray diffraction, vibrational spectroscopy and theoretical methods

Intermolecular forces of C–HO, C–Hπ, COCl and ππ types are present in the stable triclinic crystal structure of 5-chloro-1-indanone. They are analysed from a geometrical point of view supported in some extent by the analysis of the vibrational spectrum of the titled compound. Moreover, the molecular structure of the isolated species is calculated by using ab initio as well as density functional theory (DFT) methods together an assortment of basis sets. In order to obtain some information about the influence of intermolecular forces on the molecular structure, the calculated geometries of a free molecule were compared with the experimental solid phase geometry determined by X-ray crystallography.An analysis and assignment of the vibrational spectrum of the 5-chloro-1-indanone is accomplished by using IR and Raman experimental data along with Pulay et al.’s scaled quantum mechanical force field (SQM) methodology starting from the theoretical B3LYP/6-31G(d) and BLYP/6-31G(d) force fields under C_s symmetry.     

Blue-shifting intramolecular CH O(S) contacts in sterically strained systems

A group of model systems which may form chelate-type structures with intramolecular CH  Y (Y = O, S) contact is investigated computationally. The existence of several conformers permits to identify a reference molecule without the CH  Y intramolecular contact and to establish the blue-shifting character of this interaction. The CH stretching frequency in chelate forms is found to increase with respect to its value in the reference system. A parallel decrease of the CH bond distance is also established. The blue-shifting character of the intramolecular CH  Y contact is interpreted in terms of the sterically enforced repulsion between the hydrogen atom in CH and the electron donor Y. This interpretation is supported by the negative (repulsive) estimates of the energy contribution due to CH  Y contacts.     

Theoretical study of the influence of para- and meta-substituents on X-pyridineHF hydrogen bonding

The effects of O⁻, N (CH₃)₂, NH (CH₃), NH₂, C₂H₅, CH₃, OH, F, Cl, OF, Br, NO₂ and substituents in para- and meta-positions on X-pyridineHF hydrogen bond has been studied by HF, B3LYP and MP2 methods using 6-311++G(d,p) basis set. The relationship between hydrogen bond formation energy ΔE and electron donating (or withdrawing) of substituents has been investigated. In this respect, population analysis has been performed by atoms in molecules (AIM) and natural bond orbital (NBO) theories. The results of AIM and NBO analyses are in good agreement with calculated energy values. The relationship between Hammett coefficient and complexation energy has been established and the ρ constant has been calculated for hydrogen bonding. There is a relationship between σ and ΔE with a correlation coefficient equal to 0.94.     

Reaction of diacetylmonoxime with morpholine N-thiohydrazide in the absence and in presence of a metal ion: Facile synthesis of a thiadiazole derivative with non-bonded SS interaction

The condensation of diacetylmonoxime (damnx) with morpholine N-thiohydrazide (mth) in 1:1 molar ratio in ethanol (16 h) afforded a nitrogen–sulfur zwitterionic heterocyclic compound, N-(3,4-dimethyl-1,2,5-thiadiazole-2-ium-2-yl)morpholine-4-carbothioate (dtmc). However, the same reaction in presence of [Zn(OAc)₂]·2H₂O in ethanol under gentle reflux on (3 h) yielded the zinc complex, [Zn(Hdammthiol)(OAc)(H₂O)]·H₂O, where H₂dammthiol (H₂L²) is the thiol form of tridentate NNS donor thiohydrazone ligand, diacetylmonoxime morpholine N-thiohydrazone (Hdammth). Both the nitrogen–sulfur heterocyclic compound and the zinc complex have been characterized by elemental analyses, spectroscopy (IR, UV–Vis, ¹H NMR and ¹³C NMR) and single crystal X-ray crystallography. It is noteworthy that the heterocyclic compound shows SS interaction with distance 2.738 Å in its planar conformation. The heterocyclic compound forms two dimensional supramolecular sheets through C–HO and ππ interactions while the zinc complex, with distorted square pyramidal geometry, forms 1D supramolecular chain. A mechanism has been proposed for the formation of nitrogen–sulfur heterocyclic compound.     

C–HPt(II) interaction-controlled self-assembly and photophysics of chiral bis(pyrrol-2-ylmethyleneamino)cyclohexane platinum(II) complexes

Reaction of (R,R)-(−)- and (S,S)-(+)-1,2-bis(pyrrol-2-ylmethyleneamino)cyclohexane with K₂PtCl₄ afforded chiral, neutral platinum(II) Schiff base complexes of (R,R)-PtL and (S,S)-PtL with high yields. The rare C–HPt(II) intermolecular interaction was found to show considerable strength and directionality for controlling M and P helical supramolecular architectures of (R,R)-PtL and (S,S)-PtL, respectively, in crystal lattices. More importantly, the open square-planar geometry of platinum(II) complexes allows axial C–HPt(II) interaction, resulting in the ³(ππ^*) excited state with some mixing of the Pt(II) metal character observed both in concentrated solutions and in the solid state at room temperature.     

Nonadiabatic dissociation dynamics of ClHD van der Waals complex initiated by electron detachment of Cl–HD

Nuclear dynamics following the electron detachment of the Cl⁻–HD anion is investigated by a time-dependent wave packet propagation approach. Photodetachment of Cl⁻–HD promotes it to the van der Waals well region of the reactive ClHD potential energy surface. The latter is a manifold of three electronic states coupled by the electronic and (relativistic) spin-orbit coupling. Among the three surfaces, the electronic ground one is of ²Σ_1/2 type and yields products in their electronic ground state. The remaining two, ²Π_3/2 and ²Π_1/2, on the other hand, yield products in their excited electronic states. However, these two can yield products in their electronic ground state via nonadiabatic transitions to the ²Σ_1/2 state. The channel specific, HCl + D or DCl + H or Cl + HD, dissociation probabilities on this latter state are calculated both in the uncoupled and coupled surface situations. Separate initial transitions (via, photodetachment) to the ²Σ_1/2, ²Π_3/2 and ²Π_1/2 adiabatic electronic states of ClHD are considered in order to elucidate the nonadiabatic coupling effects on this important class of chemical reactions initiated by an electron detachment.     

Theoretical investigation of C–HM interactions in organometallic complexes: A natural bond orbital (NBO) study

The nature of C–HM agostic interactions in model metal complexes [M²⁺(CH₂CH₃)(PH₃)_nCl] (where M = Sc, Ti, V, Ti, Cr, Mn, Fe, Co, Ni, Cu, Zn; n = 1, 2, 3, 4) was studied with the natural bond orbital analysis (NBO) approach using density functional theory (DFT) optimized geometries at the B3LYP/6-31G(d,p) level of theory. The effect of nature of metal, coordination number, oxidation state and ligand field effects on the agostic interaction is examined. A set of 20 crystal structures of organometallic complexes taken from the Cambridge Structural Database (CSD) was studied computationally employing AIM theory and NBO analysis, and the applicability of these methods was critically accessed in demarcating the two types of interaction.     

Unimolecular chemistry of metastable dimethyl isophthalate radical cations

The MS/MS spectrum of the metastable molecular ions of dimethyl isophthalate 1 differs from that of the isomeric dimethyl terephthalate 2 by the observation of, inter alia, a quite intense loss of C,H₂,O ascribed to formaldehyde. Results obtained using a combination of mass spectrometry techniques suggest that this process could consist of an isomerization reaction of the molecular ion into an ion–neutral complex (INC) linking a benzoyl radical and neutral formaldehyde to a proton [ArCOHOCH₂]⁺. Within the complex, a proton transfer catalyzed by formaldehyde occurs resulting in the production of an ionized cyclohexadienylidene methanone (ketene) structure.     

Hydrogen-bond structures in poly(2-hydroxyethyl methacrylate): Infrared spectroscopy and quantum chemical calculations with model compounds

Hydrogen-bond structures in poly(2-hydroxyethyl methacrylate) (PHEMA) were investigated by infrared (IR) spectroscopy and quantum chemical calculations (QCC). A monomer of 2-hydroxyethyl methacrylate (HEMA) and model compounds of methyl acetate (MA) and methanol (MeOH) were also used. Evidences for OHOC and OHOH types of hydrogen-bonds were observed in an IR spectrum of a PHEMA solid. It was estimated from the present study that 47.3% of OH groups on the PHEMA side chain terminal are engaged in the OHOC type of hydrogen-bond, while the rest contributes to the OHOH type of hydrogen-bond.     

Competition between non-classical and classical hydrogen bonded sites in [BH3CN]: Spectral, energetic, structural and electronic features

Interaction of the salt (Ph₃PNPPh₃)BH₃CN with the various OH and NH proton donors in low polar media was studied by variable temperature (200–290 K) IR spectroscopy and theoretically by DFT calculations. The formation of two types of complexes containing non-classical dihydrogen bond to the hydride hydrogen (DHB) and classical hydrogen bond (HB) to nitrogen lone pair was shown in solution. The 1:1 complexes of both types (XHH and XHN) coexist in the presence of equimolar amount of proton donor. The addition of excess XH-acid leads to the increase of the classical HB content and appearance of the 1:2 complexes, where two basic sites work simultaneously. The structure, spectral characteristics, energy and electron redistribution were studied by DFT (B3LYP) method. The comparison DHB parameters of [BH₃CN]⁻ with those of the unsubstituted analogue [BH₄]⁻ allowed analyzing the electronic effects of the CN group on the basic properties of boron hydride moiety. The electronic influence of the BH₃ group on CN⁻HX hydrogen bond was also established by comparison with the corresponding classical HB to the CN⁻ anion.     

Interligand interactions involved in the molecular recognition between copper(II) complexes and adenine or related purines

The available crystal structure information in the CSD database on ternary species prepared by the reaction of diverse copper(II) complexes (CuL) and purine, adenine and guanine or related purine derivatives is considered in order to deepen the intra-molecular interligand interactions affecting the molecular recognition patterns of the ‘metal complex + purine nucleobase’ and closely related systems. The degree of protonation and the possibilities of different tautomeric forms in the purine-like moieties are taken into account. The main conclusion is a general trend to form a CuN(purine-like) coordination bond which can be reinforced by an intra-molecular interligand H-bonding interaction. NH(purines)A (O or Cl acceptor) or NH(amino ligand L)O6(oxo-purines) are commonly observed. In addition, selected examples revealed that the presence of a variety of non-coordinating groups in L or in the purine-like nucleobases can significantly influence the structurally observed molecular recognition pattern. Moreover, examples are known where binuclear cores of the types Cu^II₂(μ₂-N3,N9-adeninate)₄(aqua)₂ or Cu^I₂(μ₂-N3,N9-adeninate)₂(aqua)₂ recognise CuL chelates by means of the expectable pattern (CuN7 coordination bond + N6HO(L) interaction).     

Specific crystal structure of poly(3-hydroxybutyrate) thin films studied by infrared reflection–absorption spectroscopy

Infrared reflection–absorption (IR-RAS) and transmission spectra were measured for poly(3-hydroxybutyrate) (PHB) thin films to explore its specific crystal structure in the surface region. As IR-RAS is sensitive to the vibration mode of perpendicular orientation of the surface, differences between IR-RAS and transmission spectra indicate an orientation of the lamella structure in the surface of PHB thin films. The relative intensity of the crystalline CO stretching band in the IR-RAS spectrum is significantly weaker than that in the transmission spectrum. It may be concluded that the transient dipole moment of the CO stretching mode of the crystalline state is not oriented perpendicular but nearly parallel to the substrate surface. On the other hand, the relative intensity of the band at 3009 cm⁻¹ due to the C–H stretching mode of the C–HOC hydrogen bonding is similar between the IR-RAS and transmission spectra, suggesting that the C–H bond is oriented neither perpendicular nor parallel to the substrate surface but in an intermediate direction. Since the CO group of the C–HOC hydrogen bonding is oriented nearly parallel to the surface and its C–H group is in the intermediate direction, it is very likely that the C–HOC hydrogen bonding has a somewhat bent structure. These results are in good agreement with our previous conclusion that the C–HOC hydrogen bonding of PHB exists along the a-axis (not the b-axis) between the CH₃ group of one helix and the CO group of another helix.     

Ba2In2O4(OH)2: Proton sites, disorder and vibrational properties

The structure of Ba₂In₂O₄(OH)₂ is analysed by the explicit full optimization of a large number of possible proton arrangements using periodic density functional theory. It is shown that the experimental assignments in which protons appear to be located at high symmetry positions with unphysical bond lengths do not correspond to minima on the potential energy hypersurface. The apparent sites are averages of a number of possible proton locations involving a set of possible local structural environments in which the internuclear separations are more realistic. Such problems with structural refinements are common where profile refinement programs place the atoms at the average position due to dynamic and/or static disorder. Thus while the calculations support a previous neutron diffraction analysis of the structure in that the average structure contains two different proton sites, they also reveal substantial information about the local environments of the protons. In all optimizations, the protons moved from the average positions suggested in the neutron diffraction study with calculated O–H and OHO distances consistent with those observed in other oxides. The energies of different proton distributions vary significantly so the protons are not randomly distributed. We also present an analysis of the vibrational properties of the O–H bonds. Since the strength of the hydrogen bonds is closely related to the local structural environments of the protons, a range of vibrational frequencies is obtained providing a prediction of the vibrational spectra. In O–HO linkages, O–H stretching modes soften with increasing HO hydrogen bond strength, while the in-plane and out-of-plane bending or libration modes stiffen. Together, our results show how modern theoretical methods can provide a clearer understanding of the structure and dynamics of a complex inorganic material.     

Vibrational satellite of Na(3d ← 3s) dipole-forbidden transition in Na/CF4 mixture

Excitation spectra of Na fluorescence in mixtures with CF₄ display a new band shifted by the energy of one-vibrational quantum of the IR active ν₃-mode of CF₄ (1281 cm⁻¹) from Na 3d states. This band is attributed to a Na(3s)CF₄(ν₃ = 0) → Na(3d)CF₄(ν₃ = 1) transition and its intensity is explained by coupling with Na(4p)CF₄(v₃ = 0) resonance state which lies  180 cm⁻¹ below in energy. An analogous satellite of the Na 6p state combined with the same vibration and lying close to the Na 7p state is reported and discussed.     

Influence of hydration on the protomeric tautomerism in selenium analogue of methimazole: A computational chemistry study

Hydrogen bond assisted proton transfer reactions were investigated in 3-methyl-1H-imidazole-2(3H)-selone (MSeI) and 1H-imidazole-2(3H)-selone (SeI) at B3LYP/6-311++G(2d,2p) level of theory. The B3LYP results predict that the direct proton transfer process in MSeI and SeI is more difficult than the water-assisted one. The results also show that the selone complexes are more stable than corresponding selenol ones. Interaction energies for a single NHSe hydrogen bond in dimers MSeI and SeI are −31.3 and −32.7 kJ/mol, respectively. ZPE-corrected binding energies in the self-association complexes of the MSeI and SeI are greater than the water-associated complexes. The small negative value of H(r) obtained by AIM analysis at B3LYP/6-311++G(2d,2p) level reveals some contribution of sharing interaction (partially covalent) to the SeHN bond in dimers of the MSeI and SeI. AIM data also reveal the partially covalent nature of SeH6 interaction and electrostatic nature of OH5 interaction in water-associated complexes. Results of charge analysis show that the selenium analogue of the methimazole is more nucleophilic than the methimazole. Our results confirm that the selenium analogue of methimazole can exist as a zwitterionic form.     

Supramolecular aggregation in new crystals with nonlinear optical properties: 2-aminophenol-HClO4, 3-aminophenol-HClO4 and 4-aminophenol-HClO4

Three new hybrid crystals of 2-aminophenol-HClO₄ (2-AP-HClO₄, 1), 3-aminophenol-HClO₄ (3-AP-HClO₄, 2) and 4-aminophenol-HClO₄ (4-AP-HClO₄, 3) were obtained and their crystal structures determined. The 1 crystallises in centrosymmetric space group C2/c of monoclinic system while the other two (2 and 3) crystallise in the non-centro symmetric space group P2₁ and P2₁2₁2₁, respectively. The oppositely charged units of the crystals, i.e. positively charged 2-APH⁺, 3-APH⁺ and 4-APH⁺ and ClO₄⁻, interact via weak N⁺–HO and O–HO hydrogen bonds forming 3D-supramolecular network. Relative to KDP the SHG efficiencies are 0.62 for 2 and 0.33 for 3, measured at 1064 nm using the Kurtz–Perry method.     

Syntheses, crystal structures, spectral and thermal analysis and biological activities of copper(II)-pyridine-2,5-dicarboxylate complexes with 4-methylimidazole, imidazole, and 3,4-dimethylpyridine

In this study, three novel Cu(II)-pyridine-2,5-dicarboxylate (pydc) complexes with 4-methylimidazole (4-Meim), [Cu(pydc)(H₂O)(4-Meim)₂]·H₂O (1), imidazole (im), {[Cu(μ-pydc)(im)₂]·2H₂O}_n (2), and 3,4-dimethylpyridine (dmpy), [Cu(μ-pydc)(H₂O)(dmpy)]_n (3) have been synthesized. Elemental and thermal analyses, magnetic susceptibilities, IR and UV/vis spectroscopic studies have been performed to characterize the complexes. The molecular structures of mononuclear (1) and polynuclear (2 and 3) complexes have been determined by the single crystal X-ray diffraction technique. In 1 and 2, Cu(II) ions have distorted square planer geometry, while 3 has distorted octahedral coordination. The pyridine-2,5-dicarboxylate exhibits three different coordination modes namely bidentate (1), tridentate (2) and tetradentate (3). The complex 1 is further constructed to form three-dimensional framework by hydrogen bonding, C–Hπ and ππ stacking interactions. The adjacent chains of 2 and 3 are then mutually linked via hydrogen bonding, ππ and C–Hπ interactions, which are further assembled to form three-dimensional framework. 1 exhibits the magnetic moment value of 1.70 BM, which corresponds to one of the unpaired electron, while the polynuclear complexes 2 and 3 exhibit 1.58 and 1.46 BM, which is lower than the spin only value for one unpaired electron, indicates to antiferromagnetic effect. The first thermal decomposition process of all the complexes is endothermic dehydration. This stage is followed by partial (or complete) decomposition of the neutral and pydc ligands. In the later stage, the remained organic residue exothermically burns. The final decomposition products which identified by IR spectroscopy were the CuO.     

Synthesis, characterization and biological evaluation of a novel Cu(II) complex with the mixed ligands 2,6-pyridinedicarboxylic acid and 2-aminopyridine

A novel bridged binuclear Cu(II) complex with mixed ligands, di-μ-(2-aminopyridine(N,N′))-bis[(2,6-pyridinedicarboxylate)aquacopper(II)] tetrahydrate, formulated as [Cu(μ-ap)(dipic)(H₂O)]₂·4H₂O (1) (dipic = 2,6-pyridinedicarboxylate, ap = 2-aminopyridine), has been synthesized and characterized by elemental, spectral (IR and UV–Vis.), thermal analysis, magnetic measurements and single crystal X-ray diffraction analysis. The central Cu(II) ion resides on a centre of symmetry in a distorted square-pyramid coordination environment comprising of two N atoms, one from dipic and one from the ap ring, two carboxylate O atoms from dipic, and one O atom from water. Intermolecular N–HO and O–HO hydrogen bonds and π–π stacking interactions seem to be effective in the stabilization of the crystal structure. The free ligands and the complex were also evaluated for their antimicrobial and radical scavenging activities (DPPH = 1,1-diphenyl-2-picrylhydrazyl hydrate) using in vitro microdilution methods. Antimicrobial screening of the free ligands and their complex showed that the free ligands and the complex possess antifungal activity against Candida sp.     

H NMR Dynamic study of thermal Z/E isomerization of 5-substituted 2-alkylidene-4-oxothiazolidine derivatives: Barriers to rotation about CC bond

The rotational barriers between the configurational isomers of two structurally related push–pull 4-oxothiazolidines, differing in the number of exocyclic CC bonds, have been determined by dynamic ¹H NMR spectroscopy. The equilibrium mixture of (5-ethoxycarbonylmethyl-4-oxothiazolidin-2-ylidene)-1-phenylethanone (1a) in CDCl₃ at room temperature to 333 K consists of the E- and Z-isomers which are separated by an energy barrier ΔG^# 98.5 kJ/mol (at 298 K). The variable-temperature ¹H NMR data for the isomerization of ethyl (5-ethoxycarbonylmethylidene-4-oxothiazolidin-2-ylidene)ethanoate (2b) in DMSO-d₆, possessing the two exocyclic CC bonds at the C(2)- and C(5)-positions, indicate that the rotational barrier ΔG^# separating the (2E,5Z)-2b and (2Z,5Z)-2b isomers is 100.2 kJ/mol (at 298 K). In a polar solvent-dependent equilibrium the major (2Z,5Z)-form (>90%) is stabilized by the intermolecular resonance-assisted hydrogen bonding and strong 1,5-type S · · · O interactions within the SCCCO entity. The ¹³C NMR Δδ_C(2)C(2′) values, ranging from 58 to 69 ppm in 1a–d and 49-58 ppm in 2a–d, correlate with the degree of the push-pull character of the exocyclic C(2)C(2′) bond, which increases with the electron withdrawing ability of the substituents at the vinylic C(2′) position in the following order: COPh COEt > CONHPh > CONHCH₂CH₂Ph. The decrease of the Δδ_C(2)C(2′) values in 2a–d has been discussed for the first time in terms of an estimation of the electron donor capacity of the S fragment on the polarization of the CC bonds.     

(1,4-dabH)2MnSnS4: The first thiostannate with integrated Mn ions in an anionic chain structure

The new thiostannate (1,4-dabH)₂MnSnS₄ (1,4-dab = 1,4-diaminobutane) was synthesized under solvothermal conditions. The compound crystallizes in the non-centrosymmetric space group Fdd2 with a = 22.8124(15) Å, b = 24.7887(16) Å, c = 6.4153(6) Å, Z = 8, and V = 3627.8(5) Å³. The structure consists of one-dimensional straight anionic chains composed of alternating SnS₄ and MnS₄ tetrahedra sharing common edges. The chains are directed along [001] and are surrounded by the organic cations which form undulated chains along [100] by strong intermolecular N–HN hydrogen bonding interactions. Several SH contacts suggest weak interactions between the anionic chains and the cations. The band gap amounts to 2.9 eV indicating that the compound is a photo-conductor. The compound is stable up to about 190 °C and decomposes in two distinct steps above this temperature.