The catalytic effects of various third molecules on reaction channels of weakly bound complex CO2HF systems in the vapor phase

In this investigation, reaction channels of weakly bound complexes CO₂HF, CO₂HFH₂O, CO₂HFNH₃, CO₂HFCH₃OH, CO₂HFNH₂CH₃, CO₂HFNH(CH₃)₂ and CO₂HFN(CH₃)₃ systems were studied at the B3LYP/6-311++G(3df,2pd) level. The conformers of syn-fluoroformic acid or syn-fluoroformic acid plus a third molecule (H₂O, NH₃, CH₃OH, NH₂CH₃, NH(CH₃)₂ or N(CH₃)₃) were found to be more stable than the conformers of the related anti-fluoroformic acid or anti-fluoroformic acid plus a third molecule (H₂O, NH₃, CH₃OH, NH₂CH₃, NH(CH₃)₂ or N(CH₃)₃). However, the weakly bound complexes were found to be more stable than either the related syn- and anti- type fluoroformic acid or the acid plus third molecule (H₂O, NH₃, CH₃OH, NH₂CH₃, NH(CH₃)₂ or N(CH₃)₃) conformers. They decomposed into CO₂+HF, CO₂+H₃OF, CO₂+NH₄F, CO₂+(CH₃)OH₂F, CO₂+NH₃(CH₃)F, CO₂+NH₂(CH₃)₂F, or CO₂+NH(CH₃)₃F combined molecular systems. The weakly bound complexes have seven reaction channels, each of which includes weakly bound complexes and their related systems. Moreover, each reaction channel includes two transition state structures. The transition state between the weakly bound complex and anti-fluoroformic acid type structure (T₁₃) is significantly higher than that of internal rotation (T₂₃) between the syn- and anti-FCO₂H (or FCO₂HH₂O, FCO₂HNH₃, FCO₂HCH₃OH, FCO₂HNH₂CH₃, FCO₂HNH(CH₃)₂, or FCO₂HN(CH₃)₃) structures. However, adding the third molecule H₂O, NH₃, CH₃OH, NH₂CH₃, NH(CH₃)₂ or N(CH₃)₃ can significantly reduce the activation energy of T₁₃. The catalytic strengths of the third molecules are predicted to follow the order H₂O<NH₃<CH₃OH<.NH₂CH₃<NH(CH₃)₂<N(CH₃)₃.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

Capture of aromatic carboxylate anion through second sphere coordination: Topological complementarity of [cis-Co(en)2(N3)2] and ions

[cis-Co(en)₂(N₃)₂]C₇H₃ClNO₄·1.25H₂O (Cocnb) was synthesised and detailed packing analyses were undertaken to delineate the topological complementarity of [cis-Co(en)₂(N₃)₂]⁺ and a 2-chloro-4-nitro benzoate anion (cnb) for second sphere coordination in the crystal lattice. The complex was completely characterised by elemental analyses, spectroscopic studies (IR, UV/visible, ¹H and ¹³C NMR). The compound crystallizes in the monoclinic (space group C2/c) with a = 21.9843(18), b = 8.7959(7), c = 23.0121(18) Å, β = 116.426(1)°, V = 3984.9(6) Å³, and Z = 8. In the crystal lattice, discrete ions of [cis-Co(en)₂(N₃)₂]⁺ and cnb are arranged in A–B–A–B pattern (in both a and c directions of the lattice) forming columns of anions and cations. The anionic columns are π stacked and are involved in extensive hydrogen bonding interaction. It appears that the topological feature of [cis-Co(en)₂(N₃)₂]⁺ is conducive for generating second sphere interactions with aromatic carboxylates. This strategy may be used as a viable method for the capture of aromatic carboxylate anions.     

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.     

Molybdenum(VI) network polymers based on anion–π interaction and hydrogen bonding: Synthesis, crystal structures and oxidation catalytic application

A crystallographic investigation of anion–π interactions and hydrogen bonds on the preferred structural motifs of molybdenum(VI) complexes has been carried out. Two molybdenum(VI) network polymers MoO₂F₄·(Hinca)₂ (1) and MoO₂F₃(H₂O)·(Hinpa) (2), where inca = isonicotinamide and inpa = isonipecotamide, have been synthesized, crystallographically characterized and successfully applied to alcohol oxidation reaction. Complex 1 crystallizes in the monoclinic space C2/c: a = 16.832(3) Å, b = 8.8189(15) Å, c = 12.568(2) Å, β = 118.929(3)°, V = 1560.1(5) Å³, Z = 4. Complex 2 crystallizes in the triclinic space P-1: a = 5.459(2) Å, b = 9.189(4) Å, c = 12.204(5) Å, α = 71.341(6)°, β = 81.712(7)°, γ = 77.705(7)°, V = 564.8(4) Å³, Z = 2. Complex 1 consists of hydrogen bonding and anion–π interactions, both of which are considered as important factors for controlling the geometric features and packing characteristics of the crystal structure. The geometry of the sandwich complex of [MoO₂F₄]²⁻ with two pyridine rings indicates that the anion–π interaction is an additive and provides a base for the design and synthesis of new complexes. For complex 2, the anions and the protonated inpa ligands form a 2D supramolecular network by four different types of hydrogen contacts (N–HF, N–HO, O–HF and O–HO). The catalytic ability of complexes 1 and 2 has also been evaluated by applying them to the oxidation of benzyl alcohol with TBHP as oxidant.     

(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.     

Hydrogen bond interactions in sulfamerazine: DFT study of the O-17, N-14, and H-2 electric field gradient tensors

Hydrogen bond (HB) interactions are studied in the real crystalline structure of sulfamerazine by density functional theory (DFT) calculations of the electric field gradient (EFG) tensors at the sites of O-17, N-14, and H-2 nuclei. One-molecule (single) and four-molecule (cluster) models of sulfamerazine are created by available crystal coordinates and the EFG tensors are calculated in both models to indicate the influence of HB interactions on the tensors. Directly relate to the experiments, the calculated EFG tensors are converted to the experimentally measurable nuclear quadrupole resonance (NQR) parameters, quadrupole coupling constant (qcc) and asymmetry parameter (η_Q). The evaluated NQR parameters reveal that due to contribution of the target molecule to N–HN and N–HO types of HB interactions, the EFG tensors at the sites of various nuclei are influenced from single model to the target molecule in cluster. Additionally, O2, N4, and H2 nuclei of the target molecule are significantly influenced by HB interactions, consequently, they have the major contributions to HB interactions in cluster model of sulfamerazine. The calculations are performed employing B3LYP method and 6-311++G** basis set using GAUSSIAN 98 suite of program.     

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.     

Crystal structure of olanzapine and its solvates. Part 3. Two and three-component solvates with water, ethanol, butan-2-ol and dichloromethane

Crystalline solvates of olanzapine (1), 2-methyl-4-(4-methyl-1-piperazinyl)-10H-thieno[2,3-b][1,5]benzodiazepine, have been characterized by an X-ray analysis and thermal (DSC) data. Crystallization of 1 from ethanol gives a solid containing both water and ethanol molecules; the solvate 1 · H₂O · EtOH (2:2:1) is monoclinic with the space group P2₁/c and the unit-cell volume V = 3752.8(12) Å³. Butan-2-ol forms with 1 solvate which is also a three-component phase, 1 · H₂O · BuOH, but its stoichiometry is different (1:1:1). The space group for this crystal is P2₁/c and the unit-cell volume V = 2216.5(7) Å³. Crystalline olanzapine dichloromethane solvate (2:1), 1 · CH₂Cl₂, is triclinic with the space group .The characteristic feature of all crystal structures is presence of a pair of olanzapine molecules which form dimer stabilized by multiple weak C–Hπ interactions between the N-methylpiperazine fragment and the phenyl / thiophene systems. Theoretical calculations have been performed indicating that the total C–Hπ binding energy is about 8 kcal mol⁻¹. In the crystal structure, the self-assembled olanzapine molecular dimers are arranged into parallel crystal planes. Packing of the layers proceeds in two ways in which structural motives are replicated by (i) perpendicular translation forming columns, and (ii) rotation around the twofold screw axis (parallel to the layer).     

Coordination of Ce(III) and Nd(III) with pentaethylene glycol in the presence of picrate anion: Spectroscopic and X-ray structural studies

¹H NMR evidence for direct coordination between the Ln(III) ion and the oxygen atoms of the pentaethylene glycol (EO5) ligand and the picrate anion (Pic) in [Ln(Pic)₂(EO5)][Pic] {Ln = Ce and Nd} complexes are confirmed by single X-ray diffraction. No dissociation of Ln–O bonds in dimethyl sulfoxide-d solution was observed in NMR studies conducted at different temperatures ranging 25–100 °C. The Ln(III) ion was chelated to nine oxygen atoms from the EO5 ligand in a hexadentate manner and the two Pic anions in each bidentate and monodentate modes. Both compounds are isostructural and crystallized in monoclinic with space group P2₁/c. Coordination environment around the Ce1 and Nd1 atoms can be described as tricapped trigonal prismatic and monocapped square antiprismatic geometries, respectively. The crystal packing of the complexes have stabilized by one dimensional (1D) chains along the [0 0 1] direction to form intermolecular O–HO and C–HO hydrogen bonding. The molar conductance of the complexes in DMSO solution indicated that both compounds are ionic. The complexes had a good thermal stability. Under the UV-excitation, these complexes exhibited the red-shift emission.     

Molecular DFT structure and packing effect of thiodipropionic and dithiodiglycolic acids and salts

Molecular and periodic DFT structure calculations of thiodipropionic and dithiodiglycolic acids, S_n[(CH₂)(COOR)]₂ (n = 1,2, R = H, Na), were performed. Computed structures were analyzed and compared to the experimental data (a C_s conformation is favored in solution than C₂ in solid state). Four close and low-energy optimized conformations were analyzed: C_2v, C₂, C_s and C₁. Small changes in the conformation stability (ΔG) and symmetry group were observed in polar medium. Periodic DFT-GGA approaches have been performed to determine the importance of weak interaction upon the crystal structure of the thiodipropionic acid, e.g., S–H and/or O–H hydrogen bonding. More SH and OH dispersed bands were observed in the optimized structure. Using a full analysis of the DOS of O–H or S–H bonding contributions, a notable interlayer bonding in the parent structure was revealed. Therefore, the presence of such weak interaction ONa⁺ or OH may thus change the point group symmetry of the crystal upon packing effect.     

Fermi resonance and strong anharmonic effects in the absorption spectra of the ν-OH (ν-OD) vibration of solid H- and D-benzoic acid

The vibrational spectra of polycrystalline benzoic acid (BA) and its deuterated derivative were studied over the wide frequency region 4000–10 cm⁻¹ by IR and Raman methods. A theoretical analysis of the hydrogen bond frequency region and calculations at the B3LYP/6-311++G(2d, 2p) level for the benzoic acid cyclic dimer in the gas phase were made. In order to study the dynamics of proton transfer two formalisms were applied: Car–Parrinello Molecular Dynamics (CPMD) and Path Integrals Molecular Dynamics (PIMD). It was shown that the experimentally observed very broad ν-OH band absorption is the result of complex anharmonic interaction: Fermi resonance between the OH-stretching and bending vibrations and strong interaction of the ν-OH stretching with the low frequency phonons. The theoretical analysis in the framework of such an approach gave a good correlation with experiment. From the CPMD calculations it was confirmed that the O–HO bridge is not rigid, with the OO distance being described by a large amplitude motion. For the benzoic acid dimer we observed stepwise (asynchronous) proton transfer.     

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.