The intricacies of the stacking interaction in a pyrrole–pyrrole system

Extensive calculations of potential energy surfaces for parallel-displaced configurations of pyrrole–pyrrole systems have been carried out by the use of a dispersion-corrected density functional. System geometries associated with the energy minima have been found. The minimum interaction energy has been calculated as ?5.38 kcal/mol. However, bonding boundaries appeared to be relatively broad, and stacking interactions can be binding even for ring centroid distances larger than 6 Å. Though the contribution of the correlation energy to intermolecular interaction in pyrrole dimers appeared to be relatively small (around 1.6 smaller than it is in a benzene–benzene system), this system’s minimum interaction energy is lower than those calculated for benzene–benzene, benzene–pyridine and even pyridine–pyridine configurations. The calculation of the charges and energy decomposition analysis revealed that the specific charge distribution in a pyrrole molecule and its relatively high polarization are the significant source of the intermolecular interaction in pyrrole dimer systems.     

DFT study on reaction mechanisms of cyclic dipeptide generation

In this work, three possible reaction pathways (Path 1, Path 2 and Path 3) for the generation process of cyclic dipeptide from amino acid have been investigated in detail using density functional theory. Path 1 and Path 2 are the intramolecular reaction processes, while Path 3 involves the intermolecular reaction process that assisted with water molecule. Our calculated results indicate that Path 3 is more energy favorable than Path 1 and Path 2. There are four steps in Path 3 proceed from the amino acid to cyclic dipeptide. The first step is two adjacent amino acids to form precursor of dipeptide, the second step is the removal of water molecule of precursor of dipeptide for the formation of the linear dipeptide, the third step is generation of precursor of cyclic dipeptide associated with other hydrogen atom transfer, and the last step is another dehydration process to generate the final product of cyclic dipeptide. Moreover, the obtained results indicate that the generation mechanisms of different cyclic dipeptides are similar, and the energy barrier of the rate-determined step influenced somewhat by the hydrophilic or hydrophobic group linked to the C_α atom. Additionally, the potential energy profiles suggest that the generation reactions of the studied nine cyclic dipeptides are exothermic processes. The detailed mechanisms should be helpful for people to understanding the title reaction at the molecular level, and the proposed novel intermolecular process might provide valuable insights on rational improve reaction condition for this type of reaction.     

Hydrogen physisorption energies for bumpy,saturated, nitrogen-doped single-walled carbon nanotubes

Finite saturated regular carbon nanotubes (CNTs) are predicted to exhibit higher capacity as hydrogen storage media compared to unsaturated regular CNTs. In the present study, molecular hydrogen physisorption energies (MHPEs) for finite saturated and unsaturated bumpy defected CNTs were calculated by density functional theory (DFT-D3) methods at the B3LYP/6-31G(d) theory level, with rigorous inclusion of van der Waals interactions. The calculated MHPEs for both regular and bumpy defected armchair, chiral and zigzag CNTs with similar diameters and lengths, with and without nitrogen doping, were compared in terms of Eph/H₂, defined as the MHPE per hydrogen molecule adsorbed inside the nanotube. For all studied systems, Eph/H₂ increased with the number of physisorbed hydrogen molecules. Nitrogen doping of regular and bumpy CNTs resulted in an increase in the Eph/H₂ values, with the exception of bumpy chiral nanotubes. The results of this study demonstrate that bumpy defects are important nanotube structural features whose effects depend on nanotube chirality. For instance, bumpy defects were beneficial for undoped and doped zigzag nanotubes, resulting in a decrease in Eph/H₂ values for regular structures from 0.5 and 0.74 to 0.26 and 0.42 eV, respectively. By contrast, for doped armchair regular structures with an Eph/H₂ value of 0.38 eV, bumpy defects increased Eph/H₂ to 0.45 eV. These Eph/H₂ values for bumpy doped armchair and the zigzag nanotubes are all within the range of 0.1–0.5 eV/H₂ reported as ideal for reversible hydrogen storage under environmental conditions.     

Self-assembly and high anisotropy thermal expansion of compounds consisting of <Emphasis Type="Italic">T</Emphasis>O<Subscript>3</Subscript> triangular radicals

Thermal motion is the inherent driving force of crystal substances formation. In borates, carbonates and nitrates such an organizing force are the strong anisotropy of thermal vibrations of atoms in the TO₃ triangles (T = B, C, N), flat triborate and other B–O rigid groups containing TO₃ triangles. These triangles and rigid groups, due to the sharp anisotropy of thermal vibrations, tend to be arranged in the parallel (or preferable) orientation. In this case, chemical compound has usually the least energy. The examples of the self-organization of atoms, TO₃ triangles and rigid groups during crystallization process are given.     

Thermal expansion and structural complexity of strontium borates

Thermal expansion of four strontium borates has been studied by high-temperature powder X-ray diffraction. Strong anisotropy of thermal expansion is observed for the structures of Sr₃B₂O₆ (0D) and SrB₂O₄ (1D) based on triangles BO₃ only: The high expansion occurs perpendicular to the BO₃ plane, i.e. along the direction of the less strong bonds in the crystal structure. The monoclinic Sr₂B₁₆O₂₆ (3D) borate expands dramatically due to shear deformations in monoclinic plane: Monoclinic β′ angle changes significantly because it is not fixed by symmetry. In contrast to these borates, SrB₄O₇ (3D) borate built up from tetrahedra only expands almost isotropically. Average value of volume expansion is 36 × 10^?6 K^?1 for studied Sr-borates. Tendency of slight decrease in the volume thermal expansion and sharp decrease in the melting points is observed with an increase in B₂O₃ content as a result of the degree of polymerization increase. As the B₂O₃ content grows in Sr-borates, the structural complexity increases in the SrO–B₂O₃ system due to more complex anionic structure. Inverse “melting temperature decrease—structural complexity increase” correlation is revealed.     

Substituent effects in reduction-induced synthesis of <Emphasis Type="Italic">ansa</Emphasis>-titanocenes

Bis{(diphenylvinylsilyl)tetramethylcyclopentadienyl}titanium dichloride [TiCl₂{η⁵-C₅Me₄(SiPh₂CH=CH₂)}₂] (1) is reduced with a half molar equivalent of magnesium to the monochloride ([TiCl{η⁵-C₅Me₄(SiPh₂CH=CH₂)}₂] (2), whereas one molar equivalent of magnesium affords the titanocene [Ti{η⁵-C₅Me₄(SiPh₂CH=CH₂)}{η⁵:η²-C₅Me₄(SiPh₂CH=CH₂)}] (3) stabilized by η²-coordination of one of the two vinyl groups to titanium(II). In the presence of excess magnesium, the vinyl moieties of 3 undergo intramolecular coupling to afford the ansa-titanocene [Ti(η⁵:η⁵:η²-C₅Me₄SiPh₂CH=CHCH₂CH₂SiPh₂C₅Me₄)] (4) possessing the η²-coordinated double bond in lateral position of its ansa-chain. The symmetrical ansa-titanocene [Ti(η⁵:η⁵:η²-C₅Me₄SiPh₂CH₂CH=CHCH₂SiPh₂C₅Me₄)] (5) was not obtained although its DFT-calculated energy is only slightly higher than that of 4. It is considered that transient 5 gives rise to non-identified tar-like by-products which inherently accompany the formation of 4.     

Diverse topologies of three cobalt(II) coordination polymers constructed from flexible bis(benzimidazole) and dicarboxylate ligands

Three cobalt(II) coordination polymers {[Co(L1)(nda)(H₂O)₂]·2H₂O} _n (1), [Co(L2)(tbi)(H₂O)] _n (2) and [Co(L2)(bpdc)(H₂O)] _n (3) (L1 = 1,3-bis(5,6-dimethylbenzimidazol-1-yl)-2-propanol, L2 = 1,3-bis(benzimidazol-1-yl)-2-propanol, H₂nda = 2,6-naphthalenedicarboxylic acid, H₂tbi = 5-tert-butyl isophthalic acid and H₂bpdc = 4,4′-biphenyldicarboxylic acid) were synthesized and characterized by physicochemical and spectroscopic methods. Complex 1 exhibits a 1D loop-like structure, which is further extended into a 3D 3,3,4T31 network through two O–H···O hydrogen bonding interactions. Complex 2 displays a 1D ladder-like chain, arranged into a 2D supramolecular network with 3,3,4L34 topology via classical O–H···O hydrogen bonding interactions, whereas complex 3 features a 2D 3,4L13 layer structure and further assembles into a 3D framework with a twofold interpenetrating sqc65 topology through O–H···O hydrogen bonding interactions. The fluorescence and catalytic properties of these complexes for the degradation of Congo red in a Fenton-like process have been investigated.     

Naringenin Schiff base: antioxidant activity,acid–base profile,and interactions with DNA

A Schiff base derived from naringenin (NTSC) and its complex with Cu(II) ([Cu(H₃L)(OAc)]·H₂O, Cu(II)–NTSC) have been synthesized and characterized by physicochemical and spectroscopic methods. EPR studies confirmed that nitrogen, oxygen, and sulfur are the donor atoms bound to Cu(II) in the complex. The geometry of the complex has been modelled using DFT methods. Furthermore, naringenin and NTSC were used for the formation of Cu(II) complexes in solution, for comparison of biological activities. Antioxidant studies confirmed better radical scavenging activity of both NTSC and its Cu(II) complex compared to naringenin. The interaction of these compounds with calf thymus DNA was monitored by UV–Vis spectroscopy.     

The role of substituents in a bidentate <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-chelating ligand on the substitution of aqua ligands from mononuclear Pt(II) complexes

The rate of substitution of aqua ligands from three mononuclear platinum(II) complexes, namely [Pt{2-(pyrazol-1-ylmethyl)pyridine}(H₂O)₂](ClO₄)₂, [Pt(H ₂ Py)]; [Pt{2-(3,5-dimethylpyrazol-1-ylmethyl)pyridine}(H₂O)₂](ClO₄)₂, [Pt(dCH ₃ Py)] and [Pt{2-[(3,5-bis(trifluoromethyl)pyrazoly-1-ylmethyl]pyridine}(H₂O)₂](ClO₄)₂, [Pt(dCF ₃ Py)] by thiourea, N,N-dimethylthiourea and N,N,N′,N′-tetramethylthiourea, was studied in aqueous perchloric acid medium of constant ionic strength. The substitution reactions were investigated under pseudo-first-order conditions as a function of nucleophile concentration and temperature using UV/Visible and stopped-flow spectrophotometries. The observed pseudo-first-order rate constants, \( k_{{{\text{obs }}\left( {1/2} \right)}} \), for the stepwise substitution of the first and second aqua ligands obeyed the rate law: \( k_{{{\text{obs}}\left( {1/2} \right)}} = k_{{2 \left( { 1 {\text{st/2nd}}} \right)}} \left[ {\text{Nu}} \right] \). The first substitution reaction takes place trans to the pyrazole ligand, while the second entering nucleophile is stabilised at the reaction site trans to the pyridine ligand. The rate of substitution of the first aqua ligand from the complexes followed the order: Pt(dCF ₃ Py) > Pt(H ₂ Py) > Pt(dCH ₃ Py), while that of the second was Pt(H ₂ Py) ≈ Pt(dCF ₃ Py) > Pt(dCH ₃ Py). Lower pK _a values were found for the deprotonation of the aqua ligand cis to the pyrazole ring. Density functional theory calculations were performed to support the interpretation of the experimental results.