Synthesis, crystal structure and vibrational spectroscopy of a novel mixed ligands Ni(II) pentaborate: [Ni(C4H10N2)(C2H8N2)2][B5O6(OH)4]2

A novel organic-inorganic hybrid pentaborate [Ni(C₄H₁₀N₂)(C₂H₈N₂)₂][B₅O₆(OH)₄]₂ has been synthesized by hydrothermal reaction and characterized by FT-IR, Raman spectroscopy, elemental analyses and DTA-TGA. Its crystal structure was determined from single crystal X-ray diffraction. The structure consists of isolated polyborate anion [B₅O₆(OH)₄]⁻ and nickel complex cation of [Ni(C₄H₁₀N₂)(C₂H₈N₂)₂]²⁺, in which the two kinds of ligands come from the decomposition of triethylenetriamine material. The [B₅O₆(OH)₄]⁻ units are connected to one another through hydrogen bonds, forming a three-dimensional framework with large channel along the a and c axes, in which the templating [Ni(C₄H₁₀N₂)(C₂H₈N₂)₂]²⁺ cations are located. The assignments of the record FT-IR absorption frequencies and Raman shifts were given.     

Molecular interactions of the quinone electron acceptors QA,QB, and QC in photosystem II as studied by the fragment molecular orbital method

Molecular interactions of the three plastoquinone electron acceptors, Q_A, Q_B, and Q_C, in photosystem II (PSII) were studied by fragment molecular orbital (FMO) calculations. Calculations at the FMO-MP2/6-31G level using PSII models deduced from the X-ray structure of the PSII complexes from Thermosynechococcus elongatus provided the binding energies of Q_A, Q_B, and Q_C as ?56.1, ?37.9, and ?30.1 kcal/mol, respectively. The interaction energies with surrounding fragments showed that the contributions of lipids and cofactors were 0, 24 and 45 % of the total interaction energies for Q_A, Q_B, and Q_C, respectively. These results are consistent with the fact that Q_A is strongly bound to the PSII protein, whereas Q_B functions as a substrate and is exchangeable with other quinones and herbicides, and the presence of Q_C is highly dependent on PSII preparations. It was further shown that the isoprenoid tail is more responsible for the binding than the head group in all the three quinones, and that dispersion forces rather than electrostatic interactions mainly contribute to the stabilization. The relevance of the stability and molecular interactions of Q_A, Q_B, and Q_C to their physiological functions is discussed.     

Comparative analysis of surface electrostatic potentials of carbon, boron/nitrogen and carbon/boron/nitrogen model nanotubes

We have extended an earlier study, in which we characterized in detail the electrostatic potentials on the inner and outer surfaces of a group of carbon and B_xN_x model nanotubes, to include several additional ones with smaller diameters plus a new category, C_2xB_xN_x. The statistical features of the surface potentials are presented and analyzed for a total of 19 tubes as well as fullerene and a small model graphene. The potentials on the surfaces of the carbon systems are relatively weak and rather bland; they are much stronger and more variable for the B_xN_x and C_2xB_xN_x. A qualitative correlation with free energies of solvation indicates that the latter two categories should have considerably greater water solubilities. The inner surfaces are generally more positive than the corresponding outer ones, while both positive and negative potentials are strengthened by increasing curvature. The outsides of B_xN_x tubes have characteristic patterns of alternating positive and negative regions, while the insides are strongly positive. In the closed C_2xB_xN_x systems, half of the C–C bonds are double-bond-like and have negative potentials above them; the adjacent rows of boron and nitrogens show the usual B_xN_x pattern. When the C_2xB_xN_x tubes are open, with hydrogens at the ends, the surface potentials are dominated by the B⁺–H^– and N^––H⁺ linkages.Figure Calculated electrostatic potential on the molecular surface of closed (6,0) B₄₈N₄₈; a is an outside view, while b shows the interior. Color ranges, in kcal mol^–1: red, greater than 20; yellow, between 20 and 0; green, between 0 and –10; blue, between –10 and –20; purple, more negative than –20     

Biophysical study of molecular mechanism of abortificient action of prostaglandins II. The study of the long and short range interaction between different fragments of PGF2α, PGF1β and PGA1

This paper reports the study of the long and short range interactions between the ring-chain and chain-chain portions for three different forms of prostaglandins (PGF_2α, PGF_1β and PGA₁) for the possible rotations around C₁₂-C₁₃ (θ), C₇-C₈ (ψ) and C₁₄-C₁₅ (φ). The calculations were based on the long range interaction formalism of Claverie and Rein, using longitudinal and transverse polarizability data. Although the chain-chain interactions play predominant role in the stabilization of molecular geometry in the normal crystallographic forms, it is found that the ring-chain interactions and especially the interactions between the carboxylic chain and the ring vary in a specific way. They lead to the formation of several low lying conformations with the total interaction energy differing by few kcal/mole. The significant differences between the interaction energies of the active and inactive forms (in relation to their abortificient action) are noted and their relevance to the specificity of the molecular mechanism of the action discussed.     

Solution-mediated syntheses and characterizations of two new zincophosphites [C6H14N2]0.5[Zn(H2PO3)2] and [C4H12N2]0.5[(CH3)2NH2][Zn2(HPO3)3]

Two new zincophosphites [C₆H₁₄N₂]_0.5[Zn(H₂PO₃)₂] 1 and [C₄H₁₂N₂]_0.5[(CH₃)₂NH₂][Zn₂(HPO₃)₃] 2 have been solvothermally synthesized in mixed solvents of N,N-dimethylformamide (DMF) and 1,4-dioxane (DOA), respectively. Single-crystal X-ray diffraction analysis reveals that compound 1 exhibits a neutral inorganic chain formed by ZnO₄ and HPO₂(OH) units. Interestingly, the left- and right-handed hydrogen-bonded helical chains are alternately formed via the hydrogen-bonds between two adjacent chains. Compound 2 exhibits a layer structure with 4- and 12-MRs formed by ZnO₄ and HPO₃ units, in which two kinds of organic amine molecules both act as countercations to compensate the overall negative electrostatic charge of the anionic network.     

Polyoxometalate cluster [V12B18O60H6] functionalized with the copper(II) bis-ethylenediamine complex

Three compounds based on the polyoxometalate building block [V₁₂B₁₈O₆₀H₆], (Na)₁₀[(H₂O)V₁₂B₁₈O₆₀H₆]·18H₂O (1), Na₈[Cu(en)₂]₂[V₁₂B₁₈O₆₀H₆](NO₃)₂·14.7H₂O (2), Na₇[Cu(en)₂]₂[V₁₂B₁₈O₆₀H₆](NO₃)·15.5H₂O (3), (en = ethylenediamine), have been hydrothermally synthesized and characterized by single-crystal X-ray diffraction analysis and TGA. Compound 1 consists of polyoxovanadium borate [V₁₂B₁₈O₆₀H₆] clusters which are surrounded by sodium countercations in octahedral sites, stabilized by electrostatic interactions with the oxygen atoms of both vanadium and boron centres. However, compounds 2 and 3 correspond to more complicated structures, constructed from the same polyoxometalate clusters, which are interconnected by [Cu(en)₂]²⁺ moieties via the terminal oxygen atoms of the polyoxoanions, generating one-dimensional structures. The functionalization of this polyoxovanadium borate cluster has been obtained by the use of [Cu(en)₂]²⁺ complex ions, thus demonstrating the capacity of the terminal oxygen atoms of the cluster to bind transition metal centres. The structural stability of the [V₁₂B₁₈O₆₀H₆] cluster permits the formation of functionalized polyoxometalate clusters, generating various crystalline lattices.     

Molecular dynamics study of the primary charge separation reactions in Photosystem I: Effect of the replacement of the axial ligands to the electron acceptor A0

Molecular dynamics (MD) calculations, a semi-continuum (SC) approach, and quantum chemistry (QC) calculations were employed together to investigate the molecular mechanics of ultrafast charge separation reactions in Photosystem I (PS I) of Thermosynechococcus elongatus. A molecular model of PS I was developed with the aim to relate the atomic structure with electron transfer events in the two branches of cofactors. A structural flexibility map of PS I was constructed based on MD simulations, which demonstrated its rigid hydrophobic core and more flexible peripheral regions. The MD model permitted the study of atomic movements (dielectric polarization) in response to primary and secondary charge separations, while QC calculations were used to estimate the direct chemical effect of the A_0A/A_0B ligands (Met or Asn in the 688/668 position) on the redox potential of chlorophylls A_0A/A_0B and phylloquinones A_1A/A_1B. A combination of MD and SC approaches was used to estimate reorganization energies λ of the primary (λ₁) and secondary (λ₂) charge separation reactions, which were found to be independent of the active branch of electron transfer; in PS I from the wild type, λ₁ was estimated to be 390 ± 20 mV, while λ₂ was estimated to be higher at 445 ± 15 mV. MD and QC approaches were used to describe the effect of substituting Met688_PsaA/Met668_PsaB by Asn688_PsaA/Asn668_PsaB on the energetics of electron transfer. Unlike Met, which has limited degrees of freedom in the site, Asn was found to switch between two relatively stable conformations depending on cofactor charge. The introduction of Asn and its conformation flexibility significantly affected the reorganization energy of charge separation and the redox potentials of chlorophylls A_0A/A_0B and phylloquinones A_1A/A_1B, which may explain the experimentally observed slowdown of secondary electron transfer in the M688N_PsaA variant. This article is part of a Special Issue entitled: Photosynthesis research for sustainability: Keys to produce clean energy.     

An aluminoborate cluster [AlB12O14(OH)12]: Synthesis and structure of [C5H6N][AlB12O14(OH)12]

A new aluminoborate, [C₅H₆N][AlB₁₂O₁₄(OH)₁₂], has been hydrothermally synthesized at 200 °C. The single-crystal diffraction study reveals that it crystallizes in space group C2/c. It consists of aluminoborate clusters [AlB₁₂O₁₄(OH)₁₂]⁻ and counterions [C₅H₆N]⁺. The aluminoborate cluster contains an Al(OH)₆ octahedron as a core that is capped by two raft-like polyborate units [B₆O₇(OH)₆]. These clusters are further interlinked by extensive hydrogen bonding to form a three-dimensional (3D) network, containing large channels along the b-axis, in which the [C₅H₆N]⁺ cations are located.     

Electronic structure and surface properties of the mixed-valence doughnut shaped polyoxomolybdate nanocapsule Mo57V6

We report a detailed analysis of the electronic structure and results of molecular dynamics simulations for the large polyoxomolybdate [H₃Mo₅₇V₆(NO)₆O₁₈₃(H₂O)₁₈]²¹⁻ (Mo₅₇V₆) which is a highly symmetric anion with a complex electronic structure and exhibiting a unique variety of multifunctionality. The six vanadium centres are reduced with one electron each, the six Mo centres are bonded to non-innocent NO ligands and the additional six 4d electrons are mostly delocalised over the rest of molybdenum atoms. DFT calculations carried out with the solvent - modelled by a continuum approach - suggest that despite the large charge of the anion, the Mo₅₇V₆ framework can be easily reduced in polar solvents. Furthermore, the Mo₅₇V₆ cluster has 18 water molecules trapped in its internal cavity. Molecular dynamics simulations carried out with different solvent conditions suggest that the water molecules inside the cavity have a high ordered structure over a wide range of temperatures and give important information about the cluster anion interactions with the cations present in solution. The obtained results allow a better understanding of related properties of the giant ball-shaped polyoxometalates/Keplerates as the present cluster contains similar building blocks - like the (metal)₆O₆ type pores with crown ether-like structure.     

Theoretical study of the interaction between X (H,F) and graphene

This study investigates the interaction between X (X = H and F) and graphene C₅₄H₁₈ (D_6 h), and the potential energy surface of the graphene radical. The calculations on the structures and energies are further discussed thermodynamically and kinetically using the density function theory method at the B3LYP/6-31G (d) level. Our findings show that there are four distinct isomers of C₅₄H₁₈–X. C₅₄H₁₈–H² and C₅₄H₁₈–F⁴ are the most stable isomers in their own systems. In addition, the transition states, as well as reaction pathways of H transferring between different key points on representative patch, are given to explore the possible reaction mechanism. Finally, the stability of C₅₄H₁₈–X₂ is discussed through the density functional theory.     

Exploration of structure, potential energy surface, and stability of planar C3B3

The geometrical structures, potential energy surface, stability, and bonding character of low-energy isomers of planar C₃B₃ were systematically explored and investigated at the B3LYP/6-311+G(d)// CCSD(T)/6-311+G(d) level for the first time. A large number of planar structures for low-energy isomers of C₃B₃ are located and reported. In particular, isomers 1 (C_s,²A’) and 2 (C_s,²A’), with a belt-like structure corresponding to the lowest-energy structures of planar C₃B₃, are revealed. Based on molecular orbital (MO) and natural bond orbital (NBO) analyses, delocalized σ MOs, multi-centered σ MOs, and delocalized π MOs play an important role in stabilizing the structures of low-energy isomers of C₃B₃. It is interesting to note from isomerization analysis that the interconversion of isomers 2 and 7 can be realized through two isomerization channels. The results demonstrate that isomers 1, 2, 3, 4, 7, 9, 12, 17, 19, and 20 of C₃B₃ are stable both thermodynamically and kinetically at the B3LYP/ 6-311+G(d)//CCSD(T)/ 6-311+G(d) level, and that they are observable in the laboratory, which is helpful for future experimental studies of C₃B₃.     

Calculations of the C<Subscript>2</Subscript> fragmentation energies of higher fullerenes C<Subscript>80</Subscript> and C<Subscript>82</Subscript>

The C₂ fragmentation energies of the most stable isolated-pentagon-rule (IPR) isomers of the C₈₀ and C₈₂ fullerenes were evaluated with second-order Møller-Plesset (MP2) theory, density-functional theory (DFT) and the semiempirical self-consistent charge density-functional tight-binding (SCC-DFTB) method. Zero-point energy, ionization energy and empirical C₂ corrections were included in the calculation of fragmentation energies for comparison with experimental C₂ fragmentation energies of the fullerene cations. In the case of the most probable Stone-Wales pathway of C₂ fragmentation of C₈₀, the calculated \(D_{0} {\left( {{\text{C}}_{{{\text{80}}}} ^{ + } } \right)}\) agree well with experimental data, whereas in the case of C₈₂ fragmentation, the calculated \(D_{0} {\left( {{\text{C}}_{{{\text{82}}}} ^{ + } } \right)}\) exceed by up to 1.2 eV the experimental ones, which suggests that other IPR isomers may be present in sufficient amounts in experimental samples. Computer-intensive MP2 calculations and DFT calculations with larger basis sets do not yield much improved C₂ fragmentation energies, compared to those reported earlier with B3LYP/3-21G. On the other hand, semiempirical approaches such as SCC-DFTB, which are orders of magnitude less intensive, yield satisfactory fragmentation energies for higher fullerenes and may become a method of choice for routine calculations of fullerenes and carbon nanotubes.

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Figure C₂ fragmentation energies of C₈₀ and C₈₂ fullerenes have been calculated with B3LYP/6-31G* model chemistry, with semiempirical self-consistent-charge density-functional tight-binding (SCC-DFTB) method and with the more rigorous MP2 method. The influence of basis set extension and level of theory on the resulting fragmentation energies is discussed

     

Computational study of enantioselective interaction between C<Subscript>60</Subscript> fullerene and its derivatives with L-histidine

The mechanism of the enantioselective binding of L-histidine with C₆₀ fullerene and its derivatives, (1,2-methanofullerene C₆₀)-61-carboxylic acid, diethyl (1,2-methanofullerene C₆₀)-61-61-dicarboxylate and tert-butyl (1,2-methanofullerene C₆₀)-61-carboxylate based chiral selectors was studied by quantum chemical calculations. All the molecules were fully optimized at RHF/6-31G* basis set. Relative energies between the different complexes were subsequently estimated with single-point electronic energies computed using Møller-Plesset perturbation theory (MP2). Stability and feasibility of all the generated structures were supported by their respective energy minima and fundamental frequencies. It was observed that interaction of fullerene derivatives with L-histidine is due to the existence of hydrogen bonding forces during the complex formation. The intermolecular forces, flow of atomic charges, binding energy, hardness, dipole moment and localization of electrostatic potential are in agreement with enantioselective interaction of L-histidine with C₆₀ fullerene and its derivatives. It is found that theoretical evaluation to be consistent with the experimental data.     

Synthesis of tantalum and niobium complexes that contain the diamidoamine ligand, [(3,4,5-F3C6H2NCH2CH2)2NMe], and the triamidoamine ligand, [(3,5-Cl2C6H3NCH2CH2)3N]

Several niobium and tantalum compounds were prepared that contain either the diamidoamine ligand, [(3,4,5-F₃C₆H₂NCH₂CH₂)₂NMe]²⁻ ([F₃N₂NMe]²⁻), or the triamidoamine ligand, [(3,5-Cl₂C₆H₃NCH₂CH₂)₃N]³⁻ ([Cl₂N₂NMe]³⁻). The former include [F₃N₂NMe]TaCl₃, [F₃N₂NMe]NbCl₃, [F₃N₂NMe]TaMe₃, [F₃N₂NMe]NbMe₃, [(F₃N₂NMe)TaMe₂][MeB(C₆F₅)₃], [F₃N₂NMe]Ta(CHSiMe₃)(CH₂SiMe₃), [F₃N₂NMe]Ta(CH₂-t-Bu)Cl₂, [F₃N₂NMe]Ta(CH-t-Bu)(CH₃), and [F₃N₂NMe]Ta(η²-C₂H₄)(CH₂CH₃). The latter include [Cl₂N₂NMe]TaCl₂, [Cl₂N₂NMe]TaMe₂, [Cl₂N₂NMe]Ta(η²-C₂H₄), and [Cl₂N₂NMe]Ta(η²-C₂H₂).X-ray diffraction studies were carried out on [F₃N₂NMe]Ta(CHSiMe₃)(CH₂SiMe₃), [F₃N₂NMe]Ta(η²-C₂H₄)(CH₂CH₃), and [Cl₂N₂NMe]TaMe_2..     

Novel supramolecular compounds based on Cucurbit[6]uril, 1,8-diaminooctane and octahedral thiohydroxo anions with cluster core [Re6S8]

Supramolecular compounds {C₈N₂H₂₂@Cuc[6]}{Re₆S₈(H₂O)₂(OH)₄}·18H₂O (1), and K₂{C₈N₂H₂₂@Cuc[6]}{Re₆S₈(OH)₆}·14H₂O (2) were obtained by crystallization from aqueous solutions that contained the macrocyclic cavitand cucurbit[6]uril (C₃₆H₃₆N₂₄O₁₂), 1,8-diaminooctane and the cluster thiohydroxo complex [Re₆S₈(OH)₆]⁴⁻. The resultant composition of the formed compounds depends on the experiment technique. According to the X-ray diffraction analysis, 1,8-diaminooctane molecules are encapsulated within the cavity of the cucurbit[6]uril molecules in such a way that the aminogroups are above and below the plane of the cavitand. The 1,8-diaminooctane molecules formed hydrogen bonds with the cavitand and the cluster thiohydroxo complexes to give chains.     

Adducts of tin(IV) and organotin(IV) derivatives with 2,2′-azopyridine II. Crystal and molecular structure of SnMe2Br2AZP and further mössbauer and photoelectronic spectroscopic studies

A series of adducts of tin(IV) derivatives with 2,2′-azopyridine, AZP, has been studied by Mössbauer and X-ray photoelectronic spectroscopies and the crystal and molecular structure of SnMe₂Br₂- AZP has been determined. The linear correlation of the Mössbauer parameter isomer shift with partial atomic charge on tin suggests the occurrence of a single homologous series of isostructural adducts. The correlation of the Mössbauer parameter quadrupole splitting and C-Sn-C bond angle permits their calculation in SnMe₂X₂AZP adducts (X = Cl, Br). The N_1s binding energies, obtained by XPS data, pointed out two slightly different values for both pyridinic and azo-group nitrogens. The crystallographic study of the SnMe₂Br₂AZP adduct shows a new structure in which the Sn atom is seven-coordinated.     

The molecular properties of heterocyclic and homocyclic hydrogen-bonded complexes evaluated by DFT calculations and AIM densities

This theoretical study presents a comparative analysis of the molecular properties of heterocyclic (C₂H₄O⋯HF and C₂H₅N⋯HF) and homocyclic (C₃H₆⋯HF) hydrogen-bonded complexes. Initially, the equilibrium geometries of these complexes were analyzed in detail at the B3LYP/6–311++G(d,p) level of theory. Subsequently, the interaction energies and polarizabilities were also evaluated, as well as the infrared stretch frequencies and absorption intensities. In addition, by combining intermolecular criteria and charge density concepts, calculations of Bader’s theory of atoms in molecules were used to determine the maxima and minima for electron density in order to measure the strength of the n⋯H and pπ⋯H hydrogen bonds. Finally, the possibility of an F⋯H_α secondary interaction between the fluoride (F) of hydrogen fluoride and the axial hydrogen atoms (H_α) of the C₂H₄O and C₂H₅N heterocyclic rings was explored. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The heat shock protein hsp70 binds in vivo to subregions 2-48BC and 3-58D of the polytene chromosomes ofDrosophila hydei

Multiple interactions of members of the hsp70 family with cellular components have already been described. We present, however, the first evidence that upon heat shock treatment hsp70 molecules interact with specific chromosomal subdivisions of the polytene chromosomes ofDrosophila hydei. After a heat shock treatment of 20 min the protein binds to subdivision 3-58D₁ and to the heat shock inducible subdivisions 2-48B_3–6 and 2-48C_1–2. Hsp70 molecules were also observed in subdivision 3-58D₁ during recovery at 25°C but not in subdivisions 2-48B_3–6 and 2-48C_1–2. Our data suggest that this interaction is stress specific. DNase and RNase experiments suggest, moreover, that the hsp70 molecules bind to RNA from ribonucleoproteins (RNPs) in subdivisions 2-48B_3–6 and 2-48C_1–2 and to DNA in subdivision 3-58D₁. The DNA sequences in subdivision 3-58D₁ seem to have the potential to adopt the Z-DNA conformation.     

Synthesis and structure of a lead(II)-citrate: {Na(H2O)3}[Pb5(C6H5O7)3(C6H6O7)(H2O)3]·9.5H2O

The reaction of lead(II) nitrate with trisodium citrate Na₃(C₆H₅O₇) in a 1:22.5 ratio at pH 4.8 provides crystals of {Na(H₂O)₃}[Pb₅(H₂O)₃(C₆H₅O₇)₃(C₆H₆O₇)]·9.5H₂O (1). The structure of 1 is two-dimensional and exhibits five distinct Pb(II) sites and four different modes of citrate bonding. The five lead sites all display hemidirected coordination geometries, that is, irregular distribution of neighboring oxygen atoms resulting in obvious gaps in the coordination spheres. Consequently, the lead coordination geometries exhibit proximal bonding to a number of oxygen donors, as well as distal interactions with nearest neighbors. The coordination numbers vary from 8 to 10, with ‘5+3’, ‘5+4’, ‘6+4’ and ‘7+3’ coordination modes where the first number refers to the proximal ligands and the second to the distal set. The four crystallographically distinct citrate groups include three with deprotonated carboxylate groups (C₆H₅O₇)³⁻ and one with a single protonated carboxyl group (C₆H₆O₇)². The citrate ligands bridge 3, 5, 7 and 7 lead sites. Three of the citrate groups exhibit tridentate chelation coordination to a lead site through two carboxylate oxygen donors and the hydroxyl groups. One citrate group projects an uncoordinated -OH group and a pendant protonated carboxyl group into the interlamellar domain. This latter carboxyl group coordinates to a sodium cation, which exhibits five coordinate geometry defined by three aqua ligands and the carbonyl oxygen of the -CO₂H groups in the basal plane and a citrate -OH donor in the apical position.