Principles of mucin architecture: structural studies on synthetic glycopeptides bearing clustered mono-, di-, tri-, and hexasaccharide glycodomains

The structural characteristics of a mucin glycopeptide motif derived from the N-terminal fragment STTAV of the cell surface glycoprotein CD43 have been investigated by NMR. In this study, a series of molecules prepared by total synthesis were examined, consisting of the peptide itself, three glycopeptides having clustered sites of alpha-O-glycosylation on the serine and threonine side chains with the Tn, TF, and STF carbohydrate antigens, respectively, and one with the beta-O-linked TF antigen. Additionally, a glycopeptide having the sequence SSSAVAV, triglycosylated with the Le(y) epitope, was investigated. NMR data for the tri-STF-STTAV glycopeptide were used to solve the structure of this construct through restrained molecular dynamics calculations. The calculations revealed a defined conformation for the glycopeptide core rooted in the interaction of the peptide and the first N-acetylgalactosamine residue. The similarity of the NMR data for each of the alpha-O-linked glycopeptides demonstrates that this structure persists for each construct and that the mode of attachment of the first sugar and the peptide is paramount in establishing the organization of the core. The core provides a common framework on which a variety of glycans may be displayed. Remarkably, while there is a profound organizational effect on the peptide backbone with the alpha-linked glycans, attachment via a beta-linkage has little apparent consequence.     

Theoretical study on the electronic, structural, properties and reactivity of a series of mono-, di-, tri- and tetrafluorothiophenes as monomers for new conducting polymers

Electrical and structural properties of mono-, di-, tri- and tetrafluorothiophenes and their radical cations have been studied using density functional theory and B3LYP method with 6-311++G** basis set. The effects of the number and position of the substituent of fluorine atoms on the properties of the thiophene ring have been studied using optimized structures obtained for these molecules and their radical cations. Vibrational frequencies, spin-density distribution, size and direction of dipole moment vector, ionization potential, electric polarizability, HOMO-LUMO gaps and NICS values of these compounds have been calculated as well. The analysis of these data showed that double bonds in 3-fluorothiophene are more delocalized and it is the best possible candidate monomer among all fluorothiophenes for the synthesis of corresponding conducting polymers with modified characteristics.     

Search for stratospheric bromine reservoir species: theoretical study of the photostability of mono-, tri-, and pentacoordinated bromine compounds

Previous work has shown that pentacoordinated bromine compounds have their lowest excited electronic states shifted to the blue relative to monocoordinated bromine molecules, and that this shift may be large enough to render them photostable in the lower stratosphere. Our earlier work has also shown that certain pentacoordinated bromine compounds are thermodynamically stable relative to their mono- or tricoordinated isomers, suggesting that if a bromine stratospheric reservoir species exists, it may be a pentacoordinated compound. In this study we have examined the singlet and triplet excited electronic states of several bromine compounds, using time dependent density functional theory, to assess their photostability under stratospheric conditions and in order to elucidate the nature of lowest excited states in mono-, tri-, and pentacoordinated bromine molecules. The triplet states have been included due to the strong spin-orbit mixing in bromine. We have found several pentacoordinated bromine/oxygen compounds that could be photostable in the lower stratosphere, but we have also found that monovalent bromine compounds where the bromine atom is bonded to an atom with no lone-pair p-electrons is far and away the most photostable. Attachment/detachment electron density plots have been useful in ascertaining the nature of the excited electronic states and their likely path to photodissociation.     

Synthesis and liquid crystalline properties of mono-, di- and tri-O-alkyl pentaerythritol derivatives bearing tri-, di- or monogalactosyl heads: the effects of curvature of molecular packing on mesophase formation

Self-organisation and self-assembly are critical to the stability of synthetic and biological membranes. Of particular importance is consideration of the packing arrangements of the various molecular species. Both phospho- and glycolipids can pack in ways in which curvature can be introduced into self-organised or self-assembled systems. For instance, it is known that the degree of curvature can affect the structures of any condensed phases that are formed. In this article we report on a systematic study in which we have varied the shapes of glycolipids and examined the condensed phases that they form. In doing so, we have also unified the shape dependency of lyotropic liquid crystals with those of thermotropic liquid crystals. In order to undertake this systematic study a range of different pentaerythritol derivatives was synthesized, which covers combinations of one to three alkyl chains of different lengths (6,7,9,10,11,12,14,16 carbon atoms) and three to one galactosyl heads. Mono- and di-O-galactosyl derivatives were prepared directly by glycosylation of the corresponding alcohols using 2,3,4,6-tetra-O-benzoyl or acetyl-alpha-D-galactopyranosyl trichloroacetimidate or bromide as the donors; the tri-O-galactosyl derivatives were synthesized from O-alkyl-O-benzyl di-O-galactosyl pentaerythritol intermediates, followed by de-O-benzylation and glycosylation steps. All of the fully deprotected products were obtained by standard methods, and their self-organising and self-assembling properties examined.     

DFT study of molecular structure and electronic properties of fluoromethylpyrrole oligomers including di-, tri- and tetramer

Structural and electronic properties of oligomers including dimer, trimer and tetramer of fluoromethylpyrroles (FMPs), NC₄H₄-CH_nF_3−n with n = 0, 1, 2, 3, and their radical cations have been studied using DFT-B3LYP method with 6-31G(d, p) basis set. FMPs are proposed in this research as candidate monomers for conducting polymers with modified characteristics compared to polypyrrole and polymethylpyrrole. A preliminary study using a set of ab initio computations (HF) with medium basis set was carried out on di-, tri- and tetramer in order to investigate the stability of configuration of polymer chains for FMPs. The B3LYP/6-31G** optimized geometry and stereochemistry show that the selectivity of branching of the propagating polymer chain is affected by the characteristics of the substitutions of monomer and, therefore, the growth pattern of the polymer chain can be predicted upon characterization of different centers of the monomers. Also, the results of this study, including quinoid coefficients, orbital energy spacing, charge- and spin-density distributions and electric dipole moment vectors show that conducting polymers consisted of trifluoromethyl pyrrole (Py-CF₃), compared with the other FMPs, are the most favorable to be used as monomers for conducting polymer structural and electronic properties.     

Pentacene oligomers and polymers: functionalization of pentacene to afford mono-, di-, tri-, and polymeric materials

The synthesis and characterization of defined-length di- and trimeric pentacenes and the corresponding polymers are described. The synthesis is divergent from two common pentacene building blocks, 1 and 2, allowing for structural diversity. The resulting materials are air stable and exhibit good solubility in common organic solvents.     

Theoretical study on the electronic,structural, properties and reactivity of a series of mono-, di-, tri- and tetrachlorothiophenes as well as corresponding radical cation forms as monomers for conducting polymers

In this paper, electrical and structural properties of mono-, di-, tri- and tetrachlorothiophenes and their radical cations have been studied using the density functional theory and B3LYP method with 6-311++G** basis set. The effects of the number and position of the substituent of chlorine atoms on the properties of the thiophene ring for all chlorothiophenes and their radical cations have been studied. Vibrational frequencies, nuclear chemical shielding constants, spin-density distribution, size and direction of dipole moment vector, ionization potential, electric polarizabilities and NICS values of these compounds have been calculated as well. The analysis of these data showed that double bonds in 3-chlorothiophene are more delocalized and it is the best possible candidate monomer among all chlorothiophenes for the synthesis of corresponding conducting polymers with modified characteristics.     

A theoretical and experimental study of the electronic transport properties of the compounds Cu2MTe3 (M =Ti,Zr, Hf)

A theoretical model that involves metal nonstoichiometry is proposed to explain the unexpected electronic conductivities in the close-packed ternary tellurides Cu₂MTe₃ (M =Ti, Zr, Hf). Conductivity, thermoelectric power, and Hall effect measurements indicate that these compounds are hole carriers with a concentration of the order of 5 × 10¹⁹ cm⁻³ for M =Zr at 300 K. Such a concentration corresponds to roughly 0.4% Cu vacancies or 0.2% Zr vacancies, levels below the detection limit by X-ray diffraction methods of the corresponding elements in theM =Hf compound.     

Mass spectrometric analysis of ceramide composition in mono-, di-, tri-, and tetraglycosylceramides from mouse kidney: an experimental model for uropathogenic Escherichia coli.

Many bacteria have been shown to bind to the carbohydrate part of glycosphingolipids, but also the lipid moieties of receptor-active glycolipids are of importance. To investigate the chemistry of the ceramides of kidney glycolipids to which the uropathogenic Escherichia coli bind, different mass spectrometric techniques were utilized. First, a mixture of glycolipids isolated from man and mice kidney was separated by thin-layer chromatography (TLC) and scanned by direct desorption from the plate by fast atom bombardment mass spectrometry (TLC/FAB-MS). Second, the glycolipids were purified by preparative TLC and analyzed by negative-ion FAB-MS. After methylation, further analyses were made with positive-ion FAB-MS, positive-ion electron ionization (EI)-MS, high-temperature capillary gas chromatography (GC/EI-MS) and positive-ion matrix-assisted laser desorption/ionization (MALDI)-MS. The ceramide compositions of the four glycolipids were determined using all these MS techniques and the reliability of the different methods for this type of analyses is discussed. Comparison of the mouse kidney glycolipids with the corresponding glycolipids from human kidney showed the same degree of hydroxylation of ceramides among mono- and disaccharide glycolipids, but a significantly higher degree of hydroxylation among mouse kidney glycolipids with three and four sugar residues. This result might be of relevance for the binding of P-fimbriated E. coli to the urinary tract tissues.     

RETRACTED: Ab initio and density functional study of electrical and thermochemical properties of mono-, di-, tri-, and tetrafluoropyrroles and their cations and anions

This article has been retracted by the authors.Reason: the authors have recognised that the subject matter of this article requires further examinations and that the content requires restructuring. For this reason, the authors requested that the article be retracted from Journal of Molecular Structure: THEOCHEM volume 713 issue 1–3 pages 43–49, from this journal.     

Perfluoromethyl fluorocarbonyl peroxide,CF3OOC(O)F: structure,conformations, and vibrational spectra studied by experimental and theoretical methods

The conformational properties and the geometric structure of perfluoromethyl fluorocarbonyl peroxide, CF(3)OOC(O)F, have been studied by matrix IR spectroscopy, gas electron diffraction, and quantum chemical calculations (HF, B3LYP, and MP2 methods with 6-311G* basis sets). Matrix IR spectra imply a mixture of syn and anti conformers (orientation of the C=O bond relative to the O-O bond) with DeltaH degrees = H(anti) degrees - H(syn) degrees = 2.16(22) kcal/mol. At room temperature, the contribution of the anti rotamer is about 3.0%. The O-O bond (1.422(15) A) is within the experimental uncertainties equal to those in related symmetrically substituted peroxides CF(3)OOCF(3) and FC(O)OOC(O)F (1.419(20) and 1.419(9) A, respectively), and the dihedral angle delta(COOC) (111(5) degrees ) is intermediate between the values in these two compounds (123(4) degrees and 83.5(14) degrees, respectively).     

Thermal properties of different transition metal forms of montmorillonite intercalated with mono-, di-, and triethanolammonium compounds

In the present study, different transition metal forms of montmorillonite have been intercalated with mono-, di-, and triethanolammonium cations via d coordination mechanism to investigate their thermal behavior, structural characteristics, surface properties, and elemental composition using TG, XRD, BET, and CHNS techniques. Thermogravimetric analysis showed two thermal transition steps for transition metal-exchanged montmorillonites, which attributed to desorption of the physically adsorbed water and hydrated water, and dehydroxylation of the structural water; whereas for ammonium-montmorillonite complexes, the TG curves showed three thermal transition steps which attributed to desorption of the adsorbed water and dehydration, decomposition of the ammonium cations in the interlayer space of montmorillonite, and the dehydroxylation of the structural water. The thermal analysis of ammonium-montmorillonites affirmed that the molar mass of amine compounds used affects both desorption temperature (position) and the amount of the adsorbed water (intensity). XRD results revealed that the molar mass of amine used has linear relation with the basal spacings of the corresponding ammonium-montmorillonites, indicating structural changes. BET results showed that the molar mass of amines has an inverse effect on the surface area of the studied samples. CHNS analysis for the studied samples quantitatively confirmed the intercalation of ammonium cations into the interlayer space of montmorillonite.     

Conformational studies by dynamic NMR—28 : Stereomutations in some di-, tri- and tetraalkylhydrazines

Low temperature NMR spectra allowed us to “freeze” some of the internal motions in a number of di-, tri- and tetraalkylhydrazines and to measure the corresponding free energies of activation. In particular, tetramethylhydrazine (Me₂N-NMe₂) was found to have, at - 150°, two pairs of diastereotopic methyls : this is due to the fact that both N-inversion and N,N-rotation are slow at this temperature and that a gauche conformation is adopted. The observed barrier (6.0 kcal mol^-1) has been attributed to N,N-rotation, the barrier due to N-inversion being higher and not measurable via NMR in the presence of a concomitant fast rotation. In other cases, notably PrⁱMeN-NH₂, Me₂N-NPrⁱ₂ and Prⁱ₂N-NHMe, two different motions (inversion and rotation) were detected. In the case of Me₂N-NHMe it was also possible to observe the first example of anisochronous behaviour of nitrogen-bonded methyls (Me₂N) induced by an aminic nitrogen that becomes chiral at low temperature.     

Photochemical and electronic properties of conjugated bis(azo) compounds: an experimental and computational study

We have investigated the photophysical, photochemical and electrochemical properties of two bis(azo) derivatives, (E,E)-m-1 and (E,E)-p-1. The two compounds, which can be viewed as being composed of a pair of azobenzene units sharing one of their phenyl rings, differ only for the relative position of the two azo groups on the central phenyl ring-meta and para for m-1 and p-1, respectively. The UV-visible absorption spectra and photoisomerisation properties are noticeably different for the two structural isomers; (E,E)-m-1 behaves similarly to (E)-azobenzene, while (E,E)-p-1 exhibits a substantial red shift in the absorption bands and a decreased photoreactivity. The three geometric isomers of m-1, namely the E,E, E,Z and Z,Z isomers, cannot be resolved in a mixture by absorption spectroscopy, while the presence of three distinct species can be revealed by analysis of the absorption changes observed upon photoisomerisation of (E,E)-p-1. Quantum chemical ZINDO/1 calculations of vertical excitation energies nicely reproduce the observed absorption changes and support the idea that, while the absorption spectra of the geometrical isomers of m-1 are approximately given by the sum of the spectra of the constituting azobenzene units in their relevant isomeric form, this is not the case for p-1. From a detailed study on the E-->Z photoisomerisation reaction it was observed that the photoreactivity of an azo unit in m-1 is influenced by the isomeric state of the other one. Such observations indicate a different degree of electronic coupling and communication between the two azo units in m-1 and p-1, as confirmed by electrochemical experiments and quantum chemical calculations. The decreased photoisomerisation efficiency of (E,E)-p-1 compared to (E,E)-m-1 is rationalised by modelling the geometry relaxation of the lowest pi-pi* state. These results are expected to be important for the design of novel oligomers and polymers, based on the azobenzene unit, with predetermined photoreactivity.     

Electrocatalysis of chloroacetic acids (mono-, di- and tri-) at a C60-[dimethyl-(beta-cyclodextrin)]2 and nafion chemically modified electrode

The C(60)-[dimethyl-(beta-cyclodextrin)](2) and nafion chemically modified electrode (CME) exhibits one electroreduction peak and two electro-oxidation peaks in a mixed solvent of water and acetonitrile (3:2, v/v) containing tetra-butylammonium perchlorate. The reduction of chloroacetic acids (mono-, di- and tri-) can be electrocatalyzed at this electrode, indicating that C(60)-[dimethyl-(beta-cyclodextrin)](2) is capable of mediating the electron transfer to chloroacetic acids. Values of the apparent catalytic rate constant, k, were determined by using the rotating-disk electrode (RDE).     

Synthesis of di-, tri- and tetranuclear platinum(II) and copper(I) acetylide complexes

Heterobimetallic {cis-[Pt](μ-σ,π-CCPh)₂}[Cu(NCMe)]BF₄ (3a: [Pt] = (bipy)Pt, bipy = 2,2′-bipyridine; 3b: [Pt] = (bipy′)Pt, bipy′ = 4,4′-dimethyl-2,2′-bipyridine) is accessible by the reaction of cis-[Pt](CCPh)₂ (1a: [Pt] = (bipy)Pt, 1b: [Pt] = (bipy′)Pt]) with [Cu(NCMe)₄]BF₄ (2). Substitution of NCMe by PPh₃ (4) can be realized by the reaction of 3a with 4, whereby [{cis-[Pt](μ-σ,π-CCPh)₂}Cu(PPh₃)]BF₄ (5) is formed. On prolonged stirring of 3 and 5, respectively, NCMe and PPh₃ are eliminated and tetrametallic {[{cis-[Pt](η²-CCPh)₂}Cu]₂}(BF₄)₂ (6) is produced. Addition of an excess of NCMe to 6 gives heterobimetallic 3a.When instead of NCMe or PPh₃ chelating molecules such as bipy (7) are reacted with 3a then the heterobimetallic π-tweezer molecule [{cis-[Pt](μ-σ,π-CCPh)₂}Cu(bipy)]BF₄ (8) is formed. Treatment of 8 with another equivalent of 7 produced [Cu(bipy₂)]BF₄ (9) along with [Pt](CCPh)₂. However, when 3b is reacted with 1b in a 1:1 molar ratio then 10 and 11 of general composition [{[Pt](CCPh)₂}₂Cu]BF₄ are formed. These species are isomers and only differ in the binding of the PhCC units to copper(I). A possible mechanism for the formation of 10 and 11 is presented.The solid state structures of 6, 10 and 11 are reported. In 11 the [{cis-[Pt](μ-σ,π-CCPh)₂}₂Cu]⁺ building block is set-up by two nearly orthogonal positioned bis(alkynyl) platinum units which are connected by a Cu(I) ion, whereby the four carbon-carbon triple bonds are unsymmetrical coordinated to Cu(I). In trimetallic 10 two cis-[Pt](CCPh)₂ units are bridged by a copper(I) center, however, only one of the two PhCC ligands of individual cis-[Pt](CCPh)₂ fragments is η²-coordinated to Cu(I) giving rise to the formation of a [(η²-CCPh)₂Cu]⁺ moiety with a linear alkyne-copper-alkyne arrangement (alkyne = midpoint of the CC triple bond). In 6 two almost parallel oriented [Pt](CCPh)₂ planes are linked by two copper(I) ions, whereby two individual PhCC units, one associated with each Pt building block, are symmetrically π-coordinated to Cu.     

Combined experimental and theoretical studies on the photophysical properties of cycloparaphenylenes

We studied the UV-vis absorption and fluorescence in solution/solid states of [n]cycloparaphenylene ([n]CPP: n = 9, 12, 14, 15, and 16), and conducted theoretical studies to better understand the experimental results. The representative experimental findings include (i) the most intense absorption maxima (λ(abs1)) display remarkably close values (338-339 nm), (ii) the longest-wavelength absorption maxima (λ(abs2)) are blue-shifted with increasing the ring size (395 → 365 nm), (iii) the emission maxima (λ(em)) are blue-shifted with increasing the ring size (494 → 438 nm for longest-wavelength maxima), (iv) the fluorescent quantum yields (Φ(F)) in solution are high (0.73-0.90), (v) the fluorescence lifetimes (τ(s)) of [9]- and [12]CPP are 10.6 and 2.2 ns, respectively, and (vi) the Φ(F) values slightly increase in polymer matrix but significantly decrease in the crystalline state. According to TD-DFT calculations, the longest-wavelength absorption (λ(abs2)) corresponds to a forbidden HOMO → LUMO transition and the most intense absorption (λ(abs1)) corresponds to degenerate HOMO - 1 → LUMO and HOMO → LUMO + 1 transitions with high oscillator strength. The interesting and counterintuitive optical properties of CPPs (constant λ(abs1) and blue shift of λ(abs2)) could be ascribed mainly to the ring-size effect in frontier molecular orbitals (in particular the increase of the HOMO-LUMO gap as the number of benzene rings increases). On the basis of comparative calculations using hypothetical model geometries, we conclude that the unique behavior of HOMO and LUMO of CPPs is due mainly to their lack of a conjugation length dependence in combination with a significant bending effect (particularly to HOMO) and a torsion effect (particularly to LUMO).     

Solvent effects on the geometry,electronic structure,and bonding style of Zn(N5)2: A theoretical study

Nitrogen-rich compounds involving the cyclo-pentazole anion (cyclo-N₅⁻) have attracted extensive attention due to higher energy release and environmental friendliness than traditional high energy density materials (HEDMs). However, the synthesis of stable HEDMs with cyclo-N₅⁻ is still a challenge. In this study, the effect of nine solvents on the geometrical and electronic structures and solvation energies of Zn(N₅)₂, one of the recently synthesized nitrogen-rich compounds, was studied using the density functional theory and the polarized continuum model. The results indicated an increase in the stability of Zn(N₅)₂ in the solution phase compared to the vacuum phase, and the stability of Zn(N₅)₂ increases with increasing dielectric constants. The energy gap of frontier molecular orbitals and the absolute value of total energy in water are the largest, revealing that Zn(N₅)₂ is more stable in water than in other solvents. To understand the stabilization mechanism of Zn(N₅)₂ by water, further studies were performed with the natural bond orbital (NBO) analysis and the quantum theory of atoms in molecules (QTAIM) analysis using the explicit solvent model. The charge transfer and the hydrogen bonds are observed between Zn(N₅)₂ and water, which are beneficial to improvement of the stability of Zn(N₅)₂. This may indicate the solvents that have strong interactions with the cyclo-N₅⁻ candidate may improve the possibility of success of synthesis.