A case study in conformation design: learning by doing

Efforts are described to design simple, fully flexible but conformationally preorganised omega-hydroxy-nonanoic acids that could serve as the conformation controlling unit in analogues of the potent protein-kinase C activator aplysiatoxin. Such analogues are macrodilactones incorporating the designed omega-hydroxy-nonanoic acid and 3,4-dihydroxy-pentanoic acid, which contains the pharmacophoric groups. The design process (replacement of CH(2) groups by an oxygen atom, annelation of a six-membered ring and placement of alkyl substituents) of the omega-hydroxy-nonanoic acids was monitored by force-field calculations. In the end of this process simple analogues of aplysiatoxin are proposed in which the proper disposition of the pharmacophoric groups is secured by a conformationally flexible but preorganised template structure as part of the macrodilactone ring.     

Interaction of the important species HNO and HFSO2 in the atmosphere: Theoretical study of the N?H and S?H blue‐shifted hydrogen bonds

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the N? H…O and S? H…O blue‐shifted H‐bonds in the HNO…HFSO₂ complex. The geometric structures, vibrational frequencies, and interaction energies were calculated by both standard and CP‐corrected methods. Natural bond orbital (NBO) analysis was used to investigate the origin of blue‐shifted H‐bonds, showing that the decrease in the σ*(N? H) and σ*(S? H) is due to the electron density redistribution effect. The structure reorganization effect on the blue‐shifted hydrogen bonds was discussed in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Electrochemical Evaluation of the Interaction between Avidin and Biotin at Biotinylated Polypyrrole Electrode Using a Redox Marker

The interaction between avidin and biotin was evaluated electrochemically by monitoring the change in the electrode response of redox markers. Biotin was immobilized on the electrode surface by means of the electrochemical polymerization of biotinylated pyrrole and pyrrole. When avidin was introduced onto the biotinylated polypyrrole electrode surface, the large change in the electrode response of the redox marker was detected. The fact that the change in the electrode response of a marker ion could be attributed to the electrostatic interaction between avidin on the electrode surface and the redox marker ion present in a solution was verified by replacing avidin with NutrAvidin. At a pH lower than the isoelectric point of avidin, the electrode response of ferrocyanide as an anionic marker ion increased linearly within the range of 5.0×10^?9 ?3.0×10^?8 M avidin. The relative standard deviation at 1.5×10^?8 M avidin was about 5.4% (n=5). The detection of biotin was also performed using a competitive reaction between biotin in solution and biotin that had been immobilized on the electrode surface in the form of the biotinylated polypyrrole.     

Synthesis and properties of new soluble aromatic polyamides and polyimides on the basis of N,N′‐bis(3‐aminobenzoyl)‐N,N′‐diphenyl‐1,4‐phenylenediamine

A new N‐phenylated amide (N‐phenylamide) unit containing aromatic diamine, N,N′‐bis(3‐aminobenzoyl)‐N,N′‐diphenyl‐1,4‐phenylenediamine, was prepared by the condensation of N,N′‐diphenyl‐1,4‐phenylenediamine with 3‐nitrobenzoyl chloride, followed by catalytic reduction. Two series of organosoluble aromatic poly(N‐phenylamide‐imide)s and poly(N‐phenylamide‐amide)s with inherent viscosities of 0.58–0.82 and 0.56–1.21 dL/g were prepared by a conventional two‐stage method and the direct phosphorylation polycondensation, respectively, from the diamine with various aromatic dianhydrides and aromatic dicarboxylic acids. All polyimides and polyamides are amorphous and readily soluble in many organic solvents such as N,N‐dimethylacetamide and N‐methyl‐2‐pyrrolidone. These polymers could be solution cast into transparent, tough, and flexible films with high tensile strengths. These polyimides and polyamides had glass‐transition temperatures in the ranges of 230–258 and 196–229 °C, respectively. Decomposition temperatures of the polyimides for 10% weight loss all occurred above 500 °C in both nitrogen and air atmospheres. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2564–2574, 2002     

1,4‐Addition polymerization of 1,4‐bis(4‐benzylpyridinium)butadiyne triflate in a dipolar aprotic solvent

1,4‐Bis(4‐benzylpyridinium)butadiyne triflate was aggregated in dimethylformamide and spontaneously converted into the 1,4‐addition type of polydiacetylene. The polymerization took place in a dipolar aprotic solvent with a large dielectric constant that could enhance the aggregation of the ionic diacetylene salt through the electrostatic interaction. The molecular weight of the diacetylene was leveled off after 30 h at 80 °C to reach 1.5 × 10⁴ (number‐average molecular weight) that consisted of the 1,4‐addition type of polydiacetylene similar to polydiacetylenes obtained in the conventional solid‐state polymerization. Electron spin resonance spectra revealed that diradicals were generated at the earlier state aggregation to give rise to a solution polymerization. The UV spectra also suggested the presence of the activated aggregation associated with the polymerization as well as the eximer emission spectra. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 3534–3541, 2002     

Catalytic Adsorptive Stripping Voltammetry of Cobalt in the Presence of Dimethylglyoxime and Nitrite at In Situ Plated Lead–Copper Film Electrode

A lead‐copper film electrode was proposed for Co(II) determination by catalytic adsorptive stripping voltammetry. The electrode was plated in situ and hence the exchange of a solution after plating step was not required. At optimized conditions the calibration graph for Co(II) was linear from 5×10^?10 to 2×10^?8 mol L^?1 for accumulation time of 15 s. The relative standard deviation for Co(II) determination at concentration 5×10^?9 mol L^?1 was 4.1%. The detection limits for Co(II) were 1.2×10^?10 and 1.0×10^?11 mol L^?1 for an accumulation time of 15 and 180 s, respectively. The method was applied to Co(II) determination in certified reference material and other water samples.     

Isotope‐Coded Affinity Tagging Technique Using Avidin Functional Affinity Electrophoresis: An Alternative to an Avidin Affinity Column

Avidin functional affinity electrophoresis (AFAEP) is substituted for an avidin affinity column (AAC) to capture biotinylated peptides in the Isotope‐Coded Affinity Tagging (ICAT) technique which is a valuable tool in quantitative proteomics. In this new technique, the AFAEP‐captured ICAT‐labeled biotinylated peptides are extracted with the biotin tag intact from the polyacrylamide gel piece with aqueous 95% formamide (pH 8.2) at 65 °C for 20 min, and then detected by a matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometer. Bovine serum albumin (BSA) and the ¹²C‐ and ¹³C‐ICAT reagents are used to test this AFAEP‐ICAT technique. The results show that both AFAEP and AAC methods provide quantitative information of the relative amounts of ¹²C‐ and ¹³C‐ICAT‐labeled biotinylated tryptic peptides of BSA in a sample. Compared with AAC, the AFAEP is cheaper to perform, more stringent in capturing the biotinylated peptides, and capable of simultaneously processing multiple samples.     

Design of organic semiconductors: tuning the electronic properties of pi-conjugated oligothiophenes with the 3,4-ethylenedioxythiophene (EDOT) building block

Hybrid oligothiophenes based on a various combinations of thiophene and 3,4-ethylenedioxythiophene (EDOT) groups have been synthesized. UV/Vis absorption spectra show that the number and relative positions of the EDOT groups considerably affect the width of the HOMO-LUMO gap and the rigidity of the conjugated system. Analysis of the crystallographic structure of two hybrid quaterthiophenes confirms that insertion of two adjacent EDOT units in the middle of the molecule leads to a self-rigidification of the conjugated systems by intramolecular SO interactions. Cyclic voltammetry data shows that the first oxidation potential of the oligomers decreases with increasing chain length and increasing number of EDOT groups for a given chain length. Electrochemical studies and theoretical calculations show that the positions of the EDOT units in the conjugated chain control the potential difference (DeltaE(p)) between the first and second oxidation steps. Moving the EDOT groups from the outer to the inner positions of the conjugated system increases DeltaE(p). Theoretical calculations confirm that this phenomenon reflects an increase of the intramolecular coulombic repulsion between positive charges in the dication. A thin-film field-effect transistor was fabricated by vacuum sublimation of a pentamer with alternating thiophene-EDOT structure, and the hole mobility was determined.     

Two‐ and Three‐Dimensional Molecular Organization of Schiff‐Base Derivatives

We have designed and synthesized a series of Schiff base derivatives, and studied their structural features in two‐dimensional (2D) and three‐dimensional (3D) states by combining scanning tunneling microscopy (STM) and X‐ray diffraction experiments. The Schiff‐base derivatives with short alkyl chains crystallize easily, which allows a detailed structural analysis by X‐ray diffraction. Due to the strong adsorbate–substrate interactions, those bases with long alkyl chains easily form 2D assemblies on highly oriented pyrolytic graphite (HOPG). The STM images indicate also that the introduction of two methoxy groups into the molecule can change the structure of these 2D assemblies as a result of the increased steric hindrances, for example: the Schiff‐base derivative, bearing both methoxy groups and C₁₆H₃₃ tails, forms 2D Moiré patterns, and an alignment of pairing Schiff‐base molecules may be easily resolved. Conversely, the Schiff base derivative, bearing solely C₁₆H₃₃ tails, forms 2D non‐Moiré patterns. It is demonstrated that the 3D structural features result from the compromise of intermolecular interactions of different molecular moieties. However, there is one more factor, which also governs the 2D structure: the adsorbate‐substrate interaction. The 3D crystal structure may thus help to understand many factors involved in the formation of 2D structures, and would be helpful for designing new molecular assemblies with tailoring functions.     

Remarkable reactions of cyclooctatetraene diiron-bridging carbyne complexes with amino and amido compounds: nucleophilic addition to and breaking of the cyclooctatetraene ring

The reactions of the cationic, diiron-bridging carbyne complexes [Fe(2)(mu-CAr)(CO)(4)(eta(8)-C(8)H(8))]BF(4) (1, Ar=C(6)H(5); 2, Ar=p-CH(3)C(6)H(4); 3, Ar=p-CF(3)C(6)H(4)) with LiN(C(6)H(5))(2) in THF at low temperature gave novel N-nucleophilic-addition products, namely, the neutral, diiron-bridging carbyne complexes [Fe(2)(mu-CAr)(CO)(4)(eta(7)-C(8)H(8)N(C(6)H(5))(2))] (4, Ar=C(6)H(5); 5, Ar=p-CH(3)C(6)H(4); 6, Ar=p-CF(3)C(6)H(4))). Cationic bridging carbyne complexes 1-3 react with (C(2)H(5))(2)NH, (iC(3)H(7))(2)NH, and (C(6)H(11))(2)NH under the same conditions with ring cleavage of the COT ligand to produce the novel diiron-bridging carbene inner salts [Fe(2)[mu-C(Ar)C(8)H(8)NR(2)](CO)(4)] (7, Ar=C(6)H(5), R=C(2)H(5); 8, Ar=p-CH(3)C(6)H(4), R=C(2)H(5); 9, Ar=p-CF(3)C(6)H(4), R=C(2)H(5); 10, Ar=C(6)H(5), R=iC(3)H(7); 11, Ar=p-CH(3)C(6)H(4), R=iC(3)H(7); 12, Ar=p-CF(3)C(6)H(4), R=iC(3)H(7); 13, Ar=C(6)H(5), R=C(6)H(11); 14, Ar=p-CH(3)C(6)H(4), R=C(6)H(11), 15, Ar=p-CF(3)C(6)H(4), R=C(6)H(11)). Piperidine reacts similarly with cationic carbyne complex 3 to afford the corresponding bridging carbene inner salt [Fe(2)[mu-C(Ar)C(8)H(8)N(CH(2))(5)](CO)(4)] (16). Compound 9 was transformed into a new diiron-bridging carbene inner salt 17, the trans isomer of 9, by heating in benzene. Unexpectedly, the reaction of C(6)H(5)NH(2) with 2 gave a novel COT iron-carbene complex [Fe(2)[=C(C(6)H(4)CH(3)-p)NHC(6)H(5)](mu-CO)(CO)(3)(eta(8)-C(8)H(8))] (18). However, the analogous reactions of 2-naphthylamine with 2 and of p-CF(3)C(6)H(4)NH(2) with 3 produce novel chelated iron-carbene complexes [Fe(2)[=C(C(6)H(4)CH(3)-p)NC(10)H(7)](CO)(4)(eta(2):eta(3):eta(2)-C(8)H(9))] (19) and [Fe(2)[=C(C(6)H(4)CF(3)-p)NC(6)H(4)CF(3)-p](CO)(4)(eta(2):eta(3):eta(2)-C(8)H(9))] (20), respectively. Compound 18 can also be transformed into the analogous chelated iron-carbene complex [Fe(2)[=C(C(6)H(4)CH(3)-p)NC(6)H(5)](CO)(4)(eta(2):eta(3):eta(2)-C(8)H(9))] (21). The structures of complexes 6, 9, 15, 17, 18, and 21 have been established by X-ray diffraction studies.