Anisotropy of the fluorescence from the monomer,five oligomers,and a polymer of epicatechin

The steady-state fluorescence anisotropy r has been measured at 25°C for dilute solutions of epicatechin units connected by interflavan bonds with 4β → 8 stereochemistry. The molecules studied are monodisperse oligomers from the monomer through the hexamer, and a polydisperse sample with a number-average degree of polymerization x_n of 10. The hexamer and smaller oligomers have been removed from the polydisperse sample. All samples have a very small value of r in 1,4-dioxane and in methanol. Higher values of r are seen in ethylene glycol and in glycerol. In the latter two solvents, the monomer has significantly higher r than any species with x_n > 1. This observation is interpreted as evidence for the presence of excitation migration from one monomer to another in the dimer and species of higher x_n.     

The effect of homologous amino acid replacement on the conformation of oligopeptides. II. Synthesis of co-oligopeptides containing methionine and glycine

The synthess of 18 co-oligopeptides of L -methionine and glycine is reported. A series of oligomers, Boc-Gly-Met_n-OMe (n = 1–6), and six hexamers-containing five methionyl and one glycyl residue were synthesized using the mixed anhydride procedure. Polarimetric studies give evidence that oligomers in the Boc-Gly-Met_n-Ome series are essentially disordered in hexafluoroacetone sesquihydrate but begin forming secondry structures at n > 4 in trifluorethanol. Difference in the molar rotation values found for the six hexamers in hexafluoroacetone sesquihydrate may indicate that these compounds, while primirily disordered, are present in slightly different conformations.     

Comparison of oligoribonucleotides and oligodesoxyribonucleotides. I. Formation of double helices

The ability of oligodesoxyribonucleotides of various chain lengths to form complexes has been compared with that of oligoribonucleotides. Four series of oligonucleotidcs were prepared and investigated, i.e., dC_n at acid pH versus rC_n, dA_n and dT_n versus. rA_n and rU_n at neutral pH. The results indicate that in dilute solution, the formation of complexes is greatly facilitated in the case of desoxyoligomers and occurs for shorter oligomere than in the corresponding ribooligomers. The spectrophotometric titration of deoxyribooligo C indicates the appearance of two pK values in the 4–5 pH region characteristic of the double-stranded form, which occurs for much shorter dC_n than rC_n. The circular dichroism (CD.) spectra of deoxycytidylies in dilute solution starting from the trimer are conservative, characteristic of the double-stranded helical form of poly C at acid pH. In contrast, the CD spectra of a series of corresponding ribo C_n, under identical conditions is of nonconservative character similar to that of the single-stranded form of poly C at neutral pH, but differs in the band position. This spectrum is called intermediate. Only at higher concentrations of oligonucleotidcs (i.e., 10^?3Minstead of 10^?4M) does the circular dichroism spectrum of longer ribocytidylics assume conservative character. Thermal denaturation of deoxycytidylces at acid pH are strongly dependent on chain length and concentration, its one would expect for a cooperative helix-coil transition. The circular dichroism spectra measured at different temperatures shows one isosbestic point. In dilute solution, the standard-state enthalpy change found was 5–6 kcal/mole for higher oligomers (dC₇). These properties are all in agreement with a structural transition from the d-C_n double-stranded form to a coil for n > 3. Studies of dA_n and dT_n in solutions of high ionic strength at low temperature indicate that complex formation occurs already at the level of trimer and for high oligomers. Under identical conditions a complex between rA_n and rU_n is detected only for oligomers longer than the hexamer. The nature of the “intermediate” form of oligoribo C at acid pH and low temperature was investigated by sedimentation and circular dichroism. A model of rC_n is proposed of linear molecules which are partially double-stranded and partially single-stranded, which probably are slowly rearranged by “slippage” into a regular-double-stranded helical form.     

Assessing the sequence specificity in the binding of Co(III) to DNA via a thermodynamic approach

The interaction specificities of Co(III) with DNA were investigated via consideration of thermodynamic characteristics of the duplex to single strand transition for DNA oligomers incubated in the presence of [Co(NH₃)₅(OH₂)] (ClO₄)₃. It has previously been demonstrated that incubation of the DNA oligomer [(5medC-dG)₄]₂ with this cobalt complex leads to coordination of the cobalt center to the DNA, presumably at N7 of guanine bases [D. C. Calderone, E. J. Mantilla, M. Hicks, D. H. Huchital, W. R. Murphy, Jr. and R. D. Sheardy, (1995) Biochemistry 34, 13841]. In this report, DNA oligomers of different sequence were incubated with [Co(NH₃)₅(OH₂)] (ClO₄)₃ via protocols developed previously and the treated oligomers were subjected to thermal denaturation for comparison to the untreated oligomers. The DNA oligomers were designed in order to investigate the sequence specificity, if any, in the reaction of the cobalt complex with DNA. The values of T_m, ΔH_uH, and Δn (the differential ion binding term) obtained from the thermal denaturations were used to assess the sequence specificity of the interaction. For all oligomers, treated or untreated, T_m and Δ_uH vary linearly with log [Na⁺] and hence the value of Δn is a function of the Na⁺ concentration. The results indicate no significant reaction between the cobalt complex and oligomers possessing isolated -GA- or -CG- sites; however, the thermodynamic characteristics of DNA oligomers possessing either an isolated -GG- site or an isolated -GC- site were altered by the treatment. Atomic absorption studies of the treated oligomers demonstrate that only the DNA oligomers possessing isolated -GG- or -GC- sites bind cobalt. Hence, the changes in the thermodynamic properties of these oligomers are a result of cobalt binding with a remarkable sequence specificity. © 1997 John Wiley & Sons, Inc. Biopoly 42: 549–599, 1997     

Cooperative and thermodynamic parameters for oligoinosinate-polycytidylate complexes

The cooperative nature of the binding between polycytidylate and the oligoinosinates I(pI)_5–10 has been determined. Using the data of Tazawa, Tazawa, and Ts'o, it is shown that knowledge of the slope of the adsorption isothern allows one to determine the oligomer-polymer binidng constant, the oligomer–oligomer interaction constant, and the average degree of association (cooperative clustering) of the oligomers on the polymer. Knowledge of the above equilibrium constants as a function of temperature yields the respective thermodynamic parameters; no assumptions need to be made about the nature of the equilibrium constants or the thermodynamic parameters. For very long chains of polycytidylate, simple, explicit relations are given for the determination of the equilibrium constants involved. For finite chains of polycytidylate, the calculation of a single graph for each oligomer and polymer size allows the equilibrium constants to be determined for all experimental conditions of temperature and concentration. We find that the enthalpy and entropy of binding an oligomer n, bases to be δH_n = ±13.7 ? n(6.65) and δS_n = +32.5 ? n(18.8) given, respectively, in kcal/mole and e.u.; these parameters predict a melting temperature of 81°C for the poly(I)·poly(C) complex compared with the experimental value of 75°C. If the enthalpy is interpreted as arising from a sum of hydrogen bonding and stacking interactions, then the enthalpy of stacking is ?13.7 kcal/mole while the enthalpy of hydrogen bonding is +7 ± 4 kcal/mole; the positive enthalpy of hydrogen bonding presumably is a result of the fact that in the inosine-cytosine base pair, only two of the three sites on cytosine can hydrogen bond, the third being blocked from hydrogen bonding with water. The enthalpy of interaction between neighboring bound oligomers is found to be ?10.4 kcal/mole while the corresponding entropy is ?26.1 e.u. The binding is bound to be cooperative, though the extent of clustering varies markedly with temperature; the average number of oligomers in a cluster on the polymer is found to about five at a melting temperature of 25°C. The approach and equations given have generally applicability to oligomer-polymer associations.     

The impact of Cu atoms on the reactivity of ZrO2 oligomers

A theoretical study on (ZrO₂) _n (n = 1–5) and Cu/ZrO₂ oligomers is presented, DFT/B3LYP/6-31G** calculations along with Lanl2DZ pseudopotentials on metallic centers have been used to predict ionization potentials and electron affinities, chemical potentials and bandgaps indicating that the reactivity reaches reasonably constant values at n = 5. The effect of copper atoms adsorbed on (ZrO₂) _n is discussed and the reactivity of oligomers of ZrO₂ and Cu/ZrO₂ are compared, results indicate that Cu activates the systems by localizing the specific nucleophilic and electrophilic reactivity.     

Glycoconjugate histochemistry of the digestive tract of <Emphasis Type="Italic">Triturus carnifex</Emphasis> (Amphibia,Caudata)

Summary In this study, the variety of sugar residues in the gut glycoconjugates of Triturus carnifex (Amphibia, Caudata) are investigated by carbohydrate conventional histochemistry and lectin histochemistry. The oesophageal surface mucous cells contained acidic glycoconjugates, with residues of GalNAc, Gal β1,3 GalNAc and (GlcNAc β1,4) _n oligomers. The gastric surface cells mainly produced neutral glycoproteins with residues of fucose, Gal β1-3 GalNAc, Gal-αGal, and (GlcNAc β1,4) _n oligomers in N- and O-linked glycans, as the glandular mucous neck cells, with residues of mannose/glucose, GalNAc, Gal β1,3 GalNAc, (GlcNAc β1,4) _n oligomers and fucose linked α1,6 or terminal α1,3 or α1,4 in O-linked glycans. The oxynticopeptic tubulo-vesicular system contained neutral glycoproteins with N- and O-linked glycans with residues of Gal-αGal, Gal β1-3 GalNAc and (GlcNAc β1,4) _n oligomers; Fuc linked α1,2 to Gal, α1,3 to GlcNAc in (poly)lactosamine chains and α1,6 to GlcNAc in N-linked glycans. Most of these glycoproteins probably corresponds to the H⁺K⁺-ATPase β-subunit. The intestinal goblet cells contained acidic glycoconjugates, with residues of GalNAc, mannose/ glucose, (GlcNAc β1,4) _n oligomers and fucose linked α1,2 to Gal in O-linked oligosaccharides. The different composition of the mucus in the digestive tracts may be correlated with its different functions. In fact the presence of abundant sulphation of glycoconjugates, mainly in the oesophagus and intestine, probably confers resistance to bacterial enzymatic degradation of the mucus barrier.     

DNA and RNA oligomer thermodynamics: The effect of mismatched bases on double-helix stability

The thermodynamic parameters for the double-strand formation of the molecules rCAmG + rCU_nG, m,n = 5–7, and dCA_mG + dCT_nG, m,n = 5,6, were measured from optical melting curves. Normal helices are formed when m = n. The deoxyoligomers are more stable than the ribo-oligomers, due to a more favorable enthalpy. Double helices with mismatched bases can be formed by mixing oligomers with m ≠ n. Such helices may form several possible structures. A structure with a dangling base is favored over a structure with a bulged base. The destabilization of the double strands by the formation of a bulged base was determined to be greater than 1.6 kcal/mol at 10°C. The extent of aggregation in the oligomer double strand rCA₇G·rCU₇G was determined using ultracentrifugation equilibrium. The possible effects of aggregation on the determination of the thermodynamic parameters for double-strand formation are discussed.     

Cytogenetic characterization of the sole Solea senegalensis (Teleostei: Pleuronectiformes: Soleidae): Ag-NOR, (GATA) n , (TTAGGG) n and ribosomal genes by one-color and two-color FISH

A cytogenetic analysis of the sole Solea senegalensis was carried out using silver staining for the nucleolus organizer region (Ag-NOR) identification, one-color FISH for chromosomal mapping of 45S and 5S ribosomal DNAs (rDNAs), (GATA) _n , and (TTAGGG) _n , and two-color FISH for co-localization of both rDNAs. The Ag-NORs and the 45S rDNA were mapped to a medium-sized submetacentric chromosomal pair. Hybridization with the 5S rDNA showed a major signal on the short arm of a medium-sized submetacentric chromosome pair and a minor signal on a centromeric site of a small acrocentric chromosome pair. Differences in the Ag-NOR and 45S and 5S rDNAs FISH signal sizes were observed between homologous chromosomes and among individuals. A two-color FISH co-localized 45S and 5S rDNAs to a medium-sized submetacentric chromosomal pair. The hybridization with the telomeric (TTAGGG) _n repeat displayed small signals at all chromosomal telomeres. Finally, the (GATA) _n probe produced dispersed and small hybridization signals on all chromosome spreads, showing its ubiquitous existence in the genome. These results were compared with those from other Pleuronectiformes and discussed in terms of karyotype evolution.     

Photoselective synthesis of azobenzene-containing cyclic oligosarcosine and its thermal cis → trans isomerization in solution

Oligosarcosines, which contain as azobenzene group at the center of the chain and amino groups at both ends [(Sar)_n? Azo? (Sar)_n], were prepared with the N-carboxyanhydride method. The oligomers were coupled with an equimolar amount of succinyl chloride in the presence of triethylamine. When the condensation was carried out under photo irradiation, the azobenzene group assumed the cis configuration and the intramolecular reaction (cyclization) was facilitated. Intermolecular polycondensation occurred preferentially in the dark, in which case the azo group was trans. Cyclic oligosarcosine, which contains one azo group, was isolated by gel chromatography, and its thermal cis → trans isomerization was examined in dimethylformamide. The isomerization rate depended strongly on the number of sarcosine units n in the oligomer; for very small rings (n < 5), the rate constants were less than those for open-chain analogs; for rings of medium size (n = 5 ～ 10), they were larger than those for open-chain analogs; and for longer chains, no significant difference was observed. This specific chain-length dependence was explained by the conformational restrictions of the cyclic oligomers. The ring-restricted isomerization was evidenced by an isomerization-induced conformational change observed in ¹H-nmr spectroscopy.     

Conformational investigations on glycosylated threonine-oligopeptides of increasing chain length

Stepwise solution syntheses are described of the homo-oligomers Z-(Thr)_n-NHCH₃ (n=1–4, I _1–4), Z-{[Gal(Ac)₄β]Thr}_n-NHCH₃(n=1–5, II _1–5) and Z-[(Galβ)Thr]n-NHCH₃ (n=1−5, III _1–5). Members of the III _1–5 series were obtained by de-acetylation of the corresponding oligomers of the II _1–5 series. The conformational preferences of the terminally protected homo-peptides of the three series were investigated by FT-IR absorption spectroscopy both in the solid state and in CDCl₃ solution, at various concentrations. Proton NMR measurements in CDCl₃ and in DMSO-d₆ were also carried out and the effect of temperature variation on the chemical shifts of amide protons was determined in DMSO-d₆ (range 298–335 K) and in CDCl₃ (range 298–320 K). CD spectra were recorded in water and in TFE. Solubility problems prevented measurements in CDCl₃ solution for Z-(Thr)₄-NHCH₃ and for the entire III _1–5 series. The existence of unordered structures in the carbohydrate-free oligomers and of more or less extended, organized structures in the glycosylated derivatives is indicated by the NMR and IR measurements. The sugar moieties apparently show a structure-inducing effect on the peptide chain. ©1998 European Peptide Society and John Wiley & Sons, Ltd.     

Optical activity of single-stranded polydeoxyadenylic and polyriboadenylic acids; dependence of adenine chromophore cotton effects on polymer conformation

Circular dichroism (CD) curves are reported for poly dA, (pdA)₆, (pdA)₂, poly A, ApAp, ApA, AMP, dApA, pdApA, A-2′-O-methyl pA, and A-2′-O-methyl pAp. Analysis of these curves indicated the presence of single CD bands at 228–230 mμ and at 278–280 mμ in oligomers longer than dinucleotides. In the case of dinucleotides and mononucleotides (from the literature, in addition to those studied here), the 230 mμ CD of band appears but the 280 mμ CD band does not. We assign the 230 mμ band to a very weak π–π* transition at this wavelength. From theoretical considerations, we show that the 280 mμ band is not an exciton component of the strong π–π* transition at 260 mμ in adenine. We conclude that the 280 mμ CD band must be assigned to a distinct absorption, not previously reported, which we suggest arises from an n–π* transition. The fact that the n–π* CD band at 280 mμ is not seen in mononucleotides or dinucleotides is ascribed to solvation of the adenine ring by water, which shifts the band to shorter wavelengths. Therefore, only interior residues of oligomers have the 280 mμ band, and the optical activity of a polymer cannot be computed from that of a dinucleotide, by using a nearest-neighbor approximation. The existence of this end effect hag been tested, by taking it into account in computing the rotational strengths of the 278 mμ n–π* transition for several oligomers; it is pointed out that a more sensitive test of this end effect would require CD data for the oligo dA series of 3 to 5 residues. We speculate about the structural and optical differences between poly dA and poly A, and point out the need for a theoretical treatment of n–π* Cotton effects in polynucleotides.     

The influence of asymmetric carbon atoms of the side chains on the conformational properties of polypeptides: Comparison of diastereomeric homooligopeptides of L-isoleucine and D-alloisoleucine

The conventionally protected oligopeptides of the two homologous series Boc-(L -Ile)_n-OMe and Boc-(D -aIle)_n-OMe (n = 2–6) were synthesized in a standard stepwise fashion and their uv and CD spectra in 2,2,2-trifluoroethanol, and solid-state ir spectra were investigated. In addition, two oligomeric products derived from the NCAs of L -isoleucine and of D -allo-isoleucine and having a DP of 20 and 12, respectively, were studied in the solid state by x-ray and ir. No substantial differences between the properties of the diastereomeric oligomers in the solid state were noticed, a β-structure being very likely at least for the Boc-protected hexapeptides and the higher oligomers. In contrast, differences were observed between the spectroscopic properties of the diastereomeric oligopeptides, and especially of the hexapeptides, in trifluoroethanol solution. The different properties of the hexapeptides in solution were related to the existence, in the case of Boc-(L -Ile)₆-OMe, of soluble molecular aggregates in which the peptide chains assume the β-conformation. These results provide an additional example of the influence of the configuration of asymmetric carbon atoms of the side chains on the conformational properties of peptide molecules in solution.     

Kinetics of formation of fibrin oligomers. I. Theory

The course of formation of fibrin oligomers is treated theoretically for the condition that self-assembly of fibrin monomers is rapid compared with the loss of A peptides by the enzymatic action of thrombin. The rate constant for removal of the second A peptide is taken to be larger than that for the first by an arbitrary factor q; the association of activated A sites with their complementary a sites is assumed to be random and independent of oligomer size. Two types of oligomers are considered: noncovalently bonded protofibrils formed by the staggered overlap of thrombin-activated monomers and covalently bonded linear oligomers formed by factor XIIIa-mediated end-to-end ligation of adjacent monomers within protofibrils. Oligomers of the first type, if ligated, are dissociated to oligomers of the second type by solubilization in SDS–urea. Theoretical curves are presented for x _w and x ′_w (weight-average degree of polymerization of staggered overlap and linear ligated oligomers, respectively) and for the weight fractions of monomer, dimer, and decamer of both ligated and unligated species as functions of y, the fraction of A peptide removed; and also for w_x and w′_x, the weight fractions of x-mer of the respective oligomer types, as a function of x at y = 0.5. With increasing q, the maximum w_x or w′_x that a low oligomer will reach during the reaction decreases and the size distribution is broadened toward larger oligomers. Comparison with experiment is made in a companion paper.     

Concise synthesis of 4-methylumbelliferyl-penta-N-acetylchitopentaoside and its inhibition effect on chitinase

The synthesis of 4-methylumbelliferyl (UMB)-penta-N-acetylchitopentaoside 4 and its inhibition effect on chitinase are described. The fluorophore-assisted carbohydrate electrophoresis (FACE) analysis showed that the partially N-acetylated chitooligosaccharide (COS) mixture mainly contained glucosamine (GlcN) and oligomers [(GlcN)_n, n = 2–7]. The peracetylated COSs [(GlcNAc)_n, n = 1–7] were synthesized by treating the partially N-acetylated COS mixture with Ac₂O–NaOAc. The peracetylated chitopentaoside 1 was obtained by isolation of peracetylated COS mixture. The peracetylated UMB chitopentaoside 3 was synthesized by treating compound 1 with 4-methylumbelliferone and a Lewis acid (SnCl₄) catalyst. NaOMe in dry methanol was used for deacetylation of the blocked derivative, to give the target compound 4 in an overall yield of 32%. In binding chitinase assay, it indicates that compound 4 is much more stable than the corresponding penta-N-acetylchitopentaose 2.     

Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC base pairs

Absorbance-temperature profiles have been determined for the following self-complementary oligonucleotides or equimolar paris of complementary oligonucleotides containing GC base pairs: A₂GCU₂, A₃GCU₃, A₄GCU₄, A₆CG + CGU₆, A₈CG + CGU₈, A₄G₂ + C₂U₄, A₅G₂ + C₂U₅, A₄G₃ + C₃U₄, and A₅G₃ + C₃U₅. In all cases cooperative melting transitions indicate double-helix formation. As was found previously, the stability of GC containing oligomer helices is much higher than that of AU helices of corresponding length. Moreover, helices with the same length and base composition but different sequences also have quite different stabilites. The melting curves were andlyzed using a zipper model and the thermodynamic parameters for the AU pairs determined previously. The effect of single-strand stacking was considered separately. According to this model, the formation of a GC pair from unstacked single strands is associated with an ethalpy change of ?15 kcal/mole. Due to the high degree of single-strand stacking at room temperature the enthalpy change for the formation of GC pairs from unstacked single strands is only ?5 to ?6 kcal/mole. (The corresponding parameters for AU pairs are ?10.7 kcal/mole and ?5 to ?6 kcal/mole.) The sequence dependence of helix stability seems to be primarily entropic since no differences in ΔH were seen among the sequence isomers. The kinetics of helix formation was investigated for the same molecules using the temperature jump technique. Recombination of strands is second order with rate constants in the range of 10⁵ to 10⁷M^?1 sec^?1 depending on the chain length and the nucleotide sequence. Within a series of oligomers of a given type, the rates of recombination decrease with increasing chain length. Oligomers with the sequence A_nGCU_n recombine six to eight times slower than the other oligomers of corresponding chain length. The experimental enthalpies of activation of 6 to 9 kcal/mole suggest a nucleation length of one or two GC base pairs. The helix dissociation process has rate constants between 0.5 and 500 sec^?1 and enthalpies of activation of 25 to 50 kcal/mole. An increase of chain length within a given nucleotide series leads to decreased rates of dissociation and increased enthalpies of activation. An investigation of the effect of ionic strength on A_nGCU_n helix formation showed that the rates of recombination increase considerably with increased ionic strength.     

Karyotypic characterization and genomic organization of the 5S rDNA in <Emphasis Type="Italic">Polypterus senegalus</Emphasis> (Osteichthyes,Polypteridae)

Polypteridae (Cladistia) is a family of archaic fishes, confined to African freshwaters. On account of their primitiveness in anatomical and morphological characters and mosaic relationships among lower Osteichthyans fishes, they constitute an important subject for the study of evolution in vertebrates. Very little is known about the karyological structure of these species. In this article, a cytogenetic analysis on twenty specimens of Polypterus senegalus (Cuvier, 1829) was performed using both classical and molecular techniques. Karyotype (2n = 36; FN = 72), chromosome location of telomeric sequences (TTAGGG) _n , (GATA)₇ repeats and ribosomal 5S and 18S rRNA genes were examined by using Ag-NOR, classical C-banding, CMA₃ staining and FISH. Staining with Ag-NOR showed the presence of two GC rich NORs on the p arm of the chromosome pair no. 1. CMA₃ marked all centromerical and some (no. 1 and no. 14) telomeric regions. FISH with 5S rDNA marked the subtelomeric region of the q arm of the chromosome pair no. 14. FISH with 18S rDNA marked the telomeric region of the p arm of the chromosome pair no. 1, previously marked by Ag-NOR. (GATA)₇ repeats marked the subtelomeric regions of all chromosome pairs, with the exclusion of the no. 1, 3 and 14. Hybridization with telomeric probes (TTAGGG) _n showed bright signals at the end of all chromosomes. After cloning, the 5SrDNA alignment revealed an organization of sequences made up of two different classes of tandem arrays (5S type I and 5S type II) of different lengths.     

On the amino-acid-sequence distribution in benzylglutamate-methionine copolymers prepared from N-carboxyanhydrides

The amino-acid-sequence distribution in poly(γ-benzyl-L -glutamate, L -methionine) prepared by polymerization of the respective N-carboxyanhydrides has been investigated. This copolymer was converted first to poly(L -glutamic acid, L -methionine), which was subsequently cleaved by treatment with cyanogen bromide. The resulting material was fractionated into oligomers of (glutamic acid)_n-homoserine whose relative molar amounts were determined quantitatively. The results have been compared with those for a random incorporation of the methionine in a γ-benzylglutamate host polymer. Fairly close agreement has been found.     

Homooligopeptides composed of hydrophobic amino acid residues interact in a specific manner by taking α-helix or β-structure toward lipid bilayers

In order to investigate the role of each amino acid residue in determining the secondary structure of the transmembrane segment of membrane proteins in a lipid bilayer, we made a conformational analysis by CD for lipid-soluble homooligopeptides, benzyloxycarbonyl-(Z-) Aaa_n-OEt (n = 5-7), composed of Ala, Leu, Val, and Phe, in three media of trifluoroethanol, sodium dodecyl sulfaie micelle, and phospholipid liposomes. The lipid-peptide interaction was also studied through the observation of bilayer phase transition by differential scanning cahrimetry (DSC). The CD studies showed that peptides except for Phe oligomers are present as a mainly random structure in trifluoroethanol, as a mixture of α-helix, β-sheet, β-turn, and /or random in micelles above the critical micellization concentration and preferably as an extended structure of α-helical or β-structure in dipalmitoyl-D,L -α-phosphatidylcholine (DPPC) liposomes of gel state. That the β-structure content of Val oligomers in lipid bilayers is much higher than that in micelles and the oligopeptides of Leu (n = 7) and Ala (n = 6) can take an α-helical structure with one to two turns in lipid bilayers despite their short chain lengths indicates that lipid bilayers can stabilize the extended structure of both α-helical and β-structures of the peptides. The DSC study for bilayer phase transition of DPPC / peptide mixtures showed that the Leu oligomer virtually affects neither the temperature nor the enthalpy of the transition, while Val and Ala oligomers slightly reduce the transition enthalpy without altering the transition temperature. In contrast, the Phe oligomer affects the phase transition in much more complicated manner. The decreasing tendency of the transition enthalpy was more pronounced for the Ala oligomer as compared with the Leu and Val oligomers, which means that the isopropyl group of the side chain has a less perturbing effect on the lipid acyl chain than the methyl group of Ala. © 1995 John Wiley & Sons, Inc.     

Density functional study of the electronic and optical properties of fluorene-thieno[3,2-b]thiophene-based conjugated copolymers

Quantum mechanical techniques are applied to investigate a family of π-conjugated copolymers: poly(9,9′-dimethylfluorene-alt-thiophene) (PFT), poly(9,9′-dimethylfluorene-alt-thieno[3,2-b]-thiophene) (PFTT), poly(9,9′-dimethylfluorene-alt-bithiophene) (PFT2), and poly(9,9′-dimethylfluorene-alt-α,α′-bisthieno[3,2-b]-thiophene) (PFTT2). Linear extrapolation is employed to obtain polymers' properties from oligomer calculations. That is, the HOMO–LUMO gaps (Δ_H–Ls), band gaps (E _g s), ionisation potentials and electron affinities of the copolymers are obtained by plotting the corresponding quantities of the oligomers as a function of the inverse chain length (1/n) and extrapolating them to infinite chain length. The electronic properties of the neutral, positive and negative oligomers are determined using the density functional theory (DFT) at B3LYP/6-31G* approximation. The lowest singlet excitation energies of the oligomers of PFT, PFTT, PFT2, and PFTT2 are also determined with the use of the time-dependent DFT again at B3LYP/6-31G* approximation. Comparisons are made with experimental values when possible.