Library

Notes: Carbon fibre-reinforced composites of conventional diglycidyl ether of bisphenol-A (DGEBA) and liquid diglycidyl ether of bisphenol-C (DGEBC) were prepared, using 4,4′-diaminodiphenylmethane (DDM) or 4,4′-diaminodiphenylsulfone (DDS) curing agent and evaluated for their physical properties (density, void content) and mechanical properties (flexural strength and interlaminar shear strength). Thick films of the neat resin were also prepared and their flexural strength has been studied. It is observed that DGEBC-curing agent system shows improved properties compared to DGEBA-curing agent system.

Notes: A series of new polyimides with phenylquinoxaline units have been synthesized by solution polycondensation of 2,2-bis(1,3-dioxo-1H,3H-isobenzofuran-5-yl)hexafluoropropane (hexafloroisopropylidene-diphthalic anhydride) with aromatic diamines containing preformed phenylquinoxaline units. These polymers are soluble in polar amidic solvents and can be processed into transparent, flexible films, having low dielectric constants and high thermal stability with decomposition temperatures above 400°C.

Notes: Als immobilisierbare Antioxidantien für Ethylen-Propylen-Dien-Terpolymere (EPDM) wuren 4-(Mercaptoacetamido)-diphenylaminSystematischer Name: 2-Mercapto-N-[4-phenylamino phenyl]-acetamid. (MADA) und Dithiodiglycolsäure-bis-[N-(4-anilinophenyl-amid]Systematischer Name: 2,2′-Dithiobis[N-(4-phenylamino)phenyl]-acetamid. (DAPA) hergestellt und charakterisert. Zur Simulation der Reaktionen bei der Umsetzung dieser Antioxidantien mit EPDM-Kautschuken wurden Modellreaktionen mit trans-4-Decen, 2-Ethylidennorbornan und 2,3-DihydrodicyclopentadienSystematischer Name: Tricyclo[5.2.1.02,6]-3-decen. durchgeführt. Die Reaktionsprodukte wurden chromatorgraphisch aufgetrennt und durch IR-Spektroskopie charakterisiert. Dabei wurde auch der Einfluß von Azoinitiatoren auf die Additionsreaktion untersucht.Die Umsetzung von EPDM mit den genannten Stabilisatoren wurde im BrabenderPlastographen bei 140 bis 180°C Massetemperatur untesucht. Der Gehalt an immobilisiertem Stabilisator wurde mit Hilfe der Thermoanalyse und UV-spektroskopisch bestimmt. Die höchsten Gehalte an immobilisiertem Stabilisator (73%) wurden mit MADA bei 180°C Massetemperatur erzielt. DAPA ist ebenfalls bis maximal 69%immobilisierbar. Die praktische Baruchbarkeit der Immobilisierung von Mercaptostabilisatoren an EPDM-Kautschuk wurde am Beispiel von strahlenvernetzten Kabelisoliermassen bestätigt.

Notes: Im Bereich der textilen Analytik bereitet die Bestimmung der Farbstoffkonzentration dunkler und gesättigter Fäbungen große Schwierigkeiten. Deshalb wird die Einsatzmöglichkeit der photoakustischen Spektroskopie zur Charakterisierung von Fäbungen zn Konzentrationseichreihen systematisch untersucht. Die Meßergebnisse wurden mit einer modifizierten Kubelka-Munk-Funktion angepaßt, die über einen größeren Konzentrationsbereich linear verläft als bei der Reflexionsspektroskopie. Weiterhin wurde der Einfluß der Oberflächenstruktur auf das photoakustische Signal untersucht.

Notes: After-glow plasma polymerization is described as a new method to prepare polymeric layers from unsaturated monomers. An optically active acrylic monomer is used in this investigation. The deposition rates are given as functions of plasma power, pressure, distance between plasma and deposition zone, flux and kind of auxiliary gas (He, Ne, Ar, Kr) and of monomer flux. The polymers prepared are optically active, the IR spectra comply with those of polymers synthesized in bulk. Mostly the polymers prepared by after-glow plasma polymerization are cross-linked and therefore insoluble. NMR spectra of soluble samples show that the polymers are atactic. After-glow plasma polymerization occurs by a radical chain growth mechanism. Membranes made from these polymers are able to separate racemates.

Notes: In this study, the terpolymerisation, under high pressure, has been examined for the ethylene-methyl acrylate-vinyl acetate system. The polymerisations were carried out in a high pressure polymerisation facility designed for continuous operation. To assess the effect of pressure and temperature on the reaction, polymerisation was carried out at two different pressures of 1 900 and 1 100 bar and at temperatures of 180 and 230°C. By varying the concentration of the ethylene, methyl acrylate and vinyl acetate monomers in the feed, polymers of different composition were obtained. The ratio of the monomer concentrations in the reactor was calculated from the amount of polymer weighed out and its comonomer content as well as the composition of the feed, using the mass balance for the ideal stirred tank reactor. The result was used to determine the reactivity ratios of the three possible binary copolymerisation systems ethylene/methyl acrylate, ethylene/vinyl acetate and methyl acrylate/ vinyl acetate. This made it possible to predetermine, by calculation, the composition of a product obtained by continuous polymerisation in a stirred autoclave.

Notes: The synthesis of poly(3,3-phthalidylidene-4,4′ -biphenylylene) (PPB) by precipitative Friedel-Crafts homopolycondensation of 3-(4-biphenylyl)-3-chlorophthalide was studied. The polymer-catalyst complex precipitated from the initially homogeneous reaction mixture was shown to be active and providing the growth of macromolecular chains. The polymer obtained in the form of smooth, transparent glass-like particles, depending on the reaction parameters, may have either uni- or bimodal molecular weight distribution. Molecular characteristics were not found to depend on the size of the polymer particles. “Precipitative” PPB shows improved properties and higher crystallinity in comparison with “solution” PPB.

Notes: Novel photocrosslinkable polymethacrylate systems with enhanced thermal stability and solvent resistance were synthesized. Copolymers of methyl methacrylate (MMA) or butyl acrylate (BuA) with 4-maleimido benzoic acid (MBA) were synthesized and photocrosslinkable methacrylic functions were incorporated through the pendent COOH groups. Photofunctional groups were introduced by the acid chloride route and by the epoxy-carboxy reaction. Photocrosslinking was performed using UV radiation of 350 nm in the presence of a photo-initiator. The kinetics of photocuring was studied with a model multiacrylate. The imide-modified photocured acrylate polymer exhibited enhanced solvent resistance and thermal stability, compared with the unmodified polymer.

Notes: The curing behaviour of bismethacryloyl derivative of diglycidyl ether of bisphenol A (vinyl ester VE resin) containing styrene and α-methyl styrene (MS) as reactive diluents was studied. Delayed curing was observed in samples containing increasing proportions of MS. Interfacial shear stress of untreated as well as γ-methacryloyloxy-propyl trimethoxy silane (MTS) treated, glass fibre-reinforced VE resin composites were measured by single fibre technique. In comparison to untreated glass fibres, a 30 - 50% increase in interfacial shear stress was observed in composites based on MTS treated glass fibres. Addition of up to 5 wt.-% MS to VE resin did not affect the interfacial shear strength (ILSS). This behaviour was observed by using ILSS measurement of both glass fabric-reinforced composites as well as single fibre specimens. Further increase in MS to 15 wt.-% resulted in an increase in ILSS and bending stiffness as well as flexural strength.

Notes: Durch Photopolymerisation von 4,4′-Dibenzoyldiphenylmethan und 4,4′-Bis(aαhydroxybenzy1)-diphenylmethan mit UV-Licht in benzolischer Löisung lassen sich Polybenzpinakole herstellen. Die Polymeren können durch Fällungsfraktionierung in Fraktionen mit Molekulargewichten bis etwa 20000 aufgetrennt werden. Polybenzpinakole zerfallen ebenso wie Benzpinakol thermisch in Diarylhydroxymethyl-Radikale. Diese initiieren bei 60 bis 100°C die radikalische Polymerisation von Styrol direkt und teilweise auch durch Wasserstoffübertragung von den Initiatorradikalen auf das Monomere. Mit steigender Temperatur nimmt dabei der Anteil der Wasserstoffübertragung an der Initiierung ab, was aus den Reaktionsordnungen bezüglich der Monomerkonzentration geschlossen werden kann. Soweit die Polymerisation von Styrol mit Oligo-Benzpinakol direkt durch Diarylhydroxymethyl-Radikale ausgelöst wird, entstehen Polystyrolketten mit eingebauten Oligo-Benzpinakol-Segmenten, die thermisch spaltbar sind, was durch die Abnahme der Molekulargewichte beim Erhitzen in toluolischen Lösungen bestätigt wird.

Notes: This work deals with some features of the reaction of dextran with ethyl chloroformate using triethylamine as catalyst. The presence of cyclic and acyclic carbonate groups in the resulting modified dextrans was demonstrated by IR, 1H and 13C NMR spectroscopy. Preliminary experiments have shown that the reaction of cyclic carbonate groups with several model amines is greatly dependent on the basic character of the amine. Model amino type drugs (Phenethylamine and tyramine) were quantitatively bound to activated dextran with cyclic carbonate groups. The heterogeneous hydrolysis of dextran-phenethylamine or dextran-tyramine adducts showed that no hydrolysis takes place under the applied conditions.

Notes: The free-radical copolymerization of styrene with (2-oxo-1,3-dioxolan-4-yl)methyl methacrylate (cyclic carbonate of glycidyl methacrylat; GMACC) was carried out in N,N-dimethylformamide and toluene solution under batch conditions. In toluene, a precipitate was formed during polymerization. The composition of the copolymers was determined by 1H-NMR, IR spectroscopy and elemental analysis. The monomer reactivity ratios were calculated by different methods from the copolymer composition data. The values obtained for the different techniques were compared and showed a good agreement.

Notes: The removal and recovery of indium ion (In3+) from solutions with water-insoluble amphoteric starches containing the phosphate anionic group and the quaternary ammonium or tertiary amine cationic group was investigated. The adsorption capacity of tertiary amine phosphate starch (TAP) and quaternary ammonium phosphate starch (QAP) is 0.54 meq/g and 0.48 meq/g, respectively. The adsorption process has been found to be concentration-dependent and exothermic, and follows the Langmuir isothermal adsorption. The heat of adsorption (ΔH) is equal to -5.86 kJ/mol for QAP, and equal to -90.44 kJ/mol for TAP. The amount of adsorbed In3+ ion on the adsorbents decreases when inorganic acids (HCl or H2SO4) or sodium salts (NaCl or Na2SO4) are added to the solution. The adsorbed In3+ ion can be desorbed by treating with a HCl solution (1 and 3 M); the maximum percentage of desorption reaches about 80% when 1 N HCl solution is used.

Notes: Tensile and dielectric relaxation properties of sulfobetaine polyurethane ionomers based on polyesters were studied comparatively to the non-ionic polyurethane and derived compounds with Pb2+ and Co2+, using stress-strain and thermally stimulated depolarization currents (TSDC) methods. Introduction of ionic centers into polyurethane chain improves the tensile properties and modifies the TSDC spectra. These effects are assigned to an enhancement of the microphase segregation. Complexation with Pb2+ and Co2+ diminishes the tensile properties, suggesting that an increase of phase mixing occurs determined by a partial neutralization of ionic centers. Treatment with H2S slightly increases tensile properties and changes TSDC spectra owing to the presence of the semiconducting microphases formed by clustering of the metal sulfides PbS and CoS, respectively.

Notes: Abietic acid and paraformaldehyde, taken in various molar ratios, were condensed in acid catalysis (p-toluenesulfonic acid). Toluene was used both as reaction medium and carrier for aqueous condensate. The obtained polymeric products (resins) were characterized by determination of acid number, melting point, molecular weight and viscosity. Spectral methods, e.g. I. R. and 1H-NMR, were also used in the same scope. The experimental data evidence the fact that abietic acid is a substance with a functionality of minimum 3 as against formaldehyde. There have been obtained some condensation products with three-dimensional structure and low molecular weight. The polymerization average degree of the resins was found to be 3, although some fractions with polymerization average degree of 6 have been observed. The chemical bonds established between the structural units can be of both methylenic and dimethylene ether type, depending on the molar ratio of reacting substances.

Notes: The free-radical precipitation polymerization of acrylic acid in toluene was studied in an isothermal reaction calorimeter. The polymerization shows an autocatalytic behaviour of the rate of polymerization typical for precipitation polymerizations. The rate of polymerization with respect to conversion can be modeled by taking the volume fraction of the precipitated polymer into consideration.The viscosity of the reaction mixture increases with increasing volume fraction of precipitated polymer. The viscosity runs through a maximum at high conversion. The final viscosity decrease is probably due to shear stress caused aggregation phenomena of the polymer particles. A model is discussed which can describe the increase and decrease of viscosity of the system.By means of reaction calorimetry it is possible to determine the reaction-sided heat transfer coefficient during polymerization. The comparison of the experimentally determined temperature course of the reaction mixture and the temperature course calculated with a coupled model of the polymerization and the calorimeter shows that the heat-transfer characteristic changes instantaneously during a small conversion interval at the very beginning of the polymerization.

Notes: The ability of poly(2,6-dimethyl-1,4-phenylene oxide) membranes to separate water-ethanol mixtures by pervaporation was examined. Asymmetric membranes were prepared from solutions containing chloroform as a solvent and 1-butanol as a nonsolvent by the phase-inversion process. Homogeneous, dense membranes were prepared from chloroform solutions by evaporation. Nonporous membranes (membranes precipitated from solutions with a low amount of the nonsolvent or prepared by evaporation) were preferentially permeable to water. Microporous membranes (precipitated from solutions with a high amount of the nonsolvent) were preferentially permeable to ethanol, provided the membrane is not wetted by the feed solution.

Notes: Die photoinduzierte radikalische Vernetzung von Siliconacrylaten wurde mit verschiedenen Photoinitiatoren vom Benzoyltyp untersucht. Die Photovernetzung derartiger Produkte kann mit Hilfe eines radikalischen Kettenprozesses beschrieben werden. Aus kalorimetrischen Messungen folgt, daß Sauerstoff den Kettenprozeß inhibiert und terminiert, wobei dei Vernetzungsgeschwindigkeit und die Inhibierungszeit Funktionen des Luftdrucks, der Lichtintensität und der Quantenausbeute der Initiatrophotolyse sind.Der Vernetzungsprozeß kann nur beginnen, wenn der Sauerstoff in der Schicht verbraucht ist. Mit Hilfe des 1. Fickschen Diffusionsgesetzes kann gezeigt werden, daß der in das System eindiffundierende Sauerstoff auch den Grenzumsatz bestimmt.Obwohl Sauerstoff in der Schicht die Reaktionsgeschwindigkeit, die Inhibierungszeit und den Grenzumsatz bestimmt, wurde jedoch überraschenderweise festgestellt, daß Sauerstoff auf die Netzwerkdiche keinen Einfluß besitzt.Der negative Effekt des Sauerstoffs auf den Vernetzungsprozeß kann durch eine hohe Startgeschwindigkeit (Funktion der Lichtintensität, der Absorption und der Quantenausbeute der Initiatorphotolyse) reduziert werden.Mit Hilfe von zwei kinetischen Methoden wurde ermittelt, daß die Initiierungseffizienzen der verwendeten Initiatoren verschieden sind, wobei relative Abstufungen bestimmt werden konnten.

Notes: No Abstract

Notes: 6-Ethoxy-2,2,4-trimethyl-1,2-dihydroquinoline (ethoxyquin, I) does not react with the model alkyl radical, 1-cyano-1-methylethyl, in an inert atmosphere. On the other hand, its aminyl derivative (II) reacts readily with the model alkyl radical; the main product of this reaction is 6-ethoxy-8-(1-cyano-1-methylethyl)-2,2,4-trimethyl-1,2-dihydroquinoline (V), while 6-ethoxy-1-(1-cyano-1-methylethyl)-2,2,4-trimethyl-1,2-dihydroquinoline (VI) is formed as a by-product. 6-Ethoxy-2,2,4-trimethyl-1,2-dihydroquinoline-N-oxyl (III) also effectively deactivates the model alkyl radical to form 6-ethoxy- 8-(1-cyano-1-methylethoxy)-2,2,4-trimethyl-1,2-dihydroquinoline (X).It follows from these results that I is an ineffective antidegradant in oxygen-free atmosphere. However, at very low oxygen concentrations, I becomes capable of deactivating alkyl radicals. Together with its ability to deactivate alkylperoxide radicals, this explains the high antifatigue activity of I.In the presence of silica gel, V is readily cyclized to 8-ethoxy-1,2,3,4-tetrahydro-2-imino-1,1,4,4,6-pentamethylpyrrolo[3,2,1-ij]quinoline (VIII). VI undergoes thermal decomposition into its components, i.e., aminyl II and the model radical. Photodecomposition of X on silica gel yields 6-ethoxy-2,2,4-trimethyl-8-quinolone (XIII).

Notes: Magnetic properties of metal layer deposited by reduction of polymer containing metal ions were investigated.Varying the ratio of the cobalt ion to the nickel ion in the polymer, the coercivity, the maximum flux density and the remanent flux density of the deposited metal layer were changed from 100 to 600 Oe, from 1 000 to 12 600 G and from 500 to 7 600 G, respectively. The X-ray diffraction pattern of the metal layer with excellent magnetic properties gives distinct peaks corresponding to the (101) and (100) planes of the crystal of α-Co.This suggests that such a deposited metal layer has the structure of highly crystalline metal layer.

Notes: Chitosan, [(1,4)-2-amino-2-deoxy-β-D-glucan], was reacted consecutively with epichlorohydrin and thiourea. Subsequent hydrolysis of the isothiouronium salt yielded the mercaptan derivative of chitosan, which scavenges mercury ions from solution in the presence of a considerably high concentration of chloride ions.Sulfur contents varied with reacting conditions and reached values up to 7.3%. The derivative is insoluble due to partial crosslinking of chitosan during the reaction with epichlorohydrin and was characterized by IR spectroscopy, solid-state 13C NMR, thermal analysis and pyrolysis-mass spectrometry.

Notes: A phenomenological model has been proposed to understand the development of strong anisotropy in physical properties of semicrystalline polymers on uniaxial drawing. The proposed model introduces temperature as an explicit parameter in the orientation function. The model contains two free parameters for each polymer which can be evaluated by fitting the experimental data on birefringence versus draw ratio at a particular temperature. The calculated values of elastic moduli, thermal conductivity and expansibility along and perpendicular to the drawing direction over the entire range of draw ratio and a wide range of temperature are in good agreement with experimental values.

Notes: Fasern aus Poly(acrylnitril-co-methylacrylat-co-itaconsäure) wurden unter unterschiedlichen Bedingungen verstreckt. Die verstreckten Fasern wurden bezüglich des allgemeinen Orientierungsgrads und des Orientierungsgrads und Anteils der parakristallinen Gebiete charakterisiert; mechanische Kennwerte der Fasern wurden gemessen. Aus der Korrelation der erhaltenen Werte mit der sogenannten Kompensationsspannung der Fasern wird geschlossen, daß letztere ein Maß für die Eigenspannungen in den Fasern darstellt und eine Optimierung der Herstellung und Weiterverarbeitung der Fasern ermöglicht.

Notes: Photosensitive microcapsules, which are thermally quite stable, are formed via interfacial polycondensation in which one of the shell-forming reactants contains an azo function.An azo monomer, containing α,ω-carboxylic diacid dichloride was reacted with a trifunctional aliphatic amine on the oil-water interface resulting in a shell-forming crosslinked polyamide. The size of the resulting photosensitive microcapsules was determined. It could be shown that these microcapsules can be opened by means of UV-light.

Notes: Oxime-blocked toluene diisocyanates were synthesized and characterized by infrared spectra, nuclear magnetic resonance spectra, elemental analysis etc. Thermal analyses of blocked isocyanates were done by thermogravimetry. Solubility of blocked isocyanates in various polyols was tested. Formation of isocyanate on heating the blocked isocyanate was identified by gas chromatographic analysis.

Notes: Urease enzyme was immobilized in hydrogels prepared from vinyl pyrrolidone/water/crosslinking agent ternary mixtures by γ-irradiation of the solutions at room temperature. Two types of crosslinking agents used, namely ethylene glycol dimethacrylate and trimethylol propane triacrylate, yielded hydrogels with different swelling and crosslink density properties. The activity of immobilized urease was measured at the optimum conditions of temperature and pH over a period of time. It has been determined that for hydrogels with average molecular weights between crosslinks, Mc, above 2000, urease leakage is a serious problem. When Mc is around and below this value, immobilized systems showed a long time activity.

Notes: It was shown that the etching of styrene-divinylbenzene copolymer from KESD-2 type ion-exchange membranes resulted in porous membranes. Modification of such membranes introduced both acidic or basic groups onto the pore surface. The ultrafiltration of bovine serum albumin through these membranes was mostly affected by coulombic interaction. Protein deposition on/in membrane was controlled by charge as well as hydrophilic properties of membranes. In addition, the effect of polystyrene crosslinking degree on the blend morphology was explained. The structure of polystyrene copolymer underwent the qualitative threshold when the crosslinking agent concentration reached the level of 2 wt.-%.

Notes: A method for the determination of carbon black fillers in peroxide vulcanizates or sulfur vulcanizates of natural rubber (NR, cis-1,4-polyisoprene) by metathesis degradation with 1-octene was developed using the catalyst WCl6—(C2H5)3Al2Cl3. The carbon black was separated from the reaction mixture by centrifuging and determined by weighing.In this connection, investigations were also performed with the catalyst WCl6—C2H5Al2Cl3 which was less suitable for filler determination. The rate of degradation of crosslinked NR with (E)-4-octene was measured. Metathesis reactions of 2-methyl-2-pentene (low-molecular-weight model compound of NR) with 7-tetradecene showed the importance of double bond shift for the degradation of NR.

Notes: Hydrophilic polyamides containing amino or carboxyl groups in the repeat units suitable for drug binding are synthesized by polycondensation of aliphatic dicarboxylic acids, including succinic acid, iminodiacetic acid, and ethylenediaminetetraacetic acid (reacting as a difunctional monomer in these polymerizations), with diamines, such as diethylenetriamine, 1,2-bis(3-aminopropylamino)ethane, and the two hydrosolubilizing poly(ethylene oxide) derivatives, α,ω-bis(2-aminopropyl)poly(ethylene glycol) 800 (Jeffamine ED-900) and α,ω-bis(2-aminopropyl)poly(ethylene glycol) 1900 (Jeffamine ED-2001). The reactions are conducted in polyphosphoric acid medium at the optimal temperature range of 150-165°C. The product polymers, fractionated by aqueous-phase dialysis in 12000-14000 molecular-mass cut-off membrane tubing, are isolated by freeze-drying. Yield data, ranging from 1% to nearly 40% for the material so fractionated, indicate low propensity for polycondensation under these conditions for the volatile diethylenetriamine monomer, and only moderately better performance for the thermally labile Jeffamines, yet satisfactory polymerization behaviour for the bis(aminopropylamino)ethane. The microanalytically and spectroscopically characterized polyamides fulfil the biomedically important requirement of solubility in water; inherent viscosities in this medium are in the approximate range of 5-15 ml · g-1. The drug-anchoring capabilities of these polymers will be the subject of forthcoming publications.

Notes: Polymerization tests were carried out in a stirred autoclave designed for continuous operation in order to determine the influence of the reaction pressure and temperature and of the acrylic acid methyl ester and vinyl acetate comonomers on the ethylene-acrylic acid methyl ester-vinyl acetate terpolymer formed. Pressures between 1100 and 1900 bar and temperatures of 180 and 230°C were used. The average residence time was 40 seconds. Tertiary butyl perpivalate and tertiary butyl perethyl hexanoate in concentrations of 50 to 180 mol-ppm in the ethylene feed were used as initiators. The characteristic properties of the polymers obtained were assessed by determining their composition, density, crystallinity, melting point, glass transition temperature, melt index, the average molecular weight, tensile strength and elongation at break.

Notes: A new copolymer, poly(maleimide-alt-trimethylvinylsilane) (PMVS), with a high silicon content was synthesized by free-radical copolymerization, in order to obtain a positive photoresist containing diazonaphthoquinone sulfonate as a dissolution inhibitor. PMVS shows a high etching selectivity of 1 : 16 compared to a commercially available, hard-baked photoresist (HPR-204). In addition, the rigid cyclic maleimide group is responsible for high temperature stability.

Notes: A number of benzylthiolanium salts have been synthesized, analysed and evaluated by differential scanning calorimetry and viscosity measurements with respect to their potential use as thermal curing agents for epoxy resins. Over a wide range of Hammett constants a correlation exists between initial reactivity, shelf life and the electronic substituent effects of the benzyl group. A combination with arylsulfonium salts leads in singular cases to dual cure systems with attractive properties of thermal and UV induced curing. The sensitization of benzylthiolanium salts also leads to dual cure systems. This opens up new possibilities for UV curable epoxy resins in electronic applications requiring additional curing in shaded areas.

Notes: In order to study the reactivity of different vinyl monomers, the grafting of different vinyl monomers such as acrylonitrile (AN), methylacrylate (MA), ethylacrylate (EA), methyl methacrylate (MMA), butylacrylate (BA) and vinyl acetate (VAc) onto the sodium salt of partially carboxymethylated amylose (DS = 0.313) has been carried out using ceric ammonium nitrate as an initiator. The following reactivity order of monomers has been found: AN 〉 MA 〉 EA 〉 MMA 〉 BA 〉 VAc.

Notes: The synthesis of cation exchange resins via the reaction of poly(vinyl alcohol) as a carrier, citric acid as a catalyst and reactive additive to produce resin structures with grafted carboxy groups, along with a melamine-formaldehyde precondensate, responsible for crosslinking-reinforcing and insolubilizing the resin structure as well as for fixing and binding the acidic functional groups onto the resin structure, has been investigated using varied molar ratios of reactants and varied time as well as temperature. Reaction conditions were selected to prepare a cation exchange resin based on citric acid. Two other cation exchange resins based on tartaric acid and glycolic acid, were also prepared under the same selected reaction conditions. These three resins were characterized by potentiometric titration, water solubility and swellability, as well as durability to use.

Notes: Southern bean mosaic virus (SBMV) is a spherical plant virus. It possesses an intrinsic (structural) anisotropy due to the orientation of valence bonds of the amino acid and/or nucleic acid residues. According to the light scattering theory of Rayleigh and Gans for optically anisotropic spheres, the degree of linear polarization of the scattered light depends on the intrinsic anisotropy, the relative refractive index of the sphere to the solvent, the scattering angle, and the inclination angle of linearly polarized incident light to the scattering plane. By using the theoretical expression of the degree of linear polarization, the intrinsic anisotropy parameter of southern bean mosaic virus in the compact spherical state was calculated with the appropriate experimental values. This novel method should be useful in elucidating the internal structure of spherical viruses and other spherical complexes of macromolecules. © 1993 John Wiley & Sons, Inc.

Notes: The dipole moments of small protein molecules were determined experimentally in order to validate the calculated dipole moments by previous investigators. We found that the agreements are satisfactory for some proteins. There are, however, many proteins for which the agreement is less than satisfactory. In order to find the cause of the disagreement, the dipole moments of these proteins were recalculated using the Brookhaven Protein Data Bank. We calculated the dipole moment due to fixed surface charges and the bond moments of all the carbonyl groups in main chain and side chains. The calculation consists of the mean moments and their mean square fluctuations. In addition, we investigated the effect of electrostatic interactions between charged sites for several proteins. These results show that incorporation of the interactions does not affect substantially the calculated dipole moments. The rms fluctuation of the dipole moment is found to be small but not negligible. In conclusion, recalculated dipole moments are in good agreement with the observed values. © 1993 John Wiley & Sons, Inc.

Notes: A Monte Carlo method has been developed for generating the conformations of short single-stranded DNAs from arbitrary starting states. The chain conformers are constructed from energetically favorable arrangements of the constituent mononucleotides. Minimum energy states of individual dinucleotide monophosphate molecules are identified using a torsion angle minimizer. The glycosyl and acyclic backbone torsions of the dimers are allowed to vary, while the sugar rings are held fixed in one of the two preferred puckered forms. A total of 108 conformationally distinct states per dimer are considered in this first stage of minimization. The torsion angles within 5 kcal/mole of the global minimum in the resulting optimized states are then allowed to vary by ±10° in an effort to estimate the breadth of the different local minima. The energies of a total of 2187 (37) angle combinations are examined per local conformational minimum. Finally, the energies of all dinucleotide conformers are scaled so that the populations of differently puckered sugar rings in the theoretical sample match those found in nmr solution studies. This last step is necessitated by limitations in the theoretical methods to predict DNA sugar puckering accurately. The conformer populations of the individual acyclic torsion angles in the composite dimer ensembles are found to be in good agreement with the distributions of backbone conformations deduced from nmr coupling constants and the frequencies of glycosyl conformations in x-ray crystal structures, suggesting that the low energy states are reasonable. The low energy dimer forms (consisting of 150-325 conformational states per dimer step) are next used as variables in a Monte Carlo algorithm, which generates the conformations of single-stranded d(CXnG) chains, where X = A, T and n = 3, 4, 5. The oligonucleotides are built sequentially from the 5′ end of the chain using random numbers to select the conformations of overlapping dimer units. The simulations are very fast, involving a total of 106 conformations per chain sequence. The potential errors in the buildup procedure are minimized by taking advantage of known rotational interdependences in the sugar-phosphate backbone. The distributions of oligonucleotide conformations are examined in terms of the magnitudes, positions, and orientations of the end-to-end vectors of the chains. The differences in overall flexibility and extension of the oligomers are discussed in terms of the conformations of the constituent dinucleotide steps, while the general methodology is discussed and compared with other nucleic acid model building techniques. © 1993 John Wiley & Sons, Inc.

Notes: One-dimensional and two-dimensional (2D) nmr experiments were carried out on an oligonucleotide duplex that contains an unpaired cytosine, d(GCGAACAAGCG)·d(CGCTTTTCGC), which will be referred to as the C-bulge decamer. Evidence from one-dimensional nuclear Overhauser effect (NOE) experiments on the exchangeable protons indicates that the unpaired cytosine is extrahelical. This conclusion is also supported by numerous cross-peaks in the 2D NOE spectroscopy (NOESY) spectrum of the nonexchangeable protons. The assignments for all of the resonances, with the exception of the H5′ and H5″ resonances, have been made through the use of 2D NOESY, correlated spectroscopy (COSY), and relayed COSY experiments. The temperature dependence of the C(H6) resonance chemical shifts indicates that the unpaired cytosine shows unusual behavior compared to other cytosines in the duplex. A comparison of chemical shifts for all, the assigned resonances of the duplexes with and without the unpaired cytosine suggests that the majority of the structural perturbation is localized in the A·T tract surrounding the unpaired base. The behavior of the imino resonances as a function of temperature also indicates that the perturbation to the duplex is localized and destabilizes the A·T base pairs adjacent to the unpaired base. © 1993 John Wiley & Sons, Inc.

Notes: A theory describing the shapes of polarized fluorescence photobleaching recovery (PFPR) curves for a population of fluorophores undergoing restricted rotational diffusion in two-dimensional systems such as planar membranes has been developed. In this model, restricted rotational diffusion of the fluorophores is described by using reflective boundary conditions, in which the fluorophores are assumed to diffuse freely but only within an angular space of width 2ω. The magnitude and apparent rate of the PFPR postbleach fluorescence curves are a function of both ω and the angle between the bleaching and observation beam polarizations ψ. It is shown that estimates of the degree of rotational restriction ω may be obtained from changes in the ψ-dependent postbleach fluorescence intensities.Using angle-dependent PFPR, slow rotational reorientations of the fluorescent lipid analogue 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine in distearoylphosphatidylcholine Langmuir-Blodgett monolayers deposited on octadecyltrichlorosilane-treated fused quartz were measured. As theoretically predicted for a rotationally restricted fluorophore population, both the initial Fψ(0) and final Fψ(∞) postbleach fluorescence intensities varied as a function of ψ, and no measurable change in the postbleach fluorescence intensities was observed for ψ = 45°. Using the theory for restricted rotational motion, the ψ-dependent variations of the final fluorescence intensities Fψ(∞) obtained at two bleaching intensities gave an average apparent ω ≍ 52°. However, to adequately fit the Fψ(0) data, inclusion of the theoretical effects of rapid (faster than the duration of the photobleaching pulse) fluorophore dynamics was also required. Best fits of the Fψ(0) and Fψ(∞) data were obtained when the fluorophores were assumed to rapidly wobble within a cone of semiangle δ ≍ 30°-50° while slowly rotating within an angular space defined by semiangle ω ≍ 35°-60°. Subsequent analysis of the time- and ψ-dependent changes in the postbleach fluorescence curves Fψ(t) gave apparent diffusion coefficients ranging from D ≍ 10-3 s-1 to 4 × 10-2 s-1. © 1993 John Wiley & Sons, Inc.

Notes: A highly potent and selective agonist to the tachykinin NK-3 receptor, [pGlu6, N-MePhe8, Aib9] substance P (6-11) (I), was synthesized via the solid phase method. The ED50 of I was 4n M in the guinea pig ileum in the absence of atropine (NK-1 + NK-3 receptors) and this agonist was 5000-fold less potent in the presence of atropine (NK-1 receptor). The analogue was virtually inactive in the rat vas deferens (NK-2 receptor). A detailed analysis of the solution conformation of this analogue in DMSO-d6 and in a DMSO-d6 H2O cryornixture was carried out by a combination of 1H-nmr 2D techniques (DQF-COSY, TOCSY, NOESY and ROESY) and model building based on empirical energy calculations. Peptide I exists as a mixture of isomers containing cis and trans Phe-N-MePhe peptide bonds. The main isomer, containing a cis Phe-N-MePhe peptide bond, shows a preferred folded conformation characterized by a type VI β-turn with Phe and N-MePhe in the i + 1 and i + 2 positions. The turn is followed by a helical segment extending to the C-terminal. This conformation is compared to previously reported conformations of other selective tachykinin agonists and may be a promising lead for the design of novel NK-3 agonists with additional conformational constraints. © 1993 John Wiley & Sons, Inc.

Notes: The disulphide bridged heptapeptide has been synthesized by classical solution methods. An ion binding study showed the peptide's ability to complex calcium ions with definite stoichiometry. The solution conformation of the peptide in its free and calcium-complexed form has been investigated by CD and nmr. The model structure derived from nmr data has been energy minimized and the resulting structure investigated by molecular dynamics simulation in water.The structure of the equimolar peptide/Ca2- complex in acetonitrile at room temperature shows the presence of two transannular hydrogen bonds, with the formation of two ring structures of the C10 (type VIa) and C14 type. One peptide unit (Pro-Pro) is cis, all others are trans. © 1993 John Wiley & Sons, Inc.

Notes: The conformational properties of two [D-A70, A76] and [Aib70, A76] analogues of the α67-76 Torpedo acetylcholine receptor fragment, with low binding capacity for the anti main immunogenic region (MIR) antibodies, were studied in DMSO by two-dimensional nmr techniques and molecular dynamics simulations. The results were compared to the free and bound conformations of the [A76] analogue, which has twice more affinity for the anti-MIR monoclonal antibody 6 (mAb6), than the natural Torpedo sequence. It appeared that a single substitution of the A70, at a crucial position, by the D-A70 or Aib70, could modify completely the conformational behavior of the peptide and reduced its recognition by the anti-MIR antibody. The WNPADY rigid structure at the N-terminal part was essential for antibody recognition. The adjacent more flexible C-terminal sequence (GGIK) gives additional stability to the monoclonal antibody-peptide complex probably due to an adequate orientation of the peptide side chains in the complex, by setting them in close contact with the antibody. © 1993 John Wiley & Sons, Inc.

Notes: The solid state conformations of cyclo[Gly-Proψ[CH2S]Gly-D-Phe-Pro] and cyclo[Gly-Proψ[CH2-(S)-SO]Gly-D-Phe-Pro] have been characterized by X-ray diffraction analysis. Crystals of the sulfide trihydrate are orthorhombic, P212121, with a = 10.156(3) Å, b = 11.704(3) Å, c = 21.913(4) Å, and Z = 4. Crystals of the sulfoxide are monoclinic, P21, with a = 10.662(1) Å, b = 8.552(3) Å, c = 12.947(2) Å, β = 94.28(2), and Z = 2. Unlike their all-amide parent, which adopts an all-trans backbone conformation and a type II β-turn encompassing Gly-Pro-Gly-D-Phe, both of these peptides contain a cis Gly1-Pro2 bond and form a novel turn structure, i.e., a type II′ β-turn consisting of Gly-D-Phe-Pro-Gly. The turn structure in each of these peptides is stabilized by an intramolecular H bond between the carbonyl oxygen of Gly1 and the amide proton of D-Phe4. In the cyclic sulfoxide, the sulfinyl group is not involved in H bonding despite its strong potential as a hydrogen-bond acceptor. The crystal structure made it possible to establish the absolute configuration of the sulfinyl group in this peptide. The two crystal structures also helped identify a type II′ β-turn in the DMSO-d6 solution conformers of these peptides. © 1993 John Wiley & Sons, Inc.

Notes: The molecular dynamics algorithm (MD), which simulates intramolecular motions on the subnanosecond timescale, has been modified to allow the investigation of slow conformational transitions that do not necessarily occur spontaneously in MD simulations. The method is designated CONTRA MD (CONformational TRAnsitions by Molecular Dynamics with minimum biasing). The method requires the prior definition of a single conformational variable that is required to vary monotonically from an initial conformation to a final target conformation. The simulation is broken up into a series of short free MD segments, and we determine, after each segment of MD, whether or not the system has evolved toward the final conformation. Those segments that do not move the system in that direction are deleted. Those that do move it toward the final conformation are patched together sequentially to generate a single representative trajectory along the transition pathway. The CONTRA MD method is demonstrated first by application to the simultaneous C2′-endo to C3′-endo repucker and anti to syn N-glycosidic torsion transitions in 2′-deoxyadenosine and then to the large-scale bending in phenylalanine transfer RNA. © 1993 John Wiley & Sons, Inc.

Notes: Z-Dehydrophenylalanine (ΔzPhe) possessing four oligopeptides, Boc-(L-Ala-ΔzPhe-Aib)n-OCH3 (n = 1-4: Boc, t-butoxycarbonyl; Aib, α-aminoisobutyric acid), were synthesized, and their solution conformations were investigated by 1H-nmr, ir, uv, and CD spectroscopy and theoretical CD calculation. 1H-nmr (the solvent accessibility of NH groups) and ir studies indicated that all the NH groups except for those belonging to the N-terminal L-Ala-ΔzPhe moiety participate in intramolecular hydrogen bonding in chloroform. This suggests that the peptides n = 2-4 have a 4 → 1 hydrogen-bonding pattern characteristic of 310-helical structures. The uv spectra of all these peptides recorded in chloroform and in trimethyl phosphate showed an intense maximum around 276 nm assigned to the ΔzPhe chromophores. The corresponding CD spectra of the peptides n = 2-4 showed exciton couplets with a negative peak at longer wavelengths, whereas that of the peptide n = 1 showed only weak signals. Theoretical CD spectra were calculated for the peptides n = 2-4 of several helical conformations, on the basis of exciton chirality method. This calculation indicated that the three peptides form a helical conformation deviating from the perfect 310-helix that contains three residues per turn, and that their side chains of Δz Phe residues are arranged regularly along the helix. The center-to-center distance between the nearest phenyl pair(s) was estimated to be ∼ 5.5 Å. The chemical shifts of the ΔzPhe side-chain protons (Hβ and aromatic H) for the peptides n = 2-4 indicated anisotropic shielding effect of neighboring phenyl group(s); the effect also supports a regular arrangement of the Δz Phe side chains along the helical axis. © 1993 John Wiley & Sons, Inc.

Notes: A Monte Carlo simulated annealing (MCSA) algorithm was used to generate the conformations of local regions in bovine pancreatic trypsin inhibitor (BPTI) starting from random initial conformations. In the approach explored, only the conformation of the segment is computed; the rest of the protein is fixed in the known native conformation. Rather than follow a single simulation exhaustively, computer time is better used by performing multiple independent MCSA simulations in which different starting temperatures are employed and the number of conformations sampled is varied. The best computed conformation is chosen on the basis of lowest total energy and refined further. The total energy used in the annealing is the sum of the intrasegment energy, the interaction energy of the segment with the local surrounding region, and a distance constraint to generate a smooth connection of the initially randomized segment with the rest of the protein.The rms deviations between the main-chain conformations of the computed segments in BPTI and those of the native x-ray structure are 0.94 Å for a 5-residue α-helical segment, 1.11 Å for a 5-residue β-strand segment, and 1.03, 1.61, and 1.87 Ã for 5-, 7-, and 9-residue loop segments. Side-chain deviations are comparable to the main-chain deviations for those side chains that interact strongly with the fixed part of the protein. A detailed view of the deviations at an atom-resolved level is obtained by comparing the predicted segments with their known conformations in the crystal structure of BPTI. These results emphasize the value of predetermined fixed structure against which the computed segment can nest. © 1993 John Wiley & Sons, Inc.

Notes: A formal partially dynamical approach to ergodic sampling, hybrid Monte Carlo, has been adapted for the first time from its proven application in quantum chromodynamics to realistic molecular systems. A series of simulations of pancreatic trypsin inhibitor were run using temperature-rescaled molecular dynamics and hybrid Monte Carlo. It was found that simulations run using hybrid Monte Carlo equilibrated an order of magnitude faster than those run using temperature-rescaled molecular dynamics. Certain aspects of improved performance obtained using hybrid Monte Carlo are probably due to the increased efficiency with which this algorithm explores phase space. To discuss this we introduce the notion of “trajectory stiffness”. © 1993 John Wiley & Sons, Inc.

Notes: The rise of the birefringence following the application of an electric field to DNA in an agarose gel has been quantitatively analyzed to demonstrate the major role played by the chain overstretching. By analyzing the field free decay after short times, we demonstrate that the overshoot is completely due to overstretching. Its time of appearance τov varies with the field and DNA length in fair agreement with the E-lN0ln N0 prediction of Lim et al. [ (1990), Journal of Chemical Physics, Vol. 92, pp. 709-721]. The τov is also the time corresponding to one tube renewal after relaxation of the overstretching. © 1993 John Wiley & Sons, Inc.

Notes: A mathematical frame has been established to generally formulate the correlating properties of peptides. The formulation can be used to study the specificity of multisite enzymes, particularly in predicting the susceptible sites in proteins by human immunodeficiency virus (HIV) proteases, and hence can serve as a supplementary means in designing HIV protease inhibitors as potential drugs against acquired immunodeficiency syndrome. © 1993 John Wiley & Sons, Inc.

Notes: The acridine dye quinacrine and its interactions with calf thymus DNA, poly(dA-dT) · poly (dA-dT), and poly (dG-dC) · poly(dG-dC) were studied by light absorption, linear dichroism, and fluorescence spectroscopy. The transition moments of quinacrine give rise to absorption bands polarized along the short axis (400-480-nm band), and the long axis (345-nm and 290-nm bands) of the molecule, respectively. Linear dichroism studies show that quinacrine intercalates into calf thymus DNA as well as into the polynucleotides, displaying fairly homogeneous binding to poly (dA-dT) · poly (dA-dT), but more than one type of intercalation site for calf thymus DNA and poly (dG-dC) · poly(dG-dC). Fluorescence spectroscopy shows that for free quinacrine the pK = 8.1 between the mono- and diprotonated states also remains unchanged in the excited state. Quinacrine bound to calf thymus DNA and polynucleotides exhibits light absorption typical for the intercalated diprotonated form. The fluorescence enhancement of quinacrine bound to poly (dA-dT) · poly(dA-dT) may be due to shielding from water interactions involving transient H-bond formation. The fluorescence quenching in poly(dG-dC) · poly(dG-dC) may be due to excited state electron transfer from guanine to quinacrine. © 1993 John Wiley & Sons, Inc.

Notes: The solid state secondary structure of myoglobin, RNase A, concanavalin A (Con A), poly(L-lysine), and two linear heterooligomeric peptides were examined by both far-uv CD spectroscopy1 and by ir spectroscopy. The proteins associated from water solution on glass and mica surfaces into noncrystalline, amorphous films, as judged by transmission electron microscopy of carbon-platinum replicas of surface and cross-fractured layer. The association into the solid state induced insignificant changes in the amide CD spectra of all α-helical myoglobin, decreased the molar ellipticity of the α/β RNase A, and increased the molar ellipticity of all-β Con A with no change in the positions of the bands' maxima. High-temperature exposure of the films induced permanent changes in the conformation of all proteins, resulting in less α-helix and more β-sheet structure. The results suggest that the protein α-helices are less stable in films and that the secondary structure may rearrange into β-sheets at high temperature. Two heterooligomeric peptides and poly (L-lysine), all in solution at neutral pH with “random coil” conformation, formed films with variable degrees of their secondary structure in β-sheets or β-turns. The result corresponded to the protein-derived Chou-Fasman amino acid propensities, and depended on both temperature and solvent used. The ir and CD spectra correlations of the peptides in the solid state indicate that the CD spectrum of a “random” structure in films differs from random coil in solution. Formic acid treatment transformed the secondary structure of the protein and peptide films into a stable α-helix or β-sheet conformations. The results indicate that the proteins aggregate into a noncrystalline, glass-like state with preserved secondary structure. The solid state secondary structure may undergo further irreversible transformations induced by heat or solvent. © 1993 John Wiley & Sons, Inc.

Notes: The structural preferences of peptides (and depsipeptides) from the achiral MeAib and Hib residues, and the chiral Iva, (αMe) Val, (αMe) Leu, and (αMe) Phe residues, as determined by conformational energy computations, x-ray diffraction analyses, and 1H-nmr and spectroscopic studies, are reviewed and compared with literature data on Aib-containing peptides. The results obtained indicate that helical structures are preferentially adopted by peptides rich in these α-amino acids methylated at the α-carbon. Intriguing experimental findings on the impact of the chirality of Iva, (αMe) Val, and (αMe) Phe residues on helix screw sense are illustrated. © 1993 John Wiley & Sons, Inc.

Notes: A molecular dynamics (MD) simulation was performed on the α-helix H8-HC5, the C-terminal part of myoglobin (residue 132-153), under periodic boundary conditions in two different solutions, water and water with 30% (v/v) 2,2,2-trifluoroethanol (TFE), at 300 K to investigate the stability of the helix. In both simulations, the initial configuration was a canonical right-handed α-helix. In the course of the MD trajectory in water (200 ps), the helix clearly destabilized and began to unfold after 100 ps. In the TFE solution, two stable parts of helical regions were observed after 70 ps of a 200-ps MD simulation, supporting the notion that TFE acts as a structure-forming solvent. © 1993 John Wiley & Sons, Inc.

Notes: The crystal structures of the isovaline (Iva) containing dipeptides, Boc-D-Iva-L-Pro-OBzl and Boc-L-Iva-L-Pro-OBzl, were determined by x-ray diffraction. The diastereomeric peptides were shown to adopt unturned conformations closely similar to each other (φIva 52°, ψIva 46°, φPro-65°, and ψPro 143° for D-Iva-L-Pro sequence and φIva 52°, ψIva 44°, φPro -63°, and ψpro 148° for L-Iva-L-Pro sequence). The Pro ring of each peptide was in Cγ-endo conformation. The unusually large ∠CIva-NPro-CδPro values (131° in both peptides) were observed, that was due to steric repulsion between the δ-methylene of Pro and the alkyl side chain of Iva residue. These conformations were essentially the same as that of the corresponding α-aminoisobutyric acid (Aib)-containing peptide Boc-Aib-L-Pro-OBzl. The result has demonstrated that replacement of either one of the two methyl groups of the Aib residue in Boc-Aib-L-Pro-OBzl with an ethyl group does not cause any significant change in the unturned conformation of the dipeptide. © 1993 John Wiley & Sons, Inc.

Notes: Bradykinin (BK) is a peptide hormone with sequence Arg1-Pro2-Pro3-Gly4-Phe5-Ser6-Pro7-Phe8-Arg9 and has been implicated in a multitude of pathophysiological processes such as the ability to lower systemic blood pressure and stimulate pain. BK analogues having bulky, β-branched D-aliphatic residues at position 7 combined with bulky L-aliphatic residues at position 8 have now been observed to be strong antagonists. Conformational studies based on two-dimensional nmr experiments in methanol/water (80/20 v/v) were carried out on several such active antagonists in a polar solvent. Included in this study were the very active antagonists, [D-Arg0, Hyp3, Thi5, D-Cpg7, Cpg8]-BK [Cpg: α-cyclo-pentyl-glycine; Hyp: trans-4-hydroxy-L-proline; Thi: β-(2-thienyl)-L-alanine] (I), [D-Arg0, Hyp3, D-Cpg7, Cpg8] -BK (II), as well as its variant with D-Cpg7 replaced by Cpg7, namely [D-Arg0, Hyp3, Cpg7, Cpg8]-BK (III). A turn-like structure, which coexists with the extended conformation, was observed between residues 2 and 5 for the most active antagonists I and II, in direct correlation with the peptide activities. No turn-like structure was found for residues 6-9. In peptide III, a turn-like structure was not identified. The existence of a turn at the C-terminal end of bradykinin and its analogues has been predicted by empirical calculations and supported by nmr measurements. But the present nmr study on the most active antagonists (I, II) does not support this hypothesis. Instead, the data suggest that a turn-like structure between residues 2 and 5 could be important for antagonist activity. Finally, one weak inhibitor [D-Cpg7]-BK (IV) showed no defined secondary structure. © 1993 John Wiley & Sons, Inc.

Notes: During electrophoretic separation of anionic polyamino acids, resolution according to the number of peptide units can be achieved in capillaries filled with hydrophilic gels. While polyaspartate preparations yield single peaks for the individual oligomers at pH above 8.0, polyglutamates exhibit an anomalous behavior of peak splitting, which is attributed here to the separation of the oligopeptide conformers. An Asp-Glu (1:1) copolymer yields single peaks under similar conditions. At pH near 4.5, where polyglutamate is expected to exist in its α-helix form, peak splitting disappears. Upon heating to 95°C for at least 120 h (procedure described to transform the α-helix into a β form), peak splitting disappeared, but could be reestablished after cooling for several days. When a highly charged cation spermine was added to the operational electrolyte, triple peaks appeared in the electropherogram due to the ion-pair formation. The largest peak in every triplet has been tentatively assigned to the α-helix form. The electrophoretic results described have been largely supported by CD spectra. © 1993 John Wiley & Sons, Inc.

Notes: Individual-site isotherms for the binding of bacteriophage λ repressor to the left and right λ operators have been determined [D. F. Senear, M. Brenowitz, M. A. Shea, and G. K. Ackers (1986) Biochemistry, Vol. 25, pp. 7344-7354.] using the DNAse protection technique [ footprinting; D. J. Galas and A. Schmitz (1978) Nucleic Acids Research, Vol. 5, pp. 3157-3170]. These extensive data have been interpreted with a quantitative model that emphasized cooperative interactions between adjacently bound ligands [occupied ↔ occupied interactions; G. K. Ackers, A. D. Johnson, and M. A. Shea (1982) Proceedings of the National Academy of Science, USA, Vol. 79, pp. 1129-1133]. Overlooked in this model are the effects of cooperative interactions between a site containing a bound ligand and its neighboring unoccupied site (occupied ↔ unoccupied interactions). This paper reinterprets the existing data with a model that considers occupied ↔ unoccupied as well as occupied ↔ occupied interactions. The results yield parameters that differ substantially from those already reported. A discussion on the advisability of ignoring occupied ↔ unoccupied interactions is included. © 1993 John Wiley & Sons, Inc.

Notes: Two trans-syn cyclobutane photodimers of thymidylyl (3′-5′) deoxyuridine were formed by deamination of the corresponding trans-syn cyclobutane photodimers of thymidylyl(3′-5′) deoxycytidine and were examined by 1H-, 13C-, and 31P-nmr spectroscopy. Correlation spectroscopy, nuclear Overhauser enhancement spectroscopy, and one-dimensional heterodecoupling experiments allowed a more complete assignment of the 1H spectra, compared with previous reports by Koning et al. [ (1991) European Journal of Biochemistry, Vol. 195, pp. 29-40] and Liu and Yang [(1978) Biochemistry, Vol. 17, pp. 4865-4876]. Deoxyribose ring conformations were calculated from 1H coupling constants by pseudorotational analysis, and rotamer distributions of exocyclic bonds were calculated from the observed homonuclear and heteronuclear coupling constants. The cyclobutane ring configuration (CB) of each isomer was identified, using arguments based upon observed scalar and dipolar couplings. Glycosidic bond conformation was ascertained from nuclear Overhauser enhancements observed between base and deoxyribose protons. Isomer I (S-type class; CB-; SYN-ANTI) and isomer II (N-type class; CB+; ANTI-SYN) exhibit markedly different conformational features. 31P chemical shifts and exocyclic bond rotamer distributions indicate diminished backbone flexibility for both photoproducts relative to parent thymidylyl (3′-5′) deoxyuridine. Isomer I (SYN-ANTI) is particularly rigid, while isomer II (ANTI-S YN) maintains some flexibility. Also, 13C spectra were acquired and assigned unequivocally with the aid of short- and long-range two-dimensional heteronuclear shift correlation experiments. © 1993 John Wiley & Sons, Inc.

Notes: Interaction of a minor groove-binding drug Hoechst-33258, and an intercalating drug, proflavin, with the PSI (+) form of DNA, was studied using CD spectroscopy. Both drugs are shown to relax the suprahelical organization of DNA, leading to the formation of a B-like structure, above a certain drug to phosphate ratio. However, unlike proflavin, Hoechst-33258 brings about further structural changes after formation of the B-like structure whereas proflavin does not. A reversal of the CD signal in the 300-450-nm spectral region is also observed with Hoechst-33258, indicating a change in the handedness of the suprahelical organization of DNA. To the best of our knowledge, drug-mediated changes as presented in this paper have not been reported so far. © 1993 John Wiley & Sons, Inc.

Notes: A quantitative understanding of helix-coil dynamics will help explain their role in protein folding and in folded proteins. As a contribution to the understanding, the equilibrium and dynamical aspects of the helix-coil transition in polyvaline have been studied by computer simulation using a simplified model of the polypeptide chain. Each amino acid residue is treated as a single quasiparticle in an effective potential that approximates the potential of mean force in solution. The equilibrium properties examined include the helix-coil transition and its dependence on chain position and well depth at the coil-helix interface. A stochastic simulation of the Brownian motion of the chain in its solvent surroundings has been used to investigate dynamical properties. Time histories of the dihedral angles have been used to study the behavior of the helical structure. Auto and cross-correlation functions have been calculated from the time histories and from the state (helix or coil) functions of the residues with relaxation times of tens to hundreds of picoseconds. Helix-coil rate constants of tens of ns-1 were found for both directions of the transition. © 1993 John Wiley & Sons, Inc.

Notes: We have carried out a nanosecond molecular dynamics simulation of an analogue of the ribonuclease C-peptide in water. The overall conformation has an extended region for the first three amino acids connected to an α-helix for residues 4-13, and this basic structure is preserved throughout the simulation, with helical hydrogen bonds present 87% of the time, on average. The final helical hydrogen bond is spontaneously broken and re-formed several times, providing a detailed picture of such winding/unwinding events. The simulation was used to estimate the effects of internal motion on proton nuclear Overhauser effect spectroscopy (NOESY) intensities for several classes of important cross peaks. Within the helical regions, the effects of internal motion vary only a little from one residue to another for backbone-backbone cross peaks, and the relevant correlation functions reach plateau values within about 50 ps. The spectral simulations show, however, that it may be difficult to establish a close quantitative connection between NOESY cross-peak volumes and measures of helical content. © 1993 John Wiley & Sons, Inc.

Notes: The Z form of poly[d(G-m5C)2], in presence of Mg2+ ion, is found to be transformed into B form upon interaction with 4′,6-diamidino-2-phenylindole (DAPI). The Z → B transformation is complete at a mixing ratio of about 0.07 DAPI per DNA base pairs, i.e., each DAPI molecule may be related to the conversion of 6-7 base pairs. An interaction between DAPI and poly[d(G-m5C)2] in its Z form at low drug: DNA ratios is suggested from optical dichroism and time-resolved luminescence anisotropy results. The spectroscopic behaviour of DAPI indicates that the Z conformation of DNA does not provide normal binding sites for DAPI, such as groove or intercalation sites, but that the initial association may be of external nature. © 1993 John Wiley & Sons, Inc.

Notes: A generally applicable solid-phase methodology has been developed for the synthesis of triple-helical polypeptides incorporating native collagen sequences. Three nascent peptide chains are C-terminal linked through one Nα-amino and two Nε-amino groups of Lys, while repeating Gly-Pro-Hyp triplets induce triple helicity. Different protecting group strategies, including several three-dimensionally orthogonal schemes, have been utilized for the synthesis of four homotrimeric triple-helical polypeptides (THPs) of 79-124 residues, three of which incorporate native type IV collagen sequences. Highly efficient assemblies were achieved by 9-fluorenylmethoxycarbonyl (Fmoc) Nα-amino group protection, in situ 2-(1H-benzotriazole-l-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate mediated couplings, and 1,8-diazabicyclo [5.4.0] undec-7-ene mediated Fmoc group removal. THPs were characterized by Edman degradation sequencing, size-exclusion chromatography, mass spectrometry, reversed-phase high performance liquid chromatography, and CD spectroscopy. THP thermal stabilities ranged from 35 to 59°C, with chain length and Hyp content being the influential factors. Melting temperatures and van't Hoff enthalpies for peptide triple-helical denaturation could be correlated well to Hyp content. The THP synthetic protocol developed here will allow for the study of both structure and biological activity of specific collagen sequences in homotrimeric and heterotrimeric forms. © 1993 John Wiley & Sons, Inc.

Notes: The effects of inserting 16 base pair (bp) of alternating CG[(CG)8] near the middle of a much longer restriction fragment (1097 bp) are investigated by measuring various properties that are sensitive to secondary and tertiary structure. Results for this fragment are compared with those for a control fragment (1089 bp) with the identical sequence except at the insert. Another fragment (1382 bp), which contains a 296-bp extension at the 5′-end of the 1089-bp control fragment, is also used as a secondary control in some experiments. When the 1097-bp (CG)8 insert fragment is compared with the control fragments in 0.1M NaCl buffer, the (CG)8 insert is found to induce disproportionately large relative changes in the molar ellipticity at 273 nm ([θ)273], the torsion constant (α) measured by fluorescence polarization anisotropy, the optical melting profile, and the susceptibility to S1 nuclease. Estimates of the minimum distance over which the (CG)8 insert alters the secondary structure range from 330 to 550 bp. With increasing NaCl concentration, the 1097-bp insert fragment undergoes a structural transition between 2.0 and 2.5M that is manifested in the apparent diffusion coefficient (Dplat) from dynamic light scattering at large scattering vector. This transition, which is not exhibited by the control DNAs, is presumed to involve formation of Z-helix at the insert. However, the observed decrease in (Dplat) is attributed to an increase in bending rigidity, which perforce must be globally distributed far beyond the (CG)8 insert per se. In 4.25M NaCl (but not in 0.1M NaCl), the addition of 1 ethidium dye per 300 bp induces an extensive structural transition in the 1097 bp (CG)8 insert fragment. This transition, which also is not exhibited by the control DNAs, significantly decreases the bending rigidity, doubles [θ]273, and takes place on a time scale of a few days. Removal of ethidium and salt by dialysis vs 0.1M NaCl buffer restores the original properties of the 1097-bp (CG)8 insert fragment. The present results are consistent with a (fluctuating, long-range) description of the secondary structure in which a given short sequence transiently fluctuates among two or more distinct secondary structures that extend over much larger domains of variable position and size, and whose relative stabilities depend on distant as well as close-lying base pairs. © 1993 John Wiley & Sons, Inc.

Notes: The present study is aimed at understanding the effects of DNA sequence, local conformation, and curvature on groove geometry. Energy-optimized structures are obtained by Jumna methodology; groove geometry is analyzed by a recently developed technique that allows an accurate and continuous measurement of width and depth. The mechanics of groove deformations is also studied and analyzed in terms of helicoidal parameters. © 1993 John Wiley & Sons, Inc.

Notes: Molecular dynamics simulations of three DNA sequences using the AMBER 3.0 force field were performed with implicit inclusion of water through a distance-dependent dielectric constant and solvated counterions. Simulations of the self-complementary DNA dodecamer d(CGCGAATTCGCG) were started from a regular B-DNA structure and the x-ray single crystal B-DNA structure. Although mean convergence during the 89-ps calculation was confirmed, localized differences in backbone torsionals and base-pair helicoidals were observed. A nanosecond simulation of the nonself-complementary 14 base-pair DNA d(GGCGGAATTGGCGG) indicates that most structural parameters stabilize within the first 100-200 ps, while isolated features show low-frequency oscillations throughout the calculation. The lack of harmonic constraints on the ends of the molecules was shown not to perturb the structural dynamics of the internal oligonucleotide beyond the external 2 base pairs. Comparison of three simulations of the nonself-complementary 14 base-pair DNA d(GGCGAAATTCGCGG), identical in all respects other than the assignment of initial Maxwellian atomic velocity distributions, revealed the inherent systematic variability. The three calculations result in nearly superimposable global structures, with localized variations in torsionals and helicoidals. Our results provide a basis for performing a comparative analysis of the effect of DNA sequence on localized structure. © 1993 John Wiley & Sons, Inc.

Notes: Low-frequency collective motions in proteins are generally very important for their biological functions. To study such motions, harmonic dynamics proved most useful since it is a straightforward method; it consists of the diagonalization of the Hessian matrix of the potential energy, yielding the vibrational spectrum and the directions of internal motions. Unfortunately, the diagonalization of this matrix requires a large computer memory, which is a limiting factor when the protein contains several thousand atoms.To circumvent this limitation we have developed three methods that enable us to diagonalize large matrices using much less computer memory than the usual harmonic dynamics. The first method is approximate; it consists of diagonalizing small blocks of the Hessian matrix, followed by the coupling of the low-frequency modes obtained for each block. It yields the low-frequency vibrational spectrum with a maximum error of 20%. The second method consists, after diagonalizing small blocks, of coupling the high- and low-frequency modes using an iterative procedure. It yields the exact low-frequency normal modes, but requires a long computational time with convergence problems. The third method, DIMB (Diagonalization in a Mixed Basis), which has the best performance, consists of coupling the approximate low-frequency modes with the mass-weighted cartesian coordinates, also using an iterative procedure. It reduces significantly the required computer memory and converges rapidly. The eigenvalues and eigenvectors obtained by this method are without significant error in the chosen frequency range. Moreover, it is a general method applicable to any problem of diagonalization of a large matrix.We report the application of these methods to a deca-alanine helix, trypsin inhibitor, a neurotoxin, and lysozyme. © 1993 John Wiley & Sons, Inc.

Notes: Elasticity theory of naturally curved rods is employed to study the effects of intrinsic curvature on the properties of the equilibrium conformations of supercoiled DNA. The results stand in sharp contrast to those obtained when the molecule is viewed as being straight in its relaxed form. Starting from very fundamental principles of the theory, we show that the torsion of an open segment with a curved duplex axis can vary when the temperature, and along with it, the intrinsic twist is changed. Conversely, an imposed helicity, such as might be associated with binding to a histone, can change the intrinsic twist. It is also shown that another consequence of the presence of naturally curved sequences is that the twist density will, in general, vary with position along the chain in all equilibrium states. Then portions of the molecule will be more or less susceptible to interaction with other agents sensitive to such a variation. Finally, some closed equilibrium global structures uniquely associated with intrinsic curvature are discussed. © 1993 John Wiley & Sons, Inc.

Notes: The cyclic hexapeptide cyclo[-Pro1-Gly2-Glu3(OBzl)-Pro4-Phe5-Leu6-] (1; OBzl: benzyl ester) was modeled and synthesized to be used as a chiral site for the separation of enantiomers. Total correlation spectroscopy and nuclear Ovehauser effect spectroscopy spectra of the peptide in CDCl3 showed the presence of three stereoisomers. The two dominant stereoisomers 1a and 1b exchanged chemically with each other, while the minor stereoisomer 1c exchanged exclusively with the stereoisomer 1b. Stereoisomer 1a had two cis proline peptide bonds while stereoisomer 1b had all-trans peptide bonds. The stereoisomer 1c had, for nonstrained peptides, an unusual cis phenylalanine peptide bond while both proline peptide bonds were trans. © 1993 John Wiley & Sons, Inc.

Notes: The comprehensive structural analysis reported herein of eight N-glycopeptides, in three different solvents, is based on quantitative CD experiments, homonuclear nuclear Overhauser effect measurements, and molecular dynamics (MD) calculations. Although several orientations of the two amide planes attached to the carbohydrate pyranose ring are possible, according to NOE, CD data, and MD simulations, of all of the glycopeptide models, regardless of the type of the carrier peptide, only one dominant conformer population was found. This conformer is characterized by a nearly trans orientation of the CH and NH hydrogens of both acetamido groups. This finding is in perfect agreement with x-ray crystallographic data on the solid state conformation of the 1-N-acetyl- and 1-N-(β-aspartoyl)-2-acetamido-2-deoxy-β-D-glucopyranosylamine. The precise identification of this dominant conformer of N-glycopeptides in solution was the major question addressed herein by the structural analyses. A “CD additivity” experiment was carried out using an equimolar solution of Boc-Pro-Asp-NHCH3 and l-N-acetyl-3,4,6-tri-O-acetyl-2-acetamido-2-deoxy-β-D-gluco-pyranosylamine at ambient temperature in acetonitrile. The CD spectrum obtained from the equimolar solution of the above two molecules (the “spectroscopic sum”) was identical with the CD curve obtained from the algebraic summation of the individually recorded CD spectra of the peptide and the carbohydrate moiety (“mathematical sum”).The global picture of the CD spectral analyses of the eight parent peptides with the eight N-glycopeptides revealed that in trifluoroethanol and acetonitrile, the side-chain modification of the Asn models (natural N-glycopeptide analogues) by N-glycosylation has a significant effect on the conformation of the carrier peptide, resulting in a decrease in the original type I β-turn content. Simultaneously, the type II β-turn conformational percentage increased to ≈ 20%. Such a conformational ratio change seems to be larger than the expected errors arising from the CD analyses, and agrees with the results of MD calculations. N-glycosylation of Asn residues causes perturbations, not only through the covalent bond, but also through specific hydrogen bonds between the backbone and side chain atoms. CD spectroscopy, augmented by efficient CD curve deconvolution techniques, has proved to be a useful tool for studying multicomponent conformer mixtures of small linear peptides in solution and changes of conformational equilibria caused by N-glycosylation. © 1993 John Wiley & Sons, Inc.

Notes: Elastic and quasi-elastic light scattering studies were performed on aqueous solutions of poly (Val-Pro-Gly-Gly), a representative synthetic bioelastomer that differs from the previously studied poly (Val-Pro-Gly-Val-Gly) by the deletion of the hydrophobic Val in position four. When the spinodal line was approached from the region of thermodynamic stability, the intensity of light scattered by fluctuations, and the related lifetime and correlation length, were observed to diverge with mean-field critical exponents for both systems. Fitting of the experimental data allowed determining the spinodal and binodal (coexistence) lines that characterize the phase diagrams of the two systems, and it also allowed a quantitative sorting out of the enthalpic and entropic contributions to the Flory-Huggins interaction parameters. The contribution of valine is derived by comparison of the two cases. This can be viewed as sorting out the effect of a modulation of the solute. The same approach may allow sorting out the entropic and enthalpic effect of modulations of the solvent by cosolutes (or by cosolvents). This could be of particular interest in the case of small osmolytes, affording important adaptive roles in nature, at the cost of very limited changes in genetic information.Finally, the suggestion is further supported that statistical fluctuations of anomalous amplitude, such as those occurring in proximity of the spinodal line, have a role in promoting the process of self-assembly of extended supramolecular structures. On the practical side, the present approach appears useful in the design of novel synthetic model systems for bioelastomers. © 1993 John Wiley & Sons, Inc.

Notes: In order to investigate the Conformational change of the α-aminoisobutyric acid (Aib) containing peptide by the D/L replacement of an amino acid residue, single crystals of two diastereomers, Dnp-L-Val-Aib-Gly-L-Leu-pNA (L-L isomer) and Dnp-D-Val-Aib-Gly-L-Leu-pNA (D-L isomer), were prepared from aqueous methanol solutions as CH3OH and CH3OH · H2O solvates, respectively, and were analyzed by the x-ray diffraction method. Molecular conformation of L-L isomer adopts consecutive two different types of β-turns, a type II′ β-turn bent at Aib-Gly, and a type III β-turn bent at Gly-Leu, stabilized by two intramolecular (Leu) NH … O=C (Val) and (pNA) NH … O=C(Aib) hydrogen bonds. In contrast, these two intramolecular hydrogen bonds lead the D-L isomer to a distorted 310-helix conformation consisting of consecutive two type-III β-turn of Aib-Gly-Leu sequence. The most significant structural difference between these diastereomers is the mutual orientation between the Dnp and pNA chromophores. While the extensive stacking of both the chromophores is intramolecularly formed for the folded conformation of L-L isomer, they are oriented toward an opposite direction in the open conformation of D-L isomer and are intermolecularly stacked with each other. The large separation between these diastereomers observed in the chromatography is discussed in the relation with their Conformational differences. © 1993 John Wiley & Sons, Inc.

Notes: Recent advances in the application of solid state nmr spectroscopy to uniformly aligned biopolymers have opened a window through which to view the detailed structure of biological macromolecules that are unable to be seen with standard techniques for structure determination such as x-ray diffraction. Atomic resolution structural details are obtained from solid state nmr data in the form of bond orientations, which yield the relative positions of specific atoms within the molecule. For static aligned systems such as fibers, in which rapid reorientation about the axis of alignment does not occur, it has generally been necessary to perform trial and error line-shape simulations to extract structural details from nmr spectra arising from a single type of nuclear spin interaction. In the present work, a new method is developed in which solid state 15N-nmr spectra obtained from uniaxially aligned molecules placed with the axis of alignment both parallel and perpendicular to the magnetic field are analyzed to yield the orientations of specific molecular bonds. Analytical expressions are derived that utilize spectral features read from 15N chemical shift anisotropy line shapes to calculate a discrete number of possible orientations for a specific site. The 15N-1H dipolar interaction is employed to further narrow the number of unique orientations possible for a given site. With this method, a neighborhood of possible orientations is quickly determined, and full line-shape simulations within this region of allowed space can be performed to refine the limits of orientation. This technique demonstrates the use of a single type of isotopic label to determine the orientation of a specific molecular group such as a peptide plane within a protein. Results from the application of this method to the Bombyx mori silk fibroin protein provide structural detail that is consistent with currently accepted structural models based on fiber diffraction studies. © 1993 John Wiley & Sons, Inc.

Notes: The unfolding and refolding of T4 thioredoxin was observed by equilibrium and kinetic size exclusion chromatographic measurements in guanidine hydrochloride at 4°C and pH 7.0. All the observed chromatographic profiles can be simulated by a cubic mechanism using a consistent set of equilibrium and kinetic parameters describing each of the coupled transitions. The four components in the folded protein and in the unfolded protein are interrelated by configurational transitions having parameters characteristic for proline peptide isomerizations. Only two of the four folded conformations are significantly populated at equilibrium. Each of the four unfolded components can refold by a unique Conformational transition. No transiently populated folding intermediates are detected having hydrodynamic volumes intermediate between those characteristic for the folded and unfolded protein. © 1993 John Wiley & Sons, Inc.

Notes: Quasi-elastic light scattering studies on some polyelectrolyte systems exhibit a somewhat “bizarre” behavior in the profile of the apparent diffusion coefficient Dapp as a function of the salt concentration Cs. As Cs is decreased, Dapp first increases in accordance with polyelectrolyte theories, and then undergoes a precipitous drop in value by over an order of magnitude at a well-defined critical value Cs = Cso-e. This “transition” from Cs 〉 Co-es (ordinary) to Cs 〈 Co-es (extraordinary) is referred to as the “ordinary-extraordinary” (o-e) transition.Ghosh, Peitzsch, and Reed [(1992) Biopolymers, Vol. 32, pp. 1105-1122] proposed a “filterable aggregate” (FA) and “other particle” interpretation for the o-e transition and its reversibility in regard to ionic strength changes. The present communication examines in detail the FA model as applied to the o-e transition. It is shown that the FA model fails to account of the established characteristics of the o-e transition. © 1993 John Wiley & Sons, Inc.

Notes: The coil-helix transitions of poly (L-glutamic acid) in aqueous alcohol solutions have been investigated for mixed counterion systems. It has been found that coexistence of two kinds of counterion species, i.e., two alkali metal counterions, alkali and alkaline earth metal, and two alkaline earth metals, specifically stabilizes or destabilizes the helix conformation depending upon the combination of the counterion species. The most striking enhancement of the helix content was observed for the combination of Li+ and K+ counterions. It has been suggested that the helix stabilization is attributed to the reduction of the free energy in the contact ion pair formation between the polymer charges and the counterions in the mixed counterion systems. © 1993 John Wiley & Sons, Inc.

Notes: Structural changes can be induced in a peptide by selective substitution of coded α-amino acid residues by noncoded α-amino acid residues and the consequent production of analogues with modified structure and conformational preferences.In this review article we summarize the solid state structural results and the conformational preferences of two classes of “building blocks”: (a) the linear and cyclic symmetrically α, α-disubstituted glycines in which either two identical n-alkyl groups replace the hydrogen atoms of the glycine residue or a cyclic aliphatic side-chain system is formed by linking the two α-carbon side chains, respectively; and (b) the β-alanine residue. Examples, whenever possible, of the use of these residues for the elucidation of the bioactive conformation in the appropriate biological systems will be given. © 1993 John Wiley & Sons, Inc.

Notes: An overview of CD of proline-rich peptides is reported. First, structural characteristics, theoretical CD studies, and the biological relevance of polyproline II structure in such peptides are discussed. Second, a CD study of peptides belonging to the repetitive domain of maize glutelin-2, H-(Val-His-Leu-Pro-Pro-Pro)n-OH (n = 3, 5, 8), is described. This series of peptides displayed the CD features of polyproline II structure in water (5°C, pH5). Moreover, it was shown that the addition of increasing amounts of the polyanionic molecule heparin forced a displacement of the conformational equilibrium of those peptides toward higher proportions of the polyproline II structure. In contrast, when the temperature is raised such a structure gradually disappears, leading to more disordered conformations. © 1993 John Wiley & Sons, Inc.

Notes: An outline of the basic considerations that are under development for the rational design of biologically active peptides and peptidomimetics is given. The necessary interplay of biophysical, chemical, and biological considerations is emphasized. The importance of properly designed biological assays to provide chemical information analogous to that from biophysical studies is discussed. The development of asymmetric synthesis in conjunction with conformational considerations for the preparation of specialized amino acids and amino acid mimetics is a critical aspect of the approach. The overall approach is illustrated with three examples from our laboratory: (1) the redesign of somatostatin to a highly potent and selective μ-opioid receptor antagonist using conformational and topographical considerations in design and for obtaining insights into the pharmacophor; (2) the use of topographical considerations for obtaining oxytocin antagonists; and (3) the application of designer amino acids prepared by asymmetric synthesis to obtain insight into the topographical requirements at δ-opioid receptors. © 1993 John Wiley & Sons, Inc.

Notes: A winter flounder antifreeze polypeptide (HPLC-6) has been studied in vacuo and in aqueous solution using molecular dynamics computer simulation techniques. The helical conformation of this polypeptide was found to be stable both in vacuum and in solution. The major stabilizing interactions were found to be the main-chain hydrogen bonds, a salt-bridge interaction, and solute-solvent hydrogen bonds. A significant bending in the middle of the polypeptide chain was observed both in vacuo and in solvent at 300 K. Possible causes of the bending are discussed. From simulations of mutant polypeptide molecules in vacuo, it is concluded that the bend in the native polypeptide was caused by side chain to backbone hydrogen bond competition involving the Thr 24 side chain and facilitated by strains on the helix resulting from the Lys 18-Glu 22 salt bridge. © 1993 John Wiley & Sons, Inc.

Notes: Aqueous solutions formed by polypeptides, simple models of proteins, and bile salts (sodium cholate and deoxycholate, NaC and NaDC, respectively) or bilirubin-IXα (BR) have been studied by CD measurements. They could mimic more complicated biliary systems, thus supplying a possible interpretation of the behavior of some amino acid residues in the biliary proteins. The aggregation of NaDC and NaC in water can be monitored by CD measurements. Bile salts, in submicellar and micellar form, stabilize poly (L-Lys) (PLL) in α-helical conformation. The α-helix content increases with increasing bile salt concentration and ionic strength. NaDC seems to be a slightly better stabilizing agent of the α-helix conformation than NaC. Models characterized by hydrogen bonds between bile salts and PLL are proposed, also resorting to previous data available on the systems formed by NaDC and poly(L-Leu-L-Leu-L-Lys) (PLLL) or poly(L-Leu-L-Leu-L-Asp) (PLLA). Binding of BR to PLL, poly(D-Lys), poly(L-Glu), PLLL, and PLLA in water has been investigated by CD spectra in order to clarify the nature of the association complexes and the mechanism of the BR enantioselective complexation. Potential energy calculations provide binding models capable of explaining the enantioselective ability of the PLL and PLLL α-helices toward the left- and right-handed enantiomer of BR, respectively. BR is bound to -NH2 groups of PLL and PLLL lying on a right- and left-handed spiral, respectively. These results, together with those formerly obtained for some bile salts-BR systems, indicate that the selectivity originates from a binding that involves large regions of the BR molecule and gives rise, very probably, to moderate conformational changes from the “ridge tile” structure observed in the crystals. In some cases van der Waals forces can play a crucial role in the chiral recognition of bilirubin. Moreover, possible interaction models of BR with human serum albumin are proposed on the basis of a recent x-ray crystal structure of the protein. © 1993 John Wiley & Sons, Inc.

Notes: We have obtained the UV excited resonance Raman spectra of five mononucleotides bound to cisplatin and to carboplatin using excitation in resonance with the first electronic absorption bands of the nucleotide bases. Substantial changes in the spectra are observed following interaction with both platinum drugs, indicating modifications to nucleotide structure. Pt (II) binds to base portions of the nucleotide molecules, altering their normal modes of vibration significantly. We present comparative data of cisplatin and carboplatin, and discuss the implications of these results. The kinetics of the drug/nucleotide reactions differ, but final products are found to be similar. © 1993 John Wiley & Sons, Inc.

Notes: CD, electron spin resonance, and fluorescence spectroscopy have been utilized to study the adenine binding site of ricin and its toxic A-subunit. At acidic (4.5) and physiological (7.3) pH, adenine or a spin-labeled analogue of adenine, N6-(2,2,6,6-tetramethyl-1-oxypiperidin-4-yl) adenine, alters the near uv CD spectra of the ricin A-chain as well as intact ricin, whereas the far uv CD spectra of all proteins remain unchanged. Electron spin resonance data show that the adenine spin-labeled analogue interacts strongly with the A-chain both at pH 4.5 and 7.3, but no or very weak binding is observed for the intact ricin or the isolated B-chain. The adenine spin label gets highly immobilized (2AII = 65.5G) by the A-chain. The apparent dissociation constant Kd for the toxic A-chain ligand complex is 1.55 × 10-4 M and 5.6 × 10-5 M at pH 7.3 and 4.5, respectively. Fluorescence intensity of ricin A-chain bound 1,8-anilinonaphthalenesulfonic acid (ANS) decreases by ∼55% at pH 4.5 with the addition of the spin-labeled analogue of adenine, implying that both the ANS and adenine spin label (ADSL) bind to the hydrophobic domain of the A-chain. Fluorescence of the only intrinsic tryptophan probe of the A-chain is also efficiently quenched by ADSL, indicating that the tryptophan residue and the hydrophobic adenine binding site are closely located. All spectroscopic measurements indicate that adenine or its spin-labeled analogue has a single binding site adjacent to the TRP211 residue in the A-chain. Expansion of the A-chain globule and subsequent exposure of the hydrophobic binding site seem to be responsible for the increased binding of adenine at pH 4.5. © 1993 John Wiley & Sons, Inc.

Notes: Depolarization ratios of Raman bands, excited at 488.0 nm, of guanosine-5′-monophosphoric 4 acid, cytidine-5′-monophosphoric acid, adenosine-5′-monophosphoric acid, thymidine-5′-monophosphoric acid, and uridine-5′-monophosphoric acid have been measured in their H2O and D2O solutions in the spectral region from 300 to 1800 cm-1. For comparison, the disodium salt of 2′-deoxyadenosine-5′-monophosphoric acid was also subjected to the depolarization measurement in its H2O solution. The results have been correlated with possible orientations of the principal axes of the Raman scattering tensors as well as with the relative magnitudes of the tensor components. Results should be useful for future polarized Raman studies of synthetic and natural DNA. © 1993 John Wiley & Sons, Inc.

Notes: CD spectra and melting curves were collected for a 28 base-pair DNA fragment in the form of a DNA dumbbell (linked on both ends by T4 single-strand loops) and the same DNA sequence in the linear form (without end loops). The central 16 base pairs (bp) of the 28-bp duplex region is the poly(pu) sequence: 5′-AGGAAGGAGGAAAGAG-3′. Mixtures of the dumbbell and linear DNAs with the 16-base single-strand sequence 5′-TCCTTCCTCCTTTCTC-3′ were also prepared and studied. At 22°C, CD measurements of the mixtures in 950 mM NaCl, 10 mM sodium acetate, 1 mM EDTA, pH 5.5, at a duplex concentration of 1.8 μM, provided evidence for triplex formation. Spectroscopic features of the triplexes formed with either a dumbbell or linear substrate were quite similar. Melting curves of the duplex molecules alone and in mixtures with the third strand were collected as a function of duplex concentration from 0.16 to 2.15 μM. Melting curves of the dumbbell alone and mixtures with the third strand were entirely independent of DNA concentration. In contrast, melting curves of the linear duplex alone or mixed with the third strand were concentration dependent. At identical duplex concentrations, the dumbbell alone melts ∼20°C higher than the linear duplex. The curve of the linear duplex displayed a significant pretransition probably due to end fraying.On melting curves of mixtures of the dumbbell or linear duplex with the third strand, a low temperature transition with much lower relative hyperchromicity change (∼ 5%) was observed. This transition was attributed to the melting of a new molecular species, e.g., the triplex formed between the duplex and single-strand DNA molecules. In the case of the dumbbell/single-strand mixture, these melting transitions of the triplex and the dumbbell were entirely resolvable. In contrast, the melting transitions of the linear duplex and the triplex overlapped, thereby preventing their clear distinction. To analyze the data, a three-state equilibrium model is presented. The analysis utilizes differences in relative absorbance vs temperature curves of dumbbells (or linear molecules) alone and in mixtures with the third strand. From the model analysis a straightforward derivation of fT(T), the fraction of triplex as a function of temperature, was obtained. Analysis of fT vs temperature curves, in effect melting curves of the triplexes, provided evaluation of thermodynamic parameters of the melting transition. For the triplex formed with the dumbbell substrate, the total transition enthalpy is ΔHT = 118.4 ± 12.8 kcal/mol (7.4 ± 0.8 kcal/mol per triplet unit) and the total transition entropy is ΔST = 344 ± 36.8 cal/K · mol (eu) (21.5 ± 2.3 eu per triple unit). The transition curves of the triplex formed with the linear duplex substrate displayed two distinct regions. A broad pretransition region from fT = 0 to 0.55 and a higher, sharper transition above fT = 0.55. The transition parameters derived from the lower temperature region of the curve are ΔH′T = 44.8 ± 9.6 kcal/mol and ΔS′T = 112 ± 33.6 eu (or ΔH′ = 2.8 ± 0.6 kcal/mol and ΔS′ = 7.0 ± 2.1 eu per triplet). These values are probably too small to correspond to actual melting of the triplex but instead likely reveal effects of end fraying of the duplex substrate on triplex stability. Transition parameters of the upper transition are ΔH′T = 128.0 ± 2.3 kcal/mol and ΔS′T = 379.2 ± 6.4 eu (ΔH′ = 8.0 ± 0.2 kcal/mol and ΔS′ = 23.7 ± 0.4 eu per triplet) in good agreement (within experimental error) with the transition parameters of the triplex formed with the dumbbell substrate. Supposing this upper transition reflects actual dissociation of the third strand from the linear duplex substrate this triplex is comparable in thermodynamic stability to the triplex formed with a dumbbell substrate. Even so, the biphasic melting character of the linear triplex obscures the whole analysis, casting doubt on its absolute reliability. Apparently triplexes formed with a dumbbell substrate offer technical advantages over triplexes formed from linear or hairpin duplex substrates for studies of DNA triplex stability. © 1993 John Wiley & Sons, Inc.

Notes: In this paper, we explore the possibility of using experimental observations in the Monte Carlo chain growth method that we have previously developed. In this method, the macromolecule (peptide, protein, nucleic acid, etc.) is grown atom-by-atom (or residue-by-residue, etc.) and partial chains are replicated according to their Boltzmann weights. Once the molecule completed, we are left with a Boltzmann-distributed ensemble of configurations. For long molecules, an efficient sampling of the (extremely large) phase space is difficult for obvious reasons (existence of many local minima, limited computer memory, etc.). In the case in which one is mainly interested in the low energy conformations, we have incorporated in the growth scheme experimental observations taken from the Protein Data Banks. More precisely, we have considered the case of twenty-L-alanine and we have used the (experimental) Ramachandran's plot for this residue. The biased growth procedure goes as follows: (a) each time one adds along the main backbone chain, either a carbon atom belonging to a carbonyl group, or a nitrogen atom, its dihedral angle (φ) or (ψ) is drawn with a probability law that reflects the experimental Ramachandran (φ,ψ) plot; (b) the bias introduced in this way is canceled through an extra term in the energy (replication energy = true energy + bias energy); (c) the configurations, generated at T = 1000 K, are then energy minimized. We have worked with an all-atom CHARMM force field, and Ramachandran's plot for the alanine was modeled through three angular zones (α-helix, β-sheet, coil). In our calculations, the probabilities of the α (pα) and β (pβ) regions have been varied in large proportions (pα between 0.64 and 0.19, the “experimental” value being 0.59). The results, based on 35 “unbiased” and 25 “biased” (or “guided”) distinct minimized configurations clearly demonstrate the efficiency of the method. The low energy configurations, for all tested values of pα, have a total (or almost total) a helix content. The unbiased configurations have much higher energies (in general, even higher than the left-handed helix). Note that the method is not “α helix in-α helix out,” since working at T = 300 K with the experimental (pα = 0.59) value yields configurations partially frozen in a Ced7 alanine dipeptide type of local minima. © 1993 John Wiley & Sons, Inc.

Notes: The benzyl-protected glycosyl acetates 1, 6, 11, and 15 react with MeOPPh2 under catalysis by TMSOTf to yield diastereoselectively the glycosylphosphine oxides 2, 3, 8, 12, 13, and 16, with a strong preference for the 1,2-cis-configurated anomers. Hydrogenolysis of the major products gave the crystalline, unprotected phosphine oxides 4, 9, 14, and 17, of which 4 was transformed in to the acetate 5, and 9 into the benzoate 10. The benzylated phosphine oxides 4, 8, 12, and 16 were reduced with Cl3SiH in the presence of a tertiary amine to form the phosphines 18, 21, 24, and 26, which were transformed into the phosphine sulfides 19, 22, 25, and 27. Moreover, 18 and 21, were characterized as the borane adducts 20, and 23. The structure of the (arabinofuranosyl)phosphine oxide 12, the corresponding sulfide 25, and of the borane complex 20 were established by X-ray analysis. According to NMR spectroscopy, the equatorial pyranosylphosphine oxide 8, the sulfide 22, and the borane complex 23 adopt a 4C1 conformation. The axial phosphine oxide 2 is a flattened 4C1, the sulfide 19 exists as a B2,5, and the borane complex 20 is a flattened 4C1 in the solid sate and a B2,5 in solution. Thus, the conformational behavior of these α-D-glucopyranose derivatives reflects the steric requirement of the P-substituents.

Notes: High-yield chemical syntheses of phosphoramidite building blocks of the four arabinonucleosides aUrd (1), aCyd (2), aAdo (3), and aGuo (4), suitable for (3′-5′)oligoarabinonucleotide synthesis are described. The problem of 2′-hydroxy group protection was solved by introduction of the versatile 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) residue, which was also used for aglycon protection.