Library

Notes: In this study, we have separated the contributions of DNA and protein to the absorption and linear dichroism (LD) of each of four phages: fd, IKe, Pf1, and Pf3. We have found that the DNA packaged in each of the phages is hypochromic relative to the purified single stranded DNA, suggesting that bases are stacked in all of the phages. We have oriented the phages by flow and for the first time report the intrinsic LD from 320 to 190 nm for each of these phages. From the intrinsic LD of the phages and the isotropic absorption of the individual components, we have determined the reduced dichroism of the DNA within the phages and, subsequently, the maximum angle of inclination of the DNA bases (from the helix axis) for the packaged DNA. The maximum angles were 63° and 64° for the DNAs of class I phages fd and IKe, respectively. The angles were significantly less, 51° and 49°, for the DNAs of the class II phages Pf1 and Pf3, respectively. Thus, the two classes of phage differ in the structures of their packaged DNA, the DNA bases of the class II phages being more parallel to the long axis of the phage than are the DNA bases of the class I phages.

Notes: The interaction between poly(9-vinyladenine) (PVAd) and poly[r (U)] was investigated by means of uv, CD, 1H-, and 31P-nmr spectroscopies. The interaction was dependent on the molecular weight of PVAd determined by uv and CD spectroscopies. Based on imino proton nmr, it was clearly found that PVAd formed the complex with poly [r(U)] by complementary hydrogen bonding. The interaction of PVAd with double- and triple-stranded helices of RNA was also investigated by uv melting behavior and 31P-nmr spectroscopy. The results suggested that PVAd could not interact with the double-stranded poly [r (A)] · poly[r(U)] but did with the triple-stranded RNA.

Notes: Optical melting curves of seven DNA dumbbells with the 16 base-pair duplex sequence 5′G-C-A-T-A-G-A-T-G-A-G-A-A-T-G-C3′ linked on both ends by Tn (n = 2, 3, 4, 6, 8, 10, and 14) loops measured in 30, 70, and 120 mM Na+ are analyzed in terms of the numerically exact statistical thermodynamic model of DNA melting. The construction and characterization of these molecules were described in the previous paper (Amaratunga et al., 1992). As was recently reported for hairpins (T. M. Paner, M. Amaratunga, M. J. Doktycz, and A. S. Benight, 1990, Biopolymers, Vol. 29, pp. 1715-1734) theoretically calculated melting curves were fitted to experimental curves by simultaneously adjusting the parameters representing loop and circle formation to optimize the fits. The systematically determined empirical parameters provide evaluations of the free energies of hairpin loop formation ΔGloop(n) and single-strand circles ΔGcircle(N), as a function of end loop size, n = 2-14, and circle size, N = 32 + 2n. The dependence of these quantities on solvent ionic strength over the range from 30 to 120 mM Na+ was evaluated. An approximately analytical expression for the partition function Q(T) of the dumbbells was formulated that allowed a means for determining the transition enthalpy ΔH° and entropy ΔS° for every dumbbell, revealing the dependence of these quantities on loop size. In this multistate approach a manifold of partially melted intermediate microstates are considered and therefore no assumptions regarding the nature of the melting transitions (that they are two-state) are required. The transition thermodynamic parameters were also determined from a van't Hoff analysis of the melting curves. Comparisons between the results of the multistate analysis and the two-state van't Hoff analysis revealed significant differences for the dumbbells with larger end loops, indicating that the melting transitions of the larger looped dumbbells deviate considerably from two-state behavior. Results are then compared with published melting studies of much larger DNA dumbbells (D. B. Naritsin and Y. L. Lyubchenko, 1990, Journal of Biomolecular Structure and Dynamics, Vol. 8, pp. 1-13), of small hairpins (Paner et al., 1990; M. J. Doktycz, T. M. Paner, M. Amaratunga and A. S. Benight, 1990, Biopolymers, Vol. 30, pp. 829-845) and another dumbbell (A. S. Benight, J. M. Schurr, P. F. Flynn, B. R. Reid, and D. E. Wemmer, 1988) Journal of Molecular Biology, Vol. 200, (pp. 377-399). ΔGloop (n = 4) and ΔGcircle (40) were also evaluated from analysis of the melting curves of the 15 DNA dumbbells with 16 base-pair stems presented in the first paper (Doktycz et al., 1992). With the exception of the dumbbell with the central sequence 5′-T-T-A-A-3′, these quantities were found to be virtually independent of the sequence identity of the central 4 base pairs of the stem.

Notes: Elongational flow techniques are used to investigate the birefringent response and flow-induced molecular scission of monodisperse phage-DNA samples in aqueous solution. A 4-roll mill apparatus was used to characterize the solutions ac low stain rates, \documentclass{article}\pagestyle{empty}\begin{document}$ \dot \varepsilon $\end{document} ≤ 300 s-1, and the opposed jets apparatus used to study fracture of the DNA molecules at strain rates up to 15 × 103 S-1. The molecular weight values were measured before and after fracture in elongational flow using the high-resolution technique of pulsed field gel electrophoresis (PFGE). The birefringent response incorporates both rigid and flexible components. The birefringence is nonlocalized and rises gradually to a plateau value, similar to rigid-rod behavior. In addition a certain minimum value in the strain rate is necessary, an onset value \documentclass{article}\pagestyle{empty}\begin{document}$ \dot \varepsilon $\end{document}0, before the signal appears, indicating a flexible component. This behavior is consistent with a hinged-rod model and is similar to that observed for the protein collagen molecule at elevated temperature. We propose that this type of behavior is likely for multistrand rope-like macromolecules where localized separation or partial untwisting of the intertwined chains occurs, creating temporary hinges, in accordance with biochemical evidence for sequence-specific sites of flexibility. Results are presented on the entanglement effects at high concentrations. We have calculated rotational diffusion rates as a function of concentration and molecular weight. Using PFGE to measure the molecular weight profiles, our fracture studies at high strain rates demonstrate chain halving and quartering in accordance with the predictions of the thermally activated barrier to scission theory for single-chain polymers.

Notes: To optimize antigen-antibody reactions, we have synthesized chemically well-defined hy-drophilic microspheres. Proteins or haptens were covalently linked to these carriers. When the microsphere conjugates were agglutinated by the corresponding antiserum, the size of the complex artificially increased during the immunological reaction. After optimizing var-ious parameters such as the hydrophilic character, repulsion charges, and amount of antigen coupled to the microspheres, we developed a rapid and sensitive immunoassay based on laser light scattering by the complexes.

Notes: Discontinuous volume changes in polymer gels carrying negatively ionized groups were studied by varying the molarities of univalent and bivalent cations in the bathing solution. These studies offer a sound basis for elucidating the origin of rapid swelling and heat production in nerve fibers associated with the process of excitation.

Notes: Twelve dinucleotides (one complete turn) of left-handed, flexible, double-helix poly(dG- dC) Z-DNA have been simulated in aqueous solution with K+ counterions for 70 ps. Most of the d(GpC) phosphates have rotated in accordance with a ZI → ZII transition. The ZII conformation was probably partly stabilized by counterions, which coordinate one of the anionic oxygens and the guanine-N7 of the next (5′ → 3′ direction) base. The presence of base-coordinating ions close to the helical axis rotated and pulled about half of the d (CpG) phosphates further into the groove. These ions also gave rise to rather large deviations from the crystal structure (ZI) with their tendency of pulling the bases closer toward the helical axis. A flipping of the orientation about the glycosyl bond from the +sc to the -sc region was observed for one guanosine, also leading to deviations from the crystal structure. Many bridges containing one or two water molecules were found, with a dominance for the latter. They essentially formed a network of intra- and interstrand bridges between anionic and esterified phosphate oxygens. A “spine” of water molecules could be distinguished as a dark zig-zag pattern in the water density map. The lifetime of a bridge containing one water was about twice as long as that of a two-water bridge and it lasted 5-15 times longer than a hydrogen bond in water. The lifetimes were also calculated for a selection of bridge types, in order of decreasing stability: O1P/O2P… W…O′4 ≫ O1P/O2P… W… guanine-N2 〉 O1P/O2P… W…O1P/O2P. The reorientational motion of water molecules in the first hydration shell around selected groups was slowed down considerably compared to bulk water and the decreasing order of correlation times was guanine-N2 〉 O′4 〉 O′3/ O′5 〉 O1P/O2P. © 1992 John Wiley & Sons, Inc.

Notes: High-resolution proton spectra at 620 MHz of human angiotensin II (1-8), angiotensin II (1-7), and angiotensin II (1-6) have been obtained in aqueous solution at acidic pH, and in dimethylsulfoxide solution. Complete chemical shift assignments for all three angiotensin peptides were made based on two-dimensional (2D) correlated spectroscopy and 2D-CA-MELSPIN spectra. Based on the measured values of 3J HNCH, the pattern of observed transverse Overhauser effects, and side-chain coupling constants, it is concluded that all three analogues exist in H2O or DMSO-d6 as a mixture of conformers that is largely extended, with negligible content of folded structures, such as β-turns, γ-turns, or helix content. The results fit well with those of Nikiforovich et al.1, 2. © 1992 John Wiley & Sons, Inc.

Notes: Scaled quantum mechanical force fields have been calculated using the 4-31G basis for trans and cis conformers of both isolated and water-solvated N-methylacetamide (NMA). (1) A single set of scale factors for isolated NMA yields relatively correct predictions of the shifts in vibrational frequencies between the trans and cis conformers. This is also true of a single set of scale factors for trans and cis NMA in water. The total standard deviation between measured and calculated frequencies for trans NMA in both isolated and solvated states is 6 cm-1. This implies that it should be possible to use a single set of scale factors to accurately predict the vibrational spectra of a peptide in a variety of conformational states. (2) The computationally predicted effect of hydration on force constants for the supermolecule NMA · nH2O are generally consistent with the experimentally measured effects of hydration on scale factors. These results indicate that supermolecule calculations can be useful in predicting the effects of hydration on spectra. (3) Three types of scale factors are calculated as follows: (a) first from ab initio calculations on an isolated molecule using frequencies measured from isolated molecules; (b) second from calculations on an isolated molecule using frequencies measured from water-solvated or otherwise hydrogen-bonded molecules; (c) and third from supermolecule calculations on a molecule hydrogen-bonded to water, using frequencies measured from water-solvated molecules. (4) The third type of scale factors are similar to the first type, for confidently measured modes, even though some of the force constants are very different. This suggests that one set of scale factors may be transferable to both isolated and hydrogen-bonded molecules, and that the simple representation of hydration used here may be a useful approximation. The second type of scale factors yield accurate frequencies, but they may not be generally transferable.

Notes: Normal mode calculations have been done on a range of disulfide bridge conformations in order to determine how the SS stretch and CS stretch frequencies depend on structure. In addition to varying the CαCβSS and NCαCβS dihedral angles, we have varied the φ,Ψ of the adjoining peptide groups since we have shown that these also influence the above frequencies. In order to obtain structural information from the observed frequencies, we have done a study of the conformational states found in 92 disulfide bridges in 25 known protein structures. This permits making a statistically based correlation between CS stretch frequencies and the possible contributing conformers. © 1992 John Wiley & Sons, Inc.

Notes: The peptide YKGTMDSG (Tyr-Lys-Gly-Thr-Met-Asp-Ser-Gly) represents an important antigenic determinant from the glycoprotein G2 of the pathogenic Rift Valley fever virus. By preparing a series of single-residue substitution peptides, the importance to antigenicity of individual residues within this octapeptide has been determined. Here, we investigated a simple and rapid computational analysis to test for correlations between the observed antigenicity of the substitution analogue peptides and the calculated conformational preferences in local regions of the peptides. Conformational energy analyses were carried out on all dipeptide combinations represented in the wild-type octapeptide and in the singleresidue substitution analogue peptides. Conformational similarities and differences between wild-type and substitution dipeptide pairs were determined. The results of these computational analyses were then compared with the data on the relative antigenicity of the wild-type octapeptide and the substitution analogues. This comparison revealed a positive correlation. Substitution peptides showing changes in antigenicity possessed significant changes in the calculated backbone conformation relative to wild type in the dipeptides encompassing the residue substitution. Substitution peptides showing no change in antigenicity similarly showed no significant changes in dipeptide conformation. The potential utility of dipeptide conformational energy analyses and this preliminary structure-activity correlation are discussed. © 1992 John Wiley & Sons, Inc.

Notes: Fourier transform ir study on enzymatically isolated tomato fruit cuticle has been performed. Assignments of the observed frequencies to functional groups present in the cuticular membrane yield information on the polyester cross-links and the interactions among the different components that form this plant protective barrier. © 1992 John Wiley & Sons, Inc.

Notes: We have used a combined chemical-enzymatic approach to facilitate the total synthesis of the 20-residue peptaibol, alamethicin. The 1-11 segment of alamethicin, having a C-terminal Gly, and the 12-20 segment, having an N-terminal Leu, were prepared by well-established chemical methods, and then coupled using papain to afford a 54% yield of alamethicin in straightforward fashion. In contrast to the reported chemical syntheses of alamethicin requiring side-chain protection at Glu, 18 the papain-catalyzed coupling proceeded readily and selectively using a C-terminal segment having a free γ-carboxyl group at this position. Several alamethicin partial sequences were obtained via enzymatic formation of the Gly 11-Leu12 bond. The high efficiency of this route is illustrated by the enzymatic assembly of the 1-17 alamethicin fragment on a 400-mg scale in 62% yield. An alternative route to alamethicin through enzymatic formation of the Ala6-Gln7 bond was less successful because of a low yield in the final coupling. © 1992 John Wiley & Sons, Inc.

Notes: The problems concerning quantification with cross polarization (CP) and high-field 13C-nmr measurements has meant that, for ligno-cellulosic plant materials, aromatic carbons in lignins are often discriminated against. In this study, the aromatic lignin content of an American red oak sample has been determined at the relatively low field strength of 25 MHz to obviate problems with spinning side bands using both CP and Bloch decay or single pulse excitation (SPE), a more time-consuming acquisition technique but that is, in many cases, considerably more quantitative than CP. The value of 14 mole % carbon from SPE is in close agreement with that of 15% derived from elemental analysis and the Klason lignin content. Although virtually all of the carbon was observed by both SPE and CP, the latter significantly underestimated the aromatic content at contact times less than 1.5 ms and thus longer times should be used for reliable quantification. The quaternary carbon content was estimated as 11 mole % carbon by combining dipolar dephasing with SPE and CP. © 1992 John Wiley & Sons, Inc.

Notes: A systematic theoretical study of the CD of [poly(dA-dT)]2 and its complexes with achiral small molecules is presented. The CD spectra of [poly(dA-dT)]2 and of poly(dA):poly(dT) are calculated for various DNA structures using the matrix method. The calculated and experimental spectra agree reasonably well for [poly(dA-dT)]2 but less well for poly (dA):poly (dT). The calculated CD spectrum of [poly (dA-dT)]2 fails to reproduce the wavelength region of 205-245 nm of the experimental spectrum. This discrepancy can be explained by a magnetic dipole allowed transition contributing significantly to the CD spectrum in this region. The induced CD of a transition moment of a molecule bound to [poly (dA-dT)]2 is also calculated. As was the case for [poly(dG-dC)]2, the induced CD of a groove bound molecule is one order of magnitude stronger than that of an intercalated molecule. The calculations also show considerable differences between pyrimidine-purine sites and purine-pyrimidine sites. Both signs and magnitudes of the CD induced into ligands bound in the minor groove agree with experimental observations. © 1992 John Wiley & Sons, Inc.

Notes: Relative hydrophobicities of aromatic amino acid residues are investigated by using differential scanning calorimetry (DSC) on 10 synthetic copolypentapeptides of poly(VPGVG) of elastin. Utilizing the hydrophobic-driven process of the inverse temperature transition exhibited by these polypentapeptides in aqueous solution, the relative hydrophobicities of Phe, Trp, and Tyr residues are determined by the critical temperature and heat of the transition. The DSC data for the aromatic residue containing copolypentapeptide aqueous solution indicate that tryptophan is the most hydrophobic amino acid residue, phenylalanine the third most hydrophobic on basis of transition temperature and the second on basis of transition heat. For tyrosine, significant differences are observed between the phenolic and the phenoxide anionic states. At pH 7, where tyrosine is protonated, it is found to be the second most hydrophobic amino acid residue on the basis of the transition temperature, whereas on the basis of the heat of transition, it is loss hydrophobic than both tryptophan and phenylalanine. Changing the pH from pH 7 to pH 12, for example, for poly[0.8(VPGVG), 0.2(VPGYG)] in aqueous solution shifts the transition temperature from 7 to 49°C with a dramatically reduced heat. On the basis of both the transition temperature scale and the heat of transition, the hydroxylated tyrosine appears less hydrophobic than glycine. © 1992 John Wiley & Sons, Inc.

Notes: Six cyclic peptides, designed to act as topological templates in the TASP (template assembled synthetic protein) approach in protein de novo design, were investigated employing a 100-ps, 900-K molecular dynamics conformational search. The peptides are composed of two Lys-X-Lys (X = Gly, Ala) tripeptides connected at its N- and C-terminal end by a Pro-Gly motif and a cystine bridge (I), two Pro-Gly units (II), naphthalene derivatives (III), and tetrahydronaphthalene derivatives of different stereochemistry (IV-VI). The molecular dynamics conformational search established that template I had β-sheet like geometry. Templates II-VI showed different preferential geometries, among them, e.g., distinct preferences for type V turns in Pro-Gly containing peptides and close spatial arrangement of hydrophobic naphthalene moieties. The orientation of the lysine side chains within preferential geometries of the individual templates is analyzed and a tentative evaluation for their potential to stabilize TASP molecules of 4-helix bundle topology is given. © 1992 John Wiley & Sons, Inc.

Notes: The temperature dependencies of line shapes and spin lattice relaxation times Tl have been measured for 25Mg in dilute solutions of Na-DNA/NaCl containing varying amounts of added magnesium(II) ions. The 25Mg spectrum is clearly non-Lorentzian, due to the presence of motions modulating the quadrupolar interaction that are slow compared to the inverse of the Larmor frequency. The weakly temperature dependent line shapes and relaxation rates appear to be influenced by the relatively slow exchange of the Mg2+ ions between the DNA surface and the aqueous bulk phase. The observed temperature dependencies depend on the ratio of total magnesium to DNA phosphate, Mg/P. The line shape as well as the temperature dependence of the line width at half height can be qualitatively reproduced with a two-site discrete exchange model for the quadrupolar relaxation of a spin \documentclass{article}\pagestyle{empty}\begin{document}$ \frac{5}{2} $\end{document} nucleus in isotropic solution. The calculations give a value of the lifetime for magnesium bound to DNA of 4 ms at room temperature. Previously reported temperature dependent 43Ca relaxation measurements in DNA solution can be reproduced under the assumption of a mean lifetime of bound calcium that is not, larger than 2 ms but not smaller than 50 μs at room temperature. The temperature variation of T1 for 25Mg has been calculated, giving some qualitative agreement with the data. The correlation time for bound 25Mg has been found to be about 40 ns at room temperature. © 1992 John Wiley & Sons, Inc.

Notes: This paper presents a general method for studying the harmonic dynamics of large biomolecules and molecular complexes. The performance and accuracy of the method applied to a number of molecules are also reported. The basic approach of the method is to divide a macromolecule into a number of smaller components. The local normal modes of the components are first calculated by treating individual components and the interactions between nearest neighboring components. The physical displacements of all atoms are then represented in the local normal mode space, in which a selected range of high-frequency local modes is neglected. The equation of motion of the molecule in the local normal mode space will then have a smaller dimension, and consequently the normal modes of the whole structure, particularly for large molecules, can be solved much more easily. The normal modes of two polypeptides-(Ala)6 and (Ala)12-and a double-helical DNA- d(ATATA) · d(TATAT)-are analyzed with this method. Reductions on the dimensions of harmonic dynamic equations for these molecules have been made, with the fraction of the deleted high-frequency modes ranging from ½ to ⅚. The calculated low-frequency normal modes are found to be very accurate as compared to the exact solutions by standard procedure. The major advantage of the present approach on macromolecule harmonic dynamics is that the reduction on the dimensionality of the eigenvalue problems can be varied according to the size of molecules, so the method can be easily applied to large macromolecules with controlled accuracy. © 1992 John Wiley & Sons, Inc.

Notes: Thermostable, heterocyclic polyesters containing imide and phenylquinoxaline units have been synthesized by solution polycondensation of bis(hydroxyphenylquinoxaline) derivatives with diacid dichlorides containing preformed imide rings or by the reaction of bis(aminophenylquinoxaline) derivatives with dianhydrides containing ester groups. The thermal stability of these compounds is discussed and compared with related heterocyclic polymers. Electrical properties of the polycondensates were also studied.

Notes: The ageing of polyolefins is accelerated by carbon black Chezacarb EC used as a filler. Conditions for selection of suitable chain-breaking antioxidants protecting against degradation were simulated using cyclohexene doped with various amounts of carbon black and oxidized at 60°C. The results obtained reveal an acceleration of cyclohexene oxidation in the phase following the induction period (IP). The oxidation acceleration is similar to the effect caused by powdered copper(0) or copper(II) ions. Polynuclear phenolic antioxidants are able to stabilize cyclohexene for periods longer than 120 h only in the presence of low amounts of Chezacarb (up to 0.5 wt.-%). At higher Chezacarb concentrations, merely a prolongation of IP may be achieved. Arylene diamines are efficient stabilizers only if combined with a high concentration of Chezacarb (10 wt.-%). None of the chain-breaking antioxidants used was able to diminish the oxidation rate of cyclohexene in the phase after IP.

Notes: Poly(oxysilane imide)s were prepared via Diels-Alder (DA) intermolecular polymerization of bis(2-furylmethyloxy)-dimethyl silane (1) with different bis(maleimido)-compounds (2a-h). The DA reaction was carried out in tetrahydrofuran as solvent as well as in bulk followed by dehydration (aromatization) of poly(tetrahydrophthalimido)-intermidiates (3a-h) in the presence of acetic anhydride. All poly(oxysilane imide)s (4a-h) were characterized by elemental analyses, IR spectral studies, and thermogravimetry. 1 and 2 were polymerized (at 130 ± 10°C) by in-situ Diels-Alder intermolecular reaction into poly(oxysilane imide)s-glass fibre composites (i.e. laminates) without evolution of by-products. The prepared composites were characterized by chemical resistivity and mechanical properties.

Notes: Photoinitiated surface grafting of acrylic monomers has been carried out onto high strength polyethylene (HSPE) yarn by means of a continuous process. The grafting reaction is initiated by UV irradiation of the yarn after presoaking in an acetone solution of initiator and monomer. Four initiators, benzophenone (BP), 4-chlorobenzophenone (4-CBP), 2-hydroxy-2-cyclohexylacetophenone (HHA), and 2,2-dimethoxy-2-phenylacetophenone (DMPA), and two monomers, acrylic acid (AA) and acrylamide (AM), have been used. After short irradiation time (10 to 20 s) successful grafting is obtained, as shown by ESCA and IR-ATR spectra, dye adsorpotion from aqueous solution, and measurements of adhesion of single filaments to epoxy resin. Grafting efficiency of 74% has been reached for AA as monomer (26% is homopolymer). The tensile strength and modulus of the HSPE yarn are retained in the grafting process. The degree of surface grafting is mainly a function of structure and concentration of monomer and photoinitiator in the presoaking solution and of the irradiation conditions used. Increasing irradiation time gives increasing amounts of grafted polymer up to a certain limiting value. The reactivities of the four initiators have been compared showing the highest grafting yields of AA with BP and of AM with 4-CBP as photoinitiator. AA grafted HSPE yarn can be dyed to rather deep color by dipping in an aqueous solution of Crystal Violet. Increased dye absorption by a factor of up to seven has been measured for yarn grafted with AA to the maximum level obtained. The filaments of the grafted yarn show increased adhesion to epoxy resin by a factor of up to five compared with the ungrafted filaments.

Notes: Es wird über die Herstellung und Charakterisierung von dünnen Filmen aus Poly(p-phenylen-1, 3,4-oxadiazolen) berichtet. Die aus H2SO4-Lösungen präparierten Filme besitzen eine gute optische Transparenz und sind mechanisch stabil. Filme aus Michungen mit Polyamiden zeigen ein ähnliches Verhalten und sind aufgrund ihrer thermischen Eigenschaften für spezielle Anwendungen interessant. Bei faserverstärkten Filmen zeigen erste Untersuchungen, daß spezielle Grenzflächenbereiche entstehen.

Notes: Some materials, suitable for application in polymer-surfactant flooding used in tertiary oil recovery (EOR), have been characterized by static and dynamic light scattering and studied in respect to their suitability in various model brines by measuring their rheological and dynamic-rheological behaviour. Xanthan and polyacrylamides of different degree of hydrolysis have been used as polymers, an ethylene glycol sulfonate as surfactant.Correlations have been established between microscopic structural parameters (Hydrodynamic radius, radius of gyration, molar mass, shape of the polymers) and the macroscopic behaviour, such as viscosity and elasticity, being important rheological parameters for EOR application. Additional investigations on surface tension and long term viscosity study lead then to a judgement for the efficiency and long term stability of polymer-surfactant slugs in various reservoirs of different salinity.

Notes: Die Verwendbarkeit der aus 2-Furaldehyd erhaltenen Halogentriole 2,3-Dichlor- und 2,3-Dibrom-1,4,7-heptantriol als reaktive Flammschutzmittel für PUR-Hartschäume wurde untersucht. Zur Modifikation der Schäume wurden diese Verbindungen allein und im synergistischen System mit Antimontrioxid verwendet.

Notes: Poly-α,β-D, L-aspartamides featuring carboxy-functionalized side groups are synthesized by three different preparative routes: (i) aminolytic ring opening in polysuccinimide, (ii) N-carboxymethylation of amine-functionalized polyaspartamides, and (iii) nucleophilic addition of iminodiacetic acid to acryloylamino-substituted poly-aspartamides. The polymeric products, possessing inherent viscosities in the wide range of 5-30 ml g-1, are characterized microanalytically and spectroscopically. By virtue of the carboxylic acid side groups lending themselves to the reversible covalent bonding of suitably structured drug models, the polymers are designed to function as macromolecular carriers of chemotherapeutically active agents. Being perfectly soluble in aqueous media over a wide pH range, they fulfill a crucial precondition for carrier components in (parenterally administered) polymer-drug conjugates.

Notes: Cellulose-g-poly(glycidyl methacrylate) copolymer was reacted with aqueous solutions containing mixtures of both sodium sulfite and citric acid, in order to synthesize bifunctional cation exchangers containing both sulfonic and carboxylic acid groups. Factors affecting the reaction, such as percent neutralization of citric acid with sodium carbonate, time, temperature, liquor ratio, reagents-to-epoxide molar ratio, and monosodium salt of citric acid-to-epoxide molar ratio were studied. Reaction conditions were selected to prepare five kinds of cation exchangers of different sulfonic and carboxy contents. These exchangers were characterized by potentiometric titrations, durability tests, and water solubility.

Notes: Polymerization of β,β′-(ethylenedithio)dipropionitrileIUPAC name: 4,7-dithiadecane dinitrile. with formaldehyde in the presence of sulfuric acid was carried out in order to permit the synthesis of polymides containing thioether groups. The obtained poly(amide thioether)s were characterized; they coordinate mercury (II) with a high degree of selectivity.

Notes: Redox polymerization of methylmethacrylate (MMA) using Ce(IV) with poly(oxyethylene) having azo and hydroxy functions was carried out to yield methylmethacrylate-ethylene glycol block copolymers with labile azo linkages in the main chain. These prepolymers were used to initiate the radical polymerization of styrene through the thermal decomposition of the azo group, resulting in the formation of multiblock copolymers. Successful blocking has been confirmed by fractional precipitation, a strong change in the molecular weight distribution and spectral measurements.

Notes: Photoinitiated surface grafting of acrylic acid (AA), acrylamide (AM) and 4-vinyl pyridine (VP) onto poly(ethylene terephthalate) (PET) fibers (a commercial textile yarn) has been studied using benzophenone (BP) as photoinitiator. A continuous process as previously described has been applied, which involves presoaking of the PET yarn in a solution of initiator and monomer in acetone and UV irradiation in nitrogen atmosphere. The resulting grafted polymer on the fiber surface has been analyzed by ESCA, titration of carboxy groups (grafted AA), and dye absorption. The relative ESCA intensities (RI) of O1s/C1s and N1s/C1s are used as measure for grafted AA, AM and VP, respectively, after recording the RI-values for ungrafted fibers. For grafting with AA, the RI-values increased from 32.8% (background) to 48.6% after 20 s irradiation time. The amount of carboxy groups measured by titration increased from 0.045 to 0.106 mmol/m2. Assuming an even coverage of grafted AA polymer, this means a grafted layer of 4.8 nm thickness. After grafting, the adsorption of the dye Crystal Violet (CV) from aqueous solution increased by about 3 times. With AM as monomer, the RI-values increased from 2.6 (background) to 14.8% and the adsorption of a direct dye Sirius Lichtbordo B-LL increased by about 6 times. With VP as grafted monomer, the RI-values increased from about 2.6 (background) to 5.1% and the adsorption of the direct dye increased by about 4 times.

Notes: The thermal degradation of poly(vinyl chloride) (PVC) has been studied by differential scanning calorimetry (DSC). Due to crosslinking, the glass transition temperature (Tg) of PVC raises during the degradation. The thermal degradation of PVC has also been studied for heterogeneous 1:1 (w/w) blends of PVC with polystyrene (PC), poly(styrene-co-acrylonitrile) (SAN), high-impact PS (poly(styrene-g-butadiene)) (HIPS) and poly(SAN-g-butadiene) (ABS). Tg of the PVC phase raises slower during degradation in the PVC/PS-blend, whereas in the other blends the crosslinking is accelerated, due to a negative influence of the double bonds and/or the nitrile groups on the thermal stability of PVC. Since most methods use the determination of eliminated HCl to study the degradation of PVC, the DSC method is very useful in investigations on PVC-containing polymer blends, if there might be a reaction of HCl with one of the blend components.

Notes: The effects of initiator concentration, ionic strength of polymerization medium, polymerization temperature, and monomer/water phase ratio on particle size, particle size distribution and molecular weight of the resulting polymers prepared by an emulsifier-free emulsion polymerization of styrene, methyl methacrylate and glycidyl methacrylate have been studied. Optimal conditions for preparation of uniformly sized polystyrene particles larger than 1 μm have been found. An attempt to synthesize monodisperse particles of similar size from methacrylate monomers and crosslinked particles has failed. It is shown that the swelling ability of “non-activated” latex particles does not exceed 70 fold increase in the volume and strongly depends on the size of the original particles.

Notes: Woven cotton and cotton/polyester blend fabrics of similar construction were treated with solutions of poly(ethylene glycol) (PEG, Mn of 600, 1000 and 1450 g/mol) containing tetrafunctional dimethyloldihydroxyethyleneureaSystematic name: 1,3-Bis(hydroxymethyl)-4,5-dihydroxyimidazoline-2-one. (DMDHEU) and a mixed acid catalyst. Subsequent curing of these fabrics under selected mild conditions produced fabrics containing bound and crosslinked polyols with several improved functional properties (thermal storage and release, flex and flat abrasion resistance, soil release and hydrophilicity). These functional property improvements are due to structural aspects of the crosslinked polyol. These structural aspects are high latent heat due to energy required to break intra- and intermolecular hydrogen bonds and the elastomeric and hydrophilic nature of the polymer in the fiber matrix. When the fabrics were cured under the mildest conditions, these enhanced functional properties were obtained without adversely affecting the softness or hand and the air permeability of these fabrics. Best results were obtained with the PEG-1000/DMDHEU solutions for an overall balance of improved fabric properties. Relative to untreated fabrics, treated 100% cotton fabrics had the most dramatic increase in their flex life, sometimes over an order of magnitude greater than before treatment and curing.

Notes: Es wurde die Copolymerissation von Butadien und Ethen in Gegenwart des katalysatorsystems Dineopetyloxyvanadiumoxychlorid/Aluminiumtriisobutyl untersucht. Die Variation der grundlegenden Reaktionsparameter [A1]/[V]-Verhältnis, Zusammensetzung der Monomermischug und Polymerisationstemperature ergab einen signifikanten Einfluß auf den Verlauf der Reaction, den Umsatz der Moomeren die, Molmasse und die Polydispersität der erhaltenen Copolymeren. NMR-Untersuchngen belegen einen hohen Alternierungsgrad.Bei der Variation des Verhaltnisses der Katalysatorkomponenten wurde ein Maximum für Umsatz und die Molmasse bei einem Verhältnis [A1]/[V] ≍ 7 ermittelt. Die Erhöhung des Ethengehaltes in der Moomermischung führt ebenfalls zu einer Erhöhung des Umsatzes. Dabei werden die Molmassen jedoch erniedrigt. Die Variation der Polymerisationstemparatur im Bereich von -25°C bis +40°C ergab für den Umsatz und die Molmasse Abhängigkeiten mit Minimum bzw. Maximum. Bei Polymerisationstemperaturen oberhalb +20°C ist ein Anwachsen der 1,2 -Addition des Butadiens und eine zunehmende Vernetzung der Produkte zu verzeichnen.

Notes: The viscoelastic response of plasticized PVC was determined from stress-relaxation data over a wide range of time at different temperatures. The relaxation modulus as a function of time was determined from these data. The relaxation curves were then shifted horizontally to obtain a master curve at a reference temperature. The amount of shift was evaluated using the WLF equation. The coefficients C10 and C20 used in the equation for the PVC were determined according to the method of reduced variables.

Notes: A fully saturated, alicyclic hydrocarbon resin (IST) was blended with isotactic polypropylene (iPP). IST is a random co-oligomer of low average molecular weight obtained by oligomerization of indene, α-methyl styrene and vinyl toluene, followed by hydrogenation.The crystallization and thermal behaviour of iPP/IST blends were analyzed by microscopy and differential scanning calorimetry (DSC). The influence of blend composition on the spherulite growth rate and on the overall crystallization rate suggests that the two components form a miscible blend in the amorphous phase, as confirmed by the following observations: All blends show a single glass transition temperature (Tg); its value, depending on composition, lies between the iPP and IST Tg values (-14°C and 82°C, respectively), and is in good agreement with the theoretical values calculated by the Fox equation. The equilibrium melting temperature calculated for pure iPP was equal to 187°C; this value decreases with blending to 175°C for the iPP/IST 50/50 (w/w) blend. The χ12 parameter of the iPP/IST system was equal to -0.435, the negative value should suggest that the two components can form a compatible mixture which is thermodynamically stable above the equilibrium melting temperature.

Notes: The film properties and ionic conductivity behavior of polyacrylonitrile (PAN) containing various metal salts were investigated. Further, with a newly developed process, it was possible to cover the surface of polymer with a metallic layer. From water contact angle measurements it was found that the surface structure of PAN containing metal salt was greatly affected by properties of the material in contact with during film preparation. Ionic conductivity behaviors near Tg differed between the PAN containing a metal chloride and that containing a metal perchlorate; the activation energy for the rubber-like state (∊r) was greater than that for the glassy state (∊g) with the former and ∊r 〈 ∊g with the latter. It was clarified that a metal layer was formed on the polymer surface at a relatively low temperature by a reduction treatment with NaBH4 aqueous solution.

Notes: The adsorption of 4-methylbiphenyl, sodium dodecylbenzenesulfonate (NaDBS), and phenol on a β-cyclodextrin epichlorohydrin network polymers at 25°C has been studied. The isotherm of 4-methylbiphenyl fits well with the Freundlich equation at a concentration range from 10-5 to 10-4 mol/l. The isotherms of NaDBS and phenol deviate from a straight line in the investigated concentration range.

Notes: Saturated aliphatic polyesters with 1.4:3.6-dianhydrosorbitol units were mixed with poly(vinylchloride) (PVC). The mechanical properties of these mixtures were examined by differential scanning calorimetry, stress-strain experiments, and torsion pendulum measurements. Polyesters containing more than four methylene groups in the acid component are compatible with PVC. These polyesters can serve as plasticizers for PVC. On the contrary, mixtures of PVC with poly(1.4:3.6-dianhydrosorbitol adipate) are incompatible; in this case, at any blend composition, the two glass transition temperatures of the pure components are observed.

Notes: Starch-g-polystyrene and starch-g-poly(methyl acrylate) copolymers were synthesized and extruded without separating homopolymer PS or PMA. The extrusion behavior resembled that of thermoplastic melts in that these products were shear thinning and exhibited significant extrudate swelling and entrance pressure losses in capillary flow. These and other observations indicate that the materials comprise deformable polymer-grafted starch particles suspended in the corresponding homopolymer melt. Flow is apparently by superparticle, rather than continuum melt mechanisms.

Notes: Bei der industriellen Herstellung von polymeren Werkstoffen ist eine möglichst genaue Kenntnis des spezifischen Volumens v in Abhängigkeit vom Druck p und von der Temperatur T erforderlich. Dafür ist ein sogenannter „Biegeschwinger“ entwickelt worden, mit dem man v im Bereich von 1 bis 800 bar und von 20 bis 200°C ermitteln kann. Dieses wird an Testmessungen mit destilliertem Wasser bewiesen. Am Beispiel von fünf flüssigen Polymeren und Copolymeren wird die Brauchbarkeit sowohl empirischer als auch theoretisch fundierter Zustandsgleichungen überprüft. Dabei zeigt sich, daß die rein empirische Tait-Gleichung und die zum Teil theoretisch fundierte Simha-Somcynsky-Gleichung mit sechs bzw. fünf anpasbaren Parametern die Meßwerte am besten beschreiben.

Notes: An approach for the calculation of the optimal monomer addition policies for polymer composition control in emulsion terpolymerization is presented. The model allows the calculation of the composition of the initial charge of the reactor and the time dependent monomer addition rates. Monomer addition strategies for reactors with limited capacity for heat removal were obtained. A heat removal rate dependent on the latex solids content was considered. Simulation showed that the present approach leads to the production of homogeneous terpolymers in process times which are significantly shorter than that required by the classical starved process to produce a terpolymer of similar homogeneity.

Notes: Ultra low density polyethylene (PE-ULD), the newest and most recently commercialized member of polyethylene family, has been characterized in terms of structure, thermal and rheological properties, and molecular parameters. Since the prime use of PE-ULD is polyolefin modifier, emphasis is put on the melt rheology of the samples to provide data base for blending with other resins.

Notes: The UV absorption characteristics of a number of dihydroxynaphthyl-2H-benzotriazoles, their (meth)acryloyloxy derivatives and the corresponding polymers have been studied in a range of solvents of different polarity. It was shown that the formation of hydrogen bonds in these compounds strongly depends on the polarity of the solvent and an equilibrium exists between intramolecular and intermolecular hydrogenbonded states. The stability of the intramolecular hydrogen bond was determined quantitatively. The equilibrium between the intramolecular and the intermolecular hydrogen-bonded state of the molecule was strongly affected by the chemical structure of the naphthyl-2H-benzotriazole. The stability of the intramolecular hydrogen bond increased when electron-donating substituents were introduced into the benzotriazole or when the naphthyl-2-benzotriazole was fixed to a polymer backbone.

Notes: Siliconcopolyester wurden als Copolymere oder als Mischung mit Phenyltrichlorsilan-Hydrolysat hergestellt und aus der Lijsung zu Folien geformt. Durch Messung der dynamischen Kontaktwinkelhysterese wurde die für eine Diffusion von Gasen bei der Gastrennung relevante Phasenverteilung an der Oberfläche dieser Membranen untersucht. Sowohl in Copolymeren als auch in Mischungen wird die Oberfläche durch in Domänen aggregiertes Siloxan bestimmt.

Notes: Polyamide-6 (PA6) and blends of poly(ethylene terephthalate) (PET) and poly(butylene terephthalate) (PBT) characterized by amorphous initial structure and improved mechanical properties are obtained by means of an ultraquenching technique. In the case of polyamide-6, erasure of the structural memory is achieved by melt annealing above the equilibrium melting point. This procedure is applied in order to restrict the crystallization process. After quenching, further orientation of the amorphous polymers and annealing with fixed ends lead to a significant improvement of the mechanical properties. The tensile strength and elasticity modulus increase three to five times and the elongation at break decreases by half as compared with conventionally obtained polyamide-6, PET and PBT.

Notes: Komplexbildner für Kupfer, die als Nachweisreagenzien in der Analytik und als Reagenzien für die Flüssig-Flussig-Extraktion interessant sind, wurden als Kupferdesaktivatoren in vernetztem Polyethylen niedriger Dichte (XLDPE) durch Bestimmung der Induktionszeiten der Sauerstoffaufnahme von XLDPE/Cu/XLDPE-Sandwichproben bei 165 °C getestet. Neben acylierten Hydrazinen, einer für wirksame Metalldesaktivierung bereits bekannten Stoffklasse, wurden mehrere Gruppen von Chelatkomplexbildnern untersucht, wobei sich vor allem die 2-(2-Hydroxyphenyl)imidazole als wirksame Kupferdesaktivatoren in XLDPE erweisen. 2-(2-Hydroxyphenyl)oxazol, -thiazol und -oxadiazol, denen bei sehr ühnlicher chemischer Struktur der bewegliche Wasserstoff am Fünfring fehlt, sind dagegen unwirksam.

Notes: Polymer blends were prepared in the whole composition range using polymers of different polarity. Mechanical properties were characterized by tensile measurements. Surface and interfacial properties were measured and calculated and parameters characterizing the miscibility were determined. A correlation was found between the yield stress and the thermodynamic quantities characterizing the degree of miscibility. Since both the degree of miscibility and morphology are influenced by the interfacial tension, it can be regarded as the best candidate to correlate polymer/polymer interaction and mechanical properties in polymer blends.

Notes: Phosphorylation of poly(N-vinyl pyrrolidone-co-vinyl amine) and poly(N-vinyl pyrrolidone-co-glycidylcrotonateSystematic name: (2,3-Epoxypropyl)crotonate.) is realized by Atherton-Todd and Fields-Kabachnik reactions and by the means of direct interaction with phosphorus trichloride and phosphorus trichloride oxide. The composition and structure of the isolated final products was proved by NMR (1H and 31P), IR spectroscopy and elemental analysis.

Notes: Bisphenol A novolacs were synthesized in a melting process using paraformaldehyde, and in a solution process using a formalin solution and oxalic acid catalyst. 1H-NMR investigations show a higher content of methylene bridges in the novolacs synthesized in a melting process. These novolacs were analysed by HPLC, GPC, DSC and FT-IR spectroscopy. The molecular masses were determined by vapour pressure osmometry. The results were shown to be related with the molar ratio of the components. The bisphenol A novolacs were used as curing agents for epoxy resins. There exists a dependence of the gel times on the content of methylene bridges; this dependence is influenced by temperature. The activation energy for gel formation is nearly the same in all curing reactions investigated. The networks synthesized were investigated by thermomechanical analysis.

Notes: The cationic dye auramine O forms a fluorescent complex with Ca2+-liganded calmodulin. One moderately strong binding site is present, as well as one or more weaker sites. The binding site for auramine O is different from those for toluidinyl-naphthalene sulfonate. The dependence of binding upon electrolyte concentration suggests a substantial electrostatic component of the free energy of binding. The splitting of the bond between residues 77 and 78 by trypsin digestion abolishes auramine O binding; the N- and C-terminal half-molecules have virtually no binding capacity. This suggests that the primary binding site is located near the midpoint of the connecting strand and includes elements of both half-molecules. Thrombin digestion, which splits calmodulin between residues 106 and 107, also substantially reduces auramine O binding; this may be interpreted in terms of the stabilization of the structure of the connecting strand by interaction with residues within binding domain IV. The binding affinity at pH 5.0, where the helical organization of the connecting strand may be intact, is greater than at neutral pH.

Notes: In order to investigate the conformational variation of ascidiacyclamide, a cytotoxic cyclic peptide from marine tunicate Ascidian, single crystals were prepared from ethanol and aqueous ethanol solutions as its free form (crystal I) and H2O/0.5 C2H5OH solvate (crystal II), respectively, and were determined by the x-ray diffraction method. Crystal I showed a pseudo C2-symmetric saddle-shaped rectangular conformation. Similar conformations were also observed in crystal II, where there were two crystallographically independent C2-symmetric molecules (named Mol-A and -B) per asymmetric unit. Mol-A and -B included H2O and H2O/C2H5OH solvents within their ring structures, respectively. These water and ethanol molecules were located on the crystallographic dyad axes, and were stabilized by the van der Waals contacts (including hydrogen bonds) with the polar-ring N atoms and nonpolar D-Val side-chain atoms. The conformational characteristics of ascidiacyclamide and its fluctuation/variation were discussed based on the present and previously reported x-ray results.

Notes: In our attempts to design crystalline α-helical peptides, we synthesized and crystallized GAI (C11H21N3O4) in two crystal forms, GAI1 and GAI2. Form 1 (GAI1) Gly-L-Ala-L-Ile (C11H21N3O4 · 3H2O) crystals are monoclinic, space group P21 with a = 8.171(2), b = 6.072(4), c = 16.443(4) Å, β = 101.24(2)°, V = 800 Å3, Dc = 1.300 g cm-3 and Z = 2, R = 0.081 for 482 reflections. Form 2 (GAI2) Gly-L-Ala-L-Ile (C11H21N3O4 · ½H2O) is triclinic, space group P1 with a = 5.830 (1), b = 8.832 (2), c = 15.008(2) Å, α = 102.88 (1), β = 101.16(2), γ = 70.72(2)°, V = 705 Å3, Z = 2, Dc = 1.264 g cm-3, R = 0.04 for 2582 reflections. GAI1 is isomorphous with GAV and forms a helix, whereas GAI2 does not. In GAI1, the tripeptide molecule is held in a near helical conformation by a water molecule that bridges the NH+3 and COO- groups, and acts as the fourth residue needed to complete the turn by forming two hydrogen bonds. Two other water molecules form intermolecular hydrogen bonds in stabilizing the helical structure so that the end result is a column of molecules that looks like an incipient a-helix. GAI2 imitates a cyclic peptide and traps a water molecule. The conformation angles χ11 and χ12 for the side chain are ( -63.7°, 171.1°) for the helical GAI1, and (-65.1°, 58.6°) and (-65.0°, 58.9°) for the two independent nonhelical molecules in GAI2; in GAI1, both the C, atoms point away from the helix, whereas in GAI2 the Cγ atom with the g+ conformation points inward to the helix and causes sterical interaction with atoms in the adjacent peptide plane. From these results, it is clear that the helix-forming tendencies of amino acids correlate with the restrictions of side-chain rotamer conformations. Both the peptide units in GAI1 are trans and show significant deviation from planarity [ω1 = -168(1)°; ω2 = -171(1)°] whereas both the peptide units in both the molecules A and B in GAI2 do not show significant deviation from planarity [ω1 = 179.3(3)°; ω2 = -179.3(3)° for molecule A and ω1 = 179.5(3)°; omega;2 = -179.4 (3) ° for molecule B], indicating that the peptide planes in these incipient α-helical peptides are considerably bent.

Notes: Helix formation in (Lys)n · HClO4 and poly(Nε, Nε, Nε-trimethyl-L-lysine) · HClO4 [(LysMe3)n · HClO4] is dependent on peptide concentration and on molecular weight. For (LysMe3)n · HClO4 of degree of polymerization (DP) 2510 the midpoint of the coil-to-helix transition is 2 mM and for DP of 190 it is 5 mM. For (Lys)n · HC1O4 the peptide concentration for half-helix is 30-60 times as high, and is only weakly dependent, if at all, on molecular weight. Helix formation is an intermolecular process. The use of methylated (Lys)n as the perchlorate permits study of the intermolecular coil-helix transition at low concentration, instead of the high concentration (ca. 1-2M) required for (Lys)n · HBr. At constant peptide concentration helix content increases with added NaClO4. The higher the peptide concentration, the less NaClO4 is needed to induce helix.

Notes: The ir amide bands of the triple-helical polytripeptides and collagens upon hydration of films are investigated. On the basis of our assignment of the amide I components, the formation of hydrogen bonds between the peptide backbone and structural water is studied. The C1O1 - HOH hydrogen bonds are found more ordered than the C3O3 - HOH hydrogen bonds. The specific incorporation of water in the triple helix is followed by multistep conformational changes and by increasing of the interpeptide hydrogen-bond strength. The formation of the polypeptide hydrate structure depending on the amino acid composition and the chain length is examined.

Notes: The amide II vibrational CD (VCD) spectra of poly(L-glutamic acid) and poly(L-lysine) in various conformational forms and those of several proteins in H2O have been measured. Characteristic VCD patterns have been observed in the amide II region due to helix, β-sheet, and coil conformations in polypeptides. Based on their x-ray crystal structures, the proteins studied have been assigned to six categories. Proteins in the same category give rise to similar amide II VCD. While the protein conformational type is indicated using the amide II VCD, discrimination between types is less characteristic than with the previously studied amide I' VCD in D2O.

Notes: Random copolymers of lysine and alanine, 2 : 1 and 1 : 1, were trimethylated on the lysine. amino groups to quaternary ammonium groups. Methylated and unmethylated polymers were prepared with Cl- or ClO4- as the counterion. CD spectra were measured for increasing concentration of peptide without added salt, and at constant peptide concentration in increasing NaCl or NaClO4. Unmethylated peptides, as the chloride, form α-helix more readily than do the methylated peptides. The opposite occurs with ClO4- as counterion. The helix-promoting effect of methylated lysine residues (ClO4- counterion) is diminished by the presence of alanine, as compared with effects when lysine is the only type of residue. The effect of methylation of proteins on helix formation may depend on the types of anionic groups with which the protein may be involved.

Notes: The rate constant for the transition between the equatorial and axial conformations of N-acetylalanyl-N′-methylamide has been determined from Langevin dynamics (LD) simulations with no explicit solvent. The isomerization rate is maximum at collision frequency γ = 2 ps-1, shows diffusive character for γ ≥ 10 ps-1, but does not approach zero even at γ = 0.01 ps-1. This behavior differs from that found for a one-dimensional bistable potential and indicates that both collisional energy transfer with solvent and vibrational energy transfer between internal modes are important in the dynamics of barrier crossing for this system. It is suggested that conformational searches of peptides be carried out using LD with a collision frequency that maximizes the isomerization rate (i.e., γ ≈ 2 ps-1). This method is expected to be more efficient than either molecular dynamics in vacuo (which corresponds to LD with γ = 0) or molecular dynamics in solvent (where dynamics is largely diffusive).

Notes: A computer program SAINT has been developed for the investigation of the structure and for the prediction of minimum-energy structure of polysaccharide-polysaccharide complexes. The energy minimization is carried out on internal geometrical parameters - namely bond angles, torsional angles, and five parameters describing the mutual orientations of polysaccharide chains. For this purpose, the nonderivative method of conjugated directions is used. This procedure was applied to computer modeling of an idealized model of the binary gelling κ-carrageenan and galactomannan system. It is shown that the interaction between two chains influences the structure of the individual polysaccharide molecule and that in the minimum-energy structures of the complex, the conformation of the chains does not correspond to the lowest energy.

Notes: Reversed-phase high performance liquid chromatography (RP HPLC) has been found to be a convenient and powerful tool for the study of the secondary structure of peptides. Here, the ability of proline to perturb the secondary structures of peptides induced at aqueous-lipid interfaces and the induced conformation of polyproline peptides were investigated by means of RP HPLC. For these studies, four different complete sets of substitution analogues of model peptides expected to have specific induced conformations were used. In the first two studies, a single lysine was “walked” through two 18-residue polyproline sequences (one N-acetylated, the other not). In the remaining two studies, a proline was “walked” through two different sequences that had been found earlier to be induced into an α-helical conformation during RP HPLC (an 18-residue polyalanine sequence and the amphipathic 14-residue sequence Ac-LLKLLKKLLKKLKK-NH2). Sixty-eight individual analogues were synthesized for this study and the effect of the respective substitutions on retention times was determined. The results are consistent with the concept that, upon interaction with the C-18 of the stationary phase during RP HPLC, polyproline is induced into a type II helical conformation, polyalanine into an α-helical conformation, and Ac-LLKLLKKLLKKLKK-NH2 into an amphipathic α-helical array. In an extension of this study, the antimicrobial activities of Ac-LLKLLKKLLKKLKK-NH2 and its 18 proline substitution analogues were found to be inversely correlated with their RP HPLC retention times.

Notes: To map out the heavy metal binding sites of iduronic acid containing oligosaccharides isolated from human kidneys, we studied Zn (II) binding by nuclear magnetic resonance (NMR) and molecular modeling to two disaccharides isolated after nitrous acid depolymerization of heparin and two synthetic disaccharides representative of the heparin structure, namely, IdopA2S(α1,4) AnManOH, 1a, IdopA2S(α1,4)AnManOH6S, 1b, IdopA2S-(α1,4) GlcNSαMe, 2a, and IdopA2S(α1,4)GlcNS6SαMe, 2b (see previous article in this series). A conformational analysis of the metal free and metal bound solutions was made by comparing calculated 〈(NOE)〉s, 〈T1〉s, and 〈J〉s to experimental values. The 1C4, 4C1, and 2S0 conformations of the L-idopyranosiduronate ring and the 4E and 4T3 of the anhydro-D-mannitol ring are evaluated as are rotations about the C5-C6 hydroxymethylene of the AnManOH (6S) or GlcNS(6S) residues. The NOE between IdopA2S H1 and H3 and the known NOE between H2 and H5, as well as the T1 of IdopA2S H3, are introduced as NMR observables sensitive to the IdopA2S ring conformation. Similarly, a NOE between IdopA2S H5 and AnManOH (6S) or GlcNS (6S) H3 was observed that directly restricts the allowed interglycosidic conformational space. For all disaccharides, the Zn(II) bound spectral data are consistent with models in which these motions are partially “frozen” such that the 1C4 conformation of the IdopA2S is stabilized along with the 4T3 conformation of the AnManOH (6S) ring. The interglycosidic conformation is also stabilized in one of two minima. Electrostatic potential energy calculations gave the best overall agreement with experiment and suggest metal binding conformations with the carboxylate and ring oxygen of the IdopA2S residues (1C4 conformation) and either O3 of the GlcNS (6S) residues or the sulfate oxygens of the 6-sulphate for 2b providing additional chelating sites. These chelation models concur with the observation of marked 13C and 1H NMR chemical shifts for the IdopA2S resonances and of GlcNS H3 for 2a and GlcNS6S C6 for 2b. This study of model compounds implicates the IdopA2S(α1,4) GlcNS6S group as part of the heavy metal binding site in biologically important acidic oligosaccharides such as heparin.

Notes: A qualitative picture of operation modes of biological molecular energy machines is presented. It is suggested that there is mutual control between the flow of molecular energy stored in a biological molecular energy machine and the sequence of nonequilibrium conformational states through which the machine passes in doing work. If the structure of the conformational space is favorable, the set of trajectories in this space decomposes into two families, each of which accomplishes another task. This divergence of trajectories enables to distinguish molecular objects according to differences in interaction between the machine and the object, i.e., to perform a measurement on a molecular object and process the object according to the result of that measurement.

Notes: A method was developed for computing the free energy (ΔFi) of aggregates of type I collagen. The method was based on a treatment of Matheson and Flory describing phase equilibria of rigid rod polymers. It included a polymer-solvent interaction term that depended on near neighbor transfer energies. Extrahelical portions of the molecule were assigned local interaction energies differing from that assigned to the helix. Free energies of reaction for successive steps along assembly pathways (ΔFi-i+1) were computed. When allowance was made for specific pairing between extrahelical and helical domains, the so-called D-staggered (D = 670 Å) alignment of molecules was preferred, as opposed to a nonstaggered, or nematic, alignment. Based on ΔFi-i+1 alone, it appeared that 1D-staggered oligomers arise first in assembly, followed later by addition of molecules in 4D alignment.Neither 4D dimers nor 4D-8D trimers were predicted to be major intermediates in assembly. This result is contrary to previous hypotheses. When energies of activation were included in the analysis, the prediction was less certain, and specific circumstances were identified in which 4D dimers and 4D-8D trimers were the earliest aggregated species in assembly.

Notes: The partial molar volumes of some amino acid side-chains were determined in two recent studies [Makhatadzes, G. I., et al. (1990) Biopolymers 30, 1001, and Reading, J. F. & Hedwig, G. R. (1990) J. Chem. Soc. Faraday Trans. 86, 3117] using partial molar volume data, V20, in aqueous solution at 25°C for some peptides of sequence Gly-X-Gly, where X is an amino acid. These side-chain partial molar volumes are critically compared with those obtained using V20 data for amino acids. It is concluded that side-chain partial molar volumes calculated using V20 data for the tripeptides are better estimates of side-chain partial molar volumes in proteins than are those determined using V20 data for amino acids.

Notes: A previously developed theory for the delocalized binding of ions to polyelectrolytes was restricted to point ions and a structurally rigid polyelectrolyte. For the binding of substances like oligolysines and polyamines to DNA, the restriction to point ions would appear not to be realistic. For the binding of ions to flexible chains like single-stranded polynucleotides, the restriction to a rigid polyelectrolyte may not be realistic. In this article, we assess the effect of relaxation of these two restrictions. Excluded volume among bound ions is modeled by a hard-rod potential in the context of the theory of a one-dimensional fluid. The possibility that a flexible chain folds in some manner in the immediate vicinity of a bound ion is modeled by allowing the mean spacing between charged groups on the polymer to become smaller as the number of bound ions increases. We compare our results with recent data on the binding of a series of oligolysines to single-stranded polynucleotides, which conflict with the predictions of the original theory of delocalized binding of point ions to rigid polyelectrolytes. Inclusion of excluded volume among bound ions does not significantly improve agreement with the data. Substantial improvement in the level of agreement is obtained when the polyion chain is assumed to be flexible. One of our conclusions is that the excluded-site description of anticooperativity, which was designed for the binding of ligands to discrete sites on a polymer chain, and which does not include the effect of ionic forces, should not be used in cases of delocalized binding of ions.

Notes: As model compounds for Ni(II)-binding heparin-like compounds isolated from human kidneys (Templeton, D. M. & Sarkar, B. (1985) Biochem. J. 230 35-42.), we investigated two disaccharides - 4-O-(2-O-sulfo-α-L-idopyranosyluronic acid)-2,5-anhydro-D-mannitol, disodium salt (1a), and 4-O-(2-O-sulfo-α-L-idopyranosyluronic acid)-6-O-sulfo-2,5-an-hydro-D-mannitol, trisodium salt (1b) - that were isolated from heparin after nitrous acid hydrolysis and reduction. The monosulfate (1a) was active whereas the disulfate (1b) was inactive in a high-performance liquid chromatography (HPLC) binding assay with the tracer ions 63Ni(II) 54Mn(II), 65Zn(II), and 109Cd(II). This result is in accord with the isolation of two 67Cu(II) and 63Ni(II) binding fractions from a complete pool of nitrous-acid-derived heparin disaccharides using sulfate gradients and a MonoQ anion exchange column on an FPLC system. One was identified as compound (1a) and the other as a tetrasulfated trisaccharide by high resolution FAB-MS, NMR and HPLC-PAD. Similarly, two synthetic disaccharides - methyl, 2-O-sulfo-4-O-(α-L-idopyranosyluronic acid)-2-deoxy-2-sulfamido-α-D-glucosamine, trisodium salt [IdopA2S(α1,4)GlcNSαMe,2a], and 2-O-sulfo-4-O- (α-L-idopyranosyluronic acid)-2-deoxy-2-sulfamide-6-O-sulfo-α-D-glucosamine, tetrasodium salt [IdopA2S(α1,4) GlcNS6SαMe,2b] - were shown to bind tracer amounts of 63Ni and 67Cu using chromatographic assays. Subsequently, 1H NMR titrations of 1a, 1b, 2a, and 2b with Zn(OAc)2 were analyzed to yield 1:1 Zn(II)-binding constants of 472 ± 59, 698 ± 120, 8,758 ± 2,237 and 20,100 ± 5,598M-1, respectively. The values for 2a and 2b suggest chelation. It is suggested that the idopyranosiduronic acid residue is the major metal binding site. NMR evidence for this hypothesis comes from marked 1H and 13C chemical shift changes to the iduronic acid resonances after addition of diamagnetic Zn(II) ions.

Notes: A new constraint potential is proposed for the refinement of the three-dimensional structure of biomolecules in solution from nmr data. It is based on the nuclear Overhauser effect (NOE) intensity calculations, taking into account the spin diffusion phenomenon. For restrained energy minimization or molecular dynamics techniques, a constraint potential term expressed as a function of the negative inverse of the sixth power of the NOE intensities (NOE-1/6) is added to the classical potential energy function. The properties of this new NOE constraint potential are discussed and compared to those of a harmonic NOE intensity potential.The method integrated in the molecular modeling program GROMOS is tested on the regular α-helical structure of a decaglycylpeptide.

Notes: Solute partitioning data for dilute solutions have almost invariably been interpreted by equating experimental values of -RT In Kx (wherein Kx is the mole fraction partition coefficient) to Δμ∞, the standard Gibbs energy change for solute transfer from one solvent to another. Recently, it has been alleged that this relation is insufficiently general. Instead, the statistical mechanical Flory-Huggins (FH) theory has been recommended for use, because it is designed to account for disparities in molecular size between solute and solvent. Our examination of the thermodynamics of partitioning shows that: (1) The customary interpretation is not only entirely correct (providing only that the solute is dilute), but is model-independent. (2) The dilute limit of the FH theory is seen to agree entirely with the usual interpretation of -RT In Kx, once certain misnomers are cleared away. (3) The use of FH theory being urged upon us in fact serves only to extract from Δμ∞; (the latter quite correctly determined as -RT In Kx) the contact part of Δμ∞ in order to obtain information on hydrophobic interactions. Some caveats are cited concerning such use of the FH statistical mechanical model.

Notes: We synthesized and solved the crystalline structure of the oligopeptide acetyl- (glycyl-β-alanyl)2-NH propyl. The crystal is formed by layers of helical molecules with the same chirality; however, right-handed layers alternate with left-handed ones. Inside every layer, the packing of helices is pseudohexagonal with hydrogen bonds between neighbor molecules. The structure found affords direct support for the model proposed by Crick and Rich for polyglycine II and also provides an interpretation for the structure of a newly found family of polyamides that do not form sheets as observed in most nylon structures.

Notes: IR vibrational CD (VCD) has been observed for the cyclic pentapeptide cyclo-(-Gly-Pro-Gly-D -Ala-Pro-) in solution in CDBr3. The observed VCD spectra do not resemble the VCD features of any of the previously reported peptide secondary structures, such as α-helical, “random coil,” or sheet structures, and might be due to the β-turn contained in this molecule. To shed light onto the origin of the observed spectra, VCD intensity calculations, based on the solution and solid-state structures of cyclo-(-Gly-Pro-Gly-D-Ala-Pro-), have been carried out. In addition, calculated VCD data for pure β-turns are discussed. © 1992 John Wiley & Sons, Inc.

Notes: The structures of the helices II-III region and the helix IV region of B. megaterium 5S rRNA have been examined by means of energy minimization and molecular dynamics calculations. Calculated distances between neighboring hydrogen-bonded imino protons in helices II, III, and IV were between 3.5 and 4.5 Å. The overall axis for the helices II-III region is warped rather than straight. Formation of additional Watson-Crick base pairs in loop B and loop C was not evident from the atomic positions calculated by molecular dynamics. Bases in loop C are well stacked, showing no significant change during dynamics. Bulge migration in helix III does not seem to be possible; the helices II-III region prefers one conformation. Helix II is more stable than helix III. Five base pairs in helix IV were sufficiently stable to establish that helix IV is terminated by a hairpin loop of three nucleotides. U87 protrudes from loop D. Structures of the helices II-III segment and the helix IV segment of B. megaterium 5S rRNA obtained by molecular dynamics were generally consistent with the solution structure inferred from high-field proton nmr spectroscopy. © 1992 John Wiley & Sons, Inc.

Notes: The effect of mixed salt (1:1 and 2:1 electrolyte) on alginate (a charged polysaccharide) gel formation is analyzed within the Poisson-Boltzmann cell model utilizing experimental data from the literature. The concentration of calcium ions needed to induce gelation of alginate goes through a minimum as 1 : 1 electrolyte is added. The theoretical model can account for this in a qualitative manner. According to the theoretical model, however, it is only in terms of concentrations that the minimum exists. In terms of chemical potentials for the ions (or salt) the curve is monotonic. The effect is due to the highly nonideal interactions in polyelectrolyte solutions when the total salt content is low. © 1992 John Wiley & Sons, Inc.

Notes: CD spectra have been measured as a function of temperature for a number of ApA analogues with modified backbones. Oligonucleotides with these modified backbones are being used as antisense agents having potential as viral therapeutics. Results of these studies show that when a carbonyl is substituted for the phosphate to produce an uncharged backbone, the analogues that have either sugar or morpholino substitution do not stack. In contrast, when a morpholino group is substituted for the sugar and the phosphate is modified so as to be uncharged, there is strong base stacking. Stacking interactions in the phosphorus-linked morpholino analogues are at least as strong as those found in d (ApA). The stacking interactions in ApA are weak by comparison. Singular value decomposition demonstrates that the stacking is two state, and Taylor series decomposition yields a coefficient that measures base stacking interactions. The van't Hoff equation is applied to the base stacking coefficient from the Taylor series fitting to give thermodynamic parameters. © 1992 John Wiley & Sons, Inc.

Notes: The central ingredient of any structure modeling tool is a molecular model or force field that accounts for proper geometry and energy calculation. For protein and peptide modeling based on entire amino acids as building blocks, we describe a peptide force field in which each amino acid is represented by a single point in space, taken at the position of the α-carbon atom. Apart from the positional coordinates, these units carry the two torsional angles ϕ and Ψ as additional degrees of freedom to account for the orientations of the peptide links. While some of the energy terms are analogous to expressions in atomic force fields, the presence of the angular variables leads to fundamental differences with new features and additional terms with no atomic counterparts.The force field reproduces secondary structure elements with very good accuracy. Globular parts of tertiary packing stay near the experimental structures with a rms deviation in C-α positions of 0.1-0.3 nm and about 25° in ϕ and Ψ depending on the size of the structure. A tendency for larger discrepancies is observed in exposed loops or terminal segments the conformations of which may be strongly influenced by neighboring domains.Finally, a scope of possible applications is presented. They range from modeling activities, such as model building by homology, to coarse scanning of conformation space in conformation analysis and structure determination. An extension to a dynamics model would offer the possibility to eliminate the less interesting high-frequency modes that in all-atom force-field dynamics absorb most of the computational effort.

Notes: Systematic theoretical modeling of symmetric DNA oligomers, carried out earlier for the B conformation, is now extended to A-DNA. In contrast to the previous results, it is found that A-DNA shows no multiplicity of low-energy substate conformations. The possibilities of the Jumna algorithm are subsequently applied to studying deformations of the oligomers. Controlled winding and stretching deformations are used to study how the two allomorphs and different base sequences absorb such external stress. The results help explain the internal mechanics of the DNA double helix and the extent to which fine structure influences this behavior. The results point to some differences between the A and B double helices, but also to many similarities. Sequence effects on flexibility are relatively limited compared to their impact on optimal energy conformations. It is also shown that the conformational substates detected for B-DNA oligomers are preserved under deformation, but have little influence on its energetics. © 1992 John Wiley & Sons, Inc.

Notes: The “extraordinary” diffusional phase (EP) at low ionic strength, and the conditions for 1 its removability by filtration were investigated for dilute solutions of the following linear polyelectrolytes: poly(L-lysine), heparin, chondroitin-6-sulfate, hyaluronate, polystyrene sulfonate, and variably ionized polyacrylamide. The EP was not present for all the different types studied, and for heparin, for example, the phase was present only for samples from certain sources. In all cases the phase was removable by filtration through sufficiently small pore-size membranes. Once filtered, the EP remained absent for over one week. It is concluded that the extraordinary diffusional phase consists of fairly stable polyelectrolyte aggregates, and sometimes also includes other very small particulate impurities. These aggregates and other small particles are thought to be present, or at least nascent, in the dry polyelectrolyte material, so that their properties may depend critically on the manner in which such dry material is produced. Tests for “reversibility” of the EP by cycling between high and low Cs by dialysis further confirm these conclusions. The evidence is thus against the EP representing any type of temporal aggregates or local ordering, at least for the linear polyelectrolytes studied in this work Rather, due to the extremely feeble scattering of ordinary polyelectrolytes at low ionic strength, the weak scattering from residual aggregates and other particles, not removed by ordinary filtration and centrifugation procedures, give autocorrelable scattering signals with long decay times. The “loss” of the extraordinary phase as ionic strength increases appears to be due simply to the weak EP scattering signal getting buried in the sharply increasing scattering from the ordinary polyelectrolyte phase. Model calculations based on experimental data support this latter conclusion. © 1992 John Wiley & Sons, Inc.

Notes: Solution properties of fractionated ovine submaxillary mucin (OSM) and asialo OSM (aOSM) in aqueous guanidine hydrochloride have been investigated using light scattering and Theological methods. For the first time we present viscometric evidence in both dilute and concentrated solution that the molecular structure of OSM is that of a wormlike chain. The intrinsic viscosity shows molecular weight dependence consistent with the linear extended chain conformation observed by light scattering measurements. The viscoelastic behavior of the OSM fractions in aqueous guanidine hydrochloride was further examined above the overlap concentration as a function of molecular weight and temperature. Under these solvent conditions in which the role of nonbonding intermolecular interactions is minimized, OSM shows predominantly fluid like behavior. However, high molecular weight OSM shows evidence of the existence of an entanglement network at high concentration. The frequency-dependent shear storage and loss moduli at all concentrations and molecular weights can be scaled to yield a master curve by incorporating typical viscoelastic shift parameters. The entanglement molecular weight and concentration are consistent with literature data for extended, semiflexible wormlike chains. The behavior of aOSM is similar to that of intact OSM at comparable degrees of coil overlap, indicating that the terminal sialic acid residue on the carbohydrate side chain has no effect on the rheology of concentrated OSM solutions beyond that due to an increase in the hydrodynamic volume. © 1992 John Wiley & Sons, Inc.

Notes: The conformation of double-helical amylose is influenced by its water environment [A. Imberty, H. Chanzy, S. Perez, A. Buléon, and V. Tran (1988) Journal of Molecular Biology, Vol. 201, pp. 365-378; A. Imberty and S. Perez (1988) Biopolymers, Vol. 27, 1205-1221]. For several low-energy conformations of left-handed amylose double helices, we performed Monte Carlo simulations of the (N, V, T)-ensemble of configurations of water molecules surrounding a single duplex. The crucial point of this simulation is the use of cylindrical periodical boundary conditions with a relatively small asymmetric unit comprising a limited number of water molecules. The output data consists of local maxima of water density in the space near the macromolecule and information on one- and two-membered water bridges between polar groups of amylose as well as energetic characteristics of the system under study.A left-handed antiparallel-stranded conformation of the amylose double helix (rise and twist per glucose unit are 0.343 nm and -58.1°) corresponds to the global minimum of intraduplex potential energy W. Schulz and H. Sklenar (1993) Biopolymers, submitted; W. Schulz, H. Sklenar, W. Hinrichs, and W. Saenger (1993) Biopolymers, to be published. We found that this conformation is favored also by its hydration shell characteristics in comparison to parallel-stranded structures. Three hydration sites per glucose unit in the vicinity of HO6, O6, and O3 could be identified. Regular water bridges forming a network around the duplex were observed. A moderate change of the helical parameters within the family of left-handed antiparallel structures (to a rise and twist per glucose unit of 0.233 nm and -45°) does not have noteworthy consequences for the characteristics of the hydration shell. The location of the hydration sites with respect to the polar groups of amylose and the observed water bridges are in excellent agreement with the hydration geometry of the heavily hydrated antiparallel-stranded left-handed double helix of p-nitrophenyl α-maltohexose described in a high-resolution crystal study [W. Hinrichs, G. Büttner, M. Steifar, Ch. Betzel, V. Zabel, B. Pfannermüller, and W. Saenger (1987) Science, Vol. 238, pp. 205-208; W. Hinrichs and W. Saenger (1990) Journal of the American Chemical Society, Vol. 112, pp. 2789-2796].In the case of parallel-stranded (nonsymmetric or symmetric) double helices, only one hydration site near the (H) O3 group could be identified. No systematic water bridges with sufficient high probability were observed. The sum of the average potential energies of the amylose-water and water-water interactions is not favourable in comparison with the energy for antiparallel-stranded double helices. The water-water interaction is high, i.e., parallel-stranded amylose breaks the structure of liquid water. This effect would explain the insolubility of natural amylose in cold water and support the occurrence of parallel-stranded double helices in crystallites of starch granules and in amylose microcrystals having only low water content [see Imberty et al. (1988) and Imberty and Perez ( 1988) above]. Symmetric parallel-stranded double helices have very well-exposed polar groups and their conformation should be favored in crystals by the ability to form extensively interduplex hydrogen bonds directly or via single water molecules. Single water molecules incorporated into the crystal would compensate for the shortage of donors of hydrogen bonds on the surface of the symmetric parallel-stranded double helix. Indeed, in accordance with diffraction data see Imberty and Perez (1988) above; also A. Imberty, H. Chanzy, S. Perez, A. BulBon, V. Tran (1987) Macromolecules, Vol. 20, pp. 2636-26381 a critical amount of water increases the crystallinity of amylose and only symmetric parallel-stranded double helices would fit into a crystallographic unit cell with c = 1.05 nm. The unfavorable hydration of parallel-stranded double-helical amylose would increase the stability of natural starch granules (e.g., in seeds) and, therefore, be biologically sensible. © 1992 John Wiley & Sons, Inc.

Notes: In an effort to explore the influence of interfacial environments on reverse turns, we have performed a detailed analysis by nmr of the solution conformations of two cyclic pentapeptides in sodium dodecyl sulfate (SDS) micelles. The first peptide, cyclo (D-Phe1-Pro2-Gly3-D-Ala4-Pro5), adopts a single rigid conformation in solution (either chloroform or dimethylsulfoxide) and in crystals, whereas the second, cyclo (Gly1-Pro2-D-Phe3-Gly4-Val5), is much more flexible and adopts different conformations in the crystal and in solution. Both of these peptides are solubilized by SDS micelles, and nmr relaxation rates indicate that they are both partially immobilized by interaction with the micelles. Furthermore, some amide protons in both peptides participate in hydrogen bonds with water. In the presence of micelles, the former peptide retains a conformation essentially the same as that found in crystals and in solution, which consists of a β turn and an inverse γ turn. However, the micellar environment has a significant effect on the latter peptide. In particular, the population of a conformer containing a cis Gly-Pro peptide bond is increased significantly. The most likely conformation of the cis isomer, determined by a combination of nmr and restrained molecular dynamics, contains a Gly1-Pro2 δ turn and a γ turn about D-Phe3. The nmr data on the trans isomer indicate that this isomer is averaging between two conformations that differ mainly in the orientation of the D-Phe3-Gly4 peptide bond. © 1992 John Wiley & Sons, Inc.

Notes: In an attempt to understand the role of Ca2+ on the bioactive conformation of peptide hormones, we have examined the interaction between Ca2+ and the neuropeptide substance P. Using CD spectroscopy to monitor conformational changes caused by Ca2+ binding, we found no significant binding of the cation by substance P in water. However, a substantial conformational change occurred in the hormone on Ca2+ addition in trifluoroethanol or an 80:20 (v/v) mixture of acetonitrile and trifluoroethanol. A biphasic binding of Ca2+ was observed in these solvents with saturation at 2 cations per hormone molecule. Mg2+ caused a relatively smaller conformational change in the hormone. A peptide corresponding to residues 1-7 at the N-terminal fragment of substance P showed a weak nonsaturating binding of Ca2+ in the nonpolar solvents whereas the 7-11 C-terminal fragment peptide displayed a binding indicative of an 1 : 1 Ca2+ / peptide complex. Ca2+ binding by the hormone and the 7-11 fragment was also monitored by changes in fluorescence of the phenylalanyl residues. The results support the conclusion drawn from the CD data about a distinct Ca2+ binding site in the C-terminal part of substance P. The Kd values obtained from fluorescence data were 160 µM for Ca2+ and 1 mM for Mg2+ binding by substance P. The hormone and the two peptide fragments were also tested for their effect on the stability of dimyristoyl lecithin vesicles. Substance P and the N-terminal fragment caused no significant leakage of either fluorescent dyes or K+ trapped in the vesicles. Nor did they cause membrane fusion as monitored by the fluorescence quenching method. In contrast, the C-terminal 7-11 fragment caused considerable leakage of vesicular contents and promoted membrane fusion. When tested for their ability to translocate Ca2+ across the lipid bilayer in dimyristoyl lecithin vesicles containing the Ca2+ indicator Arsenazo III, both substance P and the 7-11 fragment showed significant Ca2+ transport while the 1-7 fragment showed negligible transport. The apparent transport of the 7-11 fragment is attributable to its effect on the integrity of the bilayer membrane. These data distinguish the N- and C-terminal domains of substance P in terms of their lipid-dependent interaction with Ca2+. In light of the requirement of extracellular Ca2+ for substance P action, the data are also suggestive of the possibility of the involvement of Ca2+ in the bioactive conformation of this hormone and in its interaction with the receptor. © 1992 John Wiley & Sons, Inc.

Notes: The potentials of mean force (pmfs) for rotation around the X1 aromatic side-chain dihedrals of the zwitterionic bis-penicillamine enkephalin pentapeptide have been determined in both aqueous and saline solution. These side chains are known to be associated with the pharmacophore and their conformational populations are thought to be critical for activity. It is found that the association between chloride ions and the peptide in saline solution simulations has profound effects on the relative energies of the g-, g+, and t conformations, and also the barriers between them. Using the pmfs we have also calculated the respective Boltzmann-weighted 3Jαβ vicinal coupling constants. The agreement between the calculated and experimentally determined coupling constants is poor for the pmf in pure water, but substantially improved for the pmf determined in saline solution. Reasons for these differences appear to be related to the experimental conditions. © 1992 John Wiley & Sons, Inc.

Notes: There are 10 unique dinucleotides of double-stranded DNA, but only 8 independent nearest-neighbor energies that occur in circular DNA, as shown by D. M. Gray and I. Tinoco [(1970) Biopolymers 9, 223-244]. We extend that analysis to include end effects, and show that the number of unique dinuoleotide pairs (including ends) is 14. but there are only 12 independent energies. We discuss how these 12 energies (or spectra or any other pairwise additive property) can be measured and displayed, and how they should and should not be compared between experimenters. As an example, we analyzed the recently reported melting curves [M. J. Doktycz et al. (1992) Biopolymers, 32, 849-864] of 16 DNA dumbbells in two different Na+ environments. This analysis reveals a new means for evaluating end effects and the emergence of longer than nearest-neighbor interactions at low salt concentration. © 1992 John Wiley & Sons, Inc.

Notes: In an effort to explore the residue preferences in three-residue reverse turns (so-called -γ-turns), two cyclic pentapeptides - cyclo(Gly1-Pro2-D-Phe3-Gly4-Ala5) (I) and cyclo (Gly1-Pro2-D-Phe3-Gly4-Val5) (II) - have been synthesized and analyzed by nmr. It was anticipated that the Gly-Pro-D-Phe-Gly portions of these molecules would favor a β-turn conformation, leaving the remainder of the molecule to adopt a γ turn, as seen in several previously studied model cyclic pentapeptides. The nmr data for both peptides in CDCl3 (5% DMSO-d6) and in neat DMSO-d6 indicate that the most populated conformation contains a distorted β turn around Pro2-D-Phe3, which includes a γ turn around D-Phe3. The distorsion in the β turn does not impede the formation of an inverse γ turn around residue 5, and indeed, this conformation is observed in both peptides. Both the alanine and the bulkier valine residues are therefore found to be compatible with an inverse γ turn. Molecular dynamics simulations on the title peptides are reported in the following paper. These simulations indicate that there is conformational flexibility around the D-Phe3-Gly4 peptide bond, which enables the formation of the γ turn around D-Phe3. The third paper in this series explores the impact of a micellar environment on conformational equilibria in II. © 1992 John Wiley & Sons, Inc.

Notes: Proton and 13C chemical shift assignments are reported for the neuropeptide Met-enkephalin (ME) in both aqueous solution and in the presence of 50 mM sodium dodecyl sulfate (SDS). Rotating frame nuclear Overhauser enhancement spectroscopy was used to qualitatively describe interproton distances. These distances were then used as restraints in the distance geometry based molecular modeling program Dspace, developed by Hare Research to generate sets of conformations of ME. The resulting aqueous solution conformations of ME were determined to exhibit characteristic of an extended random-coil polypeptide with no distinguishable secondary structure. The resulting set of solution conformations of ME in the presence of 50 m M SDS exhibited characteristics of an amphiphilic type IV β turn that are stabilized by hydrophobic aromatic-aromatic interactions between the side chains of Tyr1 and Phe4. © 1992 John Wiley & Sons, Inc.

Notes: The calculated molecular surfaces for some Sandalwood-odor molecules and structurally similar inactive compounds were compared with the calculated mean surface obtained from five Sandalwood odorants included in the set, and their individual agreement and deviations were estimated. Especially the investigation of selected parts of the surfaces seems very promising in finding structure subunits which might be important for an association to a possible receptor site.

Notes: Catalytic hydrogenation of the Δ3-unsaturated (9R,10 R)- and (9S,10 S)-epoxyenol lactones 3a, b., and 4a, b., respectively, affords, in addition to the expected saturated epoxylactones 5a, b and 7a, b, also open-chain products, i.e. the diastereoisomeric (9R,10R)- and (9S,10S)-9,10-expoxy-8-oxo-4,5-secosteroklastan-5-oic acids 6a, b. and 8a, b. Alkaline hydrolysis of the lactone ring of compounds 5 and 7 and subsequent acetylation of the corresponding hydroxy derivatives give as the major products the open-chain, diasteroisomeric (9R,10R)- and (9S,10S)-4-acetoxy-9,10-epoxy-methyl esters 9a, b and 11a, b, respectively, and, but only in the androstane series, the tetrahydropyran derivatives 10a and 12a, as the minor components.

Notes: The kinetics of pyridine exchange on trans-[MO2(py)4]+ have been followed by 1H-NMR in CD3NO2 for M = Re, Tc: k298S-1 = (5.5 ± 0.1) × 10-6, 0.04 ± 0.02; ΔH≠/kJmol-1 = 111 ± 3, 101 ± 9; ΔS≠/JK-1mol-1 = +28 ± 10, +68 ± 35. For the Rev complex, pyridine and oxygen exchanges have been measured simultaneously by 1H- and 17O-NMR in deuterated water: k298/s-1 = (8.6 ± 0.2) × 10-6 (py), (14.5 ± 0.3) × 10-6 (oxygen); ΔH≠/kJmol-1 = 111 ± 1, 91 ± 1; ΔS /JK-1mol-1 = +32 ± 3, -32 ± 4. For both complexes, the rate law for pyridine exchange is first-order in complex and zero-order in pyridine; together with the activation parameter values, and the fact that the rate does not depend significantly on the nature of the solvent, this strongly implies the operation of a dissociative mechanism. The ratio of pyridine exchange rates for the Tc and Re complexes at room temperature is ca. 8000. The consequences of these observations for radiopharmaceutical synthesis are discussed.

Notes: Why Pentose and Not Hexose Nucleic Acids? Part I . Introduction to the Problem, Conformational Analysis of Oligonucleotide Single Strands Containing 2′,3′-Dideoxyglucopyranosyl Building Blocks (‘Homo-DNA’), and Reflections on the Conformation of A- and B-DNA Summary in collaboration with Prof. Dr. C.E. Wintner, Haverford College, Haverford, PA 19041-1392; academic guest, ETH, March and June/July, 1991.Chemical rationalization of the structure of a biomolecule can be sought through consideration of two criteria: first, the relationship between the structure and its biological function; and second, the structure's potential for constitutional self assembly. The latter criterion convers the judgment, by chemical reasoning, of the chance of its preformation, that is, a synthetic event which must have been undergone by any molecular structure in order to have been selected (or to have selected itself) to become a biomolecule. One way to further the task of rationalizing a biomolecule's structure by experimental means is the design, synthesis, and study of structural alternatives which might have become biomolecules on the basis of either criterion, but which do not, in fact, appear in Nature today.In the formation of sugar phosphates from glycolaldehyde phosphate under basic conditions, straightforward and selective formation of rac-hexose 2,4,6-triphosphates is observed in the absence of formaldehyde, while rac-pentose 2,4-diphosphates are dominant, when (0.5 equiv.) formaldehyde is present [1]. This and other observations indicate that hexose sugars should be regarded to have had a chance of preformation comparable with that of pentose sugars. Why, then, did Nature choose pentoses and not hexoses as the sugar building blocks of nucleic acids? The reason must be functional; it must be the case that pentose nucleic acids are biologically superior to potential hexose alternatives. To the extent that biological function is a consequence of molecular structure and reactivity, the origin of this superiority should be decipherable through chemical experiment, that is, through synthesis of hexose nucleic acids, systematic study of their chemical properties, and comparison of these properties with those of their natural counterparts. This has been the object of the present investigation, initiated in 1986. The paper introduces a series of papers which will describe the results of a model study, namely, the synthesis, pairing properties and structure of homo-DNA oligonucleotides.

Notes: From a MeOH extra of Psiadia trinervia, seven phenolic compounds were isolated by gel filtration and reversed-phase chromatography. Six of them are known compounds, namely 3,4-di-O-caffeoylquinic acid (2), 3,5-di-O-caffeoylquinic acid (3), caffeic acid, and three 3-methoxyflavonoids. Compound 1 is a 3,4-di-O-caffeoyl derviative of (1S,3R,4R,5R)-1,3,4, 5-tetrahydroxycyclohexanecarboxylic acid, a novel steroisomer of (-)-quinic acid. Following hydrolytic treatment of the MeOH extract, ethyl 3-O-caffeoylquinate (4), ethyl 3,4-di-O-caffeoylquinate (5), and ethyl 3,5-O-caffeoylquinate (6) were isolated. The latter three compounds are artifacts. The configuration of 1-3 was established by NMR and CD (exciton chirality method).

Notes: The carbohydrate-derived lactone phenylsemicarbazones 3 and 4 were prepared from 5 and 8 (Scheme). Treatment with 4-phenylsemicarbazide gave 6 and 7 (77:23) and 9 and 19 (76:24), respectively. Oxidation of 6 and 9 by CrO3-pyridine to 11 and 13, followed by deprotection, yeilded 3 and 4. The structure of 3 was established by X-ray analysis. Enzyme-inhibition studies using revealed that 3 is a competitive inhibitor with Ki = 23 μm. The activity of 4 was examined using N-acetylglucosaminidase from bovine kidney, Aspergillus niger, and Artemia salina. compound 4 was found to be a competitive inhibitor of all three enzymes with Ki values of 0.13, 6.0, and 0.71 μm and KM/Ki values of 6910, 45, and 465, respectively.

Notes: Radical anions of ten monocyclic and bicyclic azoalkanes containing the azo group in (Z)-conformation, have been fully characterized by their hyperfine data with the use of ESR, ENDOR, and general-TRIPLE-resonance spectroscopy. These azoalkanes are represented by 3,3,5,5-tetramethyl-1-pyrazline (1), 2,3-diazabicyclo[2.2.1]hept-2-ene (4), and 2,3-diazabicyclo[2.2.2]oct-2-ene (9), as well as by their derivatives 2, 3, 5-8, and 10. For all radical anions \documentclass{article}\pagestyle{empty}\begin{document}$1^{- \atop \dot{}}-10^{- \atop \dot{}}$\end{document}, the 14N-coupling constant, aN, is in the range of +0.83 to +0.97 mT; this finding indicates that the spin population is essentially restricted to the π system of the azo group. The 14N-hyperfine anisotropy largely affects the width of ESR lines, particularly at low temperatures. Substantial coupling constants of 7Li-, 23K-, and 133Cs-nuclei point to a close association of the radical anions with their alkakimetal counterions. With the exception of 39K, these nuclei give rise to readily observable ENDOR signals which appear along with those stemming from protons. The prominent hyperfine features of \documentclass{article}\pagestyle{empty}\begin{document}$1^{- \atop \dot{}}-10^{- \atop \dot{}}$\end{document} are discussed.

Notes: The radical mono-ions of three azoalkanes in which the azo group is connected to the polycyclic alkane moieties at the bridgehead C-atoms, i.e. 1,1′-azonorbornane (1), 1,1′-azotwistane (2), and 1,1′-azobicyclo[3.2.1]octane (3), were studied in fluid solution by ESR spectroscopy. According to the ESR parameters and MO models, the radical cations of 1-3 should be considered as σ radicals, whereas the corresponding radical anions are π radicals. INDO calculations point to a a remarkable dependence of the 14N-coupling constants on the geometry at the N-atoms in the radical cations of aliphatic azo compounds.

Notes: The use of α,α,α′,α′ -tetraaryl-1,3-dioxolane-4,5-dimethanols ( = TADDOLs;1) as chiral NMR shift reagents (1H, 13C, 19F) is described. In many cases, the ratio of enantiomeric alcohols and amines can be determined under standard conditions of measurement (CDCl3 as solvent, room temperature). The preparation and use of a new type of TADDOL, the tetrakis(dimethylamino) derivative 1d, is described. Menthol, octan-2-ol, and oct-1-yn-3-ol are partially resolved by crystallization of clathrates with 1c and 1d.