bluuebunny/crossref_metadata_2025 huggingface dataset:
Room temperature growth of mesoporous silica fibers: A new high‐surface‐area optical waveguide
Authors: Huo Qisheng , Zhao Dongyuan , Feng Jianglin , Weston Kenneth , Buratto Steven K. , Stucky Galen D. , Schacht Stefan , Schüth Ferdi
Published: December 2004

High‐quality, hexagonal phase, mesoporous silica fibers (see Figure) can be grown by the general procedure for one‐step, two‐phase, room temperature synthesis reported here. The silica fibers, which are 1–5 μm in diameter and up to 5 cm long, have excellent long‐range order, a narrow pore size distribution, and a pore volume of up to 0.78 cm3/g. The birefringent fibers can be used as high‐surface‐area optical fibers.

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Novel N,N′‐bridged dithiadiazafulvalene trapped in situ as a cation radical salt with polyoxometalate: (DTDAF)2Mo6O19
Authors: Bellec Nathalie , Lorcy Dominique , Robert Albert , Carlier Roger , Tallec André , Rimbaud Christian , Ouahab Lahcène , Clerac Rodolphe , Delhaes Pierre
Published: December 2004

A quasi‐planar dithiadiazafulvalene (DTDAF) with high electrondonating properties is reported. The chemical synthesis of a phenyl‐N,N′‐bridged DTDAF (the Figure shows an ORTEP drawing of the DTDAF⊕⊙ cation radical) is described together with the preparation of a charge‐transfer set by an situ trapping and investigations of teh structural and magnetic properties of this salt. Evidence for mixed valence states is presented.

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Novel optical sensor materials based on solubilization of polar dyes in apolar polymers
Authors: Mohr Gerhard J. , Werner Tobias , Oehme Ines , Preininger Claudia , Klimant Ingo , Kovacs Barna , Wolfbeis Otto S.
Published: December 2004

Homogenous and fully transparent optical sensor layers have been prepared by pairing anionic indicator dyes with lipophilic quaternary ammonium halides (see Figure for an example) and then dissolving the pairs in an appropriate polymer. The synthesis of six ion pairs and the characterization of the resulting materials are described, along with the mechanisms responsible fo detection of several gascous species and ions.

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Surface analytical techniques
Authors: Wild R. K.
Published: December 2004

This review briefly describes some of the techniques available for analysing surfaces and illustrates their usefulness with a few examples. In particular, Auger electron spectroscopy (AES), X‐ray photoelectron spectroscopy (XPS), secondary ion mass spectroscopy (SIMS), sputter neutral mass spectroscopy (SNMS) and laser Raman spectroscopy are all described. In analysing a surface, AES and XPS would normally be considered first, with AES being applied where high spatial resolution is required and XPS where chemical state information is needed. SIMS and SNMS can be performed together and can detect smaller surface concentrations. Laser Raman spectroscopy is useful for determining molecular bonding. Techniques which give topographic information, such as scanning tunnelling microscopy (STM) and atomic force microscopy (AFM), have not been considered.
Impurity study of CdZnTe substrates used for LPE HgCdTe
Authors: Bollong A. B. , Feldewerth G. , Tower J. P. , Tobin S. P. , Kestigian M. , Norton P. W. , Schaake H. F. , Ard C. K.
Published: December 2004

Impurites were tracked from raw material purification through to CdZnTe processing in an effort to identify the sources of elements which impact on IR photodetector performance. Chemical analyses by GDMS and ZCGFAA effectively showed the levels of impurities introduced into CdZnTe substrate material from the manufacturing processes. A new purification process (ISDZR) for raw materials was developed, resulting in improved CdZnTe substrate purity. Substrate CU contamination was found to have detrimental effects on LPE layer and device electrical properties for lightly doped HgCdTe.
Essential language function of the right hemisphere in brain tumor patients
Authors: Thiel Alexander , Habedank Birgit , Winhuisen Lutz , Herholz Karl , Kessler Josef , Haupt Walter F. , Heiss Wolf‐Dieter
Published: December 2004

Neuroimaging studies of language networks in patients with brain lesions of the left language‐dominant hemisphere have shown activation in the right inferior frontal gyrus (IFG). We tested the functional relevance of right IFG activation using neuroimaging‐guided repetitive transcranial magnetic stimulation (rTMS) to disturb language function over bilateral IFG in right‐handed patients with brain tumors and controls. All subjects were susceptible to TMS over the left IFG. In patients, this susceptibility correlated with left‐sided the degree of language lateralization to the left. Those patients with lowest dominance were also susceptible to right‐sided TMS proving relevant language function of the right IFG. Ann Neurol 2005;57:128–131
Einfach koordinierte Palladiumspezies als Katalysatoren in Kreuzkupplungen
Authors: Christmann Ute , Vilar Ramón
Published: December 2004

Palladiumvermittelte Kreuzkupplungen sind nützliche metallorganische Transformationen zur Knüpfung von C‐C‐, C‐N‐, C‐O‐ und C‐S‐Bindungen. Obgleich sie bei Laborsynthesen häufig eingesetzt werden, haben sie keine bedeutende industrielle Anwendung gefunden, denn bis vor kurzem waren nur Verfahren für die reaktiven Arylbromide und ‐iodide bekannt, die teurer und weniger leicht erhältlich sind als die entsprechenden Arylchloride. In den letzten Jahren wurden neue Katalysatoren entwickelt, die auch weniger reaktive und sterisch gehinderte Arylchloride aktivieren. Diese Systeme beruhen auf Palladiumkomplexen mit elektronenreichen und sperrigen Phosphin‐ oder Carbenliganden. Die erhöhte Reaktivität dieser Systeme wurde dem Vorliegen von ungesättigten und reaktiven [PdL]‐Spezies zugeschrieben, die Ar‐X bereitwillig unter Bildung von [Pd(Ar)X(L)] oxidativ addieren.
Studies on dextran and dextran derivatives. II. Acid hydrolysis of native dextran
Authors: Antonini E. , Bellelli L. , Bonacci M. L. , Bruzzesi M. R. , Caputo A. , Chiancone E. , Rossi‐Fanelli A.
Published: December 2004

The kinetics of the depolymerization of native dextran in dilute hydrochloric acid at different temperatures has been followed by measurements of M̄w, M̄n, [η], 〈ρ2〉1/2, and S. The data allow the correlation of the various parameters of the total hydrolyzate at various degrees of depolymerization. At a first approximation the results conform to a random splitting of a statistical, branched polymer.
Polymerization of α‐amino acid N‐carboxy anhydrides in N,N‐dimethylformamide
Authors: Nylund Robert E. , Miller Wilmer G.
Published: December 2004

The polymerization of γ‐benzyl‐L‐glutamate NCA initiated by n‐hexylamine in DMF proceeds with two successive propagation rates whose ratio is about 1.5. The onset of the increase in rate of propagation occurred at a DPn of 7–14, which was independent of initiator to anhydride ratio and anhydride concentration and not a result of anhydride impurities. The increase in rate is likely a result of a conformational change in the polymer at a DPn of 7–14.
Synthesis and polymerization of N‐carboxyanhydrides of N‐benzyl‐β‐amino acids
Authors: Zilkha Albert , Burstein Yigal
Published: December 2004

The NCAs of the N‐benzyl derivatives of β‐alanine, β‐DL‐aminobutyric acid, and β‐DL‐aminoisobutyric acid (nonplanar six‐membered rings) were prepared by reacting the corresponding N‐chloroformyl derivatives, obtained on reaction of the N‐benzyl amino acids with phosgene, with triethylamine. Contrary to the others, the NCA of N‐benzyl‐β‐alanine polymerized readily on heating in vacuo or in solution, using n‐hexylamine or methanolic sodium methoxide as initiators. With n‐hexylamine the molecular weights of the polymers obtained in benzene, dioxan, and dimethylsulfoxide, were in accordance with DP = [NCA]/[Initiator], as was found with conventional five‐membered ring NCAs of α‐amino acids. With sodium methoxide initiation, DPs of the polymers obtained were smaller than the (NCA)/[Initiator] ratio, contrary to what was found previously with α‐amino acid NCAs. The possibility that stereochemical factors are responsible for the differences in polymerization activity of various. N‐alkyl β as well as α amino acid NCAs is discussed.
Helix‐coil transition of polo‐L‐glutamic acid film
Authors: Noguchi Hajime , Yang Jen Tsi
Published: December 2004

Water‐insoluble films (ca. 0.04 × 3 × 30 mm. in dried state) of poly‐L‐glutamic acid (PGA), crosslinked with glycerol or polyvinyl alcohol at pH 4.8, were suspended in aqueous media and their relative lengths measured as a function of pH. The films elongate in alkaline pH and contract in acidic pH; the process is completely reversible, although the equilibration time usually takes several days at each pH. A sharp transition of the polymer was observed in the pH range which corresponded with that observed in PGA solutions by other physical methods.

In NaCl, KCl, and KF solution the coiled from of the PGA film shrinks with increasing salt concentration. A notable exception is LiBr, which extends the film after a broef, rapid contraction and eventually causes it to disintegrate. Eight molar urea also caused a small elongation of film.

Curpic ion has a drastic effect on the stability of the PGA helices. As low as 0.001M Cu(CH3COO)2 at pH 6.6 converted the coiled from the of the film into the helical form. On the other hand, calcium and magnesium ions only reduced the film length, probably without coil‐to‐helix transition.
Infrared spectra of isotopic polyglycines
Authors: Suzuki S. , Iwashita Y. , Shimanouchi T. , Tsuboi M.
Published: December 2004

For infrared absorption measurements, the following five isotopic polyglycines have been prepared: ordinary polyglycine (—NHCH2CO—)n, N‐deuterated polyglycine (—NDCH2CO—)n, C‐deuterated polyglycine (—NHCD2CO—)n, completely deuterated polyglycine (—NDCD2CO—)n, and N15‐substituted polyglycine (—15NHCH2CO—)n. Infrared spectra have been observed both in the I and II forms of each of these five isotopic polyglycines in the spectral region of 4000–300 cm.−1. On the basis of the comparison of these spectra with each other, a nearly complete set of assignments of the observed bands of polyglycines has been given.
Study of biological activity regenerated by the oxidation of fully reduced insulin
Authors: Pruitt Kenneth M. , Robison Bonnie S. , Gibbs Julian H.
Published: December 2004

Various techniques for recombining the fully reduced A and H chains of insulin were studied. Best results were obtained from water solutions of the reduced chains allowed to oxidize by standing in air at 3 °C. and from metal‐catalyzed oxidation under the same conditions but in 7.6M urea solutions. Average net regeneration of insulin was 6% by weight, based on rat hemidiaphragm analysis for insulin activity. The theoretical yield for a random recombination of the A and B chains was calculated to be 3%. The 50% yield of insulin (from the oxidation of reduced insulin thiosulfate) reported by Jiang et al. could not. be confirmed.
Solvent effects on the helix–coil transition in polypeptides
Authors: Bixon Mordechai , Lifson Shneior
Published: December 2004

A simple way to incorporate the solvent–peptide interaction in any available theory of the helix–coil transition is developed. The competition between the intramolecular hydrogen bonding and the solvent–polymer hydrogen bonding is considered in multi‐component solvents where some of the components have hydrogen‐bonding capacity. Molecular averages are computed by using the theory of Lifson and Roig. The experimental data of Yang are analyzed, and the range of acceptable values of the equilibrium constants of hydrogen bond formation is deduced. The enthalpy of the transition in multicomponent solvents is calculated.
Interaction of poly‐L‐lysine with nucleic acids. II. Poly(A + U), poly(A + 2U), and rice dwarf virus RNA
Authors: Higuchi Shigesada , Tsuboi Masamichi
Published: December 2004

The optical density–temperature profile of double‐stranded poly(A + U), triple stranded poly(A + 2U), and double‐stranded RNA from rice dwarf virus in solutions with and without poly‐L‐lysine has been examined. When poly‐L‐lysine is added, more than one melting temperature Tm is observed for poly(A + U) and poly(A + 2U). One of them is considered to correspond to the melting of the polynucleotide molecule free from poly‐L‐lysine, and another to the melting of a polynucleotide–poly‐L‐lysine complex. For rice dwarf virus RNA, the Tm assignable to the complex is not found to be lower than 99°C. In every case, however, the hyperchromicity observed at the Tm of the free poly‐nucleotide molecule is lowered linearly as the amount of poly‐L‐lysine added to the solution increases. This fact is taken as indicating that there is a stoichiometric complex formed. The stoichiometric ratio lysine/nucleotide in each complex is determined by examining the relation between the amount of poly‐L‐lysine added to the solution and the percentage of hyperchromicity remaining at Tm of the free polynucleotide molecule. The ratio is found to be 2/3 for all of the three complexes. A discussion is given on the molecular conformations of four types of polynucleotide–polylysine complex hitherto found: (A) double‐stranded DNA plus poly‐L‐lysine in which the lyslne/nucleotide ratio is 1, (B) three‐stranded RNA [poly(A + 2U)] plus poly‐L‐lysine in which the ratio is 2/3, (C) double‐stranded RNA [poly (A + U) or rice dwarf virus RNA] plus poly‐L‐lysine in which the ratio is 2/3, and (D) double‐stranded RNA [poly(I + C)] plus poly‐L‐lysine in which the ratio is 1/2.
Low‐sulfur proteins from α‐keratins. Interrelationships between their amino acid compositions, α‐helix contents, and the supercontraction of the parent keratin
Authors: Crewther W. G. , Gillespie J. M. , Harrap B. S. , Inglis A. S.
Published: December 2004

S‐Carboxymethyl (SCM) kerateine preparations from a range of keratins were fractionated by acid precipitation into low‐sulfur (SCMKA) and high‐sulfur (SCMKB) fractions. Amiono acid analyses and optical rotatory dispersion measurements on the SCMKA fractions from different keratins indicated that the proportion of α‐helical material (30–64%) increased with increasing leucine and glutamic acid contents and decreased with increasing SCM‐cysteine and proline contents. It is shown that these variations in α‐helix contents are due mainly to differences in the conformations of the principal components of the SCMKA fractions, although there is also a smaller contribution arising from contamination with varying amounts of non helical components. The thiol + disulfide contents for the parent keratins were measured and compared with the SCM ‐cysteine contents of the solubilized fractions. In general the SCM‐cysteine contents of the SCMKA fractions increased with increasing thiol + disulfide content of the parent keratin, but these values were not directly proportional. The extent of total supercontraction in 8M LiBr solution was measured for the parent keratins and shown to bear no significant relationship to their disulfide contents. From the extents of first‐stage and total supercontractions the disulfide contents of the contractile structures in the fibers were calculated according to a model described previously and compared with the analytical values for the SCM ‐cysteine contents of the SCMKA and SCMKB fraction. Data for both fractions were consistent with the model in that they were in each case related to the calculated values by a constant factor. However, because of simplifying assumptions in the model, it was not possible to identity positively one or other of these protein fractions with the contractile elements in the fiber.
Collagen aggregation phenomena
Authors: Cassel James M.
Published: December 2004

Three processes by which tropocollagen units associate to yield highly specific aggregates have been examined. From the temperature coefficients of the amounts aggregated it is concluded that the complex “native” aggregation is endothermic, whereas both end‐to‐end and lateral aggregation are exothermic. These results combined with additional information lead to the conclusion that “native” aggregation is an entropy‐driven process in which hydrophobic bonding plays the dominant role. In contrast the reactions producing the lateral aggregate and the aggregate in which end‐to‐end bonding is dominant are electrostatically governed.
Frictional coefficients of multisubunit structures. I. Theory
Authors: Bloomfield V. , Dalton W. O. , Van Holde K. E.
Published: December 2004

The theory of Kirkwood for the translational frictional coefficients of structures composed of subunits has been generalized in two ways in order to consider aggregates of nonidentical subunits. One of these generalizations fails when the sizes of subunits are too disparate; the other, derived from a surface shell distribution of frictional elements, is effective over the whole range of relative sizes. It is shown that, in the limit of a continuous surface distribution, a shell model reproduces Stoke's law for a sphere. Comparison is made between the frictional coefficients of spheres, ellipsoids, and rods modeled by finite numbers of subunits and by continuous shells of frictional elements, and those calculated from other theories. Agreement is generally good, though the shell model for prolate ellipsoids of revolution deviates by a few per cent from the Perrin value.
Polarographic investigation of binding of Cu++ and Cd++ by DNA
Authors: Bach D. , Miller I. R.
Published: December 2004

The equilibrium binding constants of Cd++ and Cu++ to native and denatured calf thymus DNA were determined polarographically. The binding constants are an exponential function of the potential at the binding site and as such they vary with ionic strength and with the charge on the DNA molecule. The correlation between the fraction of sites occupied by heavy metal ions and between the thermal stability of DNA in solution is discussed.
Étude, par diffusion centrale des Rayons X, des polyelectrolytes rigides en solution. Cas des sels de Li, Na et Cs du DNA
Authors: Luzzati Vittorio , Masson F. , Mathis A. , Saludjian P.
Published: December 2004

The study of polyelectrolytes in solution by small‐angle x‐ray scattering techniques involves special problems, raised by the presence of several species: solvent, macroions, counterions, and possibly the ions of an additional electrolyte. A theoretical treatment of this problem is developed, based upon geometric concepts; the treatment applies to globular and to rodlike particles for the case of x‐ray experiments carried out on an absolute scale. The equation obtained involves several parameters: mass and radius of gyration for globular particles; mass per unit length and axial radius of gyration for rodlike particles; partial specific volumes of the neutral macromolecular component of the counterions and of the added electrolyte; solvation of the macromolecular species; fraction of the counterions osmotically free. The equation is used to interpret a series of experiments performed with the Li, Na, and Cs salts of DNA in solution in water containing variable amounts of the chlorides of each cation. The effects of concentration are first eliminated by extrapolating to infinite dilution the experiments carried out at different concentrations; then the effects of the solvation are eliminated by extrapolating to pure water the results obtained at different electrolyte concentration. The parameters still involved at this stage are the mass per unit length, the partial specific volumes of the DNA and of the counterions, and the fraction of the counterions osmotically free. If the partial specific volumes are chosen in agreement with other data of the literature, and if the fraction of the counterions osmotically free is assumed to be 0.30 for the three salts, as suggested by other workers, the structure of the DNA molecules turns out to be the same for three cations, and to agree with the Watson‐Crick model. These results are confirmed by the study of the liquid–crystalline gels, obtained at higher concentration, that lead to a direct determination of the mass per unit length of the rods. Moreover the solvation of the DNA molecules is determined as is shown to be different for each of the three cations. These results are in excellent agreement with those obtained by other techniques.
Derivatives of proteins. II. Coupling of α‐chymotrypsin to carboxyl‐containing polymers by use of N‐ethyl‐5‐phenylisoxazolium‐3′‐sulfonate
Authors: Patel R. P. , Lopiekes D. V. , Brown S. P. , Price S.
Published: December 2004

A method for covalently binding proteins to carboxyl‐containing polymers is described. N‐Ethyl‐5‐pheriylisoxazolium‐3′‐sulfonate is used to form active esters of the carboxyls, which then condense with amine groups on the protein to yield amides. Conjugates of α‐chymotrypsin with such polymers have been obtained, with nearly full retention of enzymatic activity in some preparations.
Viscosity and temperature effects on the rate of DNA strand separation in alkali
Authors: Davison Peter F.
Published: December 2004

The time required for the completion of the process of strand separation in λ bacteriophage DNA preparations exposed to strongly alkaline conditions in aqueous glycerol solutions was directly proportional to the viscosity of the solvent. This finding supports the idea that the rate‐limiting step in the denaturation of high molecular weight DNA is the uncoiling of the strands and in the course of this uncoiling the forces arising from electrostatic and entropic factors must overcome the hydrodynamic viscous drag of the solvent resisting the translation of the polynucleotide strands.
Helix‐with‐loops structure of polynucleotide. II. Poly(I + CU)
Authors: Tsuboi Masamichi , Matsuo Kimiko , Nakanishi Mamoru
Published: December 2004

Copolymers of ribocytidylic acid (C) and ribouridylic acid (U) with C contents of 66.5 and 43 mole‐% have been prepared. Ultraviolet, absorption measurements were made of aqueous solutions of the mixtures of these copolymers (poly CU) and polyriboinosinic acid (poly I). In every set of examinations, a maximum hypochromicity (at 230, 248, or 260 mμ) was observed when the solution contained equal moles of C residue in the copolymer and I residue in the homopolymer. This fact was interpreted as indicating that a helix‐with‐loops structure, similar to that proposed by Fresco and Alberts7, is formed. It was shown that this structure is formed more rapidly and melts more sharply than that observed by Fresco and Alberts. An infrared examination was also made of this “helix‐with‐loops” structure. It was found that a few absorption bands are assignable to the helix part and a few other bands to the loop part of the structure.
Conformations of model compounds of proteins. I. Acetylglycine N‐methylamide
Authors: Koyama Yasushi , Shimanouchi Takehiko
Published: December 2004

Infrared spectra in the region 4000–60 cm−1 have been measured for acetylglycine N‐methylamide and its deuterium homologs, CD3CONHCH2CONHCH3, CH3‐CONHCD2CONHCH3, CH2CONHCH2CONHCD3, and CH3CONDCH2CONDCH3. Normal frequencies have also been calculated for these molecules with various conformations. The spectra show that this compound has two crystalline modifications, form A and form B. The frequencies and their isotope shifts show that the molecular conformation (Ψ, ϕ) of form B is near (0, 120) and that of form A near (180, 120). The short‐range factors determining the conformation of peptide backbone having glycine residues are discussed.
Kinetic properties and the electric field effect of life helix–coil transition of poly(γ‐benzyl L‐glutamate) determined from dielectric relaxation measurements
Authors: Schwarz Gerhard , Seelig Joachim
Published: December 2004

Dielectric relaxation of poly(γ‐benzyl L‐glutamate) in solution has been studied in the 5 kcps‐10 Mcps range for various values of the helix content. The results give first experimental evidence for three effects of major significance. (1) The system exhibits dielectric relaxation due to a chemical rate process (namely helix formation). This confirms recent theoretical predictions. (2) The mean relaxation time τ* of the helix–coil transition could be evaluated as a function of the degree of transition. The results are in excellent agreement with a previously developed theory. At the midpoint of transition it is found τ*max = 5 × 10−7 sec. The elementary process of helical growth turns out to be practically diffusion‐controlled (with a rate constant of hydrogen bond formation of 1.3 × 1010 sec−1). (3) There is a considerable electric field effect of the helix–coil transition. This indicates that conformation changes in biological systems could be potentially caused by direct action of an electric field.
Influence of the tritium labeling of calf thymus DNA by the Wilzbach method on its physical properties
Authors: Frommer M. A. , Miller I. R.
Published: December 2004

The adsorption at the air‐water interface of calf thymus H3‐DNA labeled in the dry state by the Wilzbach method was studied by measuring surface concentration, surface tension, and surface potential. It was found that, correspondingly to the behavior of E. coli H3‐DNA labeled by incorporation of thymine H3 and described in another paper, both the rate of adsorption and the amount of material adsorbed increased with increase in DNA concentration, salt concentration, or in the valency of the counterion. Surface pressure and potential did not change in the course of adsorption, and this is also in accordance with the properties found for E. coli DNA. However, while the surface concentration of the E. coli DNA corresponds approximately to monomolecular layer adsorption, the radiation from the adsorbed layer of the calf thymus H3‐DNA indicated apparently multilayer adsorption. On comparing the physical properties of the H3‐DNA labeled by the Wilzbach method to those of nonlabeled DNA, it is found that while the chemical composition and the bihelical structure is essentially maintained in the labeled material, exposure to tritium gas results in a reduction in molecular weight and produces random breaks in the strands of the bihelix. The H3‐DNA produced by Wilzbach's method is not labeled homogeneously. The more the molecule is exposed to the gaseous tritium, the more efficient is the isotopic, exchange and the greater the alteration in physical properties. The defects in the labeled H3‐DNA molecule make it more surface active, thus H3‐DNA of higher specific radioactivity concentrates at the interface, conveying the impression of multilayer formation although actually the adsorbed layer is approximately monomolecular.
Theory of boundary spreading in velocity ultracentrifugation of polydisperse solutes
Authors: Fujita Hiroshi
Published: December 2004

Under the assumptions that the rectangular approximation to the sector‐shaped cell is valid and that both the sedimentation coefficient s and the diffusion coefficient D are independent of concentration, asymptotic solutions to the boundary spreading equation for velocity ultracentrifugation of polydisperse solutes have been derived for three cases: case A, D = constant for all s; case B, sD = constant; case C, \documentclass{article}\pagestyle{empty}\begin{document}$ \sqrt {sD} = {\rm constant} $\end{document}. Case A is the situation treated by all of the previous authors but supposed to be unrealistic for ordinary macromolecular solutes. Cases B and C may be associated with synthetic polymers under theta conditions and globular proteins in aqueous media, respectively. The solutions obtained have been used to explore the theoretical background of the empirical Gralén method for evaluating the distribution of s from sedimentation boundary curves, with special interest in the behavior of a plot for Sversus 1/t. Here S is the value of s for a fixed value of the apparent integral distribution of s and t is the time of centrifugation. It was found that when the distribution of s is Gaussian‐like and fairly narrow, this plot becomes linear over a more extended range of t in the order case B > case C > case A.
Interchain packing energies of multistranded α‐helical ropes
Authors: Parry D. A. D. , Suzuki E.
Published: December 2004

The interchain packing energy of two‐, three‐, and four‐stranded α‐helical ropes has been investigated. Poly‐L‐alanine was chosen as a model, and the interchain energies were calculated for various combinations of chain sense as a function of interchain distance, axial orientation and displacement. For comparison, the packing energies of the analogous assemblies of straight α‐helices were also computed. Only those systems in which the chains were equivalent, i.e., related by line symmetry, were considered. The results indicate that for structures in which all the chains are equivalent the interchain packing energy favors the coiled coil arrangements.
Counterion fluctuation and dielectric dispersion in linear polyelectrolytes
Authors: Oosawa Fumio
Published: December 2004

The thermal fluctuation in the concentration of counterions bound to a rodlike polyion was analyzed by expanding the fluctuation in a Fourier series along the rod. The amplitude and the relaxation time of fluctuations of various wave lengths were obtained as functions of the charge density and the length of the polyion. From these results the real and imaginary parts of the dielectric constant of the polyelectrolyte solution were derived as the sum of contributions of fluctuations of different modes. The dielectric dispersion curve or the Cole‐Cole plot obtained was found to be in good agreement with experimental data.
Testing of A size criterion for DNA–hydrocarbon binding
Authors: Craig Morrie , Isenberg Irvin
Published: December 2004

The intercalation model of DNA–hydrocarbon binding appears reasonable, but rests on indirect evidence only. To test the model, a size criterion for binding has been proposed. The size criterion is based on the assumption that hydrophobic forces play a major role in the binding of hydrocarbons to DNA. It states that hydrocarbons which are small enough to intercalate into DNA and be well protected from contact with the medium, will be found to bind to DNA; those that are too large will not. We report results on the binding of fourteen polycyclic aromatic hydrocarbons to DNA. Predictions based on the size criterion were found to be valid in all cases tested.
Investigation of fibrous structures. I. Computations for collagen
Authors: Tumanyan V. G.
Published: December 2004

The structure of collagen is investigated by means of an energy minimization procedure. There is a rather broad trough of potential energy which involves a variety of structures (all collagen II type). It is seen that the unit height and the unit twist can strongly deviate from 2.86 Å, 36° values. Some of the good conformations are presented.
The Role of ions in the acid melting of DNA
Authors: Dore E. , Frontali C. , Gratton E.
Published: December 2004

The use of a simple chemical equilibrium and of the law of mass action leads to correct prediction when applied to the study of the role of the counterions in the process of acid melting of the DNA molecule. This approach allows an estimate to be given of the enthalpy variation per base pair associated with this process. Experiments have been carried out to test (a) the linearity of the dependence of pHm vs. 1/T; (b) the stabilizing effect of Na+ concentration. The enthalphy variation per base pair, deduced from the slope of the pHm vs. 1/T plot, and from the number of H+ bound per base pair, is in agreement with direct measurement.6,8
The net hydration of phage lambda
Authors: Costello R. C. , Baldwin R. L.
Published: December 2004

The banding density of phage lambda varies with the activity of water when the phage particles are banded in a series of different cesium salts. The results are comparable to those Hearst and Vinograd for free DNA. Lambda phage ghosts show less net hydration than the phage particles and band in a fairly narrow range of densities in these cesium salts. The phage banding density may be predicted to a first approximation by a simple additive approximation: the total net hydration of the phage is approximately equal to the net hydrations of free λ DNA λ hosts, all measured at the same water activity. The simple additive approximation is not adequate, however, to explain the banding density differences between a deletion mutant and phage lambda in the different cesium salts. The density differences evidently are sensitive to second‐order effects: they apparently are affected by a restriction of DNA hydration inside the phage head, which depends both on water activity and on DNA length (or free volume inside the phage head). This becomes a striking effect in Cs2SO4 solutions where the net DNA hydration is large. Changing the phage banding density by substituting 5‐bromouracil for thymine, which increases the DNA mass while leaving the DNA volume relatively unchanged, gives results consistent with a restriction of the net DNA hydration that depends on the DNA volume. Data on the sedimentation velocity behavior that λ and λb2 in diferrent salts are presented and discussed. It appears possible to estimate the size of a DNA deletion from the phage sedimentation coefficient.
Salt bonding in proteins. A model for the abnormal hydrogen ion titration and the strong anion binding of serum albumin
Authors: Arvidsson E. O.
Published: December 2004

Serum albumin undergoes a conformational change at pH 4, known as the N–F transition. In the customary Linderstrøm‐Lang treatment of hydrogen ion titration, the carboxyl groups in serum albumin either have an abnormally low pK, or are buried in charged form, and the Linderstrøm‐Lang charging parameter ω decreases dramatically at the N–F isomerization. In the present paper partition functions are derived and distribution functions are calculated for a model permitting salt bonding between the positively and negatively charged sites on a macromolecule. The N‐form has an abnormally high salt bonding constant whereas that of the F‐form corresponds to that of small ions. The result obtained is consistent with a “normal” intrinsic pK of the carboxyl groups of serum albumin without burying of any charges and with an unchanged ω. The nature of the postulated salt bonding is discussed.

Further, it is shown that the “abnormal salt bonding” of serum albumin can explain its unusual ability to bind anions. Theoretical binding curves are calculated and compared with literature data of the Cl− binding of serum albumin. The relation of the present model to other models of hydrogen ion and anion binding to proteins is discussed. Some additional consequences of the present model are pointed out; a transition in the alkaline range, analogous to the acid transition, seems probable. Literature data support the existence of such a transition but do not allow detailed calculations at present.

A general, thermodynamic treatment of the interactions between small ligands and macromolecules is outlined. Important points are the choice of the statistical‐me‐ chanical ensemble and considerations of the fluctuations about the mean bonding, if (i) there are not only a ligand‐locus interaction but also interligand interactions (in par‐ ticular intdigand attraction), or (ii) there is a conformational change in themacromole‐ cule depending on the ligand binding. In these cases, the binding isotherms obtained from thermodynamically closed systems (canonical ensemble) may erroneously indicate a distribution about a single probability maximum, i.e., the statistical mean binding N̄, and fluctuations about this value. The description of a phase change in a bound phase or a change in the “internal” self‐interactions of a macromolecule requires a bind‐ ing equation permitting distributions about two maxima, i.e., (i) N1* < N̄ (“thin” phase) and N2* > N̄ (“condensed” phase) or (ii) two macromolecular conformations P′, and P″, having occupancy numbers N̄, and N̄2, respectively. The N–F transition is an example illustrating the relation between the complete distribution functions and the two‐state approximation.
Far from equilibrium synthesis of “prebiotic” polymers
Authors: Babloyantz Agnessa
Published: December 2004

The existing experimental data on prebiotic nonenzymic biopolymer synthesis is used to construct a model which shows autocatalysis and highly nonlinear behavior. It is shown that far from thermodynamic equilibrium such systems may exhibit multiple steady states favoring the enhancement of the polymer population in the medium. The role of step by step chain propagation and template directed autocatalysis are studied and contrasted.
Helix–coil transition in nucleoprotein—theory and applications
Authors: Li Hsueh Jei
Published: December 2004

A general theory of helix–coil transition of irreversibly complexed nucleoproteins is presented. The equations are tested by experimental results in basic polypeptide–DNA complexes, nucleohistone I and pea bud nucleohistones. They show good agreement between theory and experiments. The theory provides direct measurement of a fraction of DNA base pairs covered by proteins, yielding a value of about 75% histone‐covered base pairs in pea bud nucleohistone. It also provides a measurement of an average number of amino acid residues per nucleotide in protein‐bound regions. This number varies from 1.0 to 1.4 in DNA–polylysine or DNA–polyarginine and from 2.9 to 3.3 in nucleohistone Ia, Ib, f1, and pea bud nucleohistone.
Investigation of DNA structural changes by infrared spectroscopy
Authors: Pilet J. , Brahms J.
Published: December 2004

DNA‐oriented samples of various origins were studied under different conditions of humidiity and sodium chloride content by means of infrared spectroscopy.

(1) Oriented DNA (M. Lysodeikticus, E. coli, calf thymus and salmon sperm) films at 3–4% sodium chloride yield polarized spectra which show drastic changes at relative humidities (r.h.) between 94% and 0% indicative of conformational changes:
B form → a form → disordered form
The measurements of the infrared dichroism at frequencies of about 1230 cm−1 and at about 1090 cm−1 allow one to determine the orientation of the phosphate group, whereas the measurements at 1710 cm−1 characterize the base orientation. At humidities higher than 90% r.h. (B form) the bisector of OPO forms an angle of 70° relative to the helix axis, whereas at lower humidities, between 75% and 50% r.h. (A form) a rotation to about 45° is observed. Simultaneously, the 0—0 line of phosphate group changes its orientation from 55° to 65° to the helix when B → A transition takes place. The results are in general agreement with that of X‐ray diffraction and allow one to determine the orientation of the phosphate group with greater precision.

(2) The B–A conformational change is not observed for satellite DNA, isolated from Cancer pagurus, of which the guanine + cytosine content is below 5%. As a function of decreasing humidities, one observes the transition:
B form → disordered form
A diagram of conformational changes of DNA's as a function of base composition and of r.h., suggests that B–A transition will occur for DNA of relatively higher G + C content, whereas for high (A + T) content, base sequence may be of importance.

The B–A transition is prevented in DNA at a relatively high or very low sodium chloride content.
Packing analysis of carbohydrates and polysaccharides. II. B‐amylose
Authors: Zugenmaier P. , Sarko A.
Published: December 2004

A procedure is described for the simultaneous optimization of the bond lenglths and angles of the glucose residue and the chain conformation of the B‐amylose helix, while performing a packing analysis of the chains into a crystalline array. The results show that care must be exercised in selecting monomer residue coordinates for the packing analyis and optimum coordinates are given for the α‐D‐glucopyranose residue suitable for B‐amylose. The packing analysis shows that of the four proposed unit cells for B‐amylose the Rundle‐Daasch‐French, the Schieltz and the hexagonal unit cell of Blackwell et al. are not suitable, while the larger cell of Blackwell et al. is suitable. The most probable packing of B‐amylose chains in that cells is antiparallel, which the chains in a lefthanded sixfold helical conformation and with the O(6) atoms in the gt rotational position.
Studies on cytochrome c. Part II. Synthesis of the protected heptapeptide (sequence 17–23) of Baker's yeast iso‐1‐cytochrome c
Authors: Moroder Luis , Marchiori Fernando , Borin Gianfranco , Scoffone Ernesto
Published: December 2004

Synthesis is described for the N‐o‐nitrophenylsulfenylheptapeptide tert‐butoxycarbonylhydrazide corresponding to positions 17–23 of the amino acid sequence of baker's yeast iso‐1‐cytochrome c. Moreover a new method of selective removal of the S‐acetamidomethyl group for analytical and preparative purpose is reported.
Studies on cytochrome c. Part III. Synthesis of the protected heneicosapeptide (sequence 24–44) of Baker's yeast iso‐1‐cytochrome c
Authors: Moroder Luis , Borin Gianfranco , Marchiori Fernando , Scoffone Ernesto
Published: December 2004

Syntheses are described for two N‐benzyloxycarbonylpeptide tert‐butoxycarbonylhydrazides which correspond to positions 24–34 and 35–44, respectively, of the primary structure of baker's yeast iso‐1‐cytochrome c. The two peptide derivatives were coupled via the azide procedure to form the N‐benzyloxycarbonylheneicosapeptide tert‐butoxycarbonylhydrazide (sequence 24–44).
Interactions between chondroitin‐6‐sulfate and poly‐L‐lysine in aqueous solution: Circular dichroism studies
Authors: Gelman R. A. , Rippon W. B. , Blackwell J.
Published: December 2004

The interactions between chondroitin‐6‐sulfate (chondroitin sulfate C) and poly‐L‐lysine have been studied as models for investigation of possible complex formation between fibrous proteins and mucopolysaccharides. Results obtained using circular dichroism spectroscopy show that poly‐L‐lysine adopts the α‐helical conformation in dilute aqueous salt solution at pH 7 when mixed with chondroitin‐6‐sulfate, rather than the “charged‐coil” observed in the absence of this mucopolysaccharide. This conformation‐directing interaction is at a maximum when the ratio of lysine to disaccharide residues is 1 : 1. Changes in the CD spectrum of a 1 : 1 mixture following increase in the salt concentration, or addition of non‐polar solvents, indicate that the interaction is ionic in nature. No such effects are observed for non‐sulfated mucopolysaccharides mixed with poly‐L‐lysine, suggesting that, for chondroitin‐6‐sulfate, it is the sulfate groups rather than the carboxyls which interact with the amine groups of the polypeptide.

Elevation of the temperature leads to disruption of the interactions between the polypeptide and polysaccharide species. A sharp melting transition occurs at 47.0 ± 1.0°C, when the poly‐L‐lysine reverts to the “charged‐coil” conformation. The sharp transition suggests that regular ionic bonds are formed between the polypeptide and polysaccharide. These results suggest that a conformation‐directing interaction may occur between sulfated mucopolysaccharides and the polar regions of collagen and other fibrous proteins.
Studies on cytochrome c. Part V. Synthesis of the protected decapeptide (sequence 57–66) of Baker's yeast iso‐I‐cytochrome c
Authors: Borin Gianfranco , Moroder Luis , Marchiori Fernando , Scoffone Ernesto
Published: December 2004

The synthesis is described of the N‐benzyloxycarbonyldecapeptide tert‐butoxycarbonylhydrazide, which corresponds to the sequence 57–66 of baker's yeast iso‐1‐cytochrome c. The peptide derivative was synthesized coupling two smaller subunits via the Rudinger modified azide procedure.
Interaction of poly‐α,L‐glutamic acid with acridine orange
Authors: Hatano M. , Yoneyama M. , Sato Y.
Published: December 2004

Interaction of poly‐α,L‐glutamic acid (PGLA) with acridine orange (AO) was studied with circular dichroism and absorption spectra measurements. The following results were observed: (1) the addition of a comparable amount of AO with the glutamyl residue to the PLGA solution at pH of 4.5 reduced the fraction of helix of the polymer; (2) when AO was added to the PGLA solution, the pH range of the helix‐coil transition of the polymer shifted toward higher pH regions; and (3) when the mixture of the same amount of AO and the glutamyl residue was brought to the neutral and alkaline pH region, some induced circular dichroism bands were observed. In this case, it was assumed that PLGA in the system takes a helical form due to the neutralization of the anionized side chains by the cationic species of AO. We concluded that AO molecules bound to the carboxylate groups of the side chains of PLGA arrange to from a righthanded super‐helix which surrounds the core of the righthanded α‐helix of PLGA.
Dielectric behavior of DNA–Proflavine complex
Authors: Goswami D. N. , Das Jyotirmoy , Gupta N. N. Das
Published: December 2004

The dielectric relaxation of namtive DNA and DNA–proflavine complexes at different DNA phosphate (P) to dye (D) ratios, were investigated in the frequency range 100 c/sec to 100 Kc/sec. The proflavine molecules were found to have a profound effect on the static dielectric constant and the relaxation time of the polymers. The static dielectric constant was oberserved to decrese with increasing level of added proflavine. At P/D = 1, the variation of dielectric constant with frequency was small. Relaxation time (τ) was greater for the DNA–proflavine complexes compared to that for free DNA, Maximum value of the relaxation time was obtained at P/D = 10. The increase in the relaxation time and decrease in the static dielectric constant were attributed to the increase in length and meutralization of surface charges of the DNA molecules, respectively, as aresult of proflavine binding.
The effect of ions on the superstructures of reconstituted collagen
Authors: Chang E. P. , Chien James C. W.
Published: December 2004

The effect of a variety of electrolytes on the stabilization and destabilization of the rod‐like superstructures in reconstituted collagen membranes have been studied by small‐angle light scattering (SALE). Structural orders at two levels are effected: association–disassociation at the micron level and the helix‐coil transitions at the mollecular level. In addition to lyotropic salts, several transition metal ions were also studied. They act to disassociate collagen aggregates by the formation of stable complexes.
Histone IV binding of 3,4‐benzpyrene, pyrene, anthracene, and 9‐methylanthracene
Authors: Small Enoch W. , Craig A. Morrie , Isenberg I.
Published: December 2004

Ultraviolet absorption, fluorescence excitation and emission, and fluorescence anisotropy demonstrate that the polycyclic aromatic hydrocarbone 3,4‐benzpyrene, Pyrene, anthracene, and 9‐methylanthracene bind to histone IV after the sow conformational change in the presence of divalent phosphate anion. These hydrocarbons do not bind, within our limits of detection, to histone IV in the diosorderde form at low pH or to the form produced by the fast conformational change when the slow change is prevented. High anisotropy values for the bound hydrocarbon indicate a high degree of aggregation for the histone IV.
Conformation of malformin A: A proton magnetic resonance and a circular dichroism study
Authors: Ptak Marius
Published: December 2004

Malformin A is a cyclic pentapeptide with an intramolecular disulfide bridge. The conformation in solution of this molecule has been studied by NMR and CD. The 270 MHz Proton spectrum in dimethyl sulfoxide is well resolved and the peaks corresponding to the five residues have been assigned.

From the temperature dependence of chemical shifts of the peptide protons and from the exchange rate of these protons, it is concluded that the NH proton of one Cys is shielded from the solvent. This observation and HNαCH angles, estimated from the corresponding coupling constants, a proposed conformation of the peptide backbone. From the HβCαCH coupling constants, a P chirality for the disulfide bridge is proposed. Such a conformation is confirmed by the circular dichroism spectrum which shows a negative band at λ > 250 nm.

It is concluded that the conformation of malformin A is rigid and that the disulfide bridge is exposed to interact with biological receptors.