bluuebunny/crossref_metadata_2025 huggingface dataset:
Low‐temperature synthesis of poly(p‐phenylenevinylene) by the sulfonium salt route
Authors: Garay Raul O. , Baier Ullrich , Bubeck Christoph , Müllen Klaus
Published: December 2004

Poly(p‐phenylenevinylene), PPV, is one of the most promising candidates among the conjugated polymers for use in all‐optical signal processing or as the active layer in light emitting diodes. Here, a low‐temperature route to PPV is reported which makes the synthesis compatible with many of the thermoplastic polymers used in microelectronics and optics. The applicability of this route to device fabrication is also addressed.
Generation of optical evanescent waves in vacuum‐deposited thin films of α‐oligothiophenes
Authors: Knobloch Harald , Fichou Denis , Knoll Wolfgang , Sasabe Hiroyuki
Published: December 2004

The performance of oligothiophene‐based field‐effect transistors is thought to be dependent on the nature of the metal/semiconductor/insulator interfaces. The observation of evanescent optical waves in thin films of, for example, α‐6T (see Figure) provides a non‐destructive probe of the charge transfer processes taking place at these interfaces.

magnified image
Structural studies on Superconducting materials and fullerites by electron microscopy
Authors: van Tendeloo Gustaaf , Amelinckx Severin
Published: December 2004

High‐resolution electron microscopy (HREM) has proved invaluable in the study of local structure—i.e. defects—which in many cases govern the physical, chemical, and electrical properties of materials. The use of HREM in investigations of cuprate high‐temperature superconductors is reviewed, especially for compounds in which substituents replace some of the copper. HREM can also be very successfully combined with other techniques, such as electron diffraction, as is demonstrated by results of research on the structure and phase transitions of C60 and C70.
Conducting polymers—materials of commerce
Authors: Miller Joel S.
Published: December 2004

Conducting‐polymer‐based poducts that are commercially available are the topic of this second part of a two‐part article (the first half appeared last month). Many people are not aware that conducting polymers have reached the marketplace in the form of “coin”‐shaped batteries (see Figure). 3.5.″ floppy disks, and electrostatic loudspeakers, as well as being available for commercial processes and as raw materials.

magnified image
Template‐directed nucleation and growth of inorganic materials
Authors: Heywood Brigid R. , Mann Stephen
Published: December 2004

A new way to tailor the crystal chemistry of inorganic solids involves molecular recongnition between two‐dimensional organic templates and embryonic inorganic aggregates. Langmuir monolayers adopted as model surfaces offer opportunities for molecular engineering of the template. The Figure shows one example of oriented nucleation of vaterite under octadecylamine monolayers.

magnified image
Ring‐opening polymerization of metallocenophanes
Authors: Manners Ian
Published: December 2004

The development of processable high molecular weight polymers with skeletal transition metal atoms represents a synthetic challenge that, if overcome, can be expected to yield a variety of materials with novel electrical, optical, magnetic, or preceramic properties. Recent work has shown that the ringopening polymerization (ROP) of strained, ring‐tilted [11]‐ or [2] metallocenophanes provides a route to a variety of welldefined, ferrocene‐backbone polymers with molecular weights of over 1000000 in several cases.
Efficient luminescence from zeolites
Authors: Kynast Ulrich , Weiler Volker
Published: December 2004

Zeolites as potential luminescent materials is a subject that has received little attention previously. The optical properties–UV emission and reflectance/absorbance spectra–of zeolites X and Y prepared with various degrees of Ce doping are described and an interpretation of the results is proposed based on the occupation of the various zeolitic coordination sites (see Figure).

magnified image
Morphology‐dependent spectroelectrochemical behavior of pbs nanoparticulate films grown under surfactant monolayers
Authors: Tian Yongchi , Wu Changiun , Kotov Nicholas , Fendler Junos H.
Published: December 2004

Template‐dependent epitaxial growth of lead sulfide nanoparticulate films leads to three different morphologies, one of which is shown in the Figure. It is demonstrated that these structural differences are reflected in the spectroelectric, electric, and electrochemical properties, which is a step towards developing new colloid‐chemical techniques for fabricating nanoparticulate‐film‐based semiconductor devices.

magnified image
Self‐assembling phospholipid tubules
Authors: Schnur Joel M. , Shashidhar Ranganathan
Published: December 2004

Lipid‐based tubules serve as models for the development of advanced materials based upon molecular self‐assembly. The processes by which tubules are formed and how they are coated with metals (nickel in the Figure) or used as templates in order to increase the strength of the final material are described. Their electrical and magnetic properties are discussed.

magnified image
Molecular arrangement and thermal reorganization of merocyanine J‐aggregate monolayers on solid substrates
Authors: Wolthuus Lydia , Gnade Michael , Möbius Dietmar
Published: December 2004

Amphiphilic merocyanine dyes form J‐aggregates at the air–water interface. For any application the thermal behavior of the monolayers in an important issue and hermally induced phase transitions in monolayers have been intensively studied. Langmuir–Blodgett monolayers of two merocyanine dyes mixed with matrix molecules (see figure) have been examined and the optimization of the thermal stability of such systems discussed.

magnified image
Temperature dependence of the electroluminescent characteristics of light‐emitting diodes made from poly(methylphenylsilane)
Authors: Suzuki Hiroyuki
Published: December 2004

Polysilanes—Si‐based σ‐conjugated polymers—have electronic structures markedly different from those of π‐conjugated polymers. The temperature dependence of the electroluminescent properties of single‐layer LEDs made from poly(methylphenylsilane) is reported and it is demonstrated that these LEDs can be used as light sources in the near UV region. Observation of electroluminescence from one of the most typical polysilanes is encouraging as it indicates that there is potential for further improvements.
Microstructure of block copolymer reinforced interfaces observed with frictional force microscopy
Authors: Jandt Klaus D. , Dai Chi‐An , Krämer Edward J.
Published: December 2004

The microstructure of block copolymer‐reinforced interfaces of homopolymers has been studied by frictional force microscopy (FFM). The FFM micrograph in the Figure shows details, e.g., lamellar branching, of a poly(styrene)/poly(2‐vinylpyridine) (PS/PVP) homopolymer interface reinforced with a PVP–PS–PVP triblock copolymer. An explanation for the need to “develop” the FFM image is proposed and the advantages of FFM over TEM are discussed.

magnified image
InGaN‐based blue/green LEDs and laser diodes
Authors: Nakamura Shuji
Published: December 2004

High‐brightness blue LEDs and laser diodes for use in full color displays etc. have recently become available. Recent developments such as blue/green single‐quantum‐well (SQW) LEDs and a violet InGaN multiquantum‐well (MQW) laser diode—shown working on the inside front cover of the issue—are reviewed, including the electroluminescent and optical spectra of the devices. The results indicate the possibility that short wavelength laser diodes, from green to UV, will be realized in the near future using III–V nitride materials.
Technology‐transfer analysis of the materials research program “Matfo”
Authors: Preusser Steffen , Bremer Franz‐Josef
Published: December 2004

The commercial success of the German Federal Ministry's materials research program “Mafto” (1985–1994) was recently evaluated to determine the effectiveness of the direct‐funding model in supporting innovative industrial research. Based on the results of a questionnaire, where a 97% return rate was achieved, it was found that the results obtained in 27% of the projects have already been commercialized to some degree, for 26% of the projects a commercialization of the results is planned but has not yet taken place, and for 54% of the projects no commercialization is planned. This study included only projects where at least four years had elapsed since project completion. The reasons why scientifically and technically successfully projects were not commercialized were also surveyed.
Switchable smectic C* main chain liquid crystalline polymers
Authors: Sierra Teresa , Omenat Ana , Barberá Joaquìn , Serrano José Luis
Published: December 2004

Main chain liquid crystalline polymers (MCLCPs) are the basis of a number of high‐performance polymeric materials, examples being Kevlar and Vectra. For optical and electro‐optical applications, side‐chain LCPs have attracted much interest since their behavior is similar to low molecular weight LCs. Here, a ferroelectric MCLCP (see Figure) is reported.

magnified image
A new layer‐structured nitride superconductor. Lithium‐intercalated β‐zirconium nitride chloride, LixZrNCl
Authors: Yamanaka Shoji , Kawaji Hitoshi , Hotehama Ken‐ichi , Ohashi Masao
Published: December 2004

The first layered nitride superconductor is reported! The intercalation of lithium into the layered compound β‐ZrNCl (which is shown on the inside front cover of this issue) results in electron transfer from the lithium to the ZrN layers and the conversion of semiconducting β‐ZrNCl to a black metallic compound with a superconducting transition temperature of around 12.5 K. Interesting parallels with layered copper oxide superconductors and alkali‐metal doped fullerene superconductors should provide insight into the mechanism of high‐Tc superconductivity.
Electrophoresis of DNA. II. Specific interactions of univalent and divalent cations with DNA
Authors: Ross Philip D. , Scruggs Robert L.
Published: December 2004

The effect of small quantities of metal ions on the electrophoretic mobility of calf thymus DNA in solutions maintained at 0.2 ionic strength with weakly interacting (CH3)4N+ ions yields information about interactions occurring in a region very close to the polymer chain. By means of this technique, it is demonstrated that the binding order to DNA is Li+ > Na+ > K+ for the alkali metal ions and Mn++ > Mg ++ > Ca++ for the divalent ions studied. The quantitative details are compared to earlier work on the long‐chain polyphosphates. Close agreement between the two systems is obtained indicating that an intrinsic property of individual phosphate groups is being observed and that minor discrepancies probably arise from secondary factors. Three types of stability constants representing the binding of alkali metal ions to DNA are calculated and although differing in absolute magnitude, they all satisfactorily represent the result that the order of interaction is Li+ > Na+ > K+ with respective relative strengths of 1.5 : 1 : 0.8.
Properties and modifications of a cryomacroglobulin possessing cold agglutinin activity
Authors: Deutsch H. F.
Published: December 2004

The physical properties of a pathological γM‐globulin with cold agglutinin activity and cryoglobulin solubility could be modified by changes in temperature and pH and upon dilution. The type of changes noted appear to simulate those expected in a readily dissociable antigen‐antibody complex. Naturally occurring and chemically produced subunits of the γM‐globulin and Fc‐fragments of myeloma proteins diminished the cryoproperty of the γM‐globulin and effected changes in its physical properties but did not alter its cold agglutinin activity. Cryoglobulin properties could be conferred upon some purified γM‐globulins by reacting them with Fc‐fragments. Mercaptan dissociation of the Cryomacroglobulin produces subunits with loss of the noted activities. Reaggregation of these subunits restores some of the native properties, but variable results which are dependent on the type of mercaptan employed are obtained. Attempts to explain the cold agglutinin activity of γM‐globulin hybrids containing variable amounts of mercaptan‐produced active and inert subunits suggest that activity requires two of the five subunits to be derived from the γM‐cold agglutinin and to be adjacent to each other.
Determination of diffusion coefficients by spreading from thin layers
Authors: Polson A. , Parkyn D. G.
Published: December 2004

Two new methods for the measurement of diffusion coefficients were introduced. In the first method the spreading is measured from a. thin layer in a cylindrical tube containing a suitable gel. To avoid convection in the gel the tube is rotated horizontally round its long axis. In the second method the diffusion spreading is measured from an initial thin layer under a column of solvent in a Tiselius electrophoresis cell or a micro cuvet of a spectrophotometer. The great advantage is the economy on the material investigated.
Intrachain potential energy of the α‐helix and of a coiled coil strand
Authors: Tarry D. A. D. , Suzuki E.
Published: December 2004

A comparison has been made of the intrachain potential energy of an infinite straight α‐helix of poly‐L‐alanine with that of the distorted form adopted in a coiled coil conformation. The energy terms included were the van der Waal's, electrostatic, hydrogen‐bond, and the rotational potential terms. The results indicate that the potential energies of the structures investigated are almost the same, and so a transformation from one state to another may occur without significant changes in potential energy. Particular care has been taken to ensure that the electrostatic and van der Waal's interaction terms are fully convergent. The values obtained for the α‐helix were compared with those already published, and some significant differences were found.
Structure of β‐chitin or parallel chain systems of poly‐β‐(1→4)‐N‐acetyl‐D‐glucosamine
Authors: Blackwell J.
Published: December 2004

The structure of β‐chitin has been reexamined in an X‐ray diffraction study of the highly crystalline material available from pogonophore tubes. Oriented specimens were prepared by suspending the dispersed deproteinized tube in a fibrin clot which was then stretched into an oriented fiber. The X‐ray diffraction patterns of pogonophore β‐chitin were explained by proposing that this material consists of a mixture of two structural phases which have been named β‐chitins A and B. This view was confirmed by the preparation of specimens which gave only the diffraction pattern of the A phase by treating the tubes with diaphanol. Both A and B phases gave rise to a series of hydrate structures. The lowest hydrate of β‐chitin A has been studied in detail and shown to consist of an anhydrous system of parallel chitin chains. For this form, the unit cell was monoclinic with dimensions a = 4.85 Å, b = 10.38 Å (fiber axis), c = 9.26 Å, and β = 97.5°, and space group P21. Reasonable agreement was obtained between the observed X‐ray intensities and those calculated for such a structure. Examination of the β‐chitin of Loligo pen and diatom spines showed that these materials also consist of these A and B phases.
Relation of amino acid composition and the moffitt parameters to the secondary structure of proteins
Authors: Goldsack D. E.
Published: December 2004

A statistical analysis of the relation between the amino acid composition of proteins and the amount of helical secondary structure as characterized by the Moffitt b0 parameter has shown a high degree of correlation of the b0 parameter with those amino acids whose homopolymers can form helical structures. Using the data for 107 proteins, a linear relation was found between b0 and the sum of the residue percentages of alanine, arginine, aspartic acid, cysteine, glutamic acid, leucine, andlysine. A statistical analysis of the Moffitt a0 parameter, on the other hand, showed no statistically significant grouping of amino acids in relation to the amount of secondary β structure in a protein. A plot of b0 versus a0–a, where a represents the a0 parameter for a fully denatured protein, for 55 proteins showed distinct nonlinearity. This nonlinearity was postulated to be due to presence of β structure, and a nomagram was constructed which allowed a semiquantitative estimate of the amount of helical and β‐type secondary structures from the b0 versus a0–a plot.
Helix–coil transition in poly(γ‐benzyl‐L‐glutamate) and poly‐ε‐carbobenzoxy‐L‐lysine
Authors: Cortijo M. , Roig A. , Blanco F. Garcia
Published: December 2004

In this paper two points are considered: the methods of evaluating the helical content θ and the calculation of the parameters of the transition from experimental data and its interpretation. The parameter ΔH obtained is in good agreement with the calorimetric one and v is found to be independent of temperature and solvent and in agreement with the ordinarily accepted value for poly(γ‐benzyl‐L‐glutamate). The different methods of estimating θ are discussed for both polypeptides.
Early time expansions for sedimentation of weakly nonideal solutions
Authors: Nossal Ralph J. , Weiss George H.
Published: December 2004

An expansion valid for short times is presented for the rectangular approximation to the Lamm equation when the sedimentation coefficient can be expressed as s = S0(1−kc). The expansion allows the study of meniscus perturbations on the Faxén approximation, as well as a determination of when reflections from the base become significant.
Local effects of partial adenine‐N1‐oxidation on poly A · poly U and poly A · 2 poly U helix conformations
Authors: Fink T. R. , Crothers D. M.
Published: December 2004

We prepared helices with noncomplementary bases by N1‐oxidation of poly A, followed by reaction with poly U. Mixing curves indicate that doubly and triply helical structures form, with only the unmodified adenines involved in base pair formation. Circular dichroism spectra were examined particularly at the absorbance maximum of the adenine N1‐oxide (A*). In the single strand poly (A,A*), there is a relatively strong pair of positive and negative CD bands from the A*. These are greatly reduced in the double helix, and abolished in the triple helix. We conclude that A* stacks in a conventional manner with A in the single strand, but is rotated out of the double and triple helix. In the double helix the A* probably maintains a preferred orientation with respect to the helix, but rotates randomly in the triple helix.
Conformational studies on actinomycin
Authors: De Santis P. , Rizzo R. , Ughetto G.
Published: December 2004

A model of the Actinomycin structure is derived on the basis of theoretical calculations taking into account available IR, NMR and x‐ray experimental data. This model contains two intercycle hydrogen bonds and accounts for all the experimental evidence.
The dichroism of DNA in electric fields
Authors: Ding Da‐Wen , Rill Randolph , Van Holde K. E.
Published: December 2004

We have studied the dichroism of various samples of calf thymus DNA (of molecular weight from 3 × 105 to 7 × 106) in pulsed electric fields. The results may be summarized as follows:

We find that calf thymus DNA behaves in electrical orientation as if it possessed a large permanent dipole moment. This apparent moment is sensitive to such effects as Mg++ binding which lower the net charge on DNA.

The limiting dichroism at infinite field corresponds to an angle of at least 80% between the transition moments at 265 nm and the helix axis, and could be consistant with a number of known forms of DNA. This result is independent of DNA molecular weight. There is evidence that the conformation may be different in 80% ethanol.

The dichroism relaxation curves contain a component with a relaxation time of about 8 μsec, which is nearly independent of molecular weight, and a longest component which behaves either according to the Broersma theory for low‐molecular‐weight samples, or the Zimm‐Rouse theory at high molecular weights.
Conformational analysis of substituted pyrrolidones
Authors: Schellman John A. , Lifson Shneior
Published: December 2004

Consistent force‐field calculations were performed on a series of methyl substituted pyrrolidones. Methyl substitution enhances the non‐planarity of the pyrrolidone ring in a way wich varies with the position of the substituent. The effect of ring distortion is to produce skeletal contributions to the rotatory strength of the nπ* transition of the amide group. Depending on position of substitution, these reinforce or oppose the substituent contribution to optical activity. There is favorable agreement between the conformational calculations and the quadrant rule for the optical activity of the nπ* transition of the peptide chromophore.
Melting studies on spin‐labeled polyadenylic–polyuridylic complexes
Authors: Pan Yu‐Ching E. , Bobst Albert M.
Published: December 2004

Temperature‐dependent conformational transitions of spin‐labeled poly rA, spin‐labeled poly rU and the two‐stranded helical complexes consisting either of spin‐labeled rA·poly rU or spin‐labeled poly rU·poly rA have been measured by electron spin resonance spectrocopy. The polynucleotides were spin labeled with 4‐(2‐iodoacetamido)2,2,6,6‐tetramethylpiperidinooxyl and the spin label to nucleotide base ratio was approximately 1:600. The relationship between the log of tumbling time τ and the reciprocal absolute temperature for the spin‐labeled single and double‐stranded polynucleotides is presented. An agreement between TmOD (optical density melting) and Tmsp (spin melting) is found for the complexes, which strongly supports the conclusion that the same temperature‐dependent structural changes are monitored with both techniques.
Theoretical optical properties of poly‐L‐proline
Authors: Tterlikkis L. , Loxsom F. M. , Rhodes William
Published: December 2004

A non‐perturbational technique is used to calculate the circular dichroism and absorption spectra of polypeptide chains having conformations similar to that of poly‐L‐proline II. The method employs a Bogoliubov exciton formalism, from which the various optical terms associated with parallel and perpendicular components of the exciton band are obtained. A simple model for the peptide unit, consisting of three Gaussian absorption bands, leads to reasonable results for the polymer spectra, provided the lowest energy peptide π → π* transition is taken at 207 mμ and the value of the Ramachandran angle Ψ is taken to be 390°. The calculations suggest that the polymer circular dichroism spectrum is the resultant of strong interference among the two Gaussian exciton terms and the non‐Gaussian helix term. Consequently, the CD spectrum is very sensitive to the value of Ψ. It is found that the small positive CD band in the vicinity of 230 mμ arises partly from the effect of the static (crystal) field interactions on the n → π* CD band.
A temperature‐jump kinetic study of the binding of proflavine to poly I·poly C
Authors: Steenbergen Charles , Mohr Scott C.
Published: December 2004

The kinetics of interaction between proflavine and poly I.poly C at 25°C, neutral pH, and moderate ionic strength have been studied by relaxation methods. The qualitative features of this system resemble those previously reported by Crothers and co‐workers for proflavine–DNA and proflavine–poly A·poly U interactions–two relaxations are observed coresponding to a fast bimolecular step followed by a slower isomerization. These results can best be accommodated by a two‐step mechanism leading from the free dye through an “outside‐bound” complex to the intercalated complex. Quantitative comparison of the various rate constants for proflavine binding to different double‐helical polynucleotides shows that the rates are slower for both ribohomopolymer pairs than for DNA. The rates for poly I·poly C are approximately three times faster than these for poly A·poly U.
Unit fibril models derived from the molecular topography of collagen
Authors: Segrest Jere P. , Cunningham Leon W.
Published: December 2004

The geometrical properties of collagen molecules place certain restrictions on possible three‐dimensional packing models. With certain reasonable assumptions involving the macromolecular structure of collagen, a model for the surface topography of the monomeric unit is developed and two possible models for molecular packing, one hexagonal and the other non‐hexagonal, are inferred. The non‐hexagonal packing model is identical to the pentagonal unit fibril first postulated by J. W. Smith on different grounds, while the hexagonal model is one of three previously suggested by us on more general assumptions. The two models are compared to available data on collagen packing, and the bulk of the evidence would seem to favor the pentagonal model.
Circular dichroism of the alkyl amino acids in the vacuum ultraviolet
Authors: Snyder Patricia Ann , Vipond Prudence M. , Johnson W. Curtis
Published: December 2004

The circular dichroism and absorption for five alkyl amino acids as zwitterions has now been measured to 160 nm. Two bands are found, the nπ* at long wavelengths and ππ* at short wavelengths. In an effort to extract conformal information from the circular dichroism measurmenths, the circular dichroism spectra for these molecules is calculated using an independent systems apporach. It is found that the signs calculated using these methods are quite reliable, but that reliable magnitudes must await more accurate data to use in the calculations. Comparing the signs for both the measured and calculated circular dichriosm it if possible to determine the region inhabited by the carboxylate anion chromophore of these amino acid zwitterions. The greatest failure of the calculations is that thay are unable to explain the sigmoidal shape of the nπ* transition in proline. The problems facing workers trying to make calculations to relate circular dichroism measurements to conformation are discussed.
Kerr constants of amides and peptides
Authors: Ingwall R. T. , Czurylo E. A. , Flory P. J.
Published: December 2004

Molar Kerr contants mK have been determined for N‐methylacetamide, N‐ethyl‐acatamide, N‐methylpropionamide, N‐acetylglycine‐N′‐methylamide, N‐acetyl‐L‐ala‐nine‐N′‐methylamide, and N‐acetyl‐L‐leucine‐N′‐methylamide from electric birefringence measurements on dilute solutions in dioxane. The resultes are compared with configurational averatges 〈mK〉 calculated on the basis of conformational energies. Values ofmK calculated for various fixed confromations on the peptides vary over a wide range depending on the choice of conformation; hece, the configurational averages 〈mK〉 are sensitive to smalll changes in the conformational enerey. Kerr constants are calculated for random coiled oligoglycine and oligoalanine peptides as functions of chain length. The Kerr constant is an especially acute index of the average conformation.
The circular dichroism of poly d(AAT): d(ATT) and poly r(AAU):r(AUU). A test of the first‐neighbor hypothesis
Authors: Gray Donald M. , Ratliff Robert L. , Williams D. Lloyd
Published: December 2004

We present absorption and circular dichroism (CD) spectra for the synthetic polymers poly d(AAT):d(AAT) and poly r(AAU):r(AAU), in both native and heat‐denatured forms. As a means of evaluating the first‐neighbor hypothesis, the CD spectra are compared with approximations derived from spectra of other synthetic polymers containing the same first‐neighbor sequences. This is the first instance where such a comparison has been possible using spectra of double‐stranded RNA sequences, and the agreement between the measured and approximated spectra for poly r(AAU):r(AUU) is surprisingly good. We have also subjected the CD spectrum of poly d(AAT):d(AAT) to a previously published analytical procedure for obtaining estimates of first‐neighbor frequencies. In this first independent test of the procedure, we find that the analysis does infer the existence of a majority (86%) of AA, TT, AT, and TA first neighbors but does not precisely indicate their relative proportions.
Surface electric potential on rod‐like polyelectrolyte
Authors: Sugai Shintaro , Nitta Katsutoshi
Published: December 2004

The electric potential on the surface of the rod‐like polyelectrolyte with uniform charge distribution or periodically changing charge distribution on the surface is solved numerically by use of a power series method and an electronic computer. The deviation from the Linderstrøm‐Lang's linear relation in the modified pH titration diagram, and the dependence of the surface electric potential on the radius of rod are discussed. Also, the radius of counterion and ionic strength, and the effect of non‐uniformity of charge distribution are considered. Molecular radii were determined by comparing the calculated results with the pH titration data. The molecular radii of stereoregular poly‐(methacrylic acid) and α‐helical poly(glutamic acid) were found to be 5.5 Å and 15.0 Å, respectively, assuming uniform charge distribution. If nonuniform charge distribution was assumed, the molecular radii were calculated to be 5.0 Å and 14.0 Å, respectively. These values are discussed in relation to their molecular structures.
The inverse problem for DNA
Authors: Ya. Azbel' M.
Published: December 2004

The DNA distribution function for a given section of DNA of a given length depends on the nucleotide composition. It can be expressed in terms of other functions, such as specific heat, optical density, etc., if they are measured in the vicinity of the DNA melting point.
The contribution of proximity and orientation to catalytic reaction rates
Authors: Delisi Charles , Crothers Donald M.
Published: December 2004

We present calculations of the possible magnitude of propinquity which has been proposed to play an important role in enzymic catalysis. The effect has been evaluated as in the past by calculating the ratio of bimolecular to intramolecular reaction rates. The ratio is estimated for intramolecular catalysis in rigid systems as well as for systems with five and six rotatable bonds. Our method differs from others mainly in the way cyclization has been treated.

The reaction rate (in all cases) is proportional to the probability that the reactive units have the appropriate spatial and orientational positioning for reaction. This probability is obtained by evaluating a distance distribution function within the spatial and angular intervals to which the units are constrained after reaction. For the bimolecular case we have made the usual assumption that the distribution function is uniform. For the intramolecular reaction, neither the spatial nor the angular part of the distribution function is uniform. The pertinent parameters in this case are the bond lengths and angles, and the statistical weight matrices describing torsional rotation. The difficulty in obtaining analytical expressions for the distribution function is circumvented by using Monte Carlo methods.

It is argued that the spatial contribution to rate accelerations in rigid systems can be as high as 107 M, depending upon the size of the volume to which the reactive units are constrained after reaction. The limitation on the smallest physically reasonable volume is estimated from considerations of energy requirements and vibrational amplitudes. Accelerations by five‐ and six‐membered ring cyclizations were estimated at 103 M, the six‐membered ring exhibiting the smaller rate enhancement.
Conformational changes in transfer RNA. I. Equilibrium theory
Authors: De Lisi Charles
Published: December 2004

We report the results of semi‐empirical calculations describing thermodynamic properties of transfer RNA conformations. The most important new features of the procedure are: (1) the use of parameters obtained from model oligoribonucleotides to evaluate the free energy of helical regions and small hairpin loops, and (2) the use of a model which is somewhat more realistic than the freely jointed chain for evaluating internal loops and intermediate size hairpin loops. The new parameters lead to important quantitative and qualitative differences from predictions which would have been made in the past and lead to a priori predictions of tRNA melting temperatures which are within about 6°C of the experimental values. The results suggest the following conclusions: (1) The early melting transition observed in several tRNA's is partly the result of tertiary unfolding, and partly the result of the loss of some secondary structure. (2) The part of the secondary structure which melts during the early transition is different for different tRNA's. For fMet and Tyr from E. coli, the calculations predict that the dihydrouradiene arm melts out early. For yeast Phe the acceptor stem and anticodon helix melt first. (3) The results also suggest the possibility that tertiary unfolding and early secondary structural melting do not occur independently but are coupled, so that the two types of structure are probably mutually stabilizing.
Structural components of alginic acid. I. The crystalline structure of poly‐β‐D‐mannuronic acid. Results of X‐ray diffraction and polarized infrared studies
Authors: Atkins E. D. T. , Nieduszynski I. A. , Mackie W. , Parker K. D. , Smolko E. E.
Published: December 2004

A Structure determination of the naturally occuring marine algal polysaccharide poly‐β‐D‐mannuronic acid is described. The structure consists of 1e → 4e linked D‐mannuronic acid chains with the monosaccharide units in the C1 chair conformation. The X‐ray fiber diffraction photograph obtained from bundles of fibers prepared from Fucus vesiculosus has been indexed to an orthorhombic unit cell in which a =7.6 Å, b (fiber axis) = 10.4 Å, c = 8.6 Å, the unit cell containing two disaccharide chain segments with space group P212121.

A sheet‐like structure involving one intra‐chain, one intra‐sheet, and one inter‐sheet hydrogen bond per monosaccharide is proposed. Features of the chain‐packing arrangement are compared with mannan.
The conformational stability of ribosomal proteins L7 and L12 from E. coli. I. Circular dichroism study of the changes induced by ionic strength and solvents
Authors: Boublik Miloslav , Brot Nathan , Weissbach Herbert
Published: December 2004

Ribosomal proteins L7 and L12 are the only acidic proteins found on the 50S ribosomal subunit of Escherichia coli. The effect of ionic strength, helix‐promoting solvents and denaturating agents on the conformation of these proteins has been studied. It has been established that the helicity of L7 and L12 proteins (approx. 45–50% α helix) can be increased to 60–70% when they are exposed to helix‐promoting solvents such as methanol or ethanol in the presence of 0.1M salt. High ionic strength by itself was without any effect on the conformation of the proteins. However, the solvent, 2,2,2‐trifluoroethanol increased the content of α helices up to 80% even in the absence of salt. Denaturating agents like urea (6M) or guanidine HCl (6M), decreased the content of the ordered structure below 20%. All conformational changes induced by salt or solvents were completely reversible and characterized by a broad transition showing a low degree of cooperativity. This might indicate the presence of discrete segments with variations in amino acid sequences and ordered structures with different stabilities.
Dielectric relaxation and orientation of DNA molecules
Authors: Hanss M. , Bernengo J. C.
Published: December 2004

A conductivity dispersion has been measured at very low frequencies (VLF) on several concentrated DNA solutions. By measuring simultaneously their electric birefringence decay, it is shown that the dielectric relaxation (which is related to the conductivity dispersion) is due to the molecular orientation. Different polarization mechanisms are discussed. It is concluded that the DNA polarizability measured in the VLF range can only be explained by the orientation of a permanent ionic dipole. It is suggested that such permanent dipoles could be caused by small differences in the ionic composition between the two molecular “ends;” the difference could either be stable (asymmetrical localization of protein impurities for instance) or transient (fluctuating dipoles explained by the Kirkwood‐Schumaker theory).
Conformational studies on alamethicin
Authors: Burgess A. W. , Leach S. J.
Published: December 2004

A conformational analysis has been carried out for the cyclic peptide antibiotic alamethicin. Unlikely structures were first eliminated by constructing van der Waals' energy maps for near‐neighbor contacts and using these maps to generate forty complete alamethicin structures free of steric overlaps. The energies of the forty conformations were minimized; optimizing all dihedral angles first in sets and then simultaneously, to give a family of five low‐energy structures. In the conformation of lowest energy three of the seven α‐amino isobutyric acid residues occur in a six‐residue α‐helix and three at the two chain reversals. Judged by the change in conformational energy as a function of the change in dihedral angle, the flexibility of the chain is determined by both the type of peptide unit and its position in the molecule.

The model has features consistent with reported circular dichorism and surface balance measurements and has two polar centers separated by a lipophilic region. It does not contain the large central pore required by some theories for the action of alamethicin on cell membrances. It therefore probably acts by altering membrance structres rather than by shuttling ions through a pore in the membrance.
Molecular mobility of polypeptides containing proline as determined by 13C magnetic resonance
Authors: Torchia D. A. , Lyerla J. R.
Published: December 2004

The molecular conformations and dynamics of poly(L‐prolyl), poly(hydroxyl‐L‐prolyl), poly(L‐prolyl‐glycyl), poly(hydroxyl‐L‐prolyl), and poly(glycyl‐glycyl‐L‐prolyl‐glycyl), in aqueous solution, have been studied using 13C pulse Fourier transform nmr spectroscopy. From a measurement of the intensities of major and minor resonances in the spectra of the copolypeptides, it was determined that 15–20% of the glycyl‐prolyl and glycyl‐hydroxyprolyl peptide bonds are cis. Effective rotational correlation times (τeff), obtained from measurements of spin‐lattice relaxation times (T1) of individual backbone and side‐chain carbons, demonstrated that backbone reorientation is approximately isotropic for the five polypeptides and is characterized by correlation times of ca. 0.3–0.6 nanoseconds as a result of rapid segmental motion. In a given polypeptide glycyl and pyrrolidine residues were found to have the same backbone correlation times, but backbone carbon τeff values did decrease as the glycyl content of the peptides increased. A semi‐quantitative analysis of Cβ, Cγ, and Cδ correlation times suggests that rapid ring motion in both prolyl and hydroxyprolyl involves primarily Cγ and Cβ, with the prolyl ring being more mobile than the hydroxyprolyl ring.
Flexibility of DNA
Authors: Schellman John A.
Published: December 2004

A model for the flexibility of DNA is proposed that is based on discrete variations in the direction of propagation in going from one subunit to the next. Expansion of the local free energy in terms of the local bending gives a Gaussian distribution function. The assumption of the independence of local bends on neighbors lead to very simple formulae for the persistence length and the characteristic ratio. Emphasis, however, is placed on the application of the formulae for molecules of finite size where the persistence length and C∞ are not defined. The formulae are worked out for two models, which should serve as limits for the real physical situation.
Kinetics of protein subunit interactions: Simulation of a polymerization overshoot
Authors: Scheele Robert B. , Schuster Todd M.
Published: December 2004

Theoretical calculations of the kinetics of a polymerization reaction have been carried out for a scheme in which there is a nucleation step that is slow relative to subsequent propagation steps.

A transient maximum (overshoot) in molecular weight can be expected in such reversibly self‐associating systems when polymerization is initiated suddenly. The extent of overshoot decreases with increasing initial concentration of true equilibrium is strongly dependent on the rate of nucleus formation and the rate of depolymerization when the absolute values of both are small relative to the rate of propagation.
Conformational analysis of DNA–basic polypeptide complexes: Possible models of nucleoprotamines and nucleohistones
Authors: De Santis P. , Forni E. , Rizzo R.
Published: December 2004

Conformational analysis of DNA–basic polypeptide complexes, based on stereo‐chemical criteria and energy calculations and experimental results, is reported. Three types of polypeptide conformations were selected: the distorted β conformation similar to that proposed by Feughelmann et al.; a structure characterized by a repetition of a right‐handed and left‐handed α helix‐type conformation; and an intermediate structure. A model of the complex between DNA and basic polypeptides was proposed, where the polypeptide chain fits the narrow groove of the B form of DNA. Van der Waals, hydrogen bond, electrostatic, and hydrophobic forces cooperate to stabilize the association complex. This structure also seems to be suitable to represent the molecular model of nucleoprotamines. In the case of nucleohistones, both grooves of DNA are involved in the interaction with the proteins. These have the nonbasic‐rich portion in the α‐helical conformation, whereas the part where a greater proportion of basic amino acids occurs presents a structure similar to nucleoprotamines and complexes between DNA and basic homopolypeptides. The distribution of basic residues of the F2A1(IV) histone on DNA is markedly disproportionate for the two opposite cylindrical sectors of the double helix. This suggests a new mechanism of supercoiling in nucleo‐histones.
Investigation of the base‐pairing structure of the anticodon hairpin from E. coli initiator tRNA by high‐resolution nmr
Authors: Wong K. Lim , Kearns David R.
Published: December 2004

The high‐resolution nmr spectrum of the anticodon hairpin from E. coli tRNAfMet has been obtained at a number of different temperatures. The positions of the resonances from interior Watson‐Crick base pairs are well accounted for (within 0.1 ppm) by a semi‐empirical ring current shift theory, but the terminal base pairs are susceptible to the exact orientation of adjacent bases in single‐stranded regions. From a careful examination of the exact way in which resonances disappear at elevated temperatures, we conclude that melting in the nmr experiments occurs when the lifetime of a base pair is reduced to several milliseconds. On the basis of these experiments we are able to assign an nmr Tm to each individual base pair and these should be useful in interpreting the melting behavior of the intact molecule. An “extra” resonance is observed at ∼11.3 ppm and, on the basis of its position and temperature sensitivity, it is tentatively assigned to the ring nitrogen proton of a “protected” U residue in the anticodon loop. A strong preference for stacking of a nonbase‐paired A residue on an adjacent GC base pair is observed even at temperatures in excess of 52°C.
Electrical birefringence study of monodisperse collagen solutions
Authors: Bernengo J. C. , Roux B. , Herbage D.
Published: December 2004

Acid‐soluble collagen solution in 0.1 M acetic acid are studied by electrical birefringence. Specific birefringence is independant of concentration (for c < 100 mg/l.) and follows Kerr's law at low fields. Birefringence decays present a single relaxation time, and reversing pulse experiments show a very low contribution of induced moment compared to permanent dipole orientation. This result is also confirmed by birefringence rise measurements.
Helix–coil transition in nucleoprotein: Renaturation of polylysine–DNA and polylysine–nucleohistone complexes
Authors: Li Hsueh Jei , Chang Catherine , Weiskopf Manuel , Brand Benjamin , Rotter Arnold
Published: December 2004

Thermal denaturation and renaturation of directly mixed and reconstituted polylysine–DNA, directly mixed polylysine–nucleohistone complexes, and NaCl‐treated nucleohistones in 2.5 × 10−4 M EDTA, pH 8.0 have been studied. At the same input ratio of polylysine to DNA, the percent of renaturation of free base pairs in a directly mixed polylysine–DNA complex is higher than that in a reconstituted complex. For a directly mixed complex, the renaturation of free base pairs is proportional to the fraction of DNA bound by polylysine or inversely proportional to the sizes of free DNA loops. A of large amount of renaturation of free base pairs has also been observed for 0.6 M and 1.6 M NaCl‐treated nucleohistones. The binding of polylysine to nucleohistone enhances the renaturation of histone‐bound base pairs. The percent of renaturation of polylysine–bound base pairs is high and is approximately independent of the extent of binding on DNA by polylysine. This is true in polylysine–DNA complexes prepared either by reconstitution or by directly mixing. It also applies for polylysine–nucleohistone complexes.

The model where polylysine‐bound base pairs collapse at Tm′ with two complementary strands still bound by polylysine is favored over the model where polylysine is dissociated from DNA during melting. The low renaturation of histone‐bound base pairs in nucleo‐histone indicates that either histones do not hold two complementary strands of DNA tightly or that histones are fully or partially dissociated from DNA when the nucleo‐histone is fully denatured.
Effects of water on the mechanical properties of gelatin films
Authors: Tanioka Akihiko , Tazawa Takashi , Miyasaka Keizo , Ishikawa Kinzo
Published: December 2004

The mechanical properties of gelatin films were studied in relation to the effect of water, and compared with those of collagen films. The S‐shaped sorption isotherm was separated into an adsorption curve C1 and dissolution curve C2. From the C2 curve, the interaction parameter χ1 of Flory–Huggins' equation was calculated. The χ1 of gelatin were larger than those of collagen at low relative humidities (RH), while they coincided with each other at high RH. It was found that a composite curve was made by shifting stress relaxation curves obtained at different humidities along the log time axis. The shift factor for the formation of the composite curve was analyzed by Fujita–Kishimoto's equation, which was based on the free volume theory. The parameter β, which expressed the extent of the contribution of sorbed water to the increase in the free volume of the system, was 0.05 in the range of C2 from 0 to 0.08 (0–65% RH). This value was much smaller than 0.16 for collagen. The value was 0.16 in the range of C2 higher than 0.08, which was equal to that of the collagen. Dynamic shear modulus G′, loss modulus G″, and tan δ were determined as functions of RH. The gelatin film extended more than 100% at 73% RH under the very small stress of about 107 dyn/cm2. This corresponds to the region where β changes from 0.05 to 0.16, although such a phenomenon was not observed in the collagen film. The wide‐angle X‐ray pattern of extended gelatin was similar to that of renatured collagen fiber.
High‐resolution analysis of the modified quarter‐stagger model of the collagen fibril
Authors: Bruns Romaine R. , Gross Jerome
Published: December 2004

The location of transverse bands within the major repeating period of positively stained collagen fibrils was determined from electron micrographs by an optical averaging procedure. From these data and the published location of bands in SLS crystallites, we have prepared a two‐dimensional representation, accurate to about 25 Å, of the modified quarter‐stagger arrangement of molecules in the collagen fibril. With this information it is possible to demonstrate the relationship of loci on individual collagen molecules within the fibril. For example, the site where the collagen molecule is cleaved by tadpole collagenase, the site where a disaccharide unit is covalently bound to the α1‐CB5 peptide, and the site of carboxyl‐terminal intermolecular cross‐linking all occur in the fibril near the amino‐terminal edge of the “hole zone;” and the site of amino‐terminal cross‐linking occurs near the carboxyl‐terminal edge of the “hole zone.”