bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecularly imprinted polymers for optochemical sensors
Authors: Dickert Franz L. , Thierer Sylvia
Published: December 2004

Molecular imprinting can be used to generate selective cavities—which are required for sensors—more easily than traditional synthesis. Polyurethanes with exactly adapted cavities, created by the evaporation of solvent vapors, are used to demonstrate the principle and also how the embedding of a dye enables optical detection to be employed. The Figure shows a polyurethane host with ethanol guest molecules.

magnified image
Self‐organization of size‐selected, nanoparticles into three‐dimensional superlattices
Authors: Motte Laurence , Billoudet Françoise , Lacaze Emanuelle , Pileni Marie‐Paule
Published: December 2004

Three‐dimensional quantum dot superlattices with fcc structure have been formed using reverse micelles and self‐organization of Ag2S nanocrystals. It is reported that the size distribution of the nanoparticles can be narrowed by a chemical treatment of the interface and by particle extraction from the micelles. The formation of well‐defined tow‐ or three‐dimensional ordered arrays is required for the development of new types of optical gratings, optical filters, antireflective surface coatings, data storage systems, and microelectronics.
Solving materials problems by computer simulation
Authors: Mumby Stephen J.
Published: December 2004

How can computer simulation best be developed in materials science? The company MSI has successfully used the approach of forming consortia to expand the boundarics of computational materials science and to transfer the technology to industry. The philosophy behind this approach is explained and the history and success of MSI's consortia outlined from the foundation of the first consortium, which focused on polymer property prediction, in 1989 to the present. Plans for the future are briefly sketched.
Skeletonization of mixed arachidic acid/cadmium arachidate LB films: A study using atomic force microscopy
Authors: Petty Michael C. , Pearson Christopher , Evenson Simon A. , Badyal Jas Pal S.
Published: December 2004

The microscopic structure of skeletonized films of cadmium arachidate has been studied by atomic force microscopy (AFM)—skeletonization is the removal of free acid from a mixed Langmuir–Blodgett (LB) films and the AFM methods used are detailed, AFM images and results from a two‐dimensional fast Fourier transform analysis are discussed, and factors affecting the overall cadmium arachidate content of the transferred film are considered.
A three‐color, three‐dimensional, solid‐state display
Authors: Kador Lothar
Published: December 2004

The display of three‐dimensional, dynamical, colored scenes in real time and under virtually any viewing angle was recently reported. The physical principles of this novel, recently published technique that allows simultaneous viewing by many people are reviewed. The construction of the prototype display is outlined, in which the image appears inside a volume of heavy‐metal fluoride glass doped with rare‐earth ions. Luminescent sports are addressed by intersecting infrared laser beams, leading to fluorescence in the visible.
A new method for chemical modification of conductive polypyrroles without destroying their conductivity
Authors: Ono Noboru , Tsukamura Chikanori , Nomura Youta , Hironaga Hideo , Murashima Takashi , Ogawa Takuji
Published: December 2004

The functionalization of conducting polypyrroles in high yields without the polypyrroles losing their conductivity is reported. The method is based on the use of substituted arenes as starting materials, onto which the pyrrole ring is ‘grown’. The resulting pyrrole rings have aryl groups substitued on the 3− and/or 4‐positions. The aryl groups themselves can carry a wide range of substituents which can be selected in order to tune the properties of the materials. The substitued pyrolle monomers can be polymerized using standard procedures.
Alteration of the electrochemistry of fullerene C60 in the presence of dioxygen: Formation of a redox‐active polymeric film
Authors: Winkler Krzysztof , Costa David A. , Fawcett W. Ronald , Balch Alan L.
Published: December 2004

A new route to the formation of an electrochemically active film that contains fullerene units is reported. The method involves the reduction of C60 to its dianion in the presence of dioxygen and produces a film (see Figure) that is similar, but not identical to films prepared by the electrochemical reduction of C60O. This new method of fullerence polymerization therefore avoids the need for the tedious preparation and purification of C60O. fig.

magnified image
Controlling the surface properties of high temperature superconductors
Authors: Mirkin Chad A. , Xu Feng , Zhu Jin
Published: December 2004

Molecular monolayer‐based surface modification has been used extensively for three of the four important classes of electronic materials, namely metals, semiconductors, and insulators. In this article recent progress in the application of t. is technique, which is commonly called “self‐assembly”, to the modification of the surfaces of high‐Tc superconductors (e.g. see Figure) is reviewed.

magnified image
Self‐oscillating gels
Authors: Yoshida Ryo , Takahashi Toshikazu , Yamaguchi Tomohiko , Ichijo Hisao
Published: December 2004

A polymer gel is crosslinked polymer network swollen in solvent. Some gels undergo abrupt volume changes by swelling–shrinking in response to external stimuli, such as temperature or electric field. Recently a new type of biometric gel has been developed which autonomously repeats its swelling‐shrinking cycles periodically in a closed solution, without any external stimuli, similar to a beating heart muscle. The new materials and their rhythmical behavior are discussed.
The phthalocyanine approach to second harmonic generation
Authors: de la Torre Germa , Torres Tomás , Agulló‐López Fernando
Published: December 2004

Phthalocyanine‐based nonlinear optical (NLO) materials are reviewed, with particular emphasis on second‐order effects. The requirements on materials and molecules for NLO activity are outlined before three recently studied families are briefly considered: asymmetrically substituted phthalocyanines (Pcs), subphthalocyanines.

magnified image
Soluble alkyl‐ and alkoxy‐substituted titaniumoxo phthalocyanines: Synthesis and photoconductivity
Authors: Haisch Peter , Winter Götz , Hanack Michael , Lüer Larry , Egelhaai Hans‐Joachim , Oelkrug Dieter
Published: December 2004

The high photosensitivity of titaniumoxo phthalocyanines makes them suitable for application as charge generation materials, e.g., in photocopiers. The synthesis, photophysical, and photochemical properties of soluble titaniumoxo phthalocyanines containing alkyl and alkoxy substitutents (see Figure) in the periphery of the phthalocyanine ring are reported, the photoconductivity and photooxidation behavior being stressed.

magnified image
Properties of self‐assembled monolayers (SAMs) from thiol‐functionalized oligothiophenes
Authors: Michalitsch Richard , Lang Philippe , Yassar Abderrahirn , Nauer Gerhard , Gamier Francis
Published: December 2004

The introduction of electroactivity into a self‐assembled monolayer (SAM) has been attempted as a step towards a tunable interface between metals and conjugated conducting polymers. The synthesis of terthiophenes bearing an alkylthiol function at their terminal position and their chemisorption onto platinum single crystals are described. The properties of this SAM were investigated by electrochemical surface analysis and contact angle measurements. The calculation of the orientation of the terthiophene units is outlined.
Elastomeric light valves
Authors: Qin Dong , Xia Younan , Whitesides G. M.
Published: December 2004

Two types of elastomeric light valves, their fabrication, performance, and application, are described. Both are thin blocks of poly(dimethylsiloxane), PDMS, with relief structures on their surfaces, either an array of square pyramids or an array of retroreflective corner cubes (see Figure). Use of the valves in a display device is demonstrated, in which the transparency can be controlled by mechanical compression.

magnified image
An alternative design strategy for thin photorefractive polymer structures
Authors: Agulló‐López Fernando , Carrascosa Mercedes , Aguilar María
Published: December 2004

Optimization of polymer photorefractive materials is complicated in conventional devices because the photorefractive material usually contains both a charge photosensitizer and a nonlinear chromophore and optimization can lead to compatibility problems. In the device design presented here, the photoconductive and electrooptic components are separated, allowing them to be optimized individually. The design strategy is described and analyzed theoretically. Its limitations are pointed out and example measures of performance given.
Growing large, well‐oriented colloidal crystals
Authors: van Blaaderen Alfons , Wiltzius Pierre
Published: December 2004

The ability to manipulate colloidal crystallization is a challenging task, a consequence of teh size and Brownian motion of the colloid particles. As a direct result, temperature is not a suitable experimental parameter, even though it is important for tuning molecular crystal growth. Large single colloidal crystals with well‐defined crystal orientations can, however, be grown through combined use of a polymer template and gravity. This and other methods that have been employed in an attempt to control colloid crystal growth, such as use of external fields, are described.
Mesoscopic systems: Will they ever be manufacturable?
Authors: Kelly Michael J.
Published: December 2004

Immense progress on the miniaturization of deviceshas been made over the last 25 years, with the microelectronics industry predicted to represent 10% of world trade by the year 2000. Questions are raised as to whether such small devices can operate increasingly more effectively and at ever reducing manufacturing cost. The implications of the present rate of progress, the limitations of the materials currently being used, and the potential of radically new routes for manufacturing mesoscopic systems are discussed.
Orientation of liquid‐crystalline suspensions of vanadium pentoxide ribbons by a magnetic field
Authors: Commeinhes Xavier , Davidson Patrick , Bourgaux Claudie , Livage Jacques
Published: December 2004

Non‐invasive alignment and rotation of liquid‐crystalline suspensions of vanadium pentoxide ribbons by a magnetic field is reported. The ribbons align as shown in the Figure if the magnetic field, initially applied along the capillary main axis, is perpendicular to the main axis but still in the plane of the figure. It is believed that this simple idea could be applied to any nematic suspension of mineral compounds.

magnified image
Magnetically modulated microwave absorption (MMMA) measurements at low magnetic fields on the ferromagnetic state of [TDAE]C60
Authors: Bele Petra , Brunner Hermann , Schilder Andreas , Gmeiner Jürgen , Scheoerer Markus
Published: December 2004

The ferromagnetic state and reported superconductivity of [TDAE]C60 (where TDAE is titrakis(dimethylamino)ethylene, see Figure) are investigated by magnetically modulated microwave absorption (MMMA). The results are compared with those‐reported using alternative physical measurement techniques, and a hypothesis proposed to explain the observed behavior. No evidence for superconductivity is found.

magnified image
Formation of metal‐laden ultrafine semiconductor particles by solid‐state diffusion
Authors: Ko Min‐Jin , Birnboim Meyer , Plawsky Joel
Published: December 2004

Fabrication of metal‐laden semiconductor particles by solide‐state diffusion is reported. The absorption spectra of the thus formed Ag/CuCl layered nanoparticles in a glass matrix are examined and explained in terms of a theory developed for partially metal‐coated copper chloride particles. Evidence that the dominant crystallite phase after diffusion of Ag into the CuCl nanocrystals is still CuCl and not AgCl is also presented. It is hoped to use this diffusion technique for the fabrication of thin‐film metal/semiconductor nanoparticle structures for optical application.
Magnetic molecular metals based on the organic donor molecule BET (BET = Bis(ethylenethio)tetrathiafulvalene): The series BET2[MCI4] (M3⊕ = Ga, Fe)
Authors: Coronado Eugenio , Falvello Lawrence R. , Galán‐Mascarós José R. , Giménez‐Saiz Carlos , Gómez‐García Carlos J. , Lauhkin Vladimir N. , Pérez‐Benítez Aaron , Rovira Concepció , Veciana Jaume
Published: December 2004

The molecular metals BET2[MCl4] with M = Fe, Ga (see article title for BET) have been prepared and their structural, transport, and magnetic properties investigated. It is shwon that the conducting layers of the organic donor BET are interleaved by the inorganic ions, which are fairly well isolated from each other in the crystal. However, in the case of the Fe, the ions are found not to be magnetically isolated but coupled by exchange interactions. A mechanism is suggested to account for the observed Fe–Fe interaction in this magnetic molecular metal.
Self‐Organized Quantum Wires and Dots in III – V semiconductors
Authors: Asahi Hajime
Published: December 2004

The fabrication of quantum wires and quantum dots in III–V semiconductors using self‐organization phenomena is reviewed. The Stranski–Krastanov (S‐K) mode growth, step‐bunching, and strain‐induced lateral composition modulation techniques are covered. The Figure shows the vertical stacking of islands that are formed by the alternate S‐K mode growth of five cycles of an In(Ga) quantum dot layer and a GaAs spacer layer.

magnified image
Highly polarized luminescence from oriented conjugated polymer/polyethylene blend films
Authors: Weder Christoph , Sarwa Christian , Bastiaansen Cees , Smith Paul
Published: December 2004

Polarized photoluminescence (PL) from conjugated polymershas, in the past, attracted less attention than polarized electroluminescence (EL), despite possible applications in liquid crystal displays. A systematic investigation is presented of the structure–property relationships in oriented films of blends of different poly(2,5‐dialkoxy‐p‐phenyleneethynylene)s with ultrahigh molecular weight polythylene, which exhibit highly polarized PL following gel processing and tensile deformation. Based on the experimental results, a new model is suggested for what occurs during orientation of the blends.
The thermal decomposition of an organometallic precursor for the preparation of YBa2Cu3O7−x
Authors: Binder Joachim R. , Wedemeyer Horst , Reuter Hans
Published: December 2004

Why are the carrier densities of YBa2Cu3O7−x smaller in thin films prepared by wet‐chemical methods than in those prepared by other methods? In order to answer this practically relevant question, the chemical reactions taking place need to be known exactly. The thermal decomposition of an organometallic precursor of YBa2Cu3O7−x—an important step in the wet‐chemical preparation–has been investigated by the simultaneous application of dynamic and static characterization methods and the results are reported here.
Measurement of CdxHgi‐xTe composition depth profiles using auger electron spectrometry on bevelled sections
Authors: Gale I. G. , Clegg J. B. , Capper P. , Maxey C. D. , Mackett P. , O'Keefe E.
Published: December 2004

The width of the band gap in the ternary system CdxHgI‐xTe (CMT) is a function of the value of x and the assessment of device structures requires reliable techniques for the measurement of x both laterally and with depth. This work describes the development of an Auger electron spectrometry (AES) method for the measurement of CMT composition depth profiles, based on measurement of the Cd/Te ratio along shallow‐angle bevelled sections through epitaxial layers. Results are accurate to within 3% relative and the depth resolution (Δz = 2σ) is about 0.04 μm even through layer structures with a total thickness of about 20 μm. Techniques for making the bevel sections are described together with the AES measurement and calibration techniques. A composition depth profile is given for a heterostructure grown by metal organic vapour phase epitaxy (MOVPE), showing the interface width (Δz = 2σ) at the composition change to be 0.3 μm. The CdTe/CMT interface widths in material grown by liquid phase epitaxy (LPE), MOVPE and molecular beam epitaxy (MBE) are shown to be highly dependent on growth temperature, with widths of 1.5, 0.2 and ⩽ 0.04 μm respectively.
Macro‐ and microsegregation of Zn in bridgman‐grown CdZnTe
Authors: Capper P. , Harris J. E. , O'Keefe E. S. , Jones C. L. , Gale I.
Published: December 2004

One of the remaining problems in the use of CdZnTe material as substrates in liquid phase epitaxy (LPE) of CdxHg1‐xTe (CMT) layers is that of variation in lattice matching, i.e. Zn content, across substrates. This wil become increasingly important in the future as larger focal plane arrays of infrared detectors are required. The basic Bridgman growth process for CdTe/Cd0.96Zn0.04Te has been extended by applying the accelerated crucible rotation technique (ACRT). A marked reduction in axial Zn segregtion is seen in 50 mm diameter ACRT material, but this effect is smaller in the case of 75 mm diameter crystals. Radial variations in Zn content are small in both sizes of crystal, demonstrating the benefits obtained from ACRT stirring. Both macro‐ and microsegregation effects have been studied in these crystals in an attempt to understand the growth mechanism. Zinc distributions have been assessed by near‐infrared transmission, X‐ray lattice parameter measurements, atomic absorption spectrometry (AAS) and Auger electron spectrometry (AES). The last technique was used for the microsegregation studies, while AAS provides the absolute calibration for Zn content. Comparisons with segregation behaviour found in the literature will be given. It will be shown that the low temperature gradient and low growth rate lead to a degree of supercooling in the first‐to‐freeze region and this leads to significant Zn segregation in both radial and axial directions. As the crystals reach full diameter, the radial variation is decreased, presumably by the action of the ACRT, and axial segregation is also reduced.
Controllable transmission of information in excitable media: The 2+ medium
Authors: Adamatzky Andrew I.
Published: December 2004

In this paper we address the problem of how to implement directed dispatching of information in homogeneous excitable media. To do this, we surveyed cellular automaton models which reveal spatial oscillating patterns of excitation. Thus we discovered a medium where any element at rest was excited if just two of its nearest neighbours were excited. A medium of this kind, the 2+ medium, does not support the spreading of ordinary autowaves, but in its evolution one can find compact movable groups of excited states. Here we demonstrate that such solitary waves with particle‐like behaviour will change their velocity vectors as a result of external singular stimulation. Thus they can be used as objects with controllable movement which transmit information in disordered surroundings. The results of this work can be utilised in the design of molecular computers.
Diffusion of iodine into CdTe at room temperature
Authors: Malzbender J. , Jones E. D. , Shaw N. , Mullin J. B.
Published: December 2004

Studies on the diffusion of iodine into CdTe at a temperature of 20°C using four widely differing types of diffusion sources are compared and discussed. The concentration profiles were measured using either a radiotracer sectioning (RTS) technique or secondary ion mass spectrometry (SIMS).

The profiles were composed of four parts to which a computer package consisting of the sum of four complementary error functions (erfc) gave accurate fits, providing four empirical values of the diffusivity. The diffusivities for the fastest component in all four cases were in agreement (∼2 × 10−14 cm2 s−1) and were consistent with previously published data. These results indicate that when iodine is diffused from the vapour it is not a suitable long‐termstable dopant in devices where sharp junctions are required.
New cubane MOCVD precursors for gallium sulphide and gallium selenide: Synthesis of [(Et2MeC)GaS]4 and [(Me2EtC)GaS]4: Structural determinations of [(Et2MeC)GaS]4 by X‐ray diffraction and [(tBu)GaSe]4 by electron diffraction
Authors: Power Michael B. , Barron Andrew R. , Hnyk Dráhomír , Robertson Heather E. , Rankin David W. H.
Published: December 2004

The gallium sulphide cubane compounds [(Me2EtC)GaS]4 and [(Et2MeC)GaS]4, have been synthesised, and their potential as MOCVD precursors for GaS is discussed. The molecular structure of [(Et2MeC)GaS]4 has been determined by X‐ray diffraction. In addition, the vapour phase structure of the GaSe precursor, [(tBu)GaSe]4 has been determined by gas phase electron diffraction and is compared with that previously determined in the solid state by X‐ray diffraction.
Fuel utilization in subjects with carnitine palmitoyltransferase 2 gene mutations
Authors: Ørngreen Mette C. , Dunø Morten , Ejstrup Rasmus , Christensen Ernst , Schwartz Marianne , Sacchetti Massimo , Vissing John
Published: December 2004

Patients with the myopathic form of carnitine palmitoyltransferase II (CPT II) deficiency typically experience muscle pain, cramps, and myoglobinuria during prolonged exercise. It has been suggested that carriers of CPT2 gene mutations also may have milder clinical symptoms, but fatty acid oxidation (FAO) has never been investigated in vivo in this group. We studied fuel utilization by indirect calorimetry and stable isotope methodology in four patients with CPT II deficiency, three subjects who carried one CPT2 gene mutation, and five healthy control subjects. Cycle exercise at a constant workload of 50% of maximal oxygen uptake capacity was used to facilitate FAO. We found that in vivo oxidation of long‐chain fatty acids was normal at rest but severely impaired during prolonged, low‐intensity exercise in patients with CPT II deficiency, and that two of the single CPT2 gene mutation carriers, who displayed symptoms of CPT II deficiency, had an FAO comparable with the patients. These results indicate that residual CPT II activity is sufficient to maintain long‐chain FAO at rest in CPT II deficiency but not to increase FAO during exercise. The findings also suggest that single CPT2 gene mutations may exert a dominant‐negative effect on the tetrameric CPT II protein. Ann Neurol 2005;57:60–66
Natural history of neurofibromatosis 1–associated optic nerve glioma in mice
Authors: Bajenaru M. Livia , Garbow Joel R. , Perry Arie , Hernandez M. Rosario , Gutmann David H.
Published: December 2004

Children affected with the inherited tumor predisposition syndrome, neurofibromatosis 1 (NF1), are prone to the development of low‐grade astrocytic optic pathway tumors (optic pathway glioma [OPG]). Previously, we developed a model of NF1‐associated astrocytoma (GFAPCre; Nf1flox/mut mice) in which mice develop optic nerve and chiasm glioma. To define the molecular pathogenesis of OPG, we used this mouse model to study the natural history of OPG formation using immunohistological and radiographic approaches. We observed that whereas astrocyte hyperplasia is present in the optic nerves associated with gross optic nerve thickening at 3 weeks of age, overt neoplastic changes were not seen until 2 months of age. Astrocyte proliferation was maximal between 3 weeks and 2 months of age, suggesting that the most rapid period of growth occurs early. Mouse OPG tumors were detected by magnetic resonance imaging at 2 months of age and exhibited contrast enhancement, as seen in human OPG. In addition, the mouse OPG tumors exhibited expression of proteins associated with astroglial progenitors, including nestin and brain lipid binding protein. Last, we observed neovascularization and microglial cell infiltration by 3 weeks of age before overt neoplastic transformation, suggesting that these cellular changes participate in the early stages of tumor formation. Ann Neurol 2005;57:119–127
p.S143F mutation in lamin A/C: A new phenotype combining myopathy and progeria
Authors: Kirschner Janbernd , Brune Thomas , Wehnert Manfred , Denecke Jonas , Wasner Christina , Feuer Anja , Marquardt Thorsten , Ketelsen Uwe‐Peter , Wieacker Peter , Bönnemann Carsten G. , Korinthenberg Rudolf
Published: December 2004

We report a young girl with a phenotype combining early‐onset myopathy and a progeria. She had myopathy and marked axial weakness during the first year of life; progeroid features, including growth failure, sclerodermatous skin changes, and osteolytic lesions, developed later. We identified the underlying cause to be a hitherto unreported de novo missense mutation in the LMNA gene (S143F) encoding the nuclear envelope proteins lamins A and C. Although LMNA mutations have been known to cause Hutchinson–Gilford progeria syndrome and Emery–Dreifuss muscular dystrophy, this is the first report of a patient combining features of these two phenotypes because of a single mutation in LMNA. Ann Neurol 2005;57:148–151
Fragile X–associated tremor/ataxia syndrome in sisters related to X‐inactivation
Authors: Berry‐Kravis Elizabeth , Potanos Kristina , Weinberg Dahlia , Zhou Lili , Goetz Christopher G.
Published: December 2004

Fragile X tremor/ataxia syndrome (FXTAS) is a recently described condition consisting of tremor, ataxia, parkinsonism, and executive dysfunction, presenting predominantly in male carriers of a fragile X mental retardation 1 premutation. In this report, we present premutation carrier sisters in whom severity of clinical signs correlated with a molecular pattern of X‐inactivation favoring higher expression of the premutation allele. In these women with a common genetic background, we suggest that symptom severity may be dictated by X‐inactivation, and thus a higher percentage of cells producing the premutation‐containing mRNA result in increased toxicity and disease. Ann Neurol 2005;57:144–147
Band centrifugation of macromolecules in self‐generating density gradients. III. Conditions for convection‐free band sedimentation
Authors: Vinograd Jerome , Bruner Robert
Published: December 2004

The conditions for convection‐free hand sedimentation are analyzed in terms of the negative density gradients associated with the leading edge of a band and the positive density gradients generated during the experiment. The amount of material necessary to perform a band‐centrifugation experiment depends on the diffusion coefficient of the macromolecules, which determines the rate at which the concentration at band maximum decreases, and on the extinction coefficient at the wavelength of observation. The maximum negative gradients in bands of macromolecules with diffusion and extinction coefficients typical of proteins, nucleic acids, and viruses are calculated. Positive density gradients generated by diffusion of small molecules between the thin lamella and the bulk solution are calculated for bulk solutions such us 1M NaCl or 95% D2O. These “diffusion gradients” are generally adequate to stabilize bands of the above macromolecules. Positive density gradients generated by sedimentation of salts within the bulk solution may be significant in providing stability near the bottom of the cell. The effects of inadequate stabilizing gradients are discussed, and are found to cause forward spreading of the band.
Cooperative interactions in single‐strand oligomers of adenylic acid
Authors: Poland Douglas , Vournakis John N. , Scheraga Harold A.
Published: December 2004

Optical rotatory dispersion measurements were made on the oligonucleotides (pA)2, (pA)4, and (pA)6 at neutral pH over the temperature range 5–85°C., and compared to similar data for polyriboadenylic acid. The data were interpreted in terms of a temperature‐dependent stacking of the bases in the single‐strand oligomers, with very little dependence of the degree of stacking on the chain length. These results can be explained by a theory of cooperative stacking. The degrees of freedom available per residue are rotations about the five backbone covalent bonds and the bond connecting the base to the ribose ring. To nucleate a stacking interaction between neighboring bases the backbone sequence must be ordered as must be the two bases. For this stack to grow by one base a backbone sequence must again be ordered, but only one additional base must be ordered. Thus, the degree of freedom of the base with respect to the ribose ring determines the extent of the cooperative effect and hence the effect of chain length. A matrix formulation of the partition function is presented which incorporates this cooperative nature of the interaction and is shown to be in fair agreement with the data. The entropy of ordering a base with respect to the ribose ring is found to be 0.68 e.u., which suggests that the purine has a torsional oscillation when unstacked, but does not have several isoenergetic positions of internal rotation available. The enthalpy of stacking is found to be −6.5 kcal./mole. A model involving neighbor and next‐nearest neighbor interactions could also account for the data. For all practical purposes, the stacking interactions of successive residues can be treated as independent, i.e., the state of one residue is essentially independent of the state of stacking of its neighbors.
The ultrasonic degradation of biological macromolecules under conditions of stable cavitation. I. Theory, methods, and application to deoxyribonucleic acid
Authors: Pritchard N. J. , Hughes D. E. , Peacocke A. R.
Published: December 2004

Solutions of calf thymus DNA have been degraded in the presence of vibrating air bubbles in ultrasonic fields of low power which would not normally induce ultrasonic cavitation. The DNA was degraded to a limiting intrinsic viscosity, after which further irradiation by ultrasound had little or no effect. This limiting intrinsic viscosity decreased with increase in the ultrasonic intensity. Previously developed theories have‐been adapted to calculate the maximum velocity gradient associated with the streaming of the solution around such vibrating air bubbles. The tensile force which is induced and which acts on the DNA has been calculated on the basis of current theories of degradation by hydrodynamic shear. These calculations indicate that the degradation of the DNA by ultrasound under conditions of “stable cavitation” is mainly the result of the shearing forces engendered in the solution around the oscillating bubbles.
Computation of the sterically allowed conformations of peptides
Authors: Leach S. J. , Némethy George , Scheraga Harold A.
Published: December 2004

The sterically permitted conformations for various di‐ and tripeptides have been described using mathematical and computer methods outlined in an earlier paper. The effects of variations in the size and shape of the side‐chain groups on the allowed conformations have been assessed. Steric restrictions, due to the backbone atoms alone, permit the peptide groups adjacent to glycyl residues to assume only about 50% of all conceivable conformations. An alanine side chain limits these to 16% and, with further side chain complexity, restrictions increase so that the backbone adjacent to valyl or isoleucyl side chains can take up only about 5% of all possible conformations. The results of the computations are therefore consistent with what is known of the ability of various residues to fit into α‐helical polypeptide chains, and of the comparative stabilities of the α‐helical forms of poly‐L‐alanine and polyglyeine. The rigid ring structures in prolyl peptides provide such severe steric restrictions that, a trans polyprolyl chain can exist only in a left‐handed helical form of the type observed experimentally for collagen II. Other factors which have been investigated are the effects of possible variations in the geometry of the planar amide backbone and in van der Waals' contact distances between atoms on the sterically permitted backbone conformations. The evaluation of steric restrictions emphasizes their important role as a determinant in protein conformation, and the results will lie useful in applying the computer techniques to the determination of the conformation of longer polypeptide chains.
Numerical solutions of the Lamm equation. II. Equilibrium sedimentation
Authors: Dishon Menachem , Weiss George H. , Yphantis David A.
Published: December 2004

The Lamm equation has been solved numerically for conditions corresponding to equilibrium runs for a nonlinear concentration dependence of the form s/s0 = (1 + kc)−1. It is shown that the approach to equilibrium is very close to being exponential (in time) as in the case k = 0. We also compare results for the nonlinear case given above with results obtained for linear c‐dependence of the form s/s0 = 1 – kc. For relatively high speeds the time required to attain equilibrium may be greatly underestimated by use of the latter approximation. Finally, we present analytic approximations for the concentration distribution at equilibrium and as a function of time.
Studies of the birefringence and birefringence dispersion of polypeptides and proteins
Authors: Oriel P. J. , Schellman John A.
Published: December 2004

An apparatus has been constructed which permits the polarimetric observation of streaming solutions of macromolecules. The apparatus is a streaming birefringence device allowing the usual measurements of birefringence parallel to the cylinder axis but which in addition transmits light in the radial direction. Installation of the apparatus between the polarizer and analyzer of a Rudolph polarimeter makes possible the measurement of changes in optical rotation, dichroism and birefringence. The present work is concerned with the latter effect. The systems studied were α‐helical polyglutamic acid, paramyosin, and collagen (ichthyocol). The combined measurements of radial and axial birefringence completely determines the refractive index ellipsoid of the streaming fluid. This result in turn permits the testing of the Peterlin‐Stuart distribution function for streaming in a Couette device, apart from a proportionality constant. The comparison between theory and experiment is very satisfactory provided the system is reasonably homogeneous with regard to molecular length and is sufficiently dilute. On the other hand, it is concluded that the Peterlin‐Stuart optical factor seriously overestimates the “form” birefringence in agreement with recent results and conclusions of Taylor and co‐workers. The apparatus permits the study of the dispersion of the birefringence in the radial direction. The dispersion of collagen follows a one‐term Sellmeier formula and is dominated by absorption bands in the neighborhood of 2000 A. On the other hand, the dispersion of the α‐helical systems is complex and requires a multiterm Sellmeier formula. This contrast between the two kinds of polypeptidc helices is similar to results obtained with other optical techniques and is attributed to the splitting of absorption bands in the α‐helix.
Effect of aggregation on the optical rotatory dispersion of poly(α,L‐glutamic acid)
Authors: Tomimatsu Y. , Vitello L. , Gaffield W.
Published: December 2004

Light‐scattering measurements show that poly(α,L‐glutamic acid) (PGA) is strongly aggregated at the low pH's (4.0–4.3) usually used to measure the mean residue rotation at the trough, [R′]233, and that [R′]233 becomes more negative with aggregation. Concurrent weight‐average molecular weight measurements by light‐scattering and [R′]233 measurements by optical rotatory dispersion as a function of pH show that a maximum negative value for [R′]233 (unaffected by aggregation) is obtained at higher pH's (4.53–4.82). Precautions should be taken to insure that the Na‐PGA sample used as standard does not aggregate at the low pH's required for its complete conversion to the helical form. An Na‐PGA sample meeting the above requirements gives [R′]233 of −14,600° ± 1.5% over the pH range 4.53–4.82 in 0.05M NaCl.
Steady‐state kinetics of enzyme‐catalyzed copolymerization on primers
Authors: Bloomfield V.
Published: December 2004

The theory of the steady‐state kinetics of irreversible enzyme‐catalyzed homopolymerization and copolymerization on primers has been developed. The rate law for homopolymerization is of the Michaelis‐Menten form, but the kinetic parameters depend on primer concentration. Copolymerization has been treated for two monomers considering both terminal and penultimate effects and for four monomers considering terminal effects. The composition equations and conditional probabilities for monomer succession are identical for enzymatic and nonenzymatic processes, because the steady‐state approximation is used in both cases. The reactivity ratios and steady‐state velocities are different, however. Examination of published results for AU and UG copolymers synthesized by polynucleotide phosphorylase permits evaluation of reactivity ratios for the AU copolymer and indicates that penultimate effects may be operative in both cases.
Electro‐optical studies of conformation and interaction of polynucleotides
Authors: Jakabhazy S. Z. , Fleming S. W.
Published: December 2004

Measurements by the technique of electric birefringence with pulsed sinusoidal electric fields on polyriboadenylic acid (poly‐A) and polyribouridylic acid (poly‐U) indicate that the kinetics of the double‐stranded helix formation of poly (A + U) in the presence of Mg2+ is second order and consists of two steps: nucleation and propagation of base pairs from nuclei. The nucleation involves approximately 7 base pairs. It seems that the requirement of 7 base pairs to start the formation of a double‐stranded helix is not peculiar to poly (A + U) but is associated with double‐stranded helices of polynucleotides in general. This implies that it may be associated with spatial requirements of the phosphate‐sugar backbone, rather than with the particular bases linked to the backbone. The decline in rate of poly (A + U) formation observed above a critical temperature is the consequence of changes in the poly‐A conformation setting in at this critical temperature, rather than resulting from an increase in the reversibility of the base‐pair propagation step of double‐stranded helix formation. The dominant role of the conformation of poly‐A in the double‐stranded helix formation of poly (A + U) is further borne out by the pH dependence of the rate which completely parallels the conformation changes known to occur in poly‐A as a function of pH. This indirectly suggests that at neutral pH poly‐A is a single‐stranded helix. The rotary diffusion coefficients attest to the flexibility of this helix, while the stacked nature of the base pairs at low temperatures is revealed by the identical increments in the specific Kerr constant on going from poly‐A to poly (A + U) and from poly (A + U) to poly (A + 2U) helices. Results suggest that Mg2+ binds to the phosphate part of the backbone. Poly‐U binds Mg2+ more strongly than poly‐A; this difference in binding strength is attributed to differences in conformation (random coil versus helix). It is also borne out by the present results that the degree of order in the structure of poly‐U, even at low temperatures and neutral pH, is at best an order of magnitude smaller than that of poly‐A under similar conditions. Furthermore, the earlier proposed double‐stranded structure of poly‐U is called into question. A hairpinlike structure seems to agree with results of this investigation. Finally, the results support the contention that the ion atmosphere polarization is responsible for orientation of polyelectrolytes in the presence of alternating electric fields in the neighborhood of 25 kc./sec. frequency.
Potentiometric titration of poly(L‐glutamic acid) in aqueous solutions and binding of divalent cations
Authors: Kono Naoko , Ikegami Akira
Published: December 2004

The potentiometric titration of poly(L‐glutamic acid) was performed under conditions of varied ionic strength and concentration of added divalent cations. From these titration curves, the amount of divalent cations, especially magnesium, bound to poly(L‐glutamic acid) was determined using a new method of analysis based on polyelectrolyte theory. By comparison with the polyelectrolyte, poly(acrylic acid), it was found that there are no specific interactions between metal ion and poly(L‐glutamic acid) in either the helical or random coil conformation. The effect of these divalent cations on the conformation of poly(L‐glutamic acid) was also discussed.
Intramolecular steric effects and hydrogen bonding in regular conformations of polyamino acids
Authors: Leach S. J. , Némethy George , Scheraga Harold A.
Published: December 2004

A survey has been made, by using computer methods, of the types of helices which polypeptide chains can form, taking into account steric requirements and intramolecular hydrogen‐bonding interactions. The influence on these two requirements, of small variations in the bond angles of the peptide residues, or of small changes in the overall dimensions of the helix (pitch and residues per turn), have been assessed for the special case of the α‐helix. Criteria for the formation of acceptable hydrogen bonds have also been applied to helices of other types, viz., the 3, γ−, ω−, and π‐helices. It was shown that the NH … O and H … OC angles in hydrogen bonds are sensitive to changes in either the NCαC′ bond angle or in the rotational angles about the NCαand CαC′ bonds. However, the variants of the α‐helix observed experimentally in myoglobin can all be constructed without distortion of the hydrogen bonds. For α‐helices, the steric and hydrogen bonding requirements are more easily fulfilled with an NCαC′ bond angle of 111°, rather than 109.5°. The decreased stability observed for the left‐handed α‐helix relative to the right‐handed one forL‐amino acids is due essentially only to interactions of the Cβatom of the side chains with atoms in adjacent peptide units in the backbone, and interactions with atoms in adjacent turns of the helical backbone are not significantly different in the two helices. Restrictions in the freedom of rotation of bulky side chains may have significant kinetic effects during the formation of the α‐helix from the “random coil” state.
On the form of the partition function for the helix–coil transition of random copolymers
Authors: Crothers D. M.
Published: December 2004

The purpose of this paper is to examine and contrast several formulations of the partition function for the helix–coil transition of random‐sequence nucleic acids. In the exact approach, the sequence of bases in a given molecule is fixed, but this leads to expressions which are difficult to evaluate. Another approach is to make a summation over all possible sequences, each weighted by the probability of its occurrence, thereby in effect allowing all sequences to a given molecule. The error in this approach is that it does not guarantee that the average base sequence is random. This difficulty can, in principle, be overcome by applying successively increasing constraints on the system to ensure that all moments of the distribution are equal to the random‐sequence values. It is shown for the particular case of short molecules which melt only from the ends that the convergence of this method to the true solution is poor. The major conclusion is that composition fluctuations which cover a sizeable region of the molecule must be included in an accurate description of the melting transition.
Enthalpy changes in the helix‐coil transition of poly(γ‐benzyl L‐glutamate)
Authors: Karasz F. E. , O'Reilly J. M.
Published: December 2004

The helix‐coil transition temperature Tc of poly(γ‐benzyl L‐glutamate) in binary solvent mixtures of dichloroacetic acid and 1,4‐dichlorobutane, 1‐chlorooctane, or 1‐chlorododecane have been measured. A treatment is presented with which the transition enthalpy can be calculated from the observed dependence of Tc on solvent composition. Results are compared with previously obtained calorimetric data. The underlying assumptions of the calculation are discussed.
Molecular weight fractionation and the self‐suppression of complex coacervation
Authors: Veis Arthur , Bodor Edward , Mussell Shirley
Published: December 2004

A marked molecular weight fractionation accompanies the demixing or phase separation resulting from the complex coacervation of mixtures of aqueous solutions of salt‐free isoionic unfractionated gelatins with pI's of 5 and 9. Viscosity studies show that the fractionation is such that the concentrated phase tends to maintain constant, homogeneous composition. A second feature, seen in phase volume and concentration measurements, is a marked self‐suppression of coacervation intensity with increasing mixing concentration. These data were interpreted in terms of a dilute‐phase aggregate model which assumes nearly equal electrostatic free energies of mixing in dilute aggregate and concentrated random phase. The driving force for phase separation is the entropy increase upon formation of the random phase but demixing also depends upon the polymer‐solvent interaction parameter χ, in the same fashion as in simple coacervation. The dilute‐phase aggregate model indicates that the sharp molecular weight selection takes place in the aggregate formation step and explains the self‐suppression. Phase equilibria studies utilizing fractionated, paucidisperse high molecular weight gelatins, emphasize the requirement for concentrated phase homogeneity and indicate that aggregates of different molecular weight may act as different components, so that χP1Q1,PkQk > 0, bringing about a separation of the system into three or more coexisting phases. The formation of several coexisting phases from a homologous polyelectrolyte system and the very marked requirement for phase homogeneity suggest that the phenomenon of complex coacervation is a very good model for some of the essential steps in the pre‐biologic organization of polymeric polyions.
Structure of branched poly‐α‐amino acids in dimethylformamide. II. Viscosity, sedimentation, and diffusion
Authors: Eliezer N. , Silberberg A.
Published: December 2004

The intrinsic viscosity, sedimentation and diffusion of a series of branched, multichain poly‐α‐amino acids having a poly(L‐lysine) backbone and poly(γ‐benzyl L‐glutamate) and poly (β‐benzyl L‐aspartate) side chains was studied at room temperature in dimethylformamide. The molecules were found to be extremely compact structures in which the molecular backbone is either lying along the major axis in a slightly twisted configuration (the longer the side chain the smaller the twist) or is coiled up in the form of a disk with backbone and side chains coplanar. Heat treatment (to 70°C.) introduces only small changes in the hydrodynamic parameters showing that the heat‐labile aggregates detected by light scattering are reversibly broken up during the hydrodynamic measurements. The above structural information concerns the initial metastable conformation of the molecules which is irreversibly destroyed by heat treatment.