bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circular dichroism and molecular conformation of copper(II)–gramicidin S complexes
Authors: Santis P. De , D'Ilario L. , Lamanna G. , Morosletti S. , Savino M. 
Published: December 2004

AbstractOptical properties in different solvents of gramicidin‐bis (salicylaldimine) Cu(II) and (5‐I‐salicyladimine) Cu(II) chelates are intercepted in terms of their molecular structure. A molecular model for the inversion of Contton effects in two different classes of solvents is proposed. This explanation is supported by the study of optical properties of model compounds.
Theory of melting of the triple helix poly (A + 2U) for a 1 : 2 mixture of Poly A to Poly U
Authors: Goldstein Byron 
Published: December 2004

AbstractThe Zimm‐Bragg theory is extended to treat the melting of the triple helix poly (A + 2U) for a solution with a 1 : 2 mole ratio of poly A to poly U. Only the case for long chains is considered. For a given set of parameters the theory predicts the fraction of segments in the triple helix, double helix, and random coil states as a function of temperature.Four nucleation parameters are introduced to describe the two order–disorder transitions (poly (A + 2U) ⇄ poly A + 2 poly U and poly (A + U) ⇄ poly A + poly U) and the single order–order transition (poly (A + 2U) ⇄ poly (A + U) + poly U). A relation between the nucleation parameters is obtained which reduces the number of independent parameters to three. A method for determining these parameters from experiment is presented. From the previously published data of Blake, Massoulié and Fresco8 for [Na+] = 0.04, we find σT = 6.0 × 10−4, σD = 1.0 × 10−3, and σσ* = 1.5 × 10−3. σT and σD are the nucleation parameters for nucleating a triple helix and double helix, respectively, from a random coil region. σσ* is the nucleation parameter for nucleating a triple helix from a double helix and a single strand.Melting curves are generated from the theory and compared with the experimental melting curves.
Etude par Spectroscopie Infrarouge de la Transformation Hélice—Chaine Statistique des Polypeptides. I. Etude Comparée de l'Interaction de la Poly‐L‐alanine et d'un Amide Modèle avec l'Acide Trifluoroacétique
Authors: Combelas P. , Garrigou‐Lagrange C. , Lascombe J. 
Published: December 2004

AbstractInfrared spectra of poly‐L‐alanine in trifluoroacetic acid‐chloroform mixtures have been investigated and compared with those of a model amide (N‐methylacetamide). The purpose of this work is to determine the nature of peptide‐acid specific interactions responsible for the helix‐random coil transition of polymer chains. Analysis is made in using amide (A, I, II, III) and acid (νCO, νOH) vibrations which are specially sensitive to molecular interactions.We examined a model compound to determine the spectral characteristics of the different complexes or species formed between amide and acid. At a low acid concentration, hydrogen‐bonded complexes: (NH) CO…︁HOOCCF3 (1) are evidenced but no association between amide NH and acid CO groups (complexes A) is observed. For higher acid concentrations complexes (I) are progressively changed into ions pairs and free ions, which result from amide protonation by acid, according to the exothermic equilibrium (I)⇌(NH)COH+, −OOCCF3(II). Amidium and carboxylate bands are localized between 1680–1705 cm−1 and 1620–1625 cm−1, respectively. If the cation band is always clearly seen, the anion band is only observed for the most acidic solutions.For the polymer, a gradual complexation of type (I) is observed for all acid concentrations. From our results, the assumption of an (A) type interaction seems very unlikely but cannot be excluded. Moreover, proton transfer—similar to that observed with a model amide—is never evidenced since, in particular, the amidium band characteristic of protonation is never seen. In contrast to previous investigations, we conclude that the helix‐random coil transition of polypeptides is not due to the protonation of the peptide functions. This transition does suggest a strong interaction by hydrogen bonds between polymer and acid molecules.
Ultraviolet circular dichroism of polyproline and oriented collagen
Authors: Mandel Richard , Holzwarth George 
Published: December 2004

AbstractThe ultraviolet absorption, linear dichroism, circular dichroism, and oriented circular dichroism of collagen are reported and the spectra are resolved into a self‐consistent set of bands in accord with exciton theory. The parallel band at 200 nm has 40% of the π → π* intensity; the perpendicular band is placed at 189 nm yielding a splitting of 2700 cm−1. The circular dichroism is resolved into two Gaussians at λ∥ and λτ (rotational strengths +14 × 10−40 and −32 × 10−40 esu2. cm2) plus a large non‐Gaussian (“helix”) band with ampplitude −25,000° at 201 nm. These data appear to be in reasonably good accord with recent calculations.Measurements of the absorption, linear dichroism and circular dichroism of polyproline I and II are also reported and are resolved into their component bands. Polyproline I is in good accord with exciton theory, whereas polyproline II remains unsatisfactory.
Studies on cytochrome c. Part VI. Synthesis of the protected pentadecapeptide (sequence 67–81) of Baker's yeast iso‐I‐cytochrome c
Authors: Moroder Luis , Marchiori Fernando , Borin Gianfranco , Scoffone Ernesto 
Published: December 2004

AbstractThe syntheses are reported of two N‐benzloxycarbonylpeptide tert‐butoxycarbonylhydrazides corresponding to the amino acid sequences 67–74 and 75–81 of the baker's yeast iso‐1‐cytochrome c and their subsequent assembly to the N‐benzyloxycarbonylpentadecapeptide tert‐butoxycarbonylhydrazide corresponding to the sequence 67–81 of the protein.
X‐Ray studies on the conformation of poly‐Nγ‐carbobenzoxy‐L‐α,γ‐diaminobutyric acid and poly‐Nδ‐carbobenzoxy‐L‐ornithine
Authors: Del Pra A. , Spadon P. , Valle G. 
Published: December 2004

AbstractX‐ray diagrams from oriented films and fibers of poly‐Nγ‐carbobenzoxy‐L‐α,γ‐diaminobutyric acid (PCLB) and of poly‐Nδ‐carbobenzoxy‐L‐ornithine (PCLO) have been examined. The conformation in the solid state for both polymers is that of an α‐helix, 18/5 for PCLB and 11/3 for PCLO, respectively.Furthermore, while the PCLB molecules are packed in a trigonal lattice whose dimensions, on hexagonal axes, are a = 27.5 and c = 27.0 Å, the PCLO unit cell is monoclinic with a = 23.3, b = 22.7, c = 16.2 Å, and γ = 119.2°.
Depolarized light scattering by amides and peptides
Authors: Ingwall R. T. , Flory P. J. 
Published: December 2004

AbstractThe Rayleigh ratios RH have been measured for the depolarized scattering dilute solutions of N‐ethylacetamide (EA), N‐methylpropionamide (MP), and N‐acetyl‐pyrrolidine (AP) in P‐dioxane, and dilute aqueous solutions of N‐methylacetamide (MA), N,N‐dimethylacetamide (DMA), EA, and MP. Squares of the optical anisot‐ropies γ of the amides are obtained through extrapolation of these mesurements to infinite dilution. Values of γ2 found for EA and MP in dioxane are in good agreement with calculations based principally on the previously evaluated polarizability tensor of the amide group in conjunction with CC and CH bond polarizabilities. The calculations also involve averaging over all conformations, each being weighted according to the estimated conformational energy. The mean‐squared optical anisotropies (γ2) of the oligoglycines and oligoalanines are calculated by similarly averaging over all skeletal conformations. The anistropic polarizability tensor \documentclass{article}\pagestyle{empty}\begin{document}$ \hat \alpha $\end{document} for the prolyl structural unit
magnified image
is derived for γ2 for AP. The much larger optical anisotropies exhibited by the amides when dissolved in water as compared with those observed in dixane are discussed.
The effect of temperature on acid condensation of DNA
Authors: Dore E. , Frontali C. , Gratton E. 
Published: December 2004

AbstractThe temperature dependence of the condensation phenomenon observed for DNA at low pH is studied in 1M NaCl. The similarity of the effects of an increase in temperature and of a decrease in pH gives some insight into the physical nature of the interactions hindering the unwinding of the DNA molecule in the condensed state.
Intensities and other spectral parameters of infrared amide bands of polypeptides in the β‐ and random forms
Authors: Chirgadze Yu. N. , Shestopalov B. V. , Venyaminov S. Yu. 
Published: December 2004

AbstractThe intensities and other spectral parameters of the main components of infrared amide bands for the random and anti‐parallel pleated sheet forms have been determined for poly‐S‐carbobenzoxymethylcysteine, poly‐S‐carboxymethylcysteine, polylysine and silk fibroin of Bombyx mori in heavy water solutions and in organic solvents. Assuming that the optical spectra of these two types of structure are additive, the method was proposed for determining relative contents and molar absorption coefficients of amide I band. Integral intensity and maximum frequency values of the main components of the amide I band for all the samples in the β‐form turned out to be specific. In contrast to this the integral intensity of the band of amide I in the random coil form varied within certain limits, while the main maximum frequency for all samples remained the same.
Vibrational spectra and dispersion curves of poly‐L‐proline II chain
Authors: Gupta V. D. , Singh R. D. , Dwivedi A. M. 
Published: December 2004

AbstractUsing Wilson's GF‐matrix method as modified by Higgs for infinite helical polymers, dispersion curves and the frequency distribution function have been calculated for poly‐L‐proline II chain. Infrared spectrum is obtained and a Urey‐Bradley force field, which provides best fit with the observed frequencies, is evaluated. The result are discussed from the viewpoint of the conformational characteristics of forms I and II.
Interactions between purine derivatives: Electronic spectral studies. I. Electronic transitions in caffeine monomer and exciton coupling in caffeine dimer
Authors: Kikkert J. N. , Kelly G. R. , Kurucsev T. 
Published: December 2004

AbstractThe concentration dependence of the ultraviolet absorption spectrum of aqueous solutions of caffeine has been studied. Individual species spectra have been derived for the monomer, dimer, and tetramer of caffeine. The emission spectrum of caffeine in aqueous solution and the dichroic spectra in oriented poly(vinyl alcohol) and polyethylene films have been measured. The long‐wavelength tail of the absorption spectrum of caffeine in non‐polar environment has been found to incorporate at least one carbonyl(π*, n) transition. Dichroic spectral data and molecular orbital calculations have been used to assign transition moment directions to the (π*,π) transitions. The lowest energy (π*,π) transition, responsible for the near‐ultraviolet absorption peak in aqueous solution of caffeine, has been used for the study of degenerate exciton interactions in the dimeric species of caffeine. Assuming that the caffeine molecules in the dimer are stacked in parallel planes, theoretical calculations of the ground‐state interactions and of the degenerate exciton interactions have been combined with experimental data and a unique model for the dimer of caffeine has been derived. The transfer rate of energy between the molecules in the dimer is of the order of 1013S−1.
Molecular field theory of hysteresis in helix–coil transitions of polynucleotides
Authors: Weisbuch G. , Neumann E. 
Published: December 2004

AbstractA molecular field theory, taking into account long‐range electrostatic forces is used to study helix–coil transitions of polynucleotides. The theory predicts the existence of hysteresis when the electrostatic interaction parameter is large compared to the thermal energy. The theory is applied to the acid–base titration of poly(A)·2 poly(U).
The vibrational spectra and conformations of some peptide compounds: An application of the additive interatomic interaction model
Authors: Dakhis M. I. , Dashevsky V. G. , Kitaigorodsky A. I. 
Published: December 2004

AbstractThe vibrational spectra of N‐methylformamide, N‐methylacetamide, and acetylglycine N‐methylamide were calculated by use of the additive model of interatomic interactions. The rotation angles ϕ,ψ for acetylglycine N‐methylamide in the crystalline form were determined by the calculation of the spectra of the compound in various conformations. In the A form these angles are equal to 120° and 180°, respectively, and in the B form to 90° and 0°, respectively. The sensitivity of the proposed method to conformational changes, the choice of parameters, and the scope of the method's application are discussed.
Interactions between mucopolysaccharides and cationic polypeptides in aqueous solution: Chondroitin 4‐sulfate and dermatan sulfate
Authors: Gelman R. A. , Blackwell J. 
Published: December 2004

AbstractCircular dichroism spectroscopy has been used to study the interactions of both dermatan sulfate and chondroitin 4‐sulfate with the cationic polypeptides; poly(L‐arginine), poly(L‐lysine), and poly(L‐ornithine). The results indicate that the mucopolysaccharides have a conformation directing effect on both poly(L‐arginine) and poly‐(L‐lysine) such that these polypeptides adopt the α‐helical conformation. The extent of interaction in each polypeptide‐polysaccharide system can be judged by the degree of induced helicity and the “melting temperature” at which the interaction is disrupted On comparison of these results with those previously obtained for chondroitin 6‐sulfate‐polypeptide mixtures, the extent of interaction can be seen to depend on the length of the amino acid side chain and the positions of the anionic groups on the mucopolysaccharide chain. Such considerations place the three mucopolysaccharides in order of increasing interaction: chondroitin 4‐sulfate < chondroitin 6‐sulfate < dermatan sulfate. These results are correlated with observations that dermatan sulfate is bound more tightly to collagen in connective tissues than are the other two polysaccharides.
Studies on the bacteriophage MS2. XXII. Conformation of MS2 RNA in acid medium
Authors: Slegers H. , Fiers W. 
Published: December 2004

AbstractMS2 RNA, which sediments at 27S in a neutral buffer, can be converted to a compact 57S conformation at pH 3.8. Requirements for this conversion, besides protonation, are small concentrations of Mg++ ions and a low ionic strength. On the other hand, after heating in the presence of EDTA and at low ionic strength, the RNA can be unfolded to an 11.7S form at pH 6.8 and to 10.5S at pH 3.8. The compact 57S form has lost at least 50% of its secondary structure, as determined by its hypochromicity. It corresponds to a monomer species, as will be shown in a following paper (XXIV). Comparative studies with the homopolymers poly A and poly C and with the heteropolymers poly A,U, poly A,C, and poly A,G indicate that the interactions involved in the acid RNA conformation are not simply explainable by the known interactions of the A–A+, C–C+, and/or A–C+ type.
Circular dichroism and proton magnetic resonance studies of random chain poly‐L‐lysine
Authors: Epand Richard M. , Wheeler Graham E. , Moscarello Mario A. 
Published: December 2004

AbstractThe 218‐nm peak, characteristic of the circular dichroism of randomly coiled poly‐α‐amino acids can be demonstrated in solutions of penta‐L‐lysine, α‐glycyl‐L‐lysine, as well as poly‐L‐lysine. The thermal stability of the particular state that gives rise to this 218‐nm band in the CD is similar for all three peptides. These results eliminate the possibility that poly‐L‐lysine forms a structure with long‐range order in acidic aqueous solution since the stability of such a structure would be expected to be greater for a higher molecular weight polymer than for a pentamer. The intrinsic viscosity of poly‐L‐lysine of molecular weight 180,000 varies only slightly between 25 and 60°C. The proton magnetic resonance spectra of poly‐L‐lysine and penta‐L‐lysine are indistinguishable on the basis of the chemical shift of all resonances, their line widths, and the exchange rates of the NH protons. This demonstrates that poly‐L‐lysine does not possess a cooperatively formed ordered structure in acidic solutions.A weak band at 238 nm is observed in the circular dichroism of poly‐L‐lysine and other peptides. It is suggested that the effects of change in temperature, salt concentration, or polymer on both the magnitude and position of the 238‐nm band may be explained if it is assumed that it is a shoulder of a lower wavelength peak.
Migration intramoléculaire de l'energie d'excitation dans la poly‐DL‐phenylalanine etude par extinction de fluorescence
Authors: Leroy E. , Lapp C. F. , Laustriat G. 
Published: December 2004

AbstractElectronic energy transfer at the singlet level in poly‐DL‐phenylalanine was studied by comparing the experimental and theoretical values of the rate constants of fluorescence quenching by CCl4 and of energy transfer on a fluorescent acceptor (biacetyl). The fitting of the experimental and calculated values leads to a diffusion coefficient of the excitation energy of 3.8 to 4.8 × 10−5 cm2/s, consistent with 40 residues implied in the migration process.
Caractéristiques géométriques de la séquence HαCαNH de l'isoquinuclidone‐3 examinée dans différents etats physiques influence sur la constante de couplage vicinal J
Authors: Aubry A. , Giessner‐Prettre C. , Cung M. T. , Marraud M. , Neel J. 
Published: December 2004

AbstractThe X‐ray structure analysis of a crystalline sample of 2‐azabicyclo‐[2,2,2]‐octanone‐3 or 3‐isoquinuclidone shows that the molecules of this compound are associated in centrosymmetrical dimers stabilized by two NHOC hydrogen bonds in which the N,H,O atoms are nearly collinear. As a consequence of this interaction, the H atom is shifted from its usual position and the CαNH angle is increased to 125°.Using infrared spectroscopy (νN–H frequency range), it is possible to demonstrate that 3‐isoquinuclidone is mainly in a dimeric form when dissolved in an inert solvent such as CCl4 and to observe the dimer‐monomer equilibrium on dilution from saturation to a low concentration (0.005 mole/l.). On the contrary, dimers are broken off when operating in a polar medium (acetonitrile, deuterochloroform).In the same experimental conditions, measurements of the J vicinal coupling constant, by nuclear magnetic resonance spectroscopy, afford a concentration‐dependent result in the case of CCl4 solutions (increasing from 5.4 to 5.7 Hz when diluting from 0.5 to 0.005 mole/l.) and a constant one (5.8 Hz) in the case of CH3CN or CDCl3 solutions. Then the 0.4‐Hz difference can be attributed to geometrical changes in the HαCαNH system when dimers are broken off and the valence angle CαNH consequently decreases from 125° to its standard value (about 115°). This experimental observation is consistent with the result of a theoretical analysis performed by the INDO method.Then it seems that the use of the formulas proposed by Karplus to account for the valence angle distorsions in ethane‐like systems, in the case of the HαCαNH sequence, could yield overstimated corrections.
Statistical thermodynamics of triple‐helix unzippering for the collagen model (Gly‐Pro‐Pro)n and implications for natural collagen
Authors: Schwarz Martin , Poland Douglas 
Published: December 2004

AbstractInterpreting the data of Kobayashi et al.1 on the thermal transitions of triple helices of (gly‐pro‐pro)n for n = 10, 15, and 20 using a simple model of unzippering and chain dissociation, the thermodynamic parameters characterizing gly‐pro‐pro triple‐helix formation have been determined. The enthalpy and entropy of triple‐helix formation per repeating unit are found to be −7.4 ± 0.8 kcal/mol and −20 ± 2 eu, respectively. Using these parameters, the nature of the unwinding has been investigated for chains containing up to 300 triplets; it is found that there is only a minor amount of helix unwinding from the ends, the major change in helical content arising from chain dissociation. Experimental data on the melting temperatures of natural collagens as a function of imino‐acid composition are used together with the thermodynamic parameters for (gly‐pro‐pro)n to estimate the thermodynamic parameters for triple‐helix formation of amino versus imino acids (the parameters for the former being found to be similar to those for α‐helix formation). Calculations are given using these parameters for model specific‐sequence collagens; it is found that heterogeneity can have a significant influence on the nature of the unwinding of the triple helix.
Enthalpies of helix–coil transitions in polypeptides
Authors: Karasz F. E. , Gajnos G. E. 
Published: December 2004

AbstractCertain discrepancies in measured heats of helix–coil transitions in polypeptides are examined in terms of the theory of the effect of solvent composition on transition temperatures and heats in such systems. It is found, generally, that disagreement between enthalpy measurements conducted at fixed solvent compositions and isothermally may be expected because of the possibility of incomplete conversion of the polypeptide from the random‐coil to the helical conformations, or vice versa in one, or both, of these regimes in the course of the transition. The magnitude of the disagreement, if any, can depend quite critically on the particular region in the transition temperature–solvent composition plane in which measurements are undertaken. Application of these results to the system, poly‐γ‐benzyl‐L‐glutamate–dichloroacetic acid‐1,2‐dichloroethane, however, suggests that previously observed discrepancies in enthalpies here cannot be attributed to this phenomenon.
The interaction of β‐cyclodextrin with dinucleoside phosphates
Authors: Formoso Carl 
Published: December 2004

AbstractCircular dichroism studies of the interaction of β‐cyclodextrin with a series of eight dinucleoside phosphates, and with 3′‐AMP are reported. From results with ApU and ApA, it is shown that β‐cyclodextrin binding is sensitive to dinucleoside stacking in approximately the same way as optical measures of stacking. Some qualitative uses of β‐cyclodextrin binding are suggested, based on the fact that the change in the CD spectrum caused by cyclodextrin binding is unique to each of the dinucleosides studied. Hoffman and Bock have previously suggested the use of β‐cyclodextrin as a probe of nucleic acid structure. Their work indicated that only binding to adenosine and inosine would have to be considered. The present paper shows that binding to other bases cannot be neglected, and will impose serious restrictions on the use of β‐cyclodextrin as a structural probe.