bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photomodulation of conformational states. IV. Integrin‐binding RGD‐peptides with (4‐aminomethyl)phenylazobenzoic acid as backbone constituent
Authors: Milbradt Alexander G. , Löweneck Markus , Krupka Simone S. , Reif Maria , Sinner Eva‐Kathrin , Moroder Luis , Renner Christian 
Published: January 2005

AbstractIn previous studies we have investigated octapeptides backbone‐cyclized by (4‐amino)phenyl azobenzoic acid (APB) or (4‐aminomethyl)phenylazobenzoic acid (AMPB) and containing the active‐site sequence Cys‐Ala‐Thr‐Cys‐Asp from the thioredoxin reductase. The conformational and redox properties of these peptides were strongly dependent on the isomeric state of the azobenzene chromophore. Using the same approach we were successful in constructing photoresponsive ligands for αvβ3 integrin containing the Arg‐Gly‐Asp (RGD) sequence as binding motif. For achieving maximal conformational restriction of the peptide a reduced ring size compared to our previous azobenzene peptides was employed in the cyclic peptide c[Asp‐D‐Phe‐Val‐AMPB‐Lys‐Ala‐Arg‐Gly‐]. Conformational properties of the trans and cis isomers of this peptide in solution were investigated by CD and NMR and were found to differ markedly from the thioredoxin derived azobenzene peptides. In a second peptide, c[Asp‐D‐Phe‐Val‐Lys‐AMPB‐Ala‐Arg‐Gly‐], shifting the position of the chromophore lead to a marked decrease in affinity. With the availability of the x‐ray structure of a cyclic RGD‐pentapeptide bound to αvβ3 integrin (PDB entry 1L5G) modeling of possible bound conformations for trans and cis isomers of both azobenzene peptides was possible. Notably, both peptides in either isomeric form share the same overall conformation in the bound state according to our molecular dynamics simulations. © 2005 Wiley Periodicals, Inc. Biopolymers 77: 304–313, 2005
Biomedical informatics and granularity
Authors: Kumar Anand , Smith Barry , Novotny Daniel D. 
Published: January 2005

AbstractAn explicit formal‐ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT). Copyright © 2004 John Wiley & Sons, Ltd.
The seventh annual Bio‐Ontologies meeting
Authors: Lord Phillip , Stevens Robert 
Published: January 2005

AbstractThe Annual Bio‐Ontologies Meeting has now reached its seventh consecutive year, running as a special interest group (SIG) of the much larger ISMB conference. This year's meeting in Glasgow had approximately 100 attendees. Since the advent of the Gene Ontology, which coincided with the first Bio‐Ontologies Meeting, we have seen a year‐on‐year strengthening of the field; bio‐ontologies has moved from being dominated by computer science to be led by biological applications; discussion is less about ‘what is an ontology?’ and more about ‘how to build an ontology which is fit for purpose?’. This strengthening of the field can be seen elsewhere. Both the main ISMB conference and this year's Pacific Symposium on Biocomputing (PSB) have seen a large number of submissions to their ontologies track. For the first time a selection of the papers from the SIG is being published in this issue of Comparative and Functional Genomics. We hope that this will complement the publications of the larger conferences, bringing to a wider audience the cutting edge research that characterizes the Bio‐Ontologies SIG. Copyright © 2004 John Wiley & Sons, Ltd.
Analysis of single‐locus tests to detect gene/disease associations
Authors: Roeder Kathryn , Bacanu Silviu‐Alin , Sonpar Vibhor , Zhang Xiaohua , Devlin B. 
Published: January 2005

AbstractA goal of association analysis is to determine whether variation in a particular candidate region or gene is associated with liability to complex disease. To evaluate such candidates, ubiquitous Single Nucleotide Polymorphisms (SNPs) are useful. It is critical, however, to select a set of SNPs that are in substantial linkage disequilibrium (LD) with all other polymorphisms in the region. Whether there is an ideal statistical framework to test such a set of ‘tag SNPs’ for association is unknown. Compared to tests for association based on frequencies of haplotypes, recent evidence suggests tests for association based on linear combinations of the tag SNPs (Hotelling T2 test) are more powerful. Following this logical progression, we wondered if single‐locus tests would prove generally more powerful than the regression‐based tests? We answer this question by investigating four inferential procedures: the maximum of a series of test statistics corrected for multiple testing by the Bonferroni procedure, TB, or by permutation of case‐control status, TP; a procedure that tests the maximum of a smoothed curve fitted to the series of of test statistics, TS; and the Hotelling T2 procedure, which we call TR. These procedures are evaluated by simulating data like that from human populations, including realistic levels of LD and realistic effects of alleles conferring liability to disease. We find that power depends on the correlation structure of SNPs within a gene, the density of tag SNPs, and the placement of the liability allele. The clearest pattern emerges between power and the number of SNPs selected. When a large fraction of the SNPs within a gene are tested, and multiple SNPs are highly correlated with the liability allele, TS has better power. Using a SNP selection scheme that optimizes power but also requires a substantial number of SNPs to be genotyped (roughly 10–20 SNPs per gene), power of TP is generally superior to that for the other procedures, including TR. Finally, when a SNP selection procedure that targets a minimal number of SNPs per gene is applied, the average performances of TP and TR are indistinguishable. Genet. Epidemiol. © 2005 Wiley‐Liss, Inc.
Reactions of unsymmetrically substituted allyl radicals with methyl radicals
Authors: Montague D. C. 
Published: January 2005

AbstractThe Hg(63P1) photosensitized decompositions of 3‐methyl‐1‐butene, 2‐methyl‐2‐butene, 3,3‐dimethyl‐1‐butene, and 2,3‐dimethyl‐1‐butene have been used to generate 1‐methylallyl, 1,2‐dimethylallyl, 1,1‐dimethylallyl, and 1,1,2‐trimethylallyl radicals in the gas phase at 24 ± 1°C. From a study of the relative yields of the CH3 combination products, the relative reactivities of the reaction centers in each of these unsymmetrically substituted ambident radicals have been determined. The more substituted centers are found to be the less reactive, and this is ascribed primarily to greater steric interaction at these centers during reaction. Measurement of the ratio of trans‐ to cis‐2‐pentene formed from the 1‐methylallyl radical, combined with published values for this ratio at higher temperatures, enabled the differences in entropy and heat of formation of the trans‐ and cis‐forms of this radical to be calculated as 0.62 ± 0.85 J mol−1 K−1 and ‐ 0.63 ± 0.25 kJ mol−1, respectively, at 298K. Approximate values of the disproportionation/combination ratios for reaction of CH3 with 1,1‐dimethylallyl and 1‐methylallyl have been estimated and used to compute rate constants for the recombinations of tert‐butyl and isopropyl radicals that are in agreement with recently published data.
Thermolysis of dimethyl sulfoxide
Authors: Thyrion F. C. , Debecker G. 
Published: January 2005

AbstractThe thermal decomposition of dimethyl sulfoxide at small extent of reaction has been studied at temperatures of 297‐350°C and pressures of 10–400 Torr. The major products CH4, C2H4, and SO2 were shown to follow first‐order kinetics. The activation energies for production of each was about 48 kcal·mole−1. A chain mechanism has been postulated in the light of the results of isotopic substitution experiments.
Investigation of the rate coefficient for O(3p) + NO2 → O2 + NO
Authors: Slanger Tom G. , Wood Bernard J. , Black Graham 
Published: January 2005

AbstractMeasurements of the rate coefficient of the reaction (O3P) + NO2 → O2 + NO have been made at 296°K and 240°K, using the technique of NO2* chemiluminescent decay. Values of 9.3 × 10−12 cm3 molec−1 sec−1 at 296°K and 10.5 × 10−12 cm3 molec−1 sec−1 at 240°K were obtained, in excellent agreement with the recent results of Davis, Herron, and Huie [1]. The earlier lower values may have resulted from loss of NO2 on surfaces.
Recalculation of data on the thermal decomposition of 1,1‐difluoroethane and 1,1,1‐trifluoroethane
Authors: Tsang Wing 
Published: January 2005

AbstractDisagreements in rate constants and parameters between published results on the decomposition of 1,1‐difluoroethane and 1,1,1‐trifluoroethane are shown to originate from incorrect specification and setting of reaction conditions in one of the studies. When corrected, applicable results are in excellent agreement.
Kinetics of diffusion‐controlled reaction between chemically asymmetric molecules. II. Approximate steady‐state solution
Authors: Šolc K. , Stockmayer W. H. 
Published: January 2005

AbstractThe previously published equation for the rate of a diffusion‐limited bimolecular reaction between chemically asymmetric molecules is studied numerically for the case that one of the reactant molecules is uniform. The results are reproduced quite well by a simple approximate chemical‐kinetic steady‐state scheme and, in principle, allow estimates of the size of the reactive region and of the activation‐controlled rate to be made from the observed dependence of rate on solvent viscosity. The simple scheme is easily generalized to the case of two nonuniform reactants. In general, restriction of reactivity to some fraction of the molecular surface (i.e., a steric factor) must reduce the observable reaction rate, but to an extent which is moderated by the rotational diffusion of the reactant molecules.
Kinetics and mechanism of the substitution of olefinic ligands by triphenylantimony in (π‐monoolefin) tetracarbonyliron complexes
Authors: Cardaci G. 
Published: January 2005

AbstractThe kinetics of the reaction

have been studied in toluene solution. The reaction occurs by a dissociative mechanism and the observation of an appreciable mass law retardation effect shows that Fe(CO)4 is produced as an intermediate. Analysis of the effect of the substituent X on the stability of the complexes leads to the conclusion that π‐backbonding between the metal and the olefinic ligand is the major cause of the M‐olefin bond strength.
Kinetics of the reactions of 2,4,6‐tri‐t‐butylphenoxyl with cumene hydroperoxide, cumylperoxyl radicals, and molecular oxygen
Authors: Griva A. P. , Denisov E. T. 
Published: January 2005

AbstractReactions of 2,4,6‐tri‐t‐butylphenoxyl (TBP) with cumene hydroperoxide (ROOH), cumylperoxyl radicals (RO2), and molecular oxygen in benzene solution have been investigated kinetically by the ESR method. The rate constant of the reaction TBP + ROOH magnified image has been estimated in the temperature range 27°‐75°C: log10(k−7/M−1sec−1) = (7.1 ± 0.4) ‐ (10.9 ± 0.6 kcal mole−1)/θThe ratio of the rate constants of reactions TBPH + RO2 magnified image products has been determined from the experimental dependence of the rate constant of reaction TBP with ROOH on [TBPH]0/[TBP]0. Putting k7 = 4.0 × 103M−1sec−1, we obtain k8 = (2.0 ± 0.2) × 108M−1sec−1 at 30°C. The reaction of TBP with O2 obeys the kinetic law −d[TBP]/dt = k′[O2][TBP]2. This is in accordance with scheme TBP + O2 ← TBP ⃛O2 [I]; TBP ⃛O2 + TBP · products, log10 (k′/M−2sec−1) = (−14.5 ± 0.9) + (27.2 ± 1.4)/θ at 66°−78°C, where ° = 2.303RT.
A simple empirical method for the estimation of activation energies in radical molecule metathesis reactions
Authors: Alfassi Ze'ev B. , Benson Sidney W. 
Published: January 2005

AbstractSeveral new empirical methods are presented for the prediction of activation energies E of the metathetical transfer reaction of single bonded atoms in radical‐molecule reactions of the type A· + BC → AB + C· The methods assign additive contributions to E for the endgroups A· and C·, neglecting the effect of the transferred atom B. Most of the predicted values agree to within l kcal mol−1 with the experimental activation energies (average error = 0.82 and standard deviation = 1.02 kcal mol−1). This is comparable to the best of the more complex schemes available for such estimation.
Kinetics into the steady state. I. study of the reaction of oxygen atoms with methyl radicals
Authors: Slagle Irene R. , Pruss Frank J. , Gutman David 
Published: January 2005

AbstractThe exponential relaxation of CH3, produced by the reaction O + C2H4 → CH3 + HCO, to its steady‐state concentration was quantitatively monitored after the reactants were mixed. The relaxation profiles yield the rate constant of the reaction O + CH3 → H2CO + H equal to (1.85 ± 0.28) × 10‐10 cm3/molecule‐sec at 300°K. Ancillary experiments yielded values for the rate constant for the reaction of O atoms with C2H4 at 300°K, the average of which is 7.7 × 10‐12 cm3/molecule‐sec. The experimental technique, which employs a fast‐flow reactor coupled to a photoionization mass spectrometer, is described in detail and its potential discussed.
Electron spin resonance and kinetic study of the photolysis of p‐Flouranil (tetrafluoro‐p‐benzoquinone) in dioxane
Authors: Vyas H. M. , Wan J. K. S. 
Published: January 2005

AbstractThe photochemistry of p‐fluoranil in dioxane was studied by electron spin resonance (ESR) and the ESR‐rotating sector technique. The transient photoradical is identified as the p‐tetrafluorobenzosemiquinone neutral radical with a hyperfine splitting of 1.1 gauss for the hydroxy proton and the fluorine hyperfine splittings of 3.8 and 14.1 gauss for the meta and ortho fluorines, respectively. The radicals decayed by self‐disproportionation with a second‐order rate constant at room temperature of approximately 3.2 × 109M−1s−1. The activation energy of the decay process is found to be about 2.4 ± 0.4 kcal/mole.
Kinetics of reactions of Schiff base complexes of iron(II). V. Reactions of the complex of the hexadentate ligand NN‴‐bis‐[α‐(2‐pyridyl)benzylidene]triethylenetetramine in acid solution and with hydroxide, cyanide, and peroxodisulphate
Authors: Gardner E. R. , Mekhail F. M. , Burgess J. 
Published: January 2005

AbstractThe preparation and characterization of the iron(II) complex of the hexadentate Schiff base ligand NN‴‐bis‐[α‐(2‐pyridyl)benzylidene]triethylenetetramine are reported. Kinetic patterns and rate constants for aquation of this complex, and for its reactions with hydroxide, cyanide, and peroxodisulphate have been determined. Activation parameters for the reaction with cyanide, in aqueous solution, are ΔH‡ = 24.3 kcal/mole and ΔS‡ = +1 cal/deg‐mole.
Pathways of proton transfer in acetal hydrolysis
Authors: Dunn Ben M. 
Published: January 2005

AbstractThe process of acetal hydrolysis is analyzed in terms of the competing steps of proton transfer and heavy atom reorganization. The results of this analysis are portrayed in a series of three‐dimensional reaction coordinate diagrams. The observed pathway of hydrolysis (A‐1, general acid catalyzed, or spontaneous) is shown to depend on the energy of the various possible intermediates in these reactions.
Molecular relaxation processes in triatomic molecules. II. The N2–CO2 system
Authors: Thommarson Ronald L. , Berend George C , Benson Sidney W. 
Published: January 2005

AbstractTranslation–vibration (T–V) and vibration–vibration (V–V) energy transfer processes in the N2–CO2 system were investigated using classical trajectory techniques. Two empirical interaction potentials were employed. One is comprised of independent, atom–atom Morse‐type functions operating between nonbonded atoms. The other included these atom–atom Morse functions plus Coulombic terms to account for the quadrupole–quadrupole intertion. Both interaction potentials led to similar T–V results. However, the result that CO2(v3) is excited ∼103 times more efficiently than N2(v = 1) was obtained, which is at variance with existing analytical theories of T–V energy transfer employing purely repulsive short‐range potentials. Different V–V energy transfer probabilities were obtained from the two interaction potentials. The most important finding is that only when electrostatic orientation effects are combined with short‐range repulsive interactions is the near‐resonant

V–V transfer found to be the dominant energy transfer path. This interaction potential also crudely accounts for the negative temperature dependence observed for this near‐resonant V–V transfer at low temperatures (300–1000°K).
Determination of D[C6F5‐I] by the toluene carrier method
Authors: Krech Michael J. , Price Stanley James W. , Yared Wayne F. 
Published: January 2005

AbstractThe pyrolysis of C6F5I has been studied by the toluene carrier method over the temperature range of 900–978°K with contact times of 0.4–2.0 seconds and total pressures of 11.2–19.5 torr. Percent decomposition ranged from 8.6 to 97.7%. With toluene‐to‐C6F5I molar ratios of greater than 150, 85–100% of the C6F5 released abstracts a hydrogen atom from toluene to produce C6F5H. No significant quantities of I2 were observed and the only major gaseous product was HI. Within the limits of the experimental method the decomposition of C6F5I was first order and homogeneous.Least squares analysis of log k1 and 103/T(C6F5I → C6F5 + I) values gives

while a weighted line of best fit yields.

Based on this latter equation D[C6F5I] at 298°K is estimated as 66.2 kcal/mole.
Oxidation of hydrocarbons in the presence of added hydroperoxide. On the determination of rate constants by the hydroperoxide method
Authors: Niki Etsuo , Okayasu Kisaburo , Kamiya Yoshio 
Published: January 2005

AbstractOxidation of tetralin in the presence of tert‐butyl hydroperoxide and tetralyl hydroperoxide, initiated with azobisisobutyronitrile, was studied at 60°C in order to examine the complications involved in the hydroperoxide method devised by Howard and Ingold. From literature data on absolute rate constants and our rates of oxidation, cross termination rate constants and contributions of each elementary propagation and termination step were computed. It was confirmed that this method was quite useful in determining the cross propagation rate constant, but it was also demonstrated that the rate of oxidation should be measured at very low conversion and with quite high concentrations of hydroperoxide, especially when the peroxy radical derived from the added hydroperoxide has a much lower termination rate constant than that from the oxidizing substrate.
Communication to the editor pentyl radical isomerizations: Evidence for a 1,2 or 1,3 hydrogen migration
Authors: Tardy D. C. 
Published: January 2005

AbstractVibrationally excited pentyl‐1, ‐2, and ‐3 radicals were formed selectively by the addition of thermal H atoms to the various pentene isomers with approximately 47 kcal/mole of vibrational energy. Decomposition products other than those expected, along with their pressure dependences, support the fact that either 1,2 or 1,3 hydrogen migrations with either a 3‐ or 4‐member cyclic transition state is occurring with a ka of approximately 3 × 105 or 6 × 105 sec−1. A corresponding critical energy of 33 or 31 kcal/mole is found.
The thermochemical kinetics of retro‐ “ene” reactions of molecules with the general structure (allyl) XYH in the gas phase. IX. The thermal unimolecular decomposition of ethyallylether in the gas phase
Authors: Egger Kurt W. , Vitins Peter 
Published: January 2005

AbstractThe thermal decomposition of ethylallylether (EAE) has been studied in the gas phase over the temperature range of 560–648°K. Propylene and acetaldehyde are the only reaction products observed. The reaction is apparently homogeneous in nature and independent of the pressure of EAE and of added foreign gases. The experimetally determined first‐order rate constants, using the internal standard technique, fit the Arrhenius relationship log k(s−1) = 11.84 ± 0.29 − (43.57 ± 0.77 kcal/mole)/2.303RT. Independently the same rate constants are obtained, based on the amounts of products formed. The observed activation parameters are in general agreement with expectations based on the concept of a 6‐center 1,5‐H‐shift retro‐“ene” reaction mechanism, and they agree with previous results obtained for the similar reactions involving alkylallylamines and olefins.
On the accuracy of the hydroperoxide method of determining absolute rate constants for hydrogen atom abstraction by the tert‐butylperoxy radical
Authors: Howard J. A. , Chenier J. H. B. 
Published: January 2005

AbstractMeasurements of rates of oxygen absorption and steady‐state peroxy radical concentrations for the autoxidation of tetralin in the presence of tert‐butyl hydroperoxide have shown that the rate constant for reaction of the tert‐butylperoxy radical with tetralin at 60°C is approximately 11.0 M−1 s−1. This rate constant is about a factor of 4 larger than the value recently reported by Niki, Okayasu, and Kamiya for this reaction.The present work emphasizes that great care should be taken when the hydroperoxide method is used to estimate cross‐propagation rate constants for a substrate as reactive as tetralin at a temperature as high as 60°C.
The kinetics and mechanism of the slow oxidation of hydrogen
Authors: Shakhnazaryan I. K. , Sachyan G. A. , Philipossyan A. G. , Nalbandyan A. B. 
Published: January 2005

AbstractA low‐temperature matrix isolation method has been developed which makes possible the isolation and detection of HO2 radicalsfrom a gas‐phase radical chain‐reaction system containing atomic H, O and OH radicals as well. The formation of HO2 radicals is demonstrated in the rarified hydrogen flame. The same radicals are observed to exist during the slow oxidation reaction of hydrogen between the second and third inflammation limitsThe kinetics of accumulation of HO2, H2O2, and H2O has been studied as a function of total pressure, composition of reacting mixtures, temperature, and diameter and the treatmentof the surface of the reaction vessel. It has been established that in a reactor treated with boric acid, the concentration of HO2 radicalsis in the order of 101 2–101 4 particles/cm3. The kinetic relationship obtained confirms the necessity of including the following step in the mechanism of slow oxidation of hydrogen:

For a quantitative description of the experimental results, calculationsof the complete mechanism of the slow reaction are performed by computer methods. The values of the rate constants of the elementary reactions that enter into the mechanism proposed were taken from published data. Some of them were varied by small intervals to give a better agreement with experimental values. The agreement justifies the mechanism proposed for the experimental conditions employed.
Ozone–olefin reactions in the gas phase 1. Rate constants and activation energies
Authors: Becker K. H. , Schurath U. , Seitz H. 
Published: January 2005

AbstractReactions of ozone with simple olefins have been studied between 6 and 800 mtorr total pressure in a 220‐m3 reactor. Rate constants for the removal of ozone by an excess of olefin in the presence of 150 mtorr oxygen were determined over the temperature range 280 to 360° K by continuous optical absorption measurements at 2537 Å. The technique was tested by measuring the rate constants k1 and k2 of the reactions (1) NO + O3 → NO2 + O2 and (2) NO2 + O3 rarr; NO3 + O2 which are known from the literature. The results for NO, NO2, C2H4, C3H6, 2‐butene (mixture of the isomers), 1,3→butadiene, isobutene, and 1,1 ‐difluoro‐ethylene are 1.7 × 10−1 4 (290°K), 3.24 × 10−17 (289°K), 1.2 × 10−1 4 exp (–4.95 ± 0.20/RT), 1.1 × 10−1 4 exp (–3.91 ± 0.20/RT), 0.94 × 10−1 4 exp ( –2.28 ± 0.15/RT), 5.45 ± 10−1 4 exp ( –5.33 ± 0.20/RT), 1.8 ×10−17 (283°K), and 8 × 10−20 cm3/molecule ·s(290°K). Productformation from the ozone–propylene reaction was studied by a mass spectrometric technique. The stoichiometry of the reaction is near unity in the presence of molecular oxygen.