bluuebunny/crossref_metadata_2025 huggingface dataset:
Sorption and partial molar volumes of C2 and C3 hydrocarbons in polypropylene copolymers
Authors: Tsuboi Akio , Kolář Petr , Ishikawa Takeshi , Kamiya Yoshinori , Masuoka Hirokatsu
Published: August 2002

The sorption of C2 and C3 hydrocarbons in two ethylene–propylene copolymers and a propylene homopolymer and the simultaneous dilation of the polymers were measured at temperatures of 287–363 K and pressures up to 4 MPa. The sorption isotherms were well described by the Flory–Huggins theory of dissolution. Dilation isotherms in the form of elongation versus pressure were similar in shape to the corresponding sorption isotherms. Solubility coefficients, partial molar volumes, and Flory–Huggins interaction parameters were determined from these isotherms. The thermal expansivities of the hydrocarbons dissolved in the polymers were 0.002–0.005 K−1, and the Flory–Huggins interaction parameters depended not only on temperature but also on concentration. At 323 K, the calculated solubilities of propylene in the ethylene–propylene‐rubber regions of the copolymers were 1.8 times higher than in the amorphous regions of the propylene homopolymer. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 1255–1262, 2001
Origin of miscibility‐induced sequential reordering and crystallization‐induced sequential reordering in binary copolyesters: a Monte Carlo simulation
Authors: Youk Ji Ho , Jo Won Ho
Published: August 2002

The effect of the repulsive interaction between the components of binary copolyesters on their sequence order was investigated with the Monte Carlo simulation method. The phase separation and ester‐interchange reactions were implemented simultaneously with a kind of one‐site bond fluctuation model. When the repulsive interaction energy was applied to the binary copolyesters, miscibility‐induced sequential reordering (MISR) was induced. The more repulsive the pair interaction was, the higher the sequence order was. During the MISR process, homoester‐interchange reactions became more favorable because of the repulsive interaction, accompanying the decrease of the interactional free energy. The sequence order resulting from MISR was independent of the relative trial ratio of phase separation to ester‐interchange reaction at a given value of interaction energy. Restoration of the sequence distribution was also simulated with and without the repulsive interaction between the components of the binary copolyesters to investigate the effect of MISR on the crystallization‐induced sequential reordering (CISR) process in binary copolyesters, where sequences with lengths longer than 6 were assumed to crystallize and could not take part in ester‐interchange reactions. The sequence distribution in the amorphous phase was restored via ester‐interchange reactions. When the repulsive interaction was applied to binary copolyesters during the CISR process, restoration of the sequence distribution was accelerated, indicating that MISR can accelerate the CISR process when a polyester blend shows upper critical solution temperature behavior. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 1337–1347, 2001
Application of a model‐free isoconversional method to the cure of phenolic systems
Authors: Li Shuyan , Järvelä Pentti
Published: August 2002

The curing process of a phenolic resole was monitored with differential scanning calorimetry under nonisothermal and isothermal conditions, the curing kinetics were analyzed with a model‐fitting approach and a model‐free isoconversional method, and the activation energy of this phenolic system was found to be close to 46 ± 4 kJ mol−1. For complicated cures, the model‐free isoconversional method was found to be a simpler and more reliable approach. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 1525–1528, 2001
Poly(ethylene terephthalate) copolymers containing 5‐nitroisophthalic units. II. Crystallization studies
Authors: Kint Darwin P. R. , De Ilarduya Antxon Martínez , Muñoz‐Guerra Sebastián
Published: August 2002

The microstructure and crystallization behavior of a set of poly(ethylene terephthalate‐co‐5‐nitroisophthalate) copolymers (PETNI) containing 5‐nitroisophthalic units in the 10–50 mol % range were examined and compared to those of poly(ethylene terephthalate) (PET) and poly(ethylene terephthalate‐co‐isophthalate) (PETI) copolymers. A 13C NMR analysis of PETNI copolymers in a trifluoroacetic acid solution indicates that they are random copolymers with average sequence lengths in accordance with ideal polycondensation statistics. Differential scanning calorimetry (DSC) studies show that PETNI containing 5‐nitroisophthalic units up to 20 mol % are able to crystallize and that crystallization takes place in these copolymers at much slower rates than in PET. Wide‐angle X‐ray diffraction from powder and fibers reveals that crystallizable PETNI adopts the same triclinic crystal structure as PET, with the nitroisophthalate units being excluded from crystallites. Fourier transform infrared in combination with cross‐polarization/magic‐angle spinning 13C NMR spectroscopy demonstrates the occurrence of a gauche–trans conversion encompassing the crystallization process. A correlation between DSC and spectroscopic data leads us to conclude that the content of trans conformer in the noncrystallized phase of PETNI is higher than in both PET and PETI copolymers and suggests that secondary crystallization in the homopolymer must proceed by a mechanism different than that in copolymers. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 1553–1564, 2001
Resonance raman spectra of poly‐(p‐phenylenebenzobisoxazole), poly‐(p‐phenylenebenzobisthiazole), and poly(pyridobisimidazole)
Authors: Takahashi Yasuhiro
Published: August 2002

Resonance Raman spectra of poly(p‐phenylenebenzobisoxazole) (PBO), poly(p‐phenylenebenzobisthazole) (PBZT), and poly(pyridobisimidazole) (PIPD) were measured. In the case of PBO, no large dependence on wavelength of excited laser can be observed, whereas in the cases of PBZT and PIPD, the spectra depends on wavelength of excited laser. This difference may be attributed to the colors of the samples: PBO is gold, and PBZT and PIPD are metallic blue, which show the different conjugated states. The spectra of PBO are rather simpler than those of PBZT and PIPD. This is considered to be reflected by the fact that only a chain passes through the unit cell of PBO, while two chains pass through the unit cell of PBZT and PIPD. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 1791–1793, 2001
Differential scanning calorimetry, small‐angle X‐ray scattering, and wide‐angle X‐ray scattering on homogeneous and heterogeneous ethylene‐α‐copolymers
Authors: Jokela K. , Väänänen A. , Torkkeli M. , Starck P. , Serimaa R. , Löfgren B. , Seppälä J.
Published: August 2002

The objective of this work was to use both X‐ray and differential scanning calorimetry techniques in a comparative study of the lamellar and crystalline structures of heterogeneous and homogeneous ethylene‐α‐copolymers. The samples differed in the comonomer type (1‐butene, 1‐hexene, 1‐octene, and hexadecene), comonomer content, and catalyst used in the polymerizations. Step crystallizations were performed with differential scanning calorimetry, and the crystallinity and lamellar thicknesses of the different crystal populations were determined. Wide‐angle X‐ray scattering was used to determine crystallinities, average sizes of the crystallites, and dimensions of the orthorhombic unit cell. The average thickness, separation of the lamellae, and volume fractions of the crystalline phase were determined by small‐angle X‐ray scattering (SAXS). The results revealed that at densities below 900 kg/m3, polymers were organized as poorly organized crystal bundles. The lamellar distances were smaller and the lamellar thickness distributions were narrower for the homogeneous ethylene copolymers than for the heterogeneous ones. Step‐crystallization experiments by SAXS demonstrated that the long period increased after annealing. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 1860–1875, 2001
Transcrystallization kinetics of poly(vinylidene fluoride)
Authors: Benkhati Hassan , That Ton , Tan Minh , Jungnickel Bernd‐J.
Published: August 2002

We report the transcrystallinity of poly(vinylidene fluoride) on several different types of substrate materials. The supermolecular structure and its development were characterized with polarization microscopy, whereas differential scanning calorimetry was used for monitoring the isothermal and nonisothermal crystallization kinetics. Although only approximately applicable, an Avrami–Ozawa analysis of the latter yielded reliable exponents, which characterized the transcrystalline nucleation conditions, the related dimensionality of growth, and the resulting texture. The results complemented and agreed quantitatively with those of light microscopy. Several polymers, including poly(ethylene terephthalate), polytetrafluoroethylene, and polyimide, induced distinct transcrystallinity, but only a spherulitic supermolecular structure developed on glass and metallic substrates. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 2130–2139, 2001
Nonpharmacologic group treatment of insomnia: a preliminary study with cancer survivors
Authors: Davidson Judith R. , Waisberg Jodie L. , Brundage Michael D. , MacLean Alistair W.
Published: August 2002

This study describes, and examines the initial efficacy of, a sleep therapy programme developed for cancer patients with insomnia. The six‐session group programme included stimulus control therapy, relaxation training, and other strategies aimed at consolidating sleep and reducing cognitive‐emotional arousal. The 12 final participants were patients of a regional cancer centre; mean age was 54.7 years (S.D. 10.4); median time from cancer diagnosis was 33.6 months; all had high performance status. Participants kept sleep diaries and rated their sleep quality, mood and functioning at baseline, week 4 and week 8. Significant improvement over baseline was observed at weeks 4 and 8 in the number of awakenings, time awake after sleep onset, sleep efficiency, sleep quality ratings, and scores on European Organization for Research and Treatment of Cancer (EORTC) QLQ‐C30 role functioning and insomnia. Total sleep time and fatigue were significantly improved at week 8.

The sleep therapy programme was associated with improved sleep, reduced fatigue and enhanced ability to perform activities in relatively well individuals attending a cancer centre. This is preliminary evidence of the efficacy of the programme. Further research is required to examine the programme's effectiveness and suitability for a wider range of people with cancer. Options for providing cancer patients with access to nonpharmacologic treatments for insomnia are discussed. Copyright © 2001 John Wiley & Sons, Ltd.
Frost heave and thaw consolidation of ploughing boulders in a mid‐alpine environment, Finse, Southern Norway
Authors: Berthling Ivar , Eiken Trond , Sollid Johan Ludvig
Published: August 2002

The frost heave and thaw consolidation of five large ploughing boulders were studied at Finse (UTM32VMN185198), southern Norway, by optical levelling from a bedrock benchmark. The boulders heave 3–7 cm, mainly during the early winter. Thaw consolidation starts while the boulders are still completely snow‐covered in spring, but accelerates considerably when a trench in the snow is melted down to the ground surface around the boulders. During four years of measurements, the vertical position of the boulders lowered by a total mean of 5 mm. Boulder heave was well correlated to the square root of the freezing index, although differences in snow cover between subsequent years had marked effects on the heave of some of the boulders. The overburden pressure of the boulders also influenced total heave. An equation was obtained, relating boulder heave to the square root of the freezing index and the average height of the boulder. Copyright © 2001 John Wiley & Sons, Ltd.

Le soulèvement par le gel et la retombée au dégel de 5 grands blocs labourant ont été observés à Finse (UTM MN185198), au sud de la Norvège, par nivellement optique à partir d'un repère fixé sur la roche en place. Le soulèvement est de 3‐7 cm et se réalise principalement pendant le début de l'hiver. L'affaissement au dégel débute au printemps alors que les blocs sont encore complètement couverts de neige, mais s'accélère beaucoup quand la neige a fondu autour des blocs. Pendant les quatre années de mesures, les blocs se sont affaissés au dégel d'une moyenne totale de 5 mm. Le soulèvement des blocs est bien corrélé avec la racine carrée de l'index de gel, quoique des différences dans la couverture de neige suivant les années ont des effets marqués sur le soulèvement de quelques blocs. La pression des blocs influence aussi le soulèvement total. Une équation a été obtenue mettant en relation le soulèvement des blocs avec la racine carrée de l'index de gel et la hauteur moyenne des blocs. Copyright © 2001 John Wiley & Sons, Ltd.
Contribution of death receptor and mitochondrial pathways to Fas‐mediated apoptosis in the prostatic carcinoma cell line PC3
Authors: Guseva Natalya V. , Taghiyev Agshin F. , Rokhlin Oskar W. , Cohen Michael B.
Published: August 2002

BACKGROUND

Two main pathways of apoptosis in mammalian cells have been described: the death receptor pathway and the mitochondrial pathway. Two different cell types have been identified for Fas‐mediated apoptosis, each using almost exclusively one of two different signaling pathways. Human prostatic carcinoma cell line, PC3 is sensitive to Fas‐mediated apoptosis, but relation of receptor and mitochondrial pathways is not clear.

METHODS

Cell viability was estimated by calcein assay. Apoptosis was determined by preparation of DNA ladder. Expression of Fas‐associated death domain‐dominant negative (FADD‐DN) and Bcl‐2, activation of caspases, PARP, DFF45, Bid cleavage, and cytochrome c release were assessed using Western blotting techniques. [35S] Methionine‐labeled caspase‐3 was transcribed in vitro and translated using the TNT kit (Promega). A vector containing caspase‐3 was prepared by the ligation of EcoR I/BamHI flanked PCR fragment of full size caspase‐3 cDNA into pBlusckript II SK(+/−) (Stratagen).

RESULTS

Overexpression of both FADD‐DN and Bcl‐2 genes prevent Fas‐mediated apoptosis in PC3. As predicted, overexpression of FADD‐DN prevented activation of caspase‐8 and Bid cleavage and attenuated the release of cytochrome c and activation of caspases ‐2, ‐7, and ‐9. Bcl‐2 overexpression did not affect caspase‐8 activation and cleavage of Bid but blocked the release of cytochrome c and activation of mitochondria localized caspases ‐2, ‐7, and–9. Overexpression of FADD‐DN and Bcl‐2 affected the activation of caspase‐3 and PARP cleavage differently: FADD‐DN attenuated the activation of caspase‐3 and PARP cleavage whereas Bcl‐2 overexpression prevented caspase‐3 activation and completely blocked cleavage of PARP.

CONCLUSIONS

These data suggest that activation of caspase‐8 is necessary but not sufficient to complete Fas‐mediated apoptosis in PC3 cells without activation of the mitochondrial pathway. In addition, caspase‐3 activation after Fas‐receptor ligation involves two steps and is dependent on mitochondrial activation. Prostate 51: 231–240, 2002. © 2002 Wiley‐Liss, Inc.
Essential domain motions in barnase revealed by MD simulations
Authors: Nolde Svetlana B. , Arseniev Alexander S. , Orekhov Vladislav Yu , Billeter Martin
Published: August 2002

The wealth of data accumulated on the bacterial ribonuclease barnase is complemented by molecular dynamics trajectories starting from four different experimental structures and covering a total of >10 ns. Using principal component analysis, the simulations are interpreted in view of dynamic domains and hinges promoting relative motions of these domains. Two domains with residues 7–22 and 52–108 for the first domain and residues 25–51 for the second domain were consistently observed. Hinge regions consist primarily of Tyr24, Ser50, Ile51, and Gly52. Earlier mutation studies have demonstrated that the residues of the hinge regions play essential roles for the stability and activity of barnase. The domain motions are correlated to inter‐domain interactions involving functionally important active site residues, such as Lys27 and Glu73. A model is presented that combines the observation of dynamic domains and their motions with the extensive mutation data from the literature. Enthalpic energy contributions originating from specific inter‐domain interactions as well as entropic energy contributions due to the domain motions are discussed in the frame of this model and compared with destabilization energies measured for corresponding mutants. Proteins 2002;46:250–258. © 2002 Wiley‐Liss, Inc.
Identifying proteins of high designability via surface‐exposure patterns
Authors: Emberly Eldon G. , Miller Jonathan , Zeng Chen , Wingreen Ned S. , Tang Chao
Published: August 2002

Using an off‐lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique lowest‐energy conformation. We find that designability is closely correlated with the pattern of surface exposure of the folded structure. For longer chains, complete enumeration of structures is impractical. Instead, structures can be randomly sampled, and relative designability estimated either from designability within the random sample, or directly from surface‐exposure pattern. We compare the surface‐exposure patterns of those structures identified as highly designable to the patterns of naturally occurring proteins. Proteins 2002;47:295–304. © 2002 Wiley‐Liss, Inc.
Expanding the nitrogen regulatory protein superfamily: Homology detection at below random sequence identity
Authors: Kinch Lisa N. , Grishin Nick V.
Published: August 2002

Nitrogen regulatory (PII) proteins are signal transduction molecules involved in controlling nitrogen metabolism in prokaryots. PII proteins integrate the signals of intracellular nitrogen and carbon status into the control of enzymes involved in nitrogen assimilation. Using elaborate sequence similarity detection schemes, we show that five clusters of orthologs (COGs) and several small divergent protein groups belong to the PII superfamily and predict their structure to be a (βαβ)2 ferredoxin‐like fold. Proteins from the newly emerged PII superfamily are present in all major phylogenetic lineages. The PII homologs are quite diverse, with below random (as low as 1%) pairwise sequence identities between some members of distant groups. Despite this sequence diversity, evidence suggests that the different subfamilies retain the PII trimeric structure important for ligand‐binding site formation and maintain a conservation of conservations at residue positions important for PII function. Because most of the orthologous groups within the PII superfamily are composed entirely of hypothetical proteins, our remote homology‐based structure prediction provides the only information about them. Analogous to structural genomics efforts, such prediction gives clues to the biological roles of these proteins and allows us to hypothesize about locations of functional sites on model structures or rationalize about available experimental information. For instance, conserved residues in one of the families map in close proximity to each other on PII structure, allowing for a possible metal‐binding site in the proteins coded by the locus known to affect sensitivity to divalent metal ions. Presented analysis pushes the limits of sequence similarity searches and exemplifies one of the extreme cases of reliable sequence‐based structure prediction. In conjunction with structural genomics efforts to shed light on protein function, our strategies make it possible to detect homology between highly diverse sequences and are aimed at understanding the most remote evolutionary connections in the protein world. Proteins 2002;48:75–84. © 2002 Wiley‐Liss, Inc.
Free energy barrier estimation of unfolding the α‐helical surfactant‐associated polypeptide C
Authors: Zangi Ronen , Kovacs Helena , van Gunsteren Wilfred F. , Johansson Jan , Mark Alan E.
Published: August 2002

Molecular dynamics simulations were conducted to estimate the free energy barrier of unfolding surfactant‐associated polypeptide C (SP‐C) from an α‐helical conformation. Experimental studies indicate that while the helical fold of SP‐C is thermodynamically stable in phospholipid micelles, it is metastable in a mixed organic solvent of CHCl3/CH3OH/0.1 M HCl at 32:64:5 (v/v/v), in which it undergoes an irreversible transformation to an insoluble aggregate that contains β‐sheet. On the basis of experimental observations, the free energy barrier was estimated to be ∼100 kJ/mole by applying Eyring's transition state theory to the experimental rate of unfolding [Protein Sci 1998;7:2533–2540]. These studies prompted us to carry out simulations to investigate the unwinding process of two helical turns encompassing residues 25–32 in water and in methanol. The results give an upper bound estimation for the free energy barrier of unfolding of SP‐C of ∼20 kJ/mole. The results suggest a need to reconsider the applicability of a single‐mode activated process theory to protein unfolding. Proteins 2001;43:395–402. © 2001 Wiley‐Liss, Inc.
Molecular dynamics simulations of a highly charged peptide from an SH3 domain: Possible sequence–function relationship
Authors: Krueger Brent P. , Kollman Peter A.
Published: August 2002

A seven‐residue peptide that is highly conserved in SH3 domains despite being far from the active site has been shown by NMR to be stable in solution. This peptide, biologically important because it is a likely folding nucleus for SH3 domains, provides a challenging subject for molecular dynamics because it is highly charged. We present stable, 10‐ns simulations of both the native‐like diverging turn structure and a helical model. Free energies of these two conformations, estimated through MM‐PBSA analysis using several force fields, suggest a comparable free energy (ΔΔG ≤6 kcal/mol) for native and helix conformations. NOE intensities calculated from the native trajectory reproduce experimental data quite well, suggesting that the conformations sampled by the trajectory reasonably represent those observed in the NMR experiment. The molecular dynamics results, as well as sequence analysis of a diverse 690‐member family of SH3 domain proteins, suggest that the presence of two elements is essential for formation of the diverging turn structure: a pair of residues with low helical propensity in the turn region and, as previously recognized, two hydrophobic residues to close the end of the diverging turn. Thus, these two sequence features may form the structural basis for the function of this peptide as a folding nucleus in this family of proteins. Proteins 2001;45:4–15. © 2001 Wiley‐Liss, Inc.
A family of proteins related to Spätzle, the toll receptor ligand, are encoded in the Drosophila genome
Authors: Parker James S. , Mizuguchi Kenji , Gay Nicholas J.
Published: August 2002

The Drosophila gene Spätzle encodes the activating ligand for the Toll receptor. This signaling pathway is required for dorso‐ventral patterning in the early embryo and an antifungal immune response in larvae and adults. The genome sequence of Drosophila shows that there are a total of eight Toll‐like receptors and these may function in other aspects of embryonic development and innate immunity. Here we describe five Drosophila homologues of Spätzle (Spz2‐6) found using an iterative searching method. All five appear to encode proteins containing neurotrophin‐like cystine‐knot domains. In addition, most retain a characteristic intron‐exon structure shared with the prototype Spätzle gene. This provides evidence that the family arose by ancient gene duplication events and indicates that the gene products may represent activating ligands for corresponding Toll receptors. Expression studies show that only Spz4 is expressed strongly in larvae and adults and thus may be involved in an ancillary antifungal response mediated by Toll‐5. By contrast, Spz6 shows a complex spatial and temporally regulated expression pattern in the late embryo. Thus the new Toll/Spätzle families of signaling molecules may have important roles in other aspects of development and immunity. Proteins 2001;45:71–80. © 2001 Wiley‐Liss, Inc.
Crystal packing interaction that blocks crystallization of a site‐specific DNA binding protein–DNA complex
Authors: Littlefield Otis , Nelson Hillary C.M.
Published: August 2002

We present here three high‐resolution crystal structures of complexes between the DNA‐binding domain of the heat‐shock transcription factor (HSF) and DNA oligomers. Although the DNA oligomers contain HSF's specific binding sequence, called a heat‐shock element, the crystal structures do not contain the specific protein–DNA complex. In one crystal structure, the 10 base pair DNA oligomer is statically disordered. In the other two related structures, the 12 base pair DNA oligomers are in unique positions, but the protein–DNA contacts in these two crystals are not sequence specific. In all three structures, the DNA appears to act as a rigid, polyanion scaffold to support columns of proteins in a crystalline lattice. A robust crystal packing interface between protein monomers obscures the true DNA‐binding surface, known from previous genetic and biochemical studies. By redesigning the protein to interfere with the crystal lattice contacts, we were able to obtain physiologically relevant crystals in a specific protein–DNA complex. Thus, a crystal‐packing interface was able to prevent the weak, but physiological relevant interactions between a protein and DNA. Proteins 2001;45:219–228. © 2001 Wiley‐Liss, Inc.
Free energy distributions in proteins
Authors: Poland Douglas
Published: August 2002

Protein molecules in solution have a broad distribution of enthalpy states. A good approximation to the distribution function for enthalpy states can be calculated, using the maximum‐entropy method, from the moments of the distribution that, in turn, are obtained from the experimental temperature dependence of the heat capacity. In the present paper, we show that the enthalpy probability distribution can then be formulated in terms of a free energy function that gives the free energy of the protein corresponding to a particular value of the enthalpy. By the location of the minima in this function, the free energy distribution graphically indicates the most probable values of the enthalpy for the protein. We find that the behavior of the free energy functions for proteins falls somewhere between two different cases: a two‐state like function with two minima, the relative levels of the two states changing with temperature; and, a single‐minimum function where the position of the minimum shifts to higher enthalpy values as the temperature is increased. We show that the temperature dependence of the free energy function can be expressed in terms of a central free energy distribution for a given, fixed temperature (which is most conveniently chosen as the temperature of the maximum in the heat capacity). The nature of this central free energy function for a given protein thus yields all of the thermodynamic behavior of that protein over the temperature range of the denaturation process. Proteins 2001;45:325–336. © 2001 Wiley‐Liss, Inc.
Stabilizing nonpolar/polar side‐chain interactions in the α‐helix
Authors: Andrew Charles D. , Penel Simon , Jones Gareth R. , Doig Andrew J.
Published: August 2002

A simplistic, yet often used, view of protein stability is that amino acids attract other amino acids with similar polarity, whereas nonpolar and polar side chains repel. Here we show that nonpolar/polar interactions, namely Val or Ile bonding to Lys or Arg in α‐helices, can in fact be stabilizing. Residues spaced i, i + 4 in α‐helices are on the same face of the helix, with potential to favorably interact and stabilize the structure. We observe that the nonpolar/polar pairs Ile‐Lys, Ile‐Arg, and Val‐Lys occur in protein helices more often than expected when spaced i, i + 4. Partially helical peptides containing pairs of nonpolar/polar residues were synthesized. Controls with i, i + 5 spacing have the residues on opposite faces of the helix and are less helical than the test peptides with the i, i + 4 interactions. Experimental circular dichroism results were analyzed with helix‐coil theory to calculate the free energy for the interactions. All three stabilize the helix with ΔG between −0.14 and −0.32 kcal · mol−1. The interactions are hydrophobic with contacts between Val or Ile and the alkyl groups in Arg or Lys. Side chains such as Lys and Arg can thus interact favorably with both polar and nonpolar residues. Proteins 2001;45:449–455. © 2001 Wiley‐Liss, Inc.
A review of in situ measurement of organic compound transformation in groundwater
Authors: Papiernik Sharon K
Published: August 2002

Laboratory assessments of the rate of degradation of organic compounds in groundwater have been criticized for producing unrepresentative results. The potential for organic compounds to be transformed in groundwater has been measured using in situ methods, which avoid problems of attempting to duplicate aquifer conditions in the laboratory. In situ assessments of transformation rates have been accomplished using transport studies and in situ microcosms (ISMs); a review of these methods is given here. In transport studies, organic solutes are injected into an aquifer and the concentrations are monitored as they are transported downgradient. The change in mass of a solute is determined by the area contained under the breakthrough curve (plot of concentration versus time). ISMs isolate a portion of the aquifer from advective flow and act as in situ batch reactors. Experiments using ISMs involve removing water from the ISM, amending it with the solutes of interest, re‐injecting the amended water, and monitoring the solute concentrations with time. In both transport and ISM studies, the loss of organic solutes from solution does not allow a distinction to be made between sorptive, abiotic and biotic transformation losses. Biological activity can be chemically suppressed in ISMs and the results from those experiments used to indicate sorption and abiotic loss. Transformation products may be monitored to provide additional information on transformation mechanisms and rates.

Published in 2001 for SCI by John Wiley & Sons, Ltd
Activity of the botanical aphicides 1,5‐diphenyl‐1‐pentanone and 1,5‐diphenyl‐2‐penten‐1‐one on two species of Aphididnae
Authors: Ping Gao , Taiping Hou , Rong Gao , Qiu Cui , Shigui Liu
Published: August 2002

1,5‐Diphenyl‐1‐pentanone (A) and 1,5‐diphenyl‐2‐penten‐1‐one (B) are natural products extracted for the first time from Stellera chamaejasme. Laboratory bioassay showed that the two products have strong contact activity and very good anti‐feedant activity against Aphis gossypii and Schizaphis graminum. Both products showed dose‐dependent relationships for both forms of activity against the two aphids, the contact activity of B being about twice that of A. Both products were inferior to methomyl in contact activity but superior in anti‐feedant activity against the two aphids. This is the first report of aphicidal activity in these two compounds, which may represent a new class of aphicide.

© 2001 Society of Chemical Industry
Quantitative structure–activity studies of insect growth regulators: XVIII. Effects of substituents on the aromatic moiety of dibenzoylhydrazines on larvicidal activity against the Colorado potato beetle Leptinotarsa decemlineata
Authors: Nakagawa Yoshiaki , Smagghe Guy , Van Paemel Marleen , Tirry Luc , Fujita Toshio
Published: August 2002

Larvicidal activity against the Colorado potato beetle Leptinotarsa decemlineata (Say) was measured for a series of N‐tert‐butyl‐dibenzoylhydrazines having various substituents on the benzoyl (A‐ring) moiety nearer to the tert‐butyl group, with the other benzoyl (B‐ring) moiety being unsubstituted. The effects of these substituent on the larvicidal activity were analyzed using classical quantitative structure‐activity relationship (QSAR) procedures. The effects of substituents on the A‐ring moiety on larvicidal activity were entirely different from those against the lepidopteran rice stem borer Chilo suppressalis (Walker) previously reported. Position‐specific steric and hydrophobic effects, as well as certain substitution patterns, were likely to participate in modifying the larvicidal activity. The activity of para‐substituted compounds was generally lower than that of un‐, ortho‐ and meta‐substituted compounds. Most multi‐substituted compounds showed an activity equivalent to or lower than that of the unsubstituted compound. Among 46 compounds tested, the 2‐sec‐butoxy analogue was most potent against L decemlineata, although this compound had previously been shown to be only weakly active against C suppressalis.

© 2001 Society of Chemical Industry
Toxicity of a formulation of the insecticide indoxacarb to the tarnished plant bug, Lygus lineolaris (Hemiptera: Miridae), and the big‐eyed bug, Geocoris punctipes (Hemiptera: Lygaeidae)
Authors: Tillman P Glynn , Hammes Glenn G , Sacher Matthew , Connair Michael , Brady E Angela , Wing Keith D
Published: August 2002

Indoxacarb is a new oxadiazine insecticide that has shown outstanding field insecticidal activity. The toxicity of a 145 g litre−1 indoxacarb SC formulation (Steward™) was studied on the tarnished plant bug Lygus lineolaris and the big‐eyed bug Geocoris punctipes. Both insect species responded very similarly to indoxacarb in topical, tarsal contact and plant feeding toxicity studies. The topical LD50 of the formulation was c 35 ng AI per insect for both species. Prolonged tarsal contact with dry indoxacarb residues did not result in mortality for either insect species. However, both species were susceptible to feeding through dried residues of indoxacarb after spraying on young cotton plants. Feeding on water‐washed plants resulted in lower mortality than that observed with unwashed plants, and toxicity declined even more dramatically after a detergent rinse, indicating that much of the indoxacarb probably resides on the cotton leaf surface or in the waxy cuticle. These results were corroborated by HPLC–mass spectrometry measurements of indoxacarb residues on the plants. Greater mortality for both species was observed in a higher relative humidity environment. Higher levels of accumulated indoxacarb and its active metabolite were detected in dead G punctipes than in L lineolaris after feeding on sprayed, unwashed plants. When female G punctipes ate indoxacarb‐treated Heliothis zea eggs, there was significant toxicity. However, only c 15% of the females consumed indoxacarb‐treated eggs, and the rest of the females showed a significant diminution of feeding in response to the insecticide. Cotton field studies have shown that indoxacarb treatments at labelled rates lead to a dramatic decline in L lineolaris, with negligible declines in beneficial populations. A major route of intoxication of L lineolaris in indoxacarb‐treated cotton fields thus appears to be via oral, and not cuticular, uptake of residues from treated cotton plants. The mechanisms for selectivity/safety for G punctipes are currently under investigation and may be a combination of differential feeding behavior and diminution of feeding by females exposed to indoxacarb‐treated eggs.

© 2001 Society of Chemical Industry
Inhibition of intestinal motility by methanol extracts of Hibiscus sabdariffa L. (Malvaceae) in rats
Authors: Salah A. M. , Gathumbi J. , Vierling W.
Published: August 2002

The methanol extracts of Hibiscus sabdariffa (p < 0.01) showed a significant dose dependent relaxant effect (IC50 = 350 μM) on rat ileal strip comparable to the effect shown by nifedipin and papaverine as reference compounds. Similarly, the extract when administered intraperitoneally significantly (p < 0.05–0.01) reduced the intestinal transit (13%–35%) in rats (IC50 = 250 μM). The extracts (40% ± 04%) and nifedipin (51% ± 05%) also potentiated the diarrhoea inducing effect of castor oil (IC50 = 350 μM). It is postulated that these effects are possibly generated by constituents such as quercetin and eugenol via a Ca2+ channel modulated mode of action. Copyright © 2002 John Wiley & Sons, Ltd.
Thermodynamic molecular switch in sequence‐specific hydrophobic interactions
Authors: Chun Paul W.
Published: August 2002

This communication will demonstrate the existence of a thermodynamic molecular switch in the pairwise, sequence‐specific hydrophobic interaction of Ile–Ile, Leu–Ile, Val–Leu, or Ala–Leu over the temperature range of 273–333 K reported by Nemethy and Scheraga in 1962. Based on Chun's development of the Planck–Benzinger methodology, the change in inherent chemical bond energy at 0 K, ΔH°(T0), is 3.0 kcal mol−1 for Ile–Ile, 2.4 for Leu–Ile, 1.8 for Val–Leu, and 1.2 kcal mol−1 for Ala–Leu. The value of ΔH°(T0) decreases as the length of the hydrophobic side chain decreases. It is clear that the strength and stability of the hydrophobic interaction is determined by the packing density of the side chains, with Ala–Leu being the most stable. At 〈Tm〉, the thermal agitation energy, \documentclass{article}\pagestyle{empty}\begin{document}$\int^{T}_{0}\Delta Cp^{\circ}(T)\,dT$\end{document}, is about five times greater than ΔH°(T0) in each case. Additionally, the thermal agitation energy for the same series, evaluated at 〈Tm〉, decreases in the same order, that is, as the length of the side chain decreases. This pairwise, sequence‐specific hydrophobic interaction is highly similar in its thermodynamic behavior to that of other biological systems, except that the negative Gibbs free energy change minimum at 〈Ts〉 occurs at a considerably higher temperature, 355 K compared to about 300 K. The melting temperature, 〈Tm〉, is also high, 470 K compared to 343 K in a biological system. The implication is that the negative Gibbs free energy minimum at a well‐defined 〈Ts〉 has it origin in the hydrophobic interactions, which are highly dependent on details of molecular structure. In addition to the four specific dipeptide interactions described, we have shown in our unpublished work the existence of a thermodynamic molecular switch in the interactions of 32 dipeptides wherein a change of sign in ΔCp°(T)reaction leads to a true negative minimum in the Gibbs free energy of reaction, and hence, a maximum in the related Keq. Indeed, all interacting biological systems that we have thus far examined using the Planck–Benzinger approach point to the universality of thermodynamic molecular switches. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Molecular determinants of recognition and activation at GABAA/benzodiazepine receptors
Authors: Filizola Marta , Harris Danni L.
Published: August 2002

Benzodiazepines (BDZ) are among the most widely prescribed drugs known to date. However, their broad spectrum of behavioral activity and lack of specificity circumscribe their effectiveness as drugs. With the goal of designing more selective benzodiazepine receptor ligands, Dr. Loew's research group has contributed to literature over the years with both experimental and computational studies. We report here a summary of the most recent computational work carried out in our laboratory on 21 structurally diverse benzodiazepine receptor ligands, using as a data set their in‐house experimental results of activity at the anxiolytic, sedative, and hyperphagic endpoints. The chemical and geometric determinants common to the overlapping binding regions of benzodiazepine agonists, antagonists, and inverse agonists were identified at each of these three behavioral endpoints. The three resulting 3D pharmacophores did not encompass all the molecular requirements for recognition and activation of GABAA/BDZ receptors. They provided instead a means of obtaining accurate bioactive conformations for use in statistical studies, such as quantitative structure‐activity relationship and multivariate discriminant analyses. These studies can serve as a guide to predict both ligand affinities and activities. In the present work, multivariate discriminant analysis of global physicochemical properties is performed to provide new hypotheses for activation selectivity at the sedation endpoint. Although this analysis relies on a relatively small set of compounds, its results can still aim at compound screening and future identification of novel selective benzodiazepine receptor ligands. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002
Mg(H2O)62+–π(cytosine) interactions in a DNA dodecamer*
Authors: Magnuson Eric C. , Koehler Jessica , Lamm Gene , Pack George R.
Published: August 2002

In a recent investigation we performed extensive Monte Carlo calculations on the sequence‐specific binding of hydrated magnesium ions to DNA. One of the DNA models considered used coordinates from a high‐resolution crystal structure of the dodecamer duplex d(CGCGAATTCGCG)2 in which a hydrated magnesium ion is outer‐sphere‐coordinated to the dodecamer. In analogy with cation–π interactions in proteins, it has been suggested that the local base unstacking observed in this structure is due to similar interactions between cytosine rings and a nearby magnesium ion. As our (and most) Monte Carlo and molecular dynamics simulations of cation–DNA interactions rely only on the electrostatic and Lennard–Jones (6–12) components of standard force fields to describe such situations, we undertook a detailed ab initio study of selected cation–π interactions in this crystal structure to gauge their strength. The results of this investigation involving the 6‐31G*, 6‐31+G*, and 6‐311++G** basis sets at the restricted Hartree–Fock, Møller–Plesset second‐order perturbation and density functional levels are presented here within the context of previous cation–π studies. We find that, for this particular crystal structure, the average binding energy between the hydrated magnesium ion and one of the three nearest cytosine bases is about −1.8±1.0 kcal/mol. We therefore rule out these specific cation–π interactions between a hydrated magnesium ion and cytosine rings as the cause of the observed base unstacking. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002
Electronic structure of some adenosine receptor antagonists: I. Equilibrium geometries, charge density distributions, and substituent effects
Authors: Moustafa H. , El‐Sawy K. M. , Hilal Rifaat
Published: August 2002

Ab initio molecular orbital calculations were implemented to investigate the variation of the electronic structure of a series of different xanthine derivatives. MP2(full)/6‐31G calculations have been carried out and used to investigate the geometric features of the studied compounds. Alkyl xanthines studied in the present work are highly polarized with the σ and π frameworks polarized in opposite directions. This polarization is sensitive to substitution. The trend observed for the variation of dipole moment with substitution is interesting. Thus, electron‐withdrawing substituents lower the magnitude of the dipole moment, which reaches its smallest value in the case of CF3 substituent. The NO2 group not only reduces the dipole moment but it also inverts its direction as well. The effect of the basis set on these geometric features has been investigated through implementation of polarization function in MP2(full)/6‐31G/6‐311G** calculations, where it was found that inclusion of the polarization function led to a noticeable redistribution of the charge density. Thus, charge density that was originally accumulated on the atomic centers is redistributed into the bonding regions and this is the reason for the smaller net charges and the larger bond orders predicted at the 6‐311G** level. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Theoretical calculation of activation energy barrier from vibrational frequencies for the reaction of O (3P) with CHFCl
Authors: Zhou Zhengyu , Cheng Xueli , Fu Aiping , Du Dongmei
Published: August 2002

The reaction of the oxygen atom with the chlorofluoromethyl radical has been investigated fully by the B3LYP method at the 6‐311++G** basis set level. Two new approaches of the adiabatic (actual) activation energy between all of the intermediates and transition states (TSs) are calculated using the computed frequencies. TSs are activated species: When intermediates agitated spectrographically, the TSs come into being. So the vibrational quantum number ν must be taken into account, and the agitated radicals can be considered as a whole to calculate the adiabatic activation energy, or the potential energy barrier. All IMs and TSs are assigned to their spectroscopic terms to determine the vibrational quantum numbers. This appears to be a good way to estimate activation energy barriers of all reaction channels. © 2002 Wiley Periodicals, Inc.; DOI 10.1002/qua.2002;10126
Closed‐form rectangular atomic wave functions of an N‐dimensional atom
Authors: Lo Shun S. , Morales Daniel A.
Published: August 2002

A closed‐form expression has been derived to obtain the N‐dimensional rectangular atomic wave functions. The wave functions can be obtained straightforwardly with the knowledge of the angular momentum quantum numbers and the dimension and there is no need to employ recursive methods as in previous works. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 88: 263–274, 2002
Radical addition to the vinyl CC bond: Quantum chemistry model of the reaction
Authors: Sokolov Alexey V.
Published: August 2002

Transition states of radical addition of C and O centered radicals to vinyl monomers were studied by MNDO UHF. Linear relationships between activation barriers and the enthalpies of addition were found in all reaction series. To expose factors of reactivity, calculated activation barriers were subjected to energy partitioning procedure, and an attempt was made to correlate those parts with monomolecular and bimolecular indexes of reactivity (such as deformation energies of monomers, CT‐energies, etc). Shown that a satisfactory 2‐parameter linear correlation can be built. Problems of PMO theory application to considered class of reactions were discussed and alternative method of calculation of CT‐energies by using monomolecular parameters proposed. Resulting scheme of reactivity applied to existing experimental data on reactivity in radical addition reactions, optimized parameters of large group of reagents tabulated. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Bounds for the total π‐electron energy
Authors: Morales Daniel A.
Published: August 2002

Upper and lower bounds for the total π‐electron energy of conjugated hydrocarbons are found in terms of the number of carbon atoms, number of carboncarbon bonds, and the determinant of the adjacency matrix of the molecular graph. From these results and the application of some theorems concerning inequalities, we have been able to express those bounds in terms of spectral moments, up to the fourth. In the particular case of benzenoids, the bounds can be expressed solely in terms of the number of vertices and edges of the graph. It is shown that the upper bounds found are better than those of McClelland and those recently reported by Koolen et al. (Chem Phys Lett 2000, 320, 213). © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Spectral density distribution moments of a Hamiltonian of N coupled Morse oscillators: The large‐N limit
Authors: Bancewicz Małgorzata
Published: August 2002

The expressions for moments of spectral density distribution of a Hamiltonian representing a system of N coupled Morse oscillators are reduced to the large‐N limit. The effect of the values of coupling constants on the spectral density distribution is analyzed. For the values of coupling constants within the pertinent range for real molecules, the relations between moments appear to be close to those for a Gaussian distribution. Outside this range, the deviations from the normal distribution are substantial. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002