Molecular size scaling in families of protein native folds

The mean size of the most compact native states of globular proteins, independent of folding type, follows the scaling law of collapsed polymers R _g ~ n ^1/3, relating the radius of gyration R _g to the number of protein residues, n. Until now, this behaviour has only been observed within a small subset of unrelated single-domain proteins with n < 300. Here, we employ the SCOP database of protein folds to study systematically the scaling behaviour of well-defined families of domains that share structural and functional characteristics. In the particular case of helical proteins, we identify the folding types that can be associated with scaling laws corresponding to compact behaviour (e.g., the cytochrome-C monodomains) and noncompact behaviour (e.g., the immunoglobulin/albumin-binding and spectrin-repeat domains). Our results quantify the size variations within some folding families, as well as reveal that some distinct folds represent structures with equivalent compactness.     

Size scaling behaviour in protein domains belonging to the all-α, all-β, α / β, and α?+?β folding classes

We studied the size scaling behaviour in an ensemble of 8,614 non-redundant protein domains belonging to the all-α, all-β, α / β, and α + β folding classes. We find that the most compact structural domains can be characterized by an effective exponent ν _eff  = 0.39 ± 0.01, which is larger than the value for “collapsed-polymers,” i.e., ν = 1/3. We also show that the global ν _eff -exponent is an average of the scaling regimes for short and long compact chains, where the values change from ν _eff ≈ 0.37 to ν _eff ≈ 0.45 at chain length of ca. 269. A transition from short-chain to long-chain scaling behaviour is found in all major folding classes, over a window of chain lengths between 216 and 269 residues. In addition, variations in scaling exponent with respect to folding class indicates that the smallest domains in the (all-β) and (α / β) families appear to be more compact structures than the smallest (all-α)- and (α + β)-domains.     

Copolymerization of acrylic acid to nylon-6 by trapped radicals—II: Liquid phase grafting and properties of copolymers

Initial rates of grafting, R_g, have been determined for film of nylon-6, which had been -,,-irradiated in vacuo and subsequently immersed in outgassed, aqueous, acrylic acid at 50'. Equilibrium swellings due to water and to monomer are attained rapidly by nylon-6 and give rise to a high R_g. During grafting a constant swelling due to water occurs immediately but the rate of uptake of monomer is less than R_g, These effects are discussed on the basis of compatibility. At a fixed equilibrium monomer concentration, [AA], in the film, R_g ∝ D^β where D is the dose and β = 0.94. At a fixed dose, R_g ∝ [AA]^α where α = 1.04. The value of β indicates mainly monomolecular termination by radical burial. This is postulated to occur by trapping of growing grafts in crystalline regions and/or transfer from them to such regions. By selectively dyeing and sectioning films of different degrees of grafting (DG), the progress of the grafting front inwards has been shown to follow closely the corresponding grafting curve of DG vs time. Grafting does not alter the moisture regain of nylon. Surface resistance and swelling in water change with DG, the effect being enhanced markedly by converting the grafts to their sodium salts.     

Partial Synthesis and Characterization of Karpoxanthins and Cucurbitaxanthin A Epimers

Karpoxanthin (=(all-E,3S,5R,6R,3′R)-5,6-dihydro-β,β-carotene-3,5,6,3′-tetrol; 7 ), 6-epikarpoxanthin (=(all-E,3S,5R,6S,3′R)-5,6-dihydro-β,β-carotene-3,5,6,3′-tetrol; 4 ), 5-epikarpoxanthin (=(all-E,3S,5S,6R,3′-R)-5,6-dihydro-β,β-carotene-3,5,6,3′-tetrol; 11 ), cucurbitaxanthin A (=(all-E,3S,5R,6R,3′R)-3,6-epoxy-5,6-dihydro-β,β-carotene-5,3′-diol; 10 ), epicucurbitaxanthin A (=(all-E-3S,5S,6R,3′R)-3,6-epoxy-5,6-dihydro-β,β-carotene-5,3′-diol; 14 ), and the corresponding mutatoxanthin epimers 8 , 9 , 12 , and 13 were prepared in crystalline state by the acid-catalyzed hydrolysis of (3S,5R,6S,3′R)- and (3S,5S,6R,3′R)-antheraxanthin ( 5 and 6 , resp.) and characterized by their UV/VIS, CD, ¹H- and ¹³C-NMR, and mass spectra.     

(all-E)-12′-Apozeaxanthinol,Persicaxanthine und Persicachrome

( all-E)-12′-Apozeanthinol, Persicaxanthine, and Persicachromes Reexamination of the so-called ‘persicaxanthins’ and ‘persicachromes’, the fluorescent and polar C₂₅-apocarotenols from the flesh of cling peaches, led to the identification of the following components: (3R)-12′-apo-β-carotene-3,12′-diol ( 3 ), (3S,5R,8R, all-E)- and (3S,5R,8S,all-E)-5,8-epoxy-5,8-dihydro-12′-apo-β-carotene-3,12′-diols (4 and 5, resp.), (3S,5R,6S,all-E)-5,6-epoxy-5,6-dihydro-l2′-apo-β-carotene-3,12′-diol =persicaxanthin; ( 6 ), (3S,5R,6S,9Z,13′Z)-5,6-dihydro-12′apo-β-carotene-3,12′-diol ( 7 ; probable structure), (3S,5R,6S,15Z)-5,6-epoxy-5,6-dihydro-12′-apo-β-carotene-3,12′-diol ( 8 ), and (3S,5R,6S,13Z)-5,6-epoxy-5,6-dihydro-12′-apo-β-carotene-3,12′-diol ( 9 ). The (Z)-isomers 7 – 9 are very labile and, after HPLC separation, isomerized predominantly to the (all-E)-isomer 6 .     

Studies on the construction of abutasterone-type and 24-epi-abutasterone-type side chains employing asymmetric dihydroxylation of (E)-20(22),24-cholestadiene

The synthesis of abutasterone-type side chain, (20R,22R,24S)-20,22,24,25-tetrahydroxy-6β-methoxy-3α,5-cyclo-5α-cholestane 4, and 24-epi-abutasterone-type side chain, (20R,22R,24R)-20,22,24,25-tetrahydroxy-6β-methoxy-3α,5-cyclo-5α-cholestane 6, by means of Sharpless asymmetric dihydroxylation of (E)-20(22),24-cholestadiene 1 is described. Construction of abutasterone-type side chain 4 was carried out by selective mono-dihydroxylation of diene 1 with (DHQ)₂AQN, followed by dihydroxylation of the corresponding (24S)-hydroxy-20(22)-cholestene 2 with (DHQD)₂AQN. In contrast, bis-dihydroxylation of 1 with either (DHQD)₂PHAL or (DHQD)₂AQN preferentially occurs to produce 24-epi-abutasterone-type side chain 6.     

The state energy and the displacements of the potential minima of the 2Ag− state in all-trans-β-carotene as determined by fluorescence spectroscopy

The fluorescence spectrum of all-trans-β-carotene was recorded at 170 K. The 1B_u⁺ → 1A_g⁻ fluorescence exhibited clear vibrational structures constituting a mirror image with those of the 1B_u⁺ ← 1A_g⁻ absorption, and the deconvolution of the entire spectrum identified the 2A_g⁻(0) → 1A_g⁻(0) transition at 14 500 cm⁻¹. The displacements of the 1B_u⁺ and 2A_g⁻ potential minima along ν₁ and ν₂ (the CC stretching and C–C stretching normal coordinates, respectively) were determined to be 1.2 and 0.9, and 1.6 and 1.5, respectively. Thus, much larger potential displacements in the 2A_g⁻ state than in the 1Bu⁺ state have been shown.     

Latoxanthin, a minor carotenoid isolated from the fruits of yellow paprika (Capsicum annuum var. lycopersiciforme flavum)

Latoxanthin was isolated as a minor carotenoid from the ripe fruits of yellow tomato shaped paprika (Capsicum annuum var. lycopersiciforme flavum) and identified as (all-E,3S,5R,6R,3′S,5′R,6′S)-5′,6′-epoxy-5,6,5′,6′-tetrahydro-β,β-carotene-3,5,6,3′-tetrol based on spectral data.     

Critical behavior of binary mixture of {x C6H5CN + (1 − x) CH3(CH2)12CH3}: Measurements of coexistence curves,turbidity, and heat capacity

(Liquid + liquid) coexistence curve, turbidity, and isobaric heat capacity per unit volume for the critical solution of {benzonitrile + n-tetradecane} have been measured. The critical exponents β, ν, γ, and α and system-dependent critical amplitudes B, ξ₀, χ₀, and A^±, corresponding to the difference of the general density variable of two coexisting phases Δρ, the correlation length ξ, the osmotic compressibility χ, and the isobaric heat capacity per unit volume C_pV^?1, have been deduced and were used to test some universal ratios. The behavior of the diameter of the coexistence curves showed good agreement with the complete scaling theory. The analysis of effective critical exponent β_eff, which was well described by the crossover model proposed by Anisimov and Sengers, and effective critical exponent α_eff indicated monotonic crossover phenomena from 3D-Ising behavior to mean-field one as the temperature departed from the critical point.     

Effect of electron-irradiation on cross-link density and crystalline structure of low- and high-density polyethylene

Low- and high-density polyethylenes (LDPE and HDPE) were cross-linked in solid state by electron beam irradiation. Molar mass between cross-link joints, M_c, and cross-link density,ν, were calculated using rubber elasticity theory and hot set data. The results showed that the ν and creep modulus increased and creep strain and M_c decreased with increasing irradiation dose. As compared to HDPE, the LDPE had higher ν and lower M_c values at a similar irradiation dose. X-ray analysis and differential scanning calorimetry investigation of first heating cycle revealed no changes in crystalline structure of the irradiated samples. This was attributed to immobilization of radicals frozen in the crystalline phase. As a result of hindered mobility of the polymeric chains, these radicals were not able to cross-link the chains in the crystalline region. However, after melting of the crystals and during subsequent re-solidification process, different levels of crystallinity were developed depending on the applied irradiation dose. The irradiated samples with higher dose had lower crystallization and melting temperatures with reduced crystallinities. These confined crystallization behaviors, observed after a series of cooling and heating cycles, could be attributed to the decrease in the M_c values. The length of chain segment needed for usual crystallization by chain folding is decreased due to formation of cross-link joints and hence the crystallization process was hindered.     

An enantiomerically pure bilirubin. Absolute configuration of (αR,α′R)-dimethylmesobilirubin-XIIIα

Enantiomerically pure (+)-(αR,α′R)-dimethylmesobilirubin-XIIIα 1 and its (αS,α′S) enantiomer ent-1 were synthesized in ten steps from simple precursors. Resolution was achieved at an early stage in the synthesis, with a racemic monopyrrole precursor rac-6 being converted to its amides 8 with (1S)-camphor-2,10-sultam. Resolution of 8 to 99% d.e. was accomplished in three crystallizations, and the absolute configuration of the acid 6 was deduced by X-ray crystallography of the more crystalline, diastereomerically pure amide 7. Circular dichroism spectroscopy of 1 showed intense bisignate Cotton effects: Δε^max₄₃₅=+344, Δε^max₃₉₁=−193 (CHCl₃), as expected for a molecular exciton, and consistent with a P-helical intramolecularly hydrogen-bonded ridge-tile conformation. The Cotton effect magnitudes of 1 match almost exactly those found for (−)-(βS,β′S)-dimethylmesobilirubin-XIIIα 11 and (+)-(αR,β′R)-dimethylmesobilirubin-XIIIα. However, the Cotton effect of the pseudo-meso diastereomer (αR,β′S)-dimethylmesobilirubin-XIIIα 12 is not zero. Its large positive exciton couplet and ¹H NMR NOE analysis confirm that an α-CH₃ exerts a greater steric demand than a β-CH₃—by a factor of ∼3.     

Aesculaxanthin,a New Carotenoid Isolated from Pollens of Aesculus hippocastanum

From the pollens of Aesculus hippocastanum, a new apocarotenoid was isolated as the main carotenoid and, based on the spectroscopic data, identified as (all-E,3R)-3-hydroxy-6′-apo-β-caroten-6′-al ( 4 , aesculaxanthin). In addition, (all-E)-lutein ( 3 ) and (all-E)-β-citraurin ( 5 ) were isolated. Furthermore, 6 (aesculaxanthol) was prepared by reduction of 4 with NaBH₄ and tentatively identified as natural carotenoid.     

Molecular dynamics and conduction mechanism of poly(vinyl chloride-co-vinyl acetate-co-2-hydroxypropyl acrylate) terpolymer containing ionic liquid

Dielectric spectroscopy (DS) measurements were performed to probe the segmental dynamics and ion mobility of poly(vinyl chloride-co-vinyl acetate-co-2-hydroxypropyl acrylate) terpolymer dopped with different amounts of tetrabutylammonium tetrafluoroborate ([TBA] [BF₄]) ionic liquid (IL). Differential scanning calorimetry (DSC) was also employed to trace the change in the glass transition temperature (T_g) at different loads of IL. The DSC measurements revealed a remarkable reduction in the PVVH T_g from 344 to 310 K just by adding 20 wt% of IL. The DS measurements revealed three relaxation processes named α, β₁, and β₂. The α-process is related to the segmental motion of PVVH while the β₁ and β₂ are due to the restricted local dynamics of side chains. The segmental relaxation times (α-relaxation) speed up with increasing the concentration of IL due to the plasticization effect of IL on polymer chains. The temperature dependence of α-relaxation follows the Vogel-Fulcher-Tammann (VFT) relation with dynamic glass transition between 323 and 294 K in agreement with the DSC measurements. The β₁ and β₂-relaxations have an Arrhenius temperature dependence. The temperature dependence of ionic conductivity obeys the VFT behavior indicating the coupling between the segmental motion of PVVH chains and ion transport. Polaronic tunneling is the predominant conduction mechanism in PVVH and its composites. The specific capacitance increases with increasing both the temperature and IL concentration.     

Application of iso-temperature method of multiple rate to kinetic analysis

A new method of the multiple rate iso-temperature was used to define the most probable mechanism g(α) of a reaction; the iterative iso-conversional procedure has been employed to estimate apparent activation energy E _a, the pre-exponential factor A was obtained on the basis of E _a and g(α). In this new method, the thermal analysis kinetics triplet of dehydration of calcium oxalate monohydrate is determined, which apparent activation energy E _a is 82.83 kJ mol^-1, pre-exponential factor A is 1.142·10⁵-1.235·10⁵ s^-1, the most probable mechanism belongs to phase boundary reaction R_n with integral form g(α)=1-(1-α)ⁿ and differential form f(α)=n(1-α)^1-(1/n), where accommodation factor n=2.40-1.40.     

Synthesis and crystal structure of three silver indium double phosphates

Three new silver indium double phosphates Ag₃In(PO₄)₂ (I), β-(II) and α-Ag₃In₂(PO₄)₃ (III) were synthesized by solid state method (I and II—700 °C, III—900 °C). Compounds I and II crystallize into a monoclinic system (I—sp. gr. C2/m, Z=2, a=8.7037(1)Å, b=5.4884(1)Å, c=7.3404(1)Å, β=93.897(1)°; II—sp. gr. C2/c, Z=4, a=12.6305(1)Å, b=12.8549(1)Å, c=6.5989(1)Å, β=113.842(1)°), and compound III crystallize into a hexagonal system (sp. gr. R-3c, Z=6, a=8.9943(1)Å, c=22.7134(1)Å). Their crystal structures were determined by the Rietveld analysis (I—R_p=6.47, R_wp=8.54; II—R_p=5.67, R_wp=6.40; III—R_p=7.30, R_wp=9.91). Structure of Ag₃In(PO₄)₂ is related to the sodium chromate structure type and is isotypic to α-Na₃In(PO₄)₂. The polymorphous modifications of β- and α-Ag₃In₂(PO₄)₃ are isostructural to sodium analogs (β- and α-Na₃In₂(PO₄)₃) and are related to alluaudite (II) and NASICON (III) structure types. Compounds I and II are not stable at temperature above 850 °C. Ag₃In(PO₄)₂ is decomposed providing silver orthophosphate Ag₃PO₄ and α-Ag₃In₂(PO₄)₂. β-Ag₃In₂(PO₄)₃ is transformed to α-Ag₃In₂(PO₄)_3.     

Preparation and shape memory behavior of novel heat-resistance epoxy networks containing phthalide cardo structure

Heat-resistance epoxy shape memory (SM) materials were prepared based on diglycidylether of bisphenol A (DGEBA) epoxy resin with the mixture of 4,4′-diaminodiphenylether (DDM) and phthalide-containing aromatic amine (PBMI-DDM), which was synthesized by Michael addition of 3,3-bis[4-(4-maleimido phenoxy)phenyl] -phthalide (PBMI) and DDM, in different molar ratios as curing agents. The chemical structure of PBMI-DDM was confirmed by Fourier transform infrared (FTIR) and nuclear magnetic resonance (NMR) spectra. The dynamical mechanical behavior and high-temperature tensile properties, and the influence of PBMI-DDM content and number of cycles on SM performance were investigated in detail. With increasing PBMI-DDM content, the glass transition temperatures (T_g) decreased, damping loss factors increased, and shape recovery ratio (R_r) and shape fixity ratio (R_f) were improved significantly. R_r and R_f of the pure PBMI-DDM cured epoxy resins are both lager than 90% with a deformation strain above 15%. The T_g and activation energies (△E) of α-relaxation for the epoxy system with unstable SM performance are constantly increased with SM cycles due to the adjustment and rearrangement of network chains.     

Reactions in dry media: reactions of cholesterol and cholestanes on silica bound ferric chloride : Cholestane—diacholestene rearrangement

Reaction of cholesterol with silica bound FeCl₃ resulted in a mixture of 3β-cholesteryl chloride and dicholesteryl ether.5-Cholestene and hydroxy- and halogeno-substituted cholestane derivatives gave on heating at 100° with this reagent a 1:1 mixture of 20-epimeric diacholestenes. The 20(R)-isomer gave with meta-chloroperbenzoic acid 20(R)-α-epoxide, while the 20(S)-gave a mixture of 20(S)-α- and 20(S)-β-epoxides.5α,6β-Dihydrocholestane reacted with the FeCl₃/SiO₂ under milder conditions (50°) to give 6β-hydroxy-20(R)-diacholestene, which was converted to the 20(R)-diacholestene.     

Synthesis and structure of organically templated lanthanum sulfate [C4N3H16][La(SO4)3]·H2O

The first organically templated one-dimensional lanthanum sulfate [C₄N₃H₁₆][La(SO₄)₃]·H₂O has been prepared employing hydrothermal methods in the presence of diethylenetriamine (DETA). The structure was determined by single-crystal X-ray diffraction (XRD). The title compound crystallizes in the triclinic system, space group P-1 (No.2) with cell parameters M=551.30, a=8.2773(7) Å, b=9.5660(6) Å, c=10.4363(6) Å, α=105.661(2)°, β=102.849(3)°, γ=104.376(3)°, V=732.72(9) Å³, Z=2, R=0.0285, wR=0.0778. The structure consists of infinite linear chains. The chains are held together by hydrogen bond interactions involving the hydrogens of the amine and the framework oxygens. The as-synthesized product is characterized by powder XRD, inductive couple plasma analysis and thermogravimetric analysis.     

Diversity of potential hydrogen bonds in cellulose I revealed by molecular dynamics simulation

We have performed molecular dynamics calculations using a revised version of the Gromos56A_carbo force field to understand the consequences of the different potential hydrogen bonding patterns on the structural stability and thermal behavior of the I_α and I_β forms of native cellulose. For each allomorph, we considered three patterns of hydrogen bonds: two patterns obtained from neutron diffraction data refinement and a regular mixture of the two. Upon annealing, the hydrogen bonding schemes of cellulose I_β, irrespective of the starting structure, re-arranged into the main hydrogen bond pattern experimentally observed (pattern A). On the other hand, the I_α structures, irrespective of the starting hydrogen bonding pattern, converged to a non-experimental structure where the adjacent chains are shifted along the chain direction by 0.12 nm in the hydrogen-bonded plane, and the hydroxymethyl group conformation alternates between gt and tg along the chain. The exotic structure in I_α might be a consequence of a deficiency in force field parameters and/or potential molecular arrangement in less crystalline cellulose.     

Analogs of ecdysteroids with a tetrasubstituted Δ<Superscript>8,14</Superscript>-bond

By hydrogenation of (20R,22R)-6α,14α,25-trihydroxy-and (20R,22R)-6β,14α,25-trihydroxy-2,3:20,22-bis(isopropylidenedioxy)-5α-cholest-7-enes on a catalyst (Raney nickel) the corresponding (5α,6α)-and (5β,6β)-epimers of previously unknown Δ^8,14-6-hydroxy derivatives of ecdysteroids were synthesized.