Methylene Groups In Side Chains Research Articles

A novel form stable phase change material with comb-like cross-linked polyurethane as supporting skeleton

To improve the homogeneity of phase-change materials (PCMs) composites for thermal energy storage, the poly(ethylene glycol monomethyl ether)-based trimethylolpropane (Ymer-N120) with long side ethyoxyl chains is employed to form comb-like polyurethane which functioned as supporting materials for PCMs. And the results of Fourier transform infrared spectroscopy (FTIR), X-ray diffraction, differential scanning calorimetry, accelerated thermal cycling testing, thermogravimetric analysis and field emission scanning electron microscopy (FESEM) suggested a crosslinked polyurethane embedded with micron grade myristic acid (MA) crystals was prepared during the thermal curing process. The obtained comb-like polyurethane (YP) can provide 3D structure supporting materials for melting MA. And the long side ethyoxyl chain of Ymer-N120 promote the melting MA form micron-sized crystals. The results of thermal reliability testing confirmed the advantages of same methylene groups in side chains and suggested the maximal hold capability of YP crosslinks is about 50 wt% of composites. With the 50 wt% addition of MA, YPM50 can supply high latent heat (over 90 J/g of YPM50) with fine thermal stability (due to its initial decomposing temperature reaches 190 °C) without leakage (after 500 times of accelerated thermal cycling testing). All results indicated this structure supplies an effective solution for the leakage of PCMs, which show a promising application in TES.

Poly(9‐undecyl‐9‐methyl‐fluorene) and poly(9‐pentadecyl‐9‐methyl‐fluorene): Synthesis, solution structure, and effect of side chain asymmetry on aggregation behavior

ABSTRACTWe report on solution aggregates and backbone conformation of poly(9‐undecyl‐9‐methyl‐fluorene) (PF1‐11) and poly(9‐pentadecyl‐9‐methyl‐fluorene) (PF1‐15), having two different side chains compared with poly(9,9‐dihexylfluorene) (PF6) and poly(9,9‐dioctylfluorene) (PF8) with two identical side chains. In the poor solvent methylcyclohexane (MCH), X‐ray scattering indicates that PF1‐11 and PF1‐15 appear as three‐dimensional aggregates (5–10 nm wide and thick), forming ribbon‐like agglomerates (correlation lengths of 100 nm). PF6 and PF8 appear as two‐dimensional aggregates (>10 nm wide and 2–3 nm thick) involving ribbon‐like agglomerates (correlation lengths much greater than 100 nm). Upon heating, all aggregates undergo a gel–sol transition which occurs at lower temperatures for PF1‐11 and PF1‐15 (<60°C) than for PF6 and PF8 (>80°C). In the good solvent toluene, PF1‐11 and PF1‐15 form networks of cylindrical particles. The mesh size and the cylinder radius are smaller in 24°C toluene (60 nm, 0.5 nm) than in 60°C MCH (300 nm, 1–2 nm). Nuclear magnetic resonance spectra in toluene‐d8 together with density functional theory calculations suggest higher torsion angles between polymer repeat units for PF6, PF8, and PF1‐11 (less planar conformation) and a gauche arrangement of the dihedral angles between the bridge carbon atom and the side chain methylene groups in PF1‐15. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019, 57, 826–837

Probing the Flexibility of the Catalytic Nucleophile in the Lyase Catalytic Pocket of Human DNA Polymerase β with Unnatural Lysine Analogues.

DNA polymerase β (Pol β) is a key enzyme in mammalian base excision repair (BER), contributing stepwise 5'-deoxyribose phosphate (dRP) lyase and "gap-filling" DNA polymerase activities. The lyase reaction is believed to occur via a β-elimination reaction following the formation of a Schiff base between the dRP group at the pre-incised apurinic/apyrimidinic site and the ε-amino group of Lys72. To probe the steric constraints on the formation and subsequent resolution of the putative Schiff base intermediate within the lyase catalytic pocket, Lys72 was replaced with each of several nonproteinogenic lysine analogues. The modified Pol β enzymes were produced by coupled in vitro transcription and translation from a modified DNA template containing a TAG codon at the position corresponding to Lys72. In the presence of a misacylated tRNACUA transcript, suppression of the UAG codon in the transcribed mRNA led to elaboration of full length Pol β having a lysine analogue at position 72. Replacement of the primary nucleophilic amine with a secondary amine in the form of N-methyllysine (4) affected mainly the stability of the Schiff base intermediate and resulted in relatively moderate inhibition of lyase activity and BER. Elongation of the side chain of the catalytic residue by one methylene group, achieved by introduction of homolysine (6) at position 72, apparently shifted the amino group to a position less favorable for Schiff base formation. Interestingly, this effect was attenuated when the side chain was elongated by replacing one side-chain methylene group with a bridging S atom (thialysine, 2). In comparison, replacement of lysine 72 with an analogue having a guanidine moiety in lieu of an ε-amino group (homoarginine, 5) or a sterically constrained secondary amine (piperidinylalanine, 3) led to almost complete suppression of dRP excision activity and the ability of Pol β to support BER. These results help to define the tolerance of Pol β to subtle local structural and functional alterations.

Role of Conserved Salt Bridges in Homeodomain Stability and DNA Binding

The sequence information available for homeodomains reveals that salt bridges connecting pairs 19/30, 31/42, and 17/52 are frequent, whereas aliphatic residues at these sites are rare and mainly restricted to proteins from homeotherms. We have analyzed the influence of salt and hydrophobic bridges at these sites on the stability and DNA binding properties of human Hesx-1 homeodomain. Regarding the protein stability, our analysis shows that hydrophobic side chains are clearly preferred at positions 19/30 and 31/42. This stabilizing influence results from the more favorable packing of the aliphatic side chains with the protein core, as illustrated by the three-dimensional solution structure of a thermostable variant, herein reported. In contrast only polar side chains seem to be tolerated at positions 17/52. Interestingly, despite the significant influence of pairs 19/30 and 31/42 on the stability of the homeodomain, their effect on DNA binding ranges from modest to negligible. The observed lack of correlation between binding strength and conformational stability in the analyzed variants suggests that salt/hydrophobic bridges at these specific positions might have been employed by evolution to independently modulate both properties.

Terminal ion pairs stabilize the second β‐hairpin of the B1 domain of protein G

The effects of terminal ion pairs on the stability of a beta-hairpin peptide corresponding to the C-terminal residues of the B1 domain of protein G were determined using thermal unfolding as monitored by nuclear magnetic resonance and circular dichroism spectroscopy. Molecular dynamics (MD) simulations were also performed to examine the effect of ion pairs on the structures. Eight peptides were studied including the wild type (G41) and the N-terminal modified sequences that had the first residue deleted (E42), replaced with a Lys (K41), or extended by an additional Gly (G40). Acetylated variants were made to examine the effect of removing the positive N-terminal charge on beta-hairpin stability. The rank in stability determined experimentally is K41 > E42 approximately G41 approximately G40 > Ac-K41 > Ac-E42 approximately Ac-G41 > Ac-G40. The Tm of the K41 peptide is 12 degrees C higher than G41, while the Tm values for the acetylated peptides are less than their unacetylated forms by more than 15 degrees C. NOE cross-peaks between side-chain methylene groups at the N- and C-termini and larger CalphaH shifts compared to random values are seen for K41. The addition of 20% methanol increases the stability in K41 and G41. The MD studies complement these results by showing that the charged N-terminus is important to stability. The type of ion pair observed varies with peptide, and when formed the simulations show that the ion pair can prevent fraying of the beta-strands through electrostatic and hydrophobic contacts. Therefore, introducing favorable electrostatic interactions at the N- and C-termini can substantially enhance beta-hairpin stability and help define the structure.

Revisions to the microstructural assignments of poly(ethyl cyanoacrylate)

The tacticity assignments from the literature for the 13C-NMR signals of the side-chain methylene group of poly(ethyl cyanoacrylate) are reversed, and new assignments of the main-chain methylene group are proposed. The assignments were made possible by a combination of DEPT and HETCOR NMR experiments on samples of varying microstructure distributions. The polymer tends toward syndiotacticity, not isotacticity as previously reported. The distribution of stereoisomers fits well to a Bernoulian statistical model. The stereochemical assignments were corroborated by similar analyses of a model compound for two cyanoacrylate repeat units. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 2219–2224, 1999

Aspartame dipeptide analogues: effect of number of side-chain methylene group spacers and C α-methylation in the second position

Our model of the active site of the sweet taste receptor is shown to be consistent with the aspartame analogues in which the L-Phe 2 residue is replaced by L-(αMe)Phg, L-(αMe)Phe or L-(αMe)Hph. The analogues containing either the first or the third C α-methylated, phenyl-containing residue in the second position of the dipeptide were synthesized and found to be approximately as sweet as aspartame itselfand its L-(αMe)Phe 2 analogue.

Use of capillary zone electrophoresis in an investigation of peptide uptake by dairy starter bacteria

A capillary zone electrophoresis (CZE) method to separate the peptide series val-gly n , where n is 1 to 4, has been evaluated and compared to separation by reversed-phase high-performance liquid chromatography (RP-HPLC). The method was able to quantitate peptides present at very low concentrations (down to 0.05 m M) with high reproducibility and accuracy and was capable of separating peptides differing in size by only a single glycine residue. It could also separate the peptides val-gly and leu-gly which differed in only a single side-chain methylene group. The method was fast, required small sample volumes, and proved to be superior to RP-HPLC. The suitability of the CZE method to analyze peptide uptake by dairy starter bacteria is discussed.

Structural factors contributing to the hydrophobic effect: the partly exposed hydrophobic minicore in chymotrypsin inhibitor 2.

The structural basis for the stability of a partly solvent-exposed hydrophobic minicore, formed by the residues Leu51, Val57, and Phe69 in the reactive loop of the serine protease inhibitor chymotrypsin inhibitor 2 (CI2), was analyzed from the stability of 17 mutant proteins, in which side chain methylene groups were deleted or rearranged. The mutations destabilize the protein by 0.3-4.8 kcal/mol, an average of 0.6 kcal per removed methylene group. Double mutant cycles show significant interaction between individual pairs of side chains. There is an excellent linear correlation (r = 0.995) between the free energy of unfolding relative to wild type (delta delta GU-F) and the packing density nC (the number of methyl and methylene groups within 6 A of the removed atoms). delta delta GU-F correlates more weakly with changes in solvent-accessible surface area upon mutation. The correlation improves when the change in solvent-accessible surface are upon mutation is separated into distinct contributions from polar atoms that are able to hydrogen bond to solvent (delta AHB) and from nonpolar atoms (delta AHP). There is also a correlation, however, between packing density and changes in surface area. Elsewhere in CI2, delta delta GU-F for mutations in the buried hydrophobic core correlates best with packing density, whereas in the exposed surface of the alpha-helix, the best correlation is with change in surface area.(ABSTRACT TRUNCATED AT 250 WORDS)

The Mobility of Tryptophan and Dansyl Fluorophores in Labelled Poly(N-ethylacrylamide) and Poly(N-ethylmethacrylamide)

The mobility of tryptophan fluorophore in N-butyl-Nα-acetyltryptophanamide and in side chain of labelled poly(N-ethylacrylamide) and poly(N-ethylmethacrylamide) was investigated by the fluorescence depolarization method. The mobility of the fluorophore in the low-molecular-weight model is much higher than in side chains of the polymers. Different steric hindrance by the polymer backbone can explain the higher mobility of the fluorophore in poly(N-ethylacrylamide) and in poly(N-ethylmethacrylamide). The mobility of 5-dimethylamino-1-naphthalenesulfonamide (dansyl) fluorophore in side chains of labelled poly(N-ethylmethacrylamide) in the high-viscosity range increases with increasing number of methylene groups in side chains. The low-viscosity range, the rate s of conformational changes in short side chains (n = 2 - 7) are approximately constant and significantly decrease in long side chains (n = 10, 12). The drop in the rates is probably due to intramolecular association of the long hydrophobic chains in water.

The Crystal Structure-Thermochromism Relationship for the Polydiacetylene ETCD

Abstract The polydiacetylene of the bis-ethylurethane of 5,7-dodecadiyn-1,12-diol (ETCD) is the best defined example of a thermochromic polymer at present. Thermochromism in poly-ETCD is associated with an endothermic first-order phase transition involving an increase in unit cell volume. The conformer population of the side-chain methylene groups changes on heating from 23 to 130°C. Hydrogen bonding and backbone planarity do not appear to be significantly disrupted during the transition. Solid state thermochromism in other polymers and examples of reversible thermochromism in inorganic and molecular organic solids are discussed in relationship to poly-ETCD.

Inhibitors of human renin. Cyclic peptide analogs containing a D-Phe-Lys-D-Trp sequence

Cyclic peptides containing a D-phenylalanine and a D-tryptophan residue have been synthesized and tested as inhibitors of human renin. Most of these are tripeptide derivatives of the type CO(CH2)3CO-D-Phe-Lys-D-Trp- or COCH2NHCH2CO-D-Phe-Lys-D-Trp- in which the individual side-chain methylene groups have been replaced with -CHMe-, -CMe2-, -CH(Ph)-, -CH(CH2Ph)-, or -CH[CH2)2CHMe2)-groups. The three amino acid residues and the size of the ring were very important features of these compounds. Reducing the ring size gave much less potent compounds. The most potent analogue of the series, CO(CH2)2CHPhCO-D-Phe-Lys-D-Trp-NH(CH2)2CHMe (14, IC50 = 26 nM), was obtained by substituting the methylene group nearer to the D-Phe residue by a -CHPh- group. Compound 14 was 15-fold more potent in inhibiting human renin than porcine renin.

Human triose-phosphate isomerase deficiency: a single amino acid substitution results in a thermolabile enzyme.

Triose-phosphate isomerase (TPI; D-glyceraldehyde-3-phosphate ketol-isomerase, EC 5.3.1.1) deficiency is a recessive disorder that results in hemolytic anemia and neuromuscular dysfunction. To determine the molecular basis of this disorder, a TPI allele from two unrelated patients homozygous for TPI deficiency was compared with an allele from a normal individual. Each disease-associated sequence harbors a G X C----C X G transversion in the codon for amino acid-104 and specifies a structurally altered protein in which a glutamate residue is replaced by an aspartate residue. The importance of glutamate-104 to enzyme structure and function is implicated by its conservation in the TPI protein of all species that have been characterized to date. The glutamate-to-aspartate substitution results in a thermolabile enzyme as demonstrated by assays of TPI activity in cultured fibroblasts of each patient and cultured Chinese hamster ovary (CHO) cells that were stably transformed with the mutant alleles. Although this substitution conserves the overall charge of amino acid-104, the x-ray crystal structure of chicken TPI indicates that the loss of a side-chain methylene group (-CH2CH2COO- ---- -CH2COO-) is sufficient to disrupt the counterbalancing of charges that normally exists within a hydrophobic pocket of the native enzyme.

Plant growth-regulating activity in homologous series of ω -phenoxyalkanecarboxylie acids and the influence of ring substitution on their breakdown by β -oxidation within plant tissues

Further evidence is presented on the occurrence of β -oxidation within the plant. The growth regulating activities of eighteen homologous series of ω -phenoxyalkanecarboxylic acids, RO(CH 2 ) n COOH with n = 1 to 6 and with chlorine and methyl groups substituted in different positions of the ring, have been assessed in the wheat cylinder, pea curvature, pea segment and tomato-leaf epinasty tests. The breakdown of a number of homologues when metabolized in wheat coleoptile or peastem tissues has been investigated using paper chromatography and ionophoresis, identification of metabolites being made by chromogenic methods and bio-assay. Growth-regulating activity is considered in relation to degradation of the side-chain by β -oxidation. In certain series the pattern of biological activity and breakdown sequence are shown to be different in wheat and pea tissues, indicating substrate specificity of the enzyme systems concerned. Evidence is presented that in both wheat and pea tissues β -oxidation of homologues containing an even-number of side-chain methylene groups is hindered at the propionicacid stage ( n = 2); this may result in an unusual pattern o f biological activity in series where the propionic homologue possesses growth-regulating properties per se . The degradation of homologues with an odd number of side-chain methylene groups normally leads to the production of the corresponding acetic derivative ( n = 1), and although the results indicate that this breakdown occurs in all series in wheat tissue, with ten of the series there is evidence that β -oxidation is hindered at the butyricacid stage ( n = 3) in pea and tomato tissue. Such hindrance of β -oxidation at the butyric stage is shown to be associated with the presence of an ortho chlorine or methyl group, though the effect is largely removed by introducing a further chlorine atom at the para but not the meta position. The fact that the β -oxidase enzymes in wheat and pea tissues show specific differences in their reactions with these phenoxy acids, and the importance of ring substitution in influencing the degree to which hindrance of β -oxidation occurs at the propionic and butyric acid stages, together provide an explanation for the different types of growth-regulating activity observed in the series examined. All the biological results are discussed in relation to these considerations, and it is concluded that hindrance of side-chain degradation by β -oxidation is associated with electronic, in addition to steric factors. Some similarity thus appears to exist between the broad class of aromatic reactions in organic chemistry which are hindered by ortho substituents and these hindered enzymatic reactions within the plant.

Formation of a β-Hydroxy Acid as an Intermediate in the Microbiological Conversion of Monochlorophenoxybutyric Acids to the Corresponding Substituted Acetic Acids

WAIN and his colleagues1 have clearly shown that the growth-regulating activity in plants of substituted ω-phenoxyalkylcarboxylic acids containing an uneven number of side-chain methylene groups can be explained by β-oxidation of the fatty acid side-chain within the plant to give the corresponding substituted acetic acids.

The beta-oxidation of omega-phenoxyalkylcarboxylic acids in the flax plant in relation to their plant growth-regulating activity.

Members of the homologous series (C 6 H 5 O(CH 2 ) n COOH) with n = 1 to 10 have been synthesized and their breakdown within flax seedlings, following absorption through the roots, has been investigated by a chemical method. The well washed plants were macerated, steam-distilled and phenol in the distillate was estimated colorimetrically. The results provide evidence that β -oxidation can occur within plant tissue. Those acids with an even number of side chain methylene groups ( n =2, 4, 6, 8, 10) gave rise to appreciable quantities of phenol, some 160μg being found in each experimental group of 200 flax seedlings. In the cases where n was an odd number, however, the acids with n = 1, 3, 5 and 7 yielded only traces (some 10μg) of phenol. 9-Phenoxynonane-1-carboxylic acid ( n = 9) was exceptional yielding about 60μg phenol. This behaviour of the nonane-acid could be explained by side-chain degradation involving ω -oxidation, and correlates with results of animal metabolism studies. All ten acids were examined as plant growth-regulators by six different methods. Uniform inactivity was shown in the tomato leaf epinasty, tomato leaf rooting, tomato parthenocarpy and Avena cylinder tests. In both the Went pea and a bean seedling test, however, an unexpected type of alternation in activity was observed in this series. This is considered in relation to the alternation in growth-regulating activity obtained with other homologous series of aryloxy-acids.