Showing papers on "Side chain published in 1999"
TL;DR: In this article, a structural model based on intrachain ordering was proposed to account for the changes of the absorption spectrum of poly(9,9-dioctylfluorene) (PFO) films under certain physicochemical treatment protocols.
Abstract: From photophysical evidence, we suggest a structural model based on intrachain ordering that can account for the changes of the absorption spectrum of poly(9,9-dioctylfluorene) (PFO) films under certain physicochemical treatment protocols. We correlate this model to the results of X-ray fiber diffraction experiments.
615 citations
TL;DR: The proposed roles of tryptophan and lysine side chains as “anchoring” residues of transmembrane proteins are investigated, and a model in which the Trp side chain has a specific affinity for a well defined site near the lipid carbonyl region is supported.
329 citations
TL;DR: Calculations of Voronoi atomic volumes showed that protein atoms buried at the interface with DNA are on average as closely packed as in the protein interior.
Abstract: We analyzed the atomic models of 75 X-ray structures of protein−nucleic acid complexes with the aim of uncovering common properties. The interface area measured the extent of contact between the protein and nucleic acid. It was found to vary between 1120 and 5800 A2. Despite this wide variation, the interfaces in complexes of transcription factors with double-stranded DNA could be broken up into recognition modules where 12 ± 3 nucleotides on the DNA side contact 24 ± 6 amino acids on the protein side, with interface areas in the range 1600 ± 400 A2. For enzymes acting on DNA, the recognition module is on average 600 A2 larger, due to the requirement of making an active site. As judged by its chemical and amino acid composition, the average protein surface in contact with the DNA is more polar than the solvent accessible surface or the typical protein−protein interface. The protein side is rich in positively charged groups from lysine and arginine side chains; on the DNA side the negative charges from pho...
325 citations
TL;DR: Fluorescence quenching has been used to study the cooperative conformational transition in a series of oligo(phenylene ethynylene)s having tri(ethylene glycol) monomethyl ether side chains as discussed by the authors.
Abstract: Fluorescence quenching has been used to study the cooperative conformational transition in a series of oligo(phenylene ethynylene)s having tri(ethylene glycol) monomethyl ether side chains. In nonpolar solvents such as chloroform, the intensity of fluorescence emission from the backbone chromophore increases smoothly as the chain lengthens from the dimer through the octadecamer. In polar solvents such as acetonitrile, on the other hand, chains having more than eight units exhibit fluorescence quenching concomitant with the growth of an intramolecular excimer-like band. This observation is consistent with π-stacking of aromatic rings for chains that are long enough to fold back on themselves, driven by solvophobic interactions. Titration experiments in which the solvent composition was gradually changed from pure acetonitrile to pure chloroform showed sigmoidal curves characteristic of a cooperative transition. These data were analyzed using a two-state approximation and a model in which the free energy di...
312 citations
TL;DR: In this paper, an electrochemically roughened silver surface, in conjunction with a Raman microprobe spectrometer, was used to obtain SER spectra of a suite of 19 l -amino acids.
294 citations
TL;DR: To achieve small, stable complexes, the use of cationic polymers with short side chains bearing primary amino groups is suggested.
269 citations
TL;DR: Helix 2 and helix 2', which are antiparallel and next to each other in the dimer conformation, constitute the interaction face between the NS1 RNA-binding domain and its RNA targets, and that the arginine side chain at position 38 and possibly the lysine sidechain at position 41 in each of these antipar parallel helices contact the phosphate backbone of the RNA target.
Abstract: The RNA-binding/dimerization domain of the NS1 protein of influenza A virus (73 amino acids in length) exhibits a novel dimeric six-helical fold. It is not known how this domain binds to its specific RNA targets, one of which is double-stranded RNA. To elucidate the mode of RNA binding, we introduced single alanine replacements into the NS1 RNA-binding domain at specific positions in the three-dimensional structure. Our results indicate that the dimer structure is essential for RNA binding, because any alanine replacement that causes disruption of the dimer also leads to the loss of RNA-binding activity. Surprisingly, the arginine side chain at position 38, which is in the second helix of each monomer, is the only amino-acid side chain that is absolutely required only for RNA binding and not for dimerization, indicating that this side chain probably interacts directly with the RNA target. This interaction is primarily electrostatic, because replacement of this arginine with lysine had no effect on RNA binding. A second basic amino acid, the lysine at position 41, which is also in helix 2, makes a strong contribution to the affinity of binding. We conclude that helix 2 and helix 2', which are antiparallel and next to each other in the dimer conformation, constitute the interaction face between the NS1 RNA-binding domain and its RNA targets, and that the arginine side chain at position 38 and possibly the lysine side chain at position 41 in each of these antiparallel helices contact the phosphate backbone of the RNA target.
264 citations
TL;DR: Using shape description methods, a database of commercially available drugs is divided into a list of common drug side chains, and it is suggested that the diversity that side chains provide to drug molecules is quite low.
Abstract: We continue our study of the common features present in drug molecules by looking in detail at drug side chains. Using shape description methods, we divide a database of commercially available drugs into a list of common drug side chains. On the basis of the atom pair shape descriptor (taking into account atom type, hybridization, and bond order), there are 1,246 different side chains among the 5,090 compounds analyzed. The average number of side chains per molecule is 4, and the average number of heavy atoms per side chain is 2. If we ignore the carbonyl side chain, then there are approximately 15,000 occurrences of side chains. Of these 15,000 approximately 11,000 are from the "top 20" group of side chains. This suggests that the diversity that side chains provide to drug molecules is quite low. We discuss ways that this work could be used to provide guidance for molecular design efforts.
249 citations
TL;DR: The results suggest that protein stability can be increased by improving the coulombic interactions among charged groups on the protein surface by reversing the charge on a side chain on the surface of a protein.
Abstract: It is difficult to increase protein stability by adding hydrogen bonds or burying nonpolar surface. The results described here show that reversing the charge on a side chain on the surface of a protein is a useful way of increasing stability. Ribonuclease T1 is an acidic protein with a pI approximately 3.5 and a net charge of approximately -6 at pH 7. The side chain of Asp49 is hyperexposed, not hydrogen bonded, and 8 A from the nearest charged group. The stability of Asp49Ala is 0.5 kcal/mol greater than wild-type at pH 7 and 0.4 kcal/mol less at pH 2.5. The stability of Asp49His is 1.1 kcal/mol greater than wild-type at pH 6, where the histidine 49 side chain (pKa = 7.2) is positively charged. Similar results were obtained with ribonuclease Sa where Asp25Lys is 0.9 kcal/mol and Glu74Lys is 1.1 kcal/mol more stable than the wild-type enzyme. These results suggest that protein stability can be increased by improving the coulombic interactions among charged groups on the protein surface. In addition, the stability of RNase T1 decreases as more hydrophobic aromatic residues are substituted for Ala49, indicating a reverse hydrophobic effect.
215 citations
TL;DR: In this paper, the surface enhanced Raman (SER) spectra of a range of small peptides and proteins were obtained from an electrochemically roughened silver surface using a Raman microprobe spectrometer, and from analysis of these spectra the orientations of these molecules on the silver were elucidated.
213 citations
TL;DR: In this paper, a network polymer electrolyte with hyperbranched ether side chains was synthesized, and a monosubstituted epoxide monomer, 2-(...
Abstract: To achieve solvent-free polymer electrolytes with high ionic conductivity, network polymer electrolytes with hyperbranched ether side chains were synthesized. A monosubstituted epoxide monomer, 2-(...
TL;DR: A stabilization of the liquid- Crystalline mesophase and thus an enlarged temperature range of the mesogenic phase is achieved by adding perfluorotriphenylene to a chiral liquid-crystalline triphenylene.
Abstract: A stabilization of the liquid-crystalline mesophase and thus an enlarged temperature range of the mesogenic phase is achieved by adding perfluorotriphenylene to a chiral liquid-crystalline triphenylene. This mesophase is based on 1:1 perfluoroarene-arene interactions (see picture). In a polymer with triphenylenes as mesogens in the side chains, the addition of perfluorotriphenylene led to crystallization.
TL;DR: In this article, the self-aggregation behavior induced by heating of the poly(N-isopropylacrylamide) (PNIPA)/water binary system was investigated.
TL;DR: In this article, the authors investigated the field effect mobility of regioregular poly(3-hexylthiophene) (PHT) derivatives with chiral alkyl side chains, bulky side chains and carboxylic side chains.
Abstract: Soluble regioregular polythiophene derivatives with chiral alkyl side chains, bulky side chains, and carboxylic side chains have been synthesized. Their thin-film field-effect transistor performance and structural characteristics have been investigated. The above properties were found to be strongly affected by the nature of the side chains. Poor molecular ordering and low crystallinity were found for regioregular polythiophenes with bulky or carboxylic-substituted side chains, and their resulting transistor devices showed poor field-effect mobilities (less than 10-5−10-4 cm2/(V s)). A chiral alkyl-substituted regioregular polythiophene showed high crystallinity. However, its π−π overlap distance between the polythiophene backbones increase substantially (i.e., to ∼4.3 vs 3.8 A for regioregular poly(3-hexylthiophene) (PHT)) through the introduction of methyl branches in the side chains. The field-effect mobility of this polymer is reasonably high for solution-processable conjugated polymers (i.e., of the ...
TL;DR: Comparison of results using a fixed versus flexible backbone reveals that, surprisingly, the two methods are almost equivalent in their abilities to predict relative experimental stabilities, but only when full side-chain flexibility is allowed.
TL;DR: In this article, two poly(p-phenylenevinylene) (PPV) based polymers functionalized with an electron-deficient oxadiazole segment as the side chain by mimicking the chemical structure of 2-(4-biphenylyl)-5-( 4-tert-butylphenyl)-1,3,4-oxadiazoles (PBD) have been successfully synthesized through the Gilch route and Wittig method.
Abstract: Two poly(p-phenylenevinylene) (PPV) based polymers functionalized with an electron-deficient oxadiazole segment as the side chain by mimicking the chemical structure of 2-(4-biphenylyl)-5-(4-tert-butylphenyl)-1,3,4-oxadiazole (PBD) have been successfully synthesized through the Gilch route and Wittig method. The obtained polymer II, which is a copolymer, is completely soluble in conventional organic solvents. However, polymer I, which is a homopolymer, is not soluble in any common organic solvents tried. The structure and purity of II have been characterized by FT-IR, 1H NMR, 13C NMR, gel permeation chromatography (GPC), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), UV−vis and photoluminescence (PL) spectroscopy, and electrochemical analysis. The TGA results indicate that II has very high thermal stability, while DSC investigation demonstrates that the glass transition temperature (Tg) of II is higher than 200 °C, which might be a merit for the long-life operation of light-emi...
TL;DR: In this article, the lower critical solution temperature (LCST) of thermophosphazenes bearing methoxy-poly(ethylene glycol) and amino acid esters as substituents was investigated.
Abstract: Novel thermosensitive poly(organophosphazenes) bearing methoxy-poly(ethylene glycol) (MPEG) and amino acid esters as substituents have been synthesized, and their lower critical solution temperature (LCST) was investigated. Differential scanning calorimetry (DSC) has shown that some of the polymers exhibit crystallinity, which is probably induced by the MPEG side chain of the polymers. Most of the polymers show their LCSTs in the range of 25.0−98.5 °C, depending on several factors such as mole ratio of the substituents, molecular weight of the MPEG, and kinds of amino acids and esters. The more hydrophilic composition of the polymers offers the higher LCST. The LCST of the polymers exhibits almost concentration-independent behavior in the range of 3−30 wt % of the polymers in aqueous solution.
TL;DR: In this paper, Fourier transform infrared (FTIR) signals of a histidine side chain were identified in flash-induced S2/S1 difference spectra of the oxygen-evolving complex (OEC) of photosystem II (PS II) using PS II membranes from globally 15N-labeled spinach and PS II core complexes from Synechocystis cells in which both the imidazole nitrogens of histidine were selectively labeled with 15N.
Abstract: Fourier transform infrared (FTIR) signals of a histidine side chain were identified in flash-induced S2/S1 difference spectra of the oxygen-evolving complex (OEC) of photosystem II (PS II) using PS II membranes from globally 15N-labeled spinach and PS II core complexes from Synechocystis cells in which both the imidazole nitrogens of histidine were selectively labeled with 15N. A negative band at 1113−1114 cm-1 was downshifted by 7 cm-1 upon both global 15N-labeling and selective [15N]His labeling, and assigned to the C−N stretching mode of the imidazole ring. This band was unaffected by H−D exchange in the PS II preparations. In addition, several peaks observed at 2500−2850 cm-1 all downshifted upon global and selective 15N-labeling. These were ascribed to Fermi resonance peaks on a hydrogen-bonding N−H stretching band of the histidine side chain. FTIR measurements of model compounds of the histidine side chain showed that the C−N stretching band around 1100 cm-1 can be a useful IR marker of the protonat...
TL;DR: The relatively immobilized state of the nitroxide side chains suggests that the channel is rigid on the electron paramagnetic resonance time scale, and the poor sulfhydryl reactivity of the cysteine at many locations indicates that theChannel is not subject to the low-frequency fluctuations that permit reaction of buried cysteines.
Abstract: KcsA is a prokaryotic potassium channel. The present study employs cysteine scanning mutagenesis and site-directed spin labeling to investigate the structure of the second transmembrane segment (residues 82−120) in functional tetrameric channels reconstituted in lipid bilayers. Spin−spin interactions are observed between nitroxide side chains at symmetry-related sites close to the 4-fold axis of symmetry. To aid in quantitative analysis of these interactions, a new diamagnetic analogue of the nitroxide side chain is used to prepare magnetically dilute samples with constant structure. Using constraints imposed by the spin−spin interactions, a packing model for this segment is deduced that is in excellent agreement with the recently reported crystal structure [Doyle, D., et al. (1998) Science 280, 69−77]. The relatively immobilized state of the nitroxide side chains suggests that the channel is rigid on the electron paramagnetic resonance time scale. Moreover, the poor sulfhydryl reactivity of the cysteine ...
TL;DR: The results indicate that the reagent 3-(methanesulfonylthiomethyl)-2,2, 5,5-tetramethylpyrrolidin-1-yloxy reacts with cysteine to give a nitroxide side chain that has a high contrast in mobility between helix surface and tertiary contact sites, effectively resolving the degeneracy.
Abstract: Previous studies have shown that the mobility of nitroxide side chains in a protein, inferred from the electron paramagnetic resonance (EPR) spectra, can be used to classify particular sites as helix surface sites, tertiary contact sites, buried sites, or loop sites. In addition, the sequence dependence of mobility can identify regular secondary structure. However, in the most widely used side chain, an apparent interaction of the nitroxide ring with the protein at some helix surface sites gives rise to EPR spectra degenerate with those at tertiary contact sites. In the present study, we use selected sites in T4 lysozyme to evaluate novel nitroxide side chains designed to resolve this degeneracy. The results indicate that the reagent 3-(methanesulfonylthiomethyl)-2,2, 5,5-tetramethylpyrrolidin-1-yloxy reacts with cysteine to give a nitroxide side chain that has a high contrast in mobility between helix surface and tertiary contact sites, effectively resolving the degeneracy. The reagent 3-(iodomercuriomethyl)-2,2,5,5-tetramethyl-2, 5-dihydro-1H-pyrrol-1-yloxy reacts with cysteine to provide a mercury-linked nitroxide that also shows reduced interaction with the protein at most helix surface sites. Thus, these new side chains may be the preferred choices for structure determination using site-directed spin labeling.
TL;DR: In this article, three qualitatively different glass transitions are observed in the shear curves at 10 rad/s: the conventional α process in the C 5 members, and an additional polyethylene-like glass transition, αPE, in the c ≥ 3 members.
Abstract: Shear data in the temperature range from −145 °C to the flow zone are presented for the poly(n-alkyl methacrylate)s from methyl (C = 1) to lauryl (C = 12). Three qualitatively different glass transitions are observed in the shear curves at 10 rad/s: (i) the conventional α process in the C 5 members, and (iii) an additional polyethylene-like glass transition, αPE, in the C ≥ 3 members. All three processes depend systematically on side chain length. Two alternative empirical pictures for the coexistence of two glass transitions are discussed: (a) a static nanophase separation between main chains and side chains and (b) a dynamic heterogeneity with two different time and length scales.
TL;DR: In this article, side chain functionalization of an oligomeric silicone has been shown to produce a material whose phase behavior in CO2 resembles that of a fluorinated polyether.
Abstract: Previous fundamental work on the solvent properties of carbon dioxide by the research groups of McHugh, DeSimone, Johnston, and Eckert has been used as a road map for the design of materials that will be miscible with CO2 at relatively moderate pressures. In this initial work, judicious side chain functionalization of an oligomeric silicone has been shown to produce a material whose phase behavior in CO2 resembles that of a fluorinated polyether. The phase behavior results are quite dramatic in that addition of only five ester-functional side chains to the silicone polymer lowers the cloud point curve at 22 °C by 2500 psi. It was also observed that addition of simple alkyl side chains raises the cloud point pressures of the silicone in CO2. This latter observation is consistent with results on the phase behavior of poly(n-alkyl acrylates) in CO2 that showed that increasing alkyl content (i.e., increasing alkyl chain length) also raises cloud point pressures.
TL;DR: In this paper, a series of polymacromonomer samples (F15) consisting only of polystyrene and having a fixed side chain length of 15 styrene residues have been prepared and studied by static light scattering in cyclohexane at different temperatures and in toluene at 15 °C.
Abstract: A series of polymacromonomer samples (F15) consisting only of polystyrene and having a fixed side chain length of 15 styrene residues have been prepared and studied by static light scattering in cyclohexane at different temperatures and in toluene at 15 °C. The measurement has also been made on polymacromonomer samples (F33) of the same kind but with 33 side chain residues in toluene. The second virial coefficient for the F15 polymer in cyclohexane vanishes at 34.5 °C, the Θ temperature for linear polystyrene, as was previously found to be the case for the F33 polymer. Analysis of the measured mean-square radii of gyration based on the wormlike chain with or without excluded volume shows that, while the contour length per main-chain residue is insensitive to the side chain length, the Kuhn segment length λ -1 (or more generally the stiffness parameter in the helical wormlike chain) under the Θ condition remarkably increases with increasing side chain length and that the λ -1 values (16 and 36 nm) for the polymacromonomers F15 and F33 in toluene, a good solvent, are about 1.6 times as large as those in the Θ solvent. Thus, it is concluded that, in addition to the high segment density around the main chain, repulsions between the main chain and side chain and between neighboring side chains play an important role in the high stiffness of polymacromonomers.
TL;DR: The solid state structures of a series of 2,5-dialkyl-substituted poly(p-phenyleneethynylene)s were investigated by X-ray powder and electron diffraction as discussed by the authors.
Abstract: The solid-state structures of a series of 2,5-dialkyl-substituted poly(p-phenyleneethynylene)s (PPEs 4, R = hexyl, dodecyl, isopentyl, ethylbutyl, ethylhexyl, H) and of 2,5-didodecyl(1,4-phenylenebutadiynylene) were investigated by X-ray powder and electron diffraction. In addition, X-ray single-crystal structures of the monomeric (1,4-dipropynyl-2,5-dialkyl)benzenes were obtained and compared to the structures of the corresponding polymers. In the case of the ethylhexyl-substituted PPE, the packing of the monomer resembles that of the polymer in the solid state. All of the examined PPEs show lamellar morphologies, in which the extended geometry of the side chains determines the value of the lamellar spacing obtained by powder diffraction. A second d value, which could be obtained for all samples represents the π−π-stacking distance of the main chains. This distance is around 3.8 A, a typical value for stacking of aromatic systems. It implies strong electronic interaction of the chromophoric backbones, le...
TL;DR: The conformational landscapes of 2-amino-1-phenylethanol and its 1:1 water complexes have been investigated by UV band contour, UV−UV hole-burning, and IR−UV ion dip spectroscopy, coupled with ab initio computation.
Abstract: The conformational landscapes of 2-amino-1-phenylethanol and its 1:1 water complexes have been investigated by UV band contour, UV−UV hole-burning, and IR−UV ion dip spectroscopy, coupled with ab initio computation. The two molecular conformers observed are both stabilized by an intramolecular hydrogen bond, located in the folded (gauche) OCCN side chain, which links the proton donor OH group to the terminal amino group and leads to a significant constriction of the side chain. In the dominant 1:1 water complex, the intramolecular hydrogen bond is disrupted by the first water molecule, which inserts between the OH group and the nitrogen atom, to form a cyclic H-bonded structure. The side chain expands significantly in order to accommodate the water molecule within the neighborhood of both the hydroxyl and amino groups.
TL;DR: In this paper, a functional phenylacetylene derivative, [4-({[6-({ [4]oxy-4-biphenylyl]carbonyl]oxy)hexyl]oxy} carbonyl)phenyl]acetylene (1), is shown to possess a stereoregular alternating double-bond backbone with a predominant cis conformation.
Abstract: The polymerizations of a functional phenylacetylene derivative, [4-({[6-({[4‘-(heptyl)oxy-4-biphenylyl]carbonyl}oxy)hexyl]oxy}carbonyl)phenyl]acetylene (1), are effected by molybdenum and tungsten halides and rhodium−diene complexes. The rhodium-initiated polymerizations produce polymers (2) of high molecular weights (Mn up to 1.2 × 105) in high yields (up to 93%). IR, UV, and NMR analyses confirm that 2 possesses a stereoregular alternating-double-bond backbone with a predominant cis conformation. DSC, POM, and XRD measurements reveal that 2 is liquid crystalline: it shows smectic A mesophase in the temperature range 135−146 °C. The cis-rich 2 undergoes active isomerization to the trans conformation at 170 °C. Intrachain cyclization followed by chain scission at ca. 200 °C releases 1,3,5-trisubstituted benzene as the sole aromatization product, proving that the repeat units of the polymer chains are linked in a regular head-to-tail fashion.
TL;DR: In this article, the results of a Monte Carlo simulation study of isolated comb copolymer cylindrical brushes are presented, showing that the conformational characteristics of molecules consisting of a flexible backbone densely grafted with side chains strongly depend on the rigidity of the side chains, which is exemplified by using both flexible and totally rigid side chains.
Abstract: We report the results of a Monte Carlo simulation study of isolated comb copolymer cylindrical brushes. The conformational characteristics of molecules consisting of a flexible backbone densely grafted with side chains strongly depend on the rigidity of the side chains, which is exemplified by using both fully flexible and totally rigid side chains. The short length scale fluctuations of the backbone are not affected by the presence of rigid rod side chains, whereas flexible side chains induce local stretching of the backbone. However, at the large length scale, the persistence length λ of the cylindrical brush is considerably larger for rigid rod side chains than for flexible side chains. Moreover, for rigid side chains the ratio between the persistence length λ and the diameter D of the brush increases approximately linearly as a function of the rod length L, thus supporting the possibility of lyotropic behavior. In contrast to this, in the case of flexible side chains, λ/D is approximately independent of the side chain length M.
Patent•
25 Mar 1999
TL;DR: In this paper, a photo-acid generating agent was used to obtain a high sensitivity and excellent preservable property, enabling the photo-sensitive wave length range to be widely selected and made utilizable as a light source including various lasers by consisting of a polymer having a heterocyclic group having a side chain bonded with mercapto group and an photo acid generating agent.
Abstract: PROBLEM TO BE SOLVED: To obtain a photosensitive composition having high sensitivity as a photosensitive material and excellent preservable property, enabling photosensitive wave length range to be widely selected and made utilizable as a light source including various lasers by consisting of a polymer having a heterocyclic group having a side chain bonded with mercapto group and an photo-acid generating agent. SOLUTION: This photosensitive composition consists of the polymer having a heterocyclic group having a side chain bonded with mercapto group and the photo-acid generating agent. As the polymer having the heterocyclic group having the side chain bonded with mercapto group, a polymer containing a repeating unit expressed by a formula or the like is mentioned. In the formula, R1 represents hydrogen atom or methine group and X1 represents nitrogen-containing heterocyclic group. L1 represents an optional connecting group to connect X1 to the polymer main chain and (n) represents 1 or 2. As the photo-acid generating agent, a S-triazine derivative substituted by a trihaloalkyl is preferable. As a result, the high sensitivity and excellent preservable property are attained as the photosensitive material, the range of the photosensitive wave length is widely selected and utilization as the light source including various lasers is enabled. COPYRIGHT: (C)2001,JPO
TL;DR: In this paper, a double-comb polysiloxane with ethylene oxide side chains, poly[bis(2-(2-(methoxyethoxy)ethoxy (ethoxy)-propylsiloxanes] (1), has been prepared.