Molecular mobility in comb-shaped copoly(methacrylates) with fluoromethylene and chromophore-containing side chains

The molecular mobility of copoly(methacrylates) with chromophore-containing side groups of various structures has been studied by the dielectric method. The region of relaxation of dipole polarization related to the segmental mobility (α process) has been discovered. At temperatures that are ～30°C higher than those corresponding to the α process, the relaxation transition reflecting the reorientation of chromophore-containing side groups (δ process) takes place. It is suggested that the occurrence of the δ process is a general phenomenon for such systems. This effect allows one to determine the temperature at which the polarization of polymer films under application of corona discharge should be carried out so that a high level of nonlinear optical properties associated with the macroscopic noncentrosymmetrical orientation of chromophores may be achieved.     

Insights into high mobility group A (HMGA) proteins from Poaceae family: An in silico approach for studying homologs

High mobility group (HMG) proteins are the major architectural proteins. Among HMG proteins, High Mobility Group A (HMGA) is characterized by AT-hook (ATH) motifs, which have an affinity for AT-rich DNA. In this study, we characterized the plant HMGAs from the Poaceae family using in silico methods. The protein sequences for rice HMGAs were retrieved and the corresponding orthologs from grasses were extracted. The phylogenetic analysis identified three major evolutionary clades of grass HMGAs and their ATH motif analysis revealed that HMGAs from clade 1 and 2, except for clade 2 HMGAs, are devoid of high-affinity DNA-binding domain. The clade 2 HMGAs also displayed a highly conserved length of all the spacers and the length of the C-terminal tail following the last ATH. Moreover, the C-terminal tail in clade 2 HMGAs is smaller than HMGAs from any other clade. Unlike clade 2, other clades of Poaceae HMGAs displayed high variability in the length of spacers. Despite several differences among HMGAs of different clades in Poaceae, the H1/H5 domain was found to be highly conserved. This study has revealed the detailed analyses of Poaceae HMGAs and it will be useful for further investigation aiming at the determination of precise biological functions and molecular mechanisms of grass HMGAs.     

Intramolecular mobility of side chains of poly(methacrylic acid) in regularly grafted copolyimides in solution

A “dark” copolyimide with regularly grafted side chains of polymethacrylic acid and a luminescence-labeled copolyimide containing an anthracene label covalently attached to side chains with an average polycondensation degree of the polyimide backbone of ～16 and an average polymerization degree of side poly(methacrylic acid) chains of ～100 are synthesized. Relaxation times τ_IMM characterizing the mobility of parts of side chains in solvents of different thermodynamic qualities for the backbone and side chains are determined through the polarized luminescence method. It is shown that, in a “common” solvent for the backbone and side chains, the values of τ_IMM are close to those characterizing the mobility of linear polymethacrylate chains. In selective solvents, changes in τ_IMM are related to not only changes in intramolecular interactions but also changes in the heterogeneity of the dynamic characteristics of parts of grafted chains arranged at different distances from the grafting point.     

Estimation of the total range of 1J(CC) couplings in heterocyclic compounds: pyridines and their N-oxides, the experimental and DFT studies

A very large set of one-bond spin-spin carbon carbon coupling constants, 1J(CC), has been measured for 32 variously mono- and disubstituted pyridine N-oxides and for 14 substituted pyridines. The N-oxides studied were 2-, 3- and 4-monosubstituted isomers, and a series of disubstituted compounds. A variety of substituents has been employed (CH3, COCH3, C5H4NO, CN, F, Br, Cl, OH, OCH3, NH2, N(CH3)2 and NO2), which allowed us to study substituent effects thoroughly. Good linear relationships between 1J(C3C4) in 3- and/or 4-substituted pyridine N-oxides and 1J(CipsoCortho) in benzenes and between 1J(C2C3) in 2- and/or 3-substituted pyridine N-oxides and 1J(CipsoCortho) in benzenes have been found. An analogous linear relationship has been observed between 1J(C3C4) in 3- and/or 4-substituted pyridines and 1J(CipsoCortho) in benzenes. It has been also concluded that, by analogy to 1J(CC) couplings in substituted benzenes, those in pyridines and their N-oxides are the substituent electronegativity dependent. The estimated total range covered by 1J(CC), couplings in substituted compounds varies, in the case of 1J(C2C3) couplings for example, from 25 Hz in 2-lithiopyridine N-oxide to ca. 100 Hz in 2,3-difluoropyridine N-oxide and from 18 Hz in 2-lithiopyridine to 92 Hz in 2,3-difluoropyridine. The DFT calculations have been carried out for the parent compounds and for a set of their 2-lithio, and variously substituted fluoro derivatives. The DFT data reproduced very well the experimental coupling values and revealed that the Fermi contact contribution is the dominating factor which governs the magnitude of the CC coupling across one bond.     

Synthesis and characterization of poly(3-alkylthiophenes) with NLO chromophoric groups in side chains

Polythiophene copolymers containing alkyl side chains of different length and partially functionalized with chromophoric groups have been synthesized by FeCl₃ oxidative coupling of 3-alkylthiophenes and functionalized 3-alkylthiophenes. Composition, molecular weigth and configuration of the soluble fraction of the copolymers have been investigated and some structure-property correlations have been evidenced.     

Variation in protein C(alpha)-related one-bond J couplings

Four types of polypeptide (1)J(C alpha X) couplings are examined, involving the main-chain carbon C(alpha) and either of four possible substituents. A total 3105 values of (1)J(C alpha H alpha), (1)J(C alpha C beta), (1)J(C alpha C'), and (1)J(C alpha N') were collected from six proteins, averaging 143.4 +/- 3.3, 34.9 +/- 2.5, 52.6 +/- 0.9, and 10.7 +/- 1.2 Hz, respectively. Analysis of variances (ANOVA) reveals a variety of factors impacting on (1)J and ranks their relative statistical significance and importance to biomolecular NMR structure refinement. Accordingly, the spread in the (1)J values is attributed, in equal proportions, to amino-acid specific substituent patterns and to polypeptide-chain geometry, specifically torsions phi, psi, and chi(1) circumjacent to C(alpha). The (1)J coupling constants correlate with protein secondary structure. For alpha-helical phi, psi combinations, (1)J(C alpha H alpha) is elevated by more than one standard deviation (147.8 Hz), while both (1)J(C alpha N') and (1)J(C alpha C beta) fall short of their grand means (9.5 and 33.7 Hz). Rare positive phi torsion angles in proteins exhibit concomitant small (1)J(C alpha H alpha) and (1)J(C alpha N') (138.4 and 9.6 Hz) and large (1)J(C alpha C beta) (39.9 Hz) values. The (1)J(C alpha N') coupling varies monotonously over the phi torsion range typical of beta-sheet secondary structure and is largest (13.3 Hz) for phi around -160 degrees. All four coupling types depend on psi and thus help determine a torsion that is notoriously difficult to assess by traditional approaches using (3)J. Influences on (1)J stemming from protein secondary structure and other factors, such as amino-acid composition, are largely independent.     

Aib-rich peptides containing lactam-bridged side chains as models of the 3(10)-helix.

Aib-rich side chain lactam-bridged oligomers with n =1, 2, 3, were designed and synthesized as putative models of the 3(10)-helix. These peptides were conformationally characterized in aqueous solution containing SDS micelles by CD, NMR, and computer simulations. The lactam bridge between the side chains of L-Glu and L-Lys in (i) and (i+3) positions was introduced in order to enhance the conformational preference toward the right-handed 3(10)-helix. The NMR results clearly indicate that there is an increase of 3(10)-helix formation upon chain elongation. In the dimer and trimer (n = 2 and n = 3, respectively, in the structure reported above) the observed NOE connectivities are compatible with the 3(10)-helical arrangement, confirmed by the temperature coefficients of the amide proton resonances which suggest the presence of a hydrogen-bonded structure. The phi and psi dihedral angles of the structures obtained by molecular dynamics calculations are also compatible with the 3(10)-helix. Identification of the hydrogen-bond pattern indicate that C=O(i)- - -HN(i+3) hydrogen bonds, typical of the 3(10)-helical conformation, are highly probable in all low-energy structures. The CD spectra of these Aib-rich lactam-bridged oligopeptides, obtained in the same solvent system used for NMR experiments, provide important insight into the spectroscopic characteristics of the 3(10)-helix.     

Insights into the reaction of transplatin with DNA and proteins: methionine-mediated formation of histidine-guanine trans-Pt(NH3)2 cross-links

Simultaneous exposure of transplatin to polypeptides and DNA was mimicked by using a model peptide-oligonucleotide conjugate. Initially formed methionine-guanine chelates evolved into adducts with histidine-guanine trans-Pt(NH3)2 cross-links that differed in constitution and stability from those formed by reaction of the same conjugate with the anticancer drug cisplatin. This finding may be due to different capacities of the two diamminedichloroplatinum(II) complexes to interfere with biological processes and may explain their differing cytotoxicities.     

The calculation of 2J(HH) couplings in benzyl groups

The results of FPT/INDO theory together with the observed ²J(HH) coupling in benzyl groups (Ph · CH₂X) leads to a simple equation ²J(HH) = A+B cos θ+C cos 2θ where θ is the C.C.C.X dihedral angle, and X = C,H. The extension to other X substituents can be obtained from additivity rules.     

Some self-consistent perturbation calculations of 1J(CC)

Self-consistent perturbation calculations of 70 ¹J(CC) values are reported within the INDO framework. A least-squares agreement between the calculated and observed couplings, for a variety of bond multiplicities, provides values of 13.503 au^?6 and 5.072 au^?6 for (S_C²(O))² and 〈r^?3〉_C², respectively. The non-contact terms are found to be important in cases of multiple bonding.     

Role of aromatic side chains in the folding and thermodynamic stability of integral membrane proteins

Aromatic residues are frequently found in helical and beta-barrel integral membrane proteins enriched at the membrane-water interface. Although the importance of these residues in membrane protein folding has been rationalized by thermodynamic partition measurements using peptide model systems, their contribution to the stability of bona fide membrane proteins has never been demonstrated. Here, we have investigated the contribution of interfacial aromatic residues to the thermodynamic stability of the beta-barrel outer membrane protein OmpA from Escherichia coli in lipid bilayers by performing extensive mutagenesis and equilibrium folding experiments. Isolated interfacial tryptophanes contribute -2.0 kcal/mol, isolated interfacial tyrosines contribute -2.6 kcal/mol, and isolated interfacial phenylalanines contribute -1.0 kcal/mol to the stability of this protein. These values agree well with the prediction from the Wimley-White interfacial hydrophobicity scale, except for tyrosine residues, which contribute more than has been expected from the peptide models. Double mutant cycle analysis reveals that interactions between aromatic side chains become significant when their centroids are separated by less than 6 A but are nearly insignificant above 7 A. Aromatic-aromatic side chain interactions are on the order of -1.0 to -1.4 kcal/mol and do not appear to depend on the type of aromatic residue. These results suggest that the clustering of aromatic side chains at membrane interfaces provides an additional heretofore not yet recognized driving force for the folding and stability of integral membrane proteins.     

UV Raman markers for structural analysis of aromatic side chains in proteins

UV Raman spectroscopy is a powerful tool for investigating the structures and interactions of the aromatic side chains of Phe, Tyr, Trp, and His in proteins. This is because Raman bands of aromatic ring vibrations are selectively enhanced with UV excitation, and intensities and wavenumbers of Raman bands sensitively reflect structures and interactions. Interpretation of protein Raman spectra is greatly assisted by using empirical correlations between spectra and structure. Many Raman bands of aromatic side chains have been proposed to be useful as markers of structures and interactions on the basis of empirical correlations. This article reviews the usefulness and limitations of the Raman markers for protonation/deprotonation, conformation, metal coordination, environmental polarity, hydrogen bonding, hydrophobic interaction, and cation-π interaction of the aromatic side chains. The utility of Raman markers is demonstrated through an application to the structural analysis of a membrane-bound proton channel protein.     

Coalescence of 3-phenyl-propynenitrile on Cu(111) into interlocking pinwheel chains

3-phenyl-propynenitrile (PPN) adsorbs on Cu(111) in a hexagonal network of molecular trimers formed through intermolecular interaction of the cyano group of one molecule with the aromatic ring of its neighbor. Heptamers of trimers coalesce into interlocking pinwheel-shaped structures that, by percolating across islands of the original trimer coverage, create the appearance of gear chains. Density functional theory aids in identifying substrate stress associated with the chemisorption of PPN's acetylene group as the cause of this transition.     

Kinetics and mechanism of platinum-thallium bond formation: the binuclear [(CN)5Pt-Tl(CN)](-) and the trinuclear [(CN)5Pt-Tl-Pt(CN)5](3-) complex

Formation kinetics of the metal-metal bonded binuclear [(CN)(5)Pt-Tl(CN)](-) (1) and the trinuclear [(CN)(5)Pt-Tl-Pt(CN)(5)](3-) (2) complexes is studied, using the standard mix-and-measure spectrophotometric method. The overall reactions are Pt(CN)(4)(2-) + Tl(CN)(2)(+) <==> 1 and Pt(CN)(4)(2-) + [(CN)(5)Pt-Tl(CN)](-) <==> 2. The corresponding expressions for the pseudo-first-order rate constants are k(obs) = (k(1)[Tl(CN)(2)(+)] + k(-1))[Tl(CN)(2)(+)] (at Tl(CN)(2)(+) excess) and k(obs) = (k(2b)[Pt(CN)(4)(2-)] + k(-2b))[HCN] (at Pt(CN)(4)(2-) excess), and the computed parameters are k(1) = 1.04 +/- 0.02 M(-2) s(-1), k(-1) = k(1)/K(1) = 7 x 10(-5) M(-1) s(-1) and k(2b) = 0.45 +/- 0.04 M(-2) s(-1), K(2b) = 26 +/- 6 M(-1), k(-2b) = k(2b)/K(2b) = 0.017 M(-1) s(-1), respectively. Detailed kinetic models are proposed to rationalize the rate laws. Two important steps need to occur during the complex formation in both cases: (i) metal-metal bond formation and (ii) the coordination of the fifth cyanide to the platinum site in a nucleophilic addition. The main difference in the formation kinetics of the complexes is the nature of the cyanide donor in step ii. In the formation of [(CN)(5)Pt-Tl(CN)](-), Tl(CN)(2)(+) is the source of the cyanide ligand, while HCN is the cyanide donating agent in the formation of the trinuclear species. The combination of the results with previous data predict the following reactivity order for the nucleophilic agents: CN(-) > Tl(CN)(2)(+) > HCN.     

Insights into regioselective oxy (-O-) and imino (-NH-) group insertions of 3-nortricyclanone.

Lactam 4-azatricyclo[3.2.1.0(2,7)]octan-3-one (16a) was proven to be formed in a previously reported reaction that claimed production of lactam 3-azatricyclo[3.2.1.0(2,7)]octan-4-one (17a). In a related reaction, bicyclo[3.1.0]hex-2-ene-endo-6-carbonitrile (15), lactam (16a), and novel hydroxycarbonitriles 19-21 were selectively formed when 3-nortricyclanone (1) was treated with aqueous hydroxylamine-O-sulfonic acid (HOSA). Since nitrile 15 neither hydrolyzed nor underwent intramolecular Ritter reaction under these conditions, mechanisms involving Beckmann rearrangement of 3 to nitrilium ion 9 (normal) and Beckmann fragmentation of 3 to cation 8 (abnormal) were investigated using semiempirical calculations. When alkaline HOSA was employed, lactams 16a and 17a were formed in a 1:2 ratio, perhaps via oxaziridine 6a. A similar selectivity was observed using an NH(3)/NaOCl reagent solution, which afforded lactone 4-oxatricyclo[3.2.1.0(2,7)]octan-3-one (16b) in addition to both lactams. Consequently, the Baeyer-Villiger oxidation of 1 with NaOCl gave 16b exclusively. Finally, the Schmidt reaction of ketone 1 gave only the lactam 17a, via cyclopropyl migration, and the same fragmentation products obtained from the acidic HOSA reaction. Migration selectivities are rationalized in terms of nucleofugacity, electronic effects, cyclopropyl regulation, and MO theory.     

Cuprophilicity-induced cocrystallization of [Cu2(4,4'-bpy)(CN)2]n sheets and [Cu(SCN)]n chains into a 3-D pseudopolyrotaxane

The cocrystallization of [Cu(SCN)]n chains and [Cu2(4,4'-bpy)(CN)2]n (4,4'-bpy = 4,4'-bipyridine) layers generated a 3-D pseudopolyrotaxane compound, [Cu2(4,4'-bpy)(CN)2].[Cu(SCN)] (1), which can also be viewed as a 3-D network constructed by linkages of 2-D sheets and 1-D chains via unsupported CuI-CuI interactions. The CuI-CuI contact of 2.651(4) A in 1 is the shortest unsupported CuI-CuI distance documented to date, indicating cuprophilic attractions.