Cooperative unit size in the gel-liquid crytalline phase transition of dipalmitoyl phosphatidylcholine-water multilayers: An estimate from raman spectroscopy

The temperature dependence of the Raman spectral transitions assigned to the acyl chain C-C stretching modes of dipalmitoyl phosphatidylcholine was determined for the gel, phase transition and liquid crystalline states of the lipid multilayers. The van't Hoff enthalpy differences $\text{ΔH}{}_{\mathrm{<mtext>VH</mtext>}}$ between trans and gauche rotational isomers were obtained from the Raman spectral data for the temperature region characteristics of each bilayer state. An average size for the cooperative unit undergoing the chain melting process during the phase transition was estimated from the ratio of the appropriate van't Hoff enthalpy to an adjusted calorimetric enthalpy.     

Solvent effects on the conformational preferences of model peptoids. MP2 study

The influence of aqueous environment on the main‐chain conformation (ω₀, ?, and ψ dihedral angles) of two model peptoids: N‐acetyl‐N‐methylglycine N’‐methylamide (Ac‐N(Me)‐Gly‐NHMe) ( 1 ) and N‐acetyl‐N‐methylglycine N’,N’‐dimethylamide (Ac‐N(Me)‐Gly‐NMe₂) ( 2 ) was investigated by MP2/6‐311++G(d,p) method. The Ramachandran maps of both studied molecules with cis and trans configuration of the N‐terminal amide bond in the gas phase and in water environment were obtained and all energy minima localized. The polarizable continuum model was applied to estimate the solvation effect on conformation. Energy minima of the Ac‐N(Me)‐Gly‐NHMe and Ac‐N(Me)‐Gly‐NMe₂ have been analyzed in terms of the possible hydrogen bonds and C = O dipole attraction. To validate the theoretical results obtained, conformations of the similar structures gathered in the Cambridge Crystallographic Data Centre were analyzed. Obtained results indicate that aqueous environment in model peptoids 1 and 2 favors the conformation F (? and ψ = ?70º, 180º), and additionally significantly increases the percentage of structures with cis configuration of N‐terminal amide bond in studied compounds. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

1H nuclear magnetic resonance studies of N-acetyl-L-proline N-methylamide. Molecular conformations,hydrogen bondings,and thermodynamic quantities in various solvents

Concentration and temperature dependences of the ¹H nmr spectra of N-acetyl-L -proline N-methylamide were observed in various solvents [CCl₄, CDCl₃, (CD₃)₂CO, (CD₃)₂SO, H₂O, and D₂O]. The fraction of the cis isomer (with respect to the bond between the acetyl carbonyl carbon and prolyl nitrogen atoms) depends greatly on the solvent used; the fraction of the cis isomer is higher in polar solvents than in nonpolar solvents. It depends also on concentration and temperature in nonpolar solvents but not in polar solvents. In nonpolar solvents the trans isomer mostly exists in the γ-turn structure with an intramolecular hydrogen bond and the cis isomer tends to form molecular aggregates by intermolecular hydrogen bonds. In polar solvents both the cis and trans isomers exist in monomeric forms which interact with solvent molecules. The pH dependences of the N-methyl proton resonances indicate that the γ-turn structure of the trans isomer is present also in aqueous solution, though its population is difficult to determine. Apparent enthalpy and entropy changes for the conversion of the trans isomer to cis isomer are evaluated for various solvents. The results are discussed in terms of the intra- and intermolecular hydrogen bondings.     

1H- and 13C-NMR studies of N-acetyl-L-alanine methylester and N-acetyl-L-alanine methylamide. I. Self-association

The ¹H- and ¹³C-NMR spectra of N-acetyl-L -alanine methylester and N-acetyl-L -alanine methylamide were measured to examine the modes of self-association of these molecules in solution. The different dilution shifts between these molecules seem to correspond to the difference in the associated state for each molecule. Consequently, for the former molecule, a dimer model forming the intermolecular hydrogen bond through Ala NH hydrogen atom in one molecule to Ala C?O oxygen atom in another molecule was proposed. Another dimer model, which coincides with that proposed recently by Neel and coworkers, was proposed for the latter molecule. This second dimer model forms an intermolecular hydrogen bond through the NH of the N-methylamide group in one molecule to the acetyl C?O in another molecule.     

Laser-raman spectroscopic study of carbohydrates: 1-thio-β-d-hexopyranosides

Some β-d-hexopyranosides of 1-thio-d-glucose, 2-acetamido-2-deoxy-1-thio-d-glucose, and 1-thio-d-galactose were examined by laser-Raman spectroscopy. An anomeric CH bending vibration was found at 891 ± 7 cm^-1 for all compounds investigated; thus, the anomers of these sugars can be differentiated by Raman spectroscopy. The N-acetyl group and carboxyl group can also be detected by Raman spectroscopy. Unlike protein samples, the carbohydrates in aqueous solution yield less useful information from Raman spectra than in the solid state; this is due to the extensive overlapping of carbohydrate OH bands with water OH bands.     

Raman spectral studies of nucleic acids. XI. Conformations of yeast tRNAPhe and E. coli ribosomal RNA in aqueous solution and in the solid state

Laser-excited Raman spectra of tRNA^Phe from yeast and of fractionated 16S and 23S rRNA from E. coli are reported for samples in aqueous solution and in the solid state. The Raman scattering spectrum of each RNA is not significantly altered by the change from an aqueous to a solid environment and displays the same characteristic frequencies and intensities associated with ordered polyribonucleotide structures. Unlike DNA, the backbone conformation of RNA thus appears to be largely insensitive to gross changes in the degree of hydration. Raman scattering from the phosphate group vibrations of aqueous tRNA_yeast^Phe is qualitatively and quantitatively the same as obtained from previously studied tRNA's and is indicative of a highly ordered conformational structure in which some 85% of the nucleotide residues are in ordered configurations. The major differences observed between spectra of tRNA and rRNA are attributed to differences in base composition of these RNA's.     

The partition of cis-parinaric acid and trans-parinaric acid among aqueous,fluid lipid,and solid lipid phases

Summary In this article, I review the current information concerning the partition of the fluorescent probes, cis-parinaric acid (9, 11, 13, 15-cis, trans, trans, cis-octadecatetraenoic acid) and trans-parinaric acid (9, 11, 13, 15-all trans-octadecatetraenoic acid) among aqueous, solid lipid, and fluid lipid phases. The association of these probes with lipid is described by a mole fraction partition coefficient whose value is typically in the range of 1–5 × 10⁶, a reasonable value in light of partition coefficients for other fatty acids between hydrophobic phases and water. The partition coefficient, in the absence of lipid phase changes, is relatively independent of temperature and only slightly dependent on the total aqueous probe concentration.In lipid samples which contain coexisting fluid and solid phases, trans-parinaric acid preferentially partitions into the solid phase, while cis-parinaric acid distributes nearly equally between fluid and solid phases. This partition behavior probably arises from the molecular shape of the cis and trans parinaric acid isomers. From measurements of the polarization of fluorescence of cis and trans parinaric acid in mixed lipid systems or membranes it is possible to evaluate the proportion of lipid components involved in phase changes or phase separation. From fluorescence energy transfer between protein typtophan residues and the parinaric acid isomers it is possible to gain information about the organization of lipids and proteins in membranes and model systems. I close the review by considering some of the membrane research areas where these probes and their various lipid derivatives may be particularly useful.     

Artificial carbohydrate antigens: The synthesis of glycopeptidic haptens with TN specificity

The synthesis of O-(2-acetamido-2-deoxy-α-d-galactopyranosyl)-N-acetyl-l-serine 8-methoxycarbonyloctanamide and O-(2-acetamido-2-deoxy-α-d-galactopyranosyl)-N-8-methoxycarbonyloctanoyl-l-serine methylamide is reported. These compounds represent the antigenic determinant of cell-membrane glycoproteins carrying T_N specificity. Both glycopeptides are functionalized for the purpose of preparing artificial antigens by attachment to immunogenic carriers and solid supports. Different schemes are needed for the synthesis of the haptens.     

Chiroptical properties of S-proline conformational isomers

The chiroptical properties of S-proline conformational isomers are examined on a theoretical model in which electronic wave functions are obtained from semiempirical molecular orbital calculations. The CNDO/S molecular orbital model is used to perform SCF-MO calculations on ground state electronic structure and excited states are constructed in the virtual orbital-configuration interaction approximation. Electronic rotatory strengths and dipole strengths are calculated directly from the complete (but approximate) molecular electronic wave functions. Zwitterionic, cationic, and anionic S-proline structures are studied twotypes of conformational variables are represented in the calculations: (1) pyrrolidine ring conformation; and (2) rotation about the C^α-COO^? bond. Rotatory strengths are found to be somewhat sensitive to rotational isomerism about the C^α-COO^? bond, but are found to be rather insensitive to conformational changes within the pyrrolidine ring. The CD spectrum of zwitterionic S-proline down to ～160 nm appears to be well accounted for by the theoretically calculated results if conformational preferences with respect to rotation about the C^α-COO^? bond can be assumed to exist in solution media. Furthermore, spectra-structure correlations are offered for the anionic and cationic forms of S-proline in solution.     

Random-phase calculation of the low-energy circular dichroism in glucans

The CD of the long-wavelength electronic transition in the α-(1 → 4)-linked glucan dimer (maltose) and polymer (amylose), and in the β-(1 → 6)-linked dimer (gentiobiose) and polymer (pustulan), are calculated in the random-phase approximation using time-dependent Hartree theory. This long-wavelength transition (180–190 nm) is assumed to be localized on the linkage oxygen atom and to be of a σ*/3 s ← n character. The zerothorder σ*/3s ← n magnetic-dipole transition moment is coupled to the CC, CO, and CH bond density of states via a polarizability approximation. We assume this coupling is dominated energetically by the electric-dipole, electric-dipole interaction terms in the context of Schellman's μ_e-μ_m coupling mechanism of rotatory power. The CD is calculated as a function of rotation about the two single bonds of the linkage oxygen atom and also as a function of rotation about the C(5)-C(6) bond. For maltose, four rotational isomers are considered, resulting from combinations of the gg and gt C(6)H₂OH group rotational isomers. The calculated CD values were then Boltzmann-averaged over an empirical potential, and the resulting CD was found to compare satisfactorily with experiment. In the case of the polymers, only structures having periodicity (helicity) were examined.     

Density functional theory study of small nickel clusters

The stable geometries and atomization energies for the clusters Ni _n (n = 2–5) are predicted with all-electron density functional theory (DFT), using the BMK hybrid functional and a Gaussian basis set. Possible isomers and several spin states of these nickel clusters are considered systematically. The ground spin state and the lowest energy isomers are identified for each cluster size. The results are compared to available experimental and other theoretical data. The molecular orbitals of the largest cluster are plotted for all spin states. The relative stabilities of these states are interpreted in terms of superatom orbitals and no-pair bonding.     

Analyse conformationnelle de la N-méthylamide de l'acide L-pyroglutamique par diffusion Rayleigh depolarisée,spectroscopie de vibration et calcul de l'energie conformationnelle

Conformational analysis of N-methylamide of pyroglutamic acid has been performed by theoretical energy calculations and experimental physical techniques, namely, laser Raman spectroscopy and depolarized Rayleigh scattering. The two theoretically predicted conformations are evidenced in crystalline state (ψ₁ = +169°) and in aqueous solution (ψ₁ ? ?20°). This study confirms the interest of a careful vibrational analysis of peptides and N-deuterated derivatives for providing an estimate of the dihedral angle ψ. The relationship between amide III frequency and ψ values is emphasized.     

1H nuclear magnetic resonance studies of histidine-containing di- and tripeptides. Estimation of the effects of charged groups on the pKa value of the imidazole ring.

The nmr titration curves of chemical shifts versus pH were observed for the protons of various histidine-containing di- and tripeptides. With these results, the macroscopic pK_a values and the chemical shifts intrinsic to each ionic species were determined by a computer curve-fitting based on a simple acid dissociation sequence. The pK_a value of the imidazole ring in N-acetyl-L -histidine methylamide was assumed to represent the intrinsic (or unperturbed) pK_a of the imidazole rings of histidine having peptide linkages at both the CO and NH sides. The pK_a values of the imidazole rings observed for most di- and tripeptides were reasonably reproduced by simple calculations using the intrinsic value and the perturbations due to the CO₂^? and NH₃⁺ groups located at various positions. Some other factors affecting the pK_a value of the imidazole ring are also discussed.     

Maternal effects of zygotic mutants affecting early neurogenesis inDrosophila

Summary The size of the neurogenic region ofDrosophila melanogaster is under the control of several genes of zygotic expression. Lack of function from any of those genes produces an increase of the size of the neurogenic region at the expense of the epidermal anlage. However, differences exist in the extent of neuralisation achieved by each of the genetic loci upon mutation. The present results show that in the case ofN andmam phenotype differences are due to different contributions of maternal gene expression. This could be shown by studying the phenotype which appeared in mutant embryos when the oocytes developed from homozygous mutant precursor cells. Clones of mutant cells were induced in the germ line of females heterozygous for the neurogenic mutationin trans over germ line dependent, dominant female sterile mutations. After removing maternal information the phenotype ofN andmam mutants became identical in both cases. Furthermore maternal information fromN ⁺ was found to be necessary for viability of the wildtype.     

Correction to: An analysis of structural phase transition and allied properties of cubic ReN and MoN compounds

The dependence of sensitivity of an explosive on its molecular structure may be mainly attributed to the molecular deformability, which can be expressed by some characteristic parameters, resonance energy for aromatic an explosive, strain energy for a strained-ring or strained-cage explosive, large π-π separation energy for a large π-π linked-explosive, bond rotational energy barriers of C–NO₂, N–NO₂, O–NO₂ for C–NO₂, N–NO₂, O–NO₂ bond-based explosives, and so on. Molecular polarizability of an explosive is also an important molecular deformability index, which can be effectively used to compare impact sensitivities of explosive’s isomers, isoelectronic species, and similar structures. Interestingly, comparing the molecular polarizabilities under external electric fields with different energy levels of isomeric N₂₀(Ih) and N₂₀(D_3d) clusters and the Mo₂N₂₀ and Re₂N₂₀ complex compounds, it is found that there are different energy thresholds of significant molecular expansion.

     

Gold Micro-Flowers: One-Step Fabrication of Efficient, Highly Reproducible Surface-Enhanced Raman Spectroscopy Platform

We present a new method enabling simultaneous synthesis and deposition of gold micro-flowers (AuMFs) on solid substrates in a one-pot process that uses two reagents, auric acid and hydroxylamine hydrochloride, in aqueous reaction mixture. The AuMFs deposited onto the substrate form mechanically stable gold layer of expanded nanostructured surface. The morphology of the AuMFs depends on and can be controlled by the composition of the reaction solution as well as by the reaction time. The nanostructured metallic layers obtained with our method are employed as efficient platforms for chemical and biological sensing based on surface-enhanced Raman spectroscopy (SERS). SERS spectra recorded by such platforms for p-mercaptobenzoic acid and phage lambda exhibit enhancement factors above 10⁶ and excellent reproducibility.     

Type II β-turn conformation of pivaloyl-L-prolyl-α-aminoisobutyryl-N-methylamide: Theoretical,spectroscopic, and X-ray studies

Pivaloyl-L -Pro-Aib-N-methylamide has been shown to possess one intramolecular hydrogen bond in (CD₃)₂SO solution, by ¹H-nmr methods, suggesting the existence of β-turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II β-turn conformations are about 2 kcal mol^?1 more stable than Type III structures. A crystallographic study has established the Type II β-turn in the solid state. The molecule crystallizes in the space group P2₁ with a = 5.865 Å, b = 11.421 Å, c = 12.966 Å, β = 97.55°, and Z = 2. The structure has been refined to a final R value of 0.061. The Type II β-turn conformation is stabilized by an intramolecular 4 → 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are ?_Pro = ?57.8°, ψ_Pro = 139.3°, ?_Aib = 61.4°, and ψ_Aib = 25.1°. The Type II β-turn conformation for Pro-Aib in this peptide is compared with the Type III structures observed for the same segment in larger peptides.     

Diamide model for the optical activity of collagen and polyproline I and II

A diamide, N-acetyl-L -proline-N,N-dimethylamide (AcProDMA), in water solution has optical rotatory dispersion (ORD) and circular dichroism (CD) spectra very similar to those of poly-L -proline II and the fibrous protein collagen. In contrast, AcProDMA in cyclohexane solution has optical activity resembling that of poly-L -proline I. Conformational analysis shows that AcProDMA is confined by steric constraints to either of two narrow regions of conformational space. The trans isomer of AcProDMA assumes conformations near those of polyproline II and collagen nearest neighbors, while cis-AcProDMA assumes conformations near that of polyproline I nearest neighbors. Nuclear magnetic resonance (NMR) experiments show that an equilibrium mixture of the cis and trans isomers of AcProDMA is present in solution. The trans isomer predominates in aqueous solution, but the equilibrium shifts to favor the cis isomer in nonpolar organic solvents such as cyclohexane. Analysis of the ORD spectra in terms of two basic spectra reveals a solvent dependent isomerization which parallels that observed by NMR. The optical activity of the pure isomers of AcProDMA can be derived from the ORD, CD and NMR data. A comparison of component cotton effects confirms the similarity in optical activity of trans-AcProDMA, polyproline II, and collagen on the one hand, and of cis-AcProDMA and Polyproline I on the other.     

Environment friendly modified chitosan hydrogels as a matrix for adsorption of metal ions, synthesis and characterization

Environment friendly modified chitosan hydrogels for metal ions absorption from aqueous systems were designed using simple technology. Chitosan was modified with [N,N′-bi-α-azidosuccinimide and N-phthalimido-α-azide succinimide] under different reaction conditions to prepare new hydrogels with high metal ion absorption efficiency. The hydrogels were characterized by FTIR, thermal stability, crystallography, solubility and swelling capacity. Promising results were obtained from this preliminary study to evaluate the efficiency of the new hydrogels to uptake copper and cobalt ions from aqueous systems.     

Tautomerism,Protonation, and Ionization of Formycin in Aqueous Solution by the pH Dependence of 13C Chemical Shifts and 13C-1H Coupling Constants

Abstract

Analyses of the pH dependence of ¹³C chemical shifts and ¹³C-¹H coupling constants of formycin in aqueous soluion revealed two pKa′s, at 4.4 and 9.7, corresponding to a protonation at N₄ and an ionization at N₁. The N₄-protonation results in the transfer of a pyrazolo ring hydrogen from N₂ to N₂-At physiological pH, formycin was found to exist as a mixture of N₁H and N₂H tautomers, with the former being predominant (>94%).