Uncoupled peptide bond vibrations in alpha-helical and polyproline II conformations of polyalanine peptides

We examined the 204-nm UV resonance Raman (UVR) spectra of the polyproline II (PPII) and alpha-helical states of a 21-residue mainly alanine peptide (AP) in different H2O/D2O mixtures. Our hypothesis is that if the amide backbone vibrations are coupled, then partial deuteration of the amide N will perturb the amide frequencies and Raman cross sections since the coupling will be interrupted; the spectra of the partially deuterated derivatives will not simply be the sum of the fully protonated and deuterated peptides. We find that the UVR spectra of the AmIII and AmII' bands of both the PPII conformation and the alpha-helical conformation (and also the PPII AmI, AmI', and AmII bands) can be exactly modeled as the linear sum of the fully N-H protonated and N-D deuterated peptides. Negligible coupling occurs for these vibrations between adjacent peptide bonds. Thus, we conclude that these peptide bond Raman bands can be considered as being independently Raman scattered by the individual peptide bonds. This dramatically simplifies the use of these vibrational bands in IR and Raman studies of peptide and protein structure. In contrast, the AmI and AmI' bands of the alpha-helical conformation cannot be well modeled as a linear sum of the fully N-H protonated and N-D deuterated derivatives. These bands show evidence of coupling between adjacent peptide bond vibrations. Care must be taken in utilizing the AmI and AmI' bands for monitoring alpha-helical conformations since these bands are likely to change as the alpha-helical length changes and the backbone conformation is perturbed.     

Benzannelated [9] and [13] annulenes: Formation,structural properties and the effect of benzannelation on the aromaticity of the (4n+2) π anionic sy

The synthesis of benzannelated [9] and [13] annulenenes is described, 1,2:3,4-dibenzocyclononatetraene 3 and its diphenyl derivative 10 show upon deprotonation the initial formation of a non-planar partially delocalized anions 4 and 11 respectively, which undergo into the planar aromatic-diatropic dibenzocyclononatetraenyl anions 4a and 12. The immediate formation of the aromatic 1,2:5,6 - dibenzocyclononatetraenyl anion 14 upon deprotonation of 1,2:5,6 - dibenzocyclononatetraene 13 precludes peri H-H repulsions in the aromaticity development of the dibenzocyclononatetraenyl anions. The deprotonation of tetrabenzo[13]annulene 15 afforded anion 17, which shows reduced diatropic character as compared with non-benzannelated[13] annulenyl anion. The spatial arrangement of 17 is discussed.     

Hydrogen-shift isomerism: mass spectrometry of isomeric benzenesulfonate and 2-, 3- and 4-dehydrobenzenesulfonic acid anions in the gas phase

The isomeric 3- and 4-dehydrobenzenesulfonic acid anions b and c were prepared by collision induced dissociation (CID) of the [M - H](-) ions of isomeric sulfobenzoic acids obtained by negative electrospray ionization (ESI). The CID spectra (MS(3)) of anions b and c are different from each other, and both are different from that of the isomeric benzenesulfonate anion a, obtained from benzenesulfonic acid. The stability of ions b and c shows that 1,2-proton transfer does not take place in this system under the conditions of the CID experiment. Density functional (DFT) calculations at B3LYP/6-31+G(2d,p) level of theory show that benzenesulfonate anion a is the most stable isomer, and the energies of isomers b and c are higher by more than 65 kcal mol(-1). The calculated energies of the transition states involved in the 1,2-hydrogen migration leading to the interconversion of the isomeric anions are very high (>120 kcal mol(-1)relative to ion a, barrier energies >55 kcal mol(-1)), much higher than those of transition structures leading to fragmentation. This situation does not allow isomerization of ions b and c to a, under the conditions of the CID experiments. The isomeric 2-dehydrobenzenesulfonic acid anion isomerizes to the benzenesulfonate anion a by a facile proton transfer from the SO(3)H group to the adjacent position 2. The results of this work indicate that the gas phase deprotonation of meta- and para-sulfobenzoic acids is a kinetically controlled process.     

Preparative separation of isomeric and stereoisomeric dicarboxylic acids by pH-zone-refining counter-current chromatography

This work involves the preparative separation of some isomeric dicarboxylic acids using pH-zone-refining counter-current chromatography (CCC), a relatively new preparative technique for the separation of ionizable compounds. The paper concentrates especially on the separation of a synthetic mixture of closely related cis and trans pairs of 1-methyl- and 1,3-dimethyl-1,3-cyclohexanedicarboxylic acids. The elution sequence of the isomers is discussed in terms of their relative acidities (pK(a) values) in solution and gas phase, hydrophobicities, and steric configuration. Two possible explanations are suggested for the mechanism of separation. They both involve the amount of retainer acid used, as it affects the separation and plays a role in the chemohydrodynamic equilibrium of the dicarboxylic acids in the column.     

Peptide bond vibrational coupling

Neutral trialanine (Ala3), which is geometrically constrained to have its peptide bond at Phi and Psi angles of alpha-helix and PPII-like conformers, are studied at the B3LYP/6-31+G(d,p) level of theory to examine vibrational interactions between adjacent peptide units. Delocalization of the amide I, amide II, and amide III3 vibrations are analyzed by calculating their potential energy distributions (PED). The vibrational coupling strengths are estimated from the frequency shifts between the amide vibrations of Ala3 and the local amide bond vibrations of isotopically substituted Ala3 derivatives. Our calculations show the absence of vibrational coupling of the amide I and amide II bands in the PPII conformations. In contrast, the alpha-helical conformation shows strong coupling between the amide I vibrations due to the favorable orientation of the C=O bonds and the strong transitional dipole coupling. The amide III3 vibration shows weak coupling in both the alpha-helix and PPII conformations; this band can be treated as a local independent vibration. Our calculated results in general agree with our previous experimental UV Raman studies of a 21-residue mainly alanine-based peptide (AP).     

Enhancing regiocontrol in carboaluminations of terminal alkynes. Application to the one-pot synthesis of coenzyme Q10

Two new "generations" of methodological advances are reported for the Negishi carboalumination of terminal alkynes. Use of simple, inexpensive additives that alter the Al-Zr complex formed between Me(3)Al and Cp(2)ZrCl(2) give rise to an especially effective reagent mix that results in virtually complete control of regiochemistry upon carboalumination of 1-alkynes. One timely application to coenzyme Q10 is highlighted. Regioisomers from subsequent coupling, which would otherwise be very difficult to separate, are avoided.     

Analysis of tear glucose concentration with electrospray ionization mass spectrometry

We have developed a mass spectrometry-based method that allows one to accurately determine the glucose concentration of tear fluid. We used a 1 microL micro-capillary to collect tear fluid from the tear meniscus with minimal irritation of the eye. We analyzed the 1 muL volume of collected tear fluid with liquid-chromatography electrospray ionization mass spectrometry with the use of D-glucose-6,6-d2 as an internal standard. Repeated measurements and a recovery experiment on pooled, onion-induced tears showed that the analysis of the glucose in tears was precise (4% relative standard deviation) and provided 100% recovery. We found the tear glucose concentration of one fasting nondiabetic subject to be 13 to 51 microM while the onion-induced tear glucose concentration of a different nondiabetic subject to be 211 to 256 microM.     

In situ observation of the internal structure and composition of biomineralized Emiliania huxleyi calcite by solid-state NMR Spectroscopy

Biomineralization, particularly the formation of calcium carbonate structures by organisms under ambient conditions, is of vast fundamental and applied interest. Organisms finely control all aspects of the formation of the biomaterials: composition, polymorph, morphology, and macroscopic properties. While in situ molecular-level characterization of the resulting biominerals is a formidable task, solid-state magic angle spinning NMR is one of the most powerful analytical techniques for this purpose. It is employed in this study to elucidate the structure and composition of biogenic calcite formed by Emiliania huxleyi, a unicellular alga distinguished by its exquisitely sculptured calcite cell coverings known as coccoliths. Strain 371 (CCMP) was grown and harvested from (15)N- and (13)C-enriched growth medium, with biosynthetic labeling to enhance the sensitivity of the NMR measurements. Crystalline and interfacial calcite environments were selectively probed using direct and indirect (cross-polarized) (13)C excitation, respectively. Different crystalline environments, in particular structural defect sites at concentrations of up to 1.4% with P and N moieties incorporated, were identified using (13)C rotational-echo double-resonance (REDOR) NMR. REDOR-derived geometrical constraints show that the P and N atoms at the defect sites are 3.2 and 2.3 (+/-0.2) A apart from a crystalline carbon carbonate. The phosphorus and nitrogen moieties within the biogenic calcite are identified as small, non-protonated moieties, attributed to inorganic ions such as PO4(3-) and NO3(-). The carbonates adjacent to these defects are chemically indistinguishable from bulk crystalline carbonates, yet their immediate environments experience reduced rigidity, as reflected by substantial T1((13)CO3(2-)) shortening. Interfacial carbonates, on the other hand, reside in structurally/chemically perturbed environments, as reflected by heterogeneous line broadening. This study is the first to directly unravel evidence on the incorporation of P/N moieties as structural defects within E. huxleyi biogenic calcite, and on the state of the adjacent crystalline carbonates.     

Progress in developing polymerized crystalline colloidal array sensors for point-of-care detection of myocardial ischemia

The difficulty of rapid, definitive diagnosis of myocardial ischemia leads to unnecessary hospital admissions and treatment delays. Previously, decreased metal binding affinity in human serum was investigated as a marker for myocardial ischemia. Polymerized Crystalline Colloidal Array (PCCA) sensors for Ni2+ may be useful in developing a point-of-care test to determine metal binding affinity in plasma and to help rule out myocardial ischemia. PCCA sensors for Ni2+, with 5-amino-8-hydroxyquinoline as a chelating agent, were tested in aqueous solutions and diluted human plasma. The peak wavelength diffracted by the sensors was monitored by reflectance spectrometry and correlated with Ni2+ concentration. The PCCA sensors show a linear response to aqueous Ni2+ concentrations between 0.2 and 1.0 mmol L(-1), and can detect changes in free Ni2+ concentration of <60 micromol L(-1). The sensors respond at physiologic pH and can be reversibly dehydrated. The PCCA sensors developed here can report on free Ni2+ concentration in the presence of human plasma. These sensors can be used to detect a decrease in the Ni2+ affinity of plasma proteins, which may indicate recent myocardial ischemia. PCCA sensors offer a practical approach to rapid, point-of-care detection of a proposed biochemical signature of myocardial ischemia.     

Structural characteristics of different types of nanoparticles synthesised in mesomorphic metal alkanoates

The class of thermotropic ionic liquid crystals (LCs) of the metal alkanoates possesses a number of unique properties, such as intrinsic ionic conductivity, high dissolving ability and ability to form time-stable mesomorphic glasses. These ionic LCs can be used as nanoreactors for the synthesis and stabilisation of different types of nanoparticles (NPs). Thus, some semiconductors, metals and core/shell NPs were chemically synthesised in the thermotropic ionic liquid crystalline phase (smectic A) of the cadmium octanoate (CdC₈) and of the cobalt octanoate (CoC₈). By applying the scanning electron microscopy, the cadmium and cobalt octanoate composites containing CdS, Au, Ag and core/shell Au/CdS NPs have been studied. NPs’ sizes and dispersion distribution of the NPs’ size in the nanocomposites have been obtained.