A study of noncovalent complexes involving single-stranded DNA and polybasic compounds using nanospray mass spectrometry

Noncovalent complexes involving a single-stranded DNA oligonucleotide and a polybasic compound (spermine, penta-L-lysine, penta-L-arginine, or polydisperse poly-L-lysine) were detected by nanospray-MS. Several control experiments tended to show that these complexes preexisted in solution and that the interactions were initially ionic ones between oligonucleotide phosphates and protonated basic sites of the polybasic compound. Collision-induced dissociation (CID) experiments carried out with these complexes allowed us to identify some differences in the nature of the interactions between the solution and the gas phase, arising from possible proton transfers. Different dissociation pathways were observed according to the nature of the polybasic compound and to the initial charge state of the complex. The complex involving spermine dissociated by cleavage of noncovalent bonds leading to the separation of the two components, whereas the one involving penta-L-arginine underwent fragmentations of covalent bonds. Both behaviors were independent of the initial charge state of the complex. On the other hand, the dissociation pathway of the complex involving penta-L-lysine has been shown to be clearly charge state dependent. Noncovalent dissociation (separation of the two components) driven by coulomb repulsion occurred for the higher charged complexes, whereas fragmentation of covalent bonds was the main pathway of the lower charged complexes. In the latter case, differences in CID behavior were observed for different lengths of poly-L-lysine.     

Q-branch linewidths of N2 perturbed by H2: experiments and quantum calculations from an ab initio potential

In this work the authors present an experimental and theoretical study about the Q-branch lines' broadening coefficients of N2 perturbed by H2. Experimental values for these parameters have been obtained at 440 and 580 K, and quantum calculations have been performed using a new ab initio potential energy surface, obtained by quantum chemistry methods. The results of these calculations are compared to experimental data obtained previously at 77 and 298 K [L. Gomez et al., Mol. Phys. 104, 1869 (2006)] and to the present measurements. A satisfactory agreement is obtained for the whole range of temperatures used in the experiments.     

Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data

Choanoflagellates are single-celled eukaryotes with complex signaling pathways. They are considered the closest non-metazoan ancestors to mammals and other metazoans and form multicellular-like states called rosettes. The choanoflagellate Monosiga brevicollis contains over 150 PDZ domains, an important peptide-binding domain in all three domains of life (Archaea, Bacteria, and Eukarya). Therefore, an understanding of PDZ domain signaling pathways in choanoflagellates may provide insight into the origins of multicellularity. PDZ domains recognize the C-terminus of target proteins and regulate signaling and trafficking pathways, as well as cellular adhesion. Here, we developed a computational software suite, Domain Analysis and Motif Matcher (DAMM), that analyzes peptide-binding cleft sequence identity as compared with human PDZ domains and that can be used in combination with literature searches of known human PDZ-interacting sequences to predict target specificity in choanoflagellate PDZ domains. We used this program, protein biochemistry, fluorescence polarization, and structural analyses to characterize the specificity of A9UPE9_MONBE, a M. brevicollis PDZ domain-containing protein with no homology to any metazoan protein, finding that its PDZ domain is most similar to those of the DLG family. We then identified two endogenous sequences that bind A9UPE9 PDZ with <100 μM affinity, a value commonly considered the threshold for cellular PDZ–peptide interactions. Taken together, this approach can be used to predict cellular targets of previously uncharacterized PDZ domains in choanoflagellates and other organisms. Our data contribute to investigations into choanoflagellate signaling and how it informs metazoan evolution.     

Determination of citric acid in soft drinks using flow injection with potentiometric detection

A flow injection analysis (FIA) system with potentiometric detection has been developed for the determination of citric acid in commercial fruit juices using a copper-selective tubular electrode. It consists of the complexation of citrate ion with copper (II) ion, monitoring the free copper (II) concentration. Linear relationships between the potential and log concentrations of citric acid in the range of 1 × 10^–3 mol/L – 1 × 10^–2 mol/L were attained with samples injected in the system without prior treatment. Repeatability was determined by assessing the relative standard deviation for ten replicate injections of different juice samples which varied from 1.2% to 3.0%. The results provided by the automated system were compared with those of an enzymatic conventional method used for the analysis of citric acid in food and a relative deviation of less than 4.0% was found. Recovery trials resulted in values from 97.0% to 101.0%. The system allows a sampling frequency of 60 samples/h.     

An experimental and theoretical investigation of gas-phase reactions of Ca2+ with glycine

The gas-phase reactions between Ca(2+) and glycine ([Ca(gly)](2+)) have been investigated through the use of mass spectrometry techniques and B3-LYP/cc-pWCVTZ density functional theory computations. The major peaks observed in the electrospray MS/MS spectrum of [Ca(gly)](2+) correspond to the formation of the [Ca,C,O(2),H](+), NH(2)CH(2) (+), CaOH(+), and NH(2)CH(2)CO(+) fragment ions, which are produced in Coulomb explosion processes. The computed potential energy surface (PES) shows that not only are these species the most stable product ions from a thermodynamic point of view, but they may be produced with barriers lower than for competing processes. Carbon monoxide is a secondary product, derived from the unimolecular decomposition of some of the primary ions formed in the Coulomb explosions. In contrast to what is found for the reactions of Ca(2+) with urea ([Ca(urea)](2+)), minimal unimolecular losses of neutral fragments are observed for the gas-phase fragmentation processes of [Ca(gly)](2+), which is readily explained in terms of the topological differences between their respective PESs.     

Tackling the chemical diversity of microbial nonulosonic acids – a universal large-scale survey approach

Nonulosonic acids, commonly referred to as sialic acids, are a highly important group of nine-carbon sugars common to all domains of life. They all share biosynthetic and structural features, but otherwise display a remarkable chemical diversity. In humans, sialic acids cover all cells which makes them important for processes such as cellular protection, immunity and brain development. On the other hand, sialic acids and other nonulosonic acids have been associated with pathological processes including cancer and viral infections. In prokaryotes, nonulosonic acids are commonly associated with pathogens, which developed through molecular mimicry a strategy to circumvent the host''s immune response. However, the remarkably large chemical diversity of prokaryotic nonulosonic acids challenges their discovery, and research on molecular characteristics essential for medical applications are often not feasible. Here, we demonstrate a novel, universal large-scale discovery approach that tackles the unmapped diversity of prokaryotic nonulosonic acids. Thereby, we utilize selective chemical labelling combined with a newly established mass spectrometric all-ion-reaction scanning approach to identify nonulosonic acids and other ulosonic acid-like sugars. In doing so, we provide a first molecular-level comparative study on the frequency and diversity across different phyla. We not only illustrate their surprisingly wide-spread occurrence in non-pathogenic species, but also provide evidence of potential higher carbon variants. Many biomedical studies rely on synthetic routes for sialic acids, which are highly demanding and often of low product yields. Our approach enables large-scale exploration for alternative sources of these highly important compounds.

A novel large-scale survey approach for microbial nonulosonic acids (sialic acids) including a first molecular level comparative study is presented.     

Unimolecular dissociations of the [2-hexanone]+˙ metastable ion

The metastable molecular ion of 2-hexanone loses a methyl radical mainly (～80%) from positions C(4) and C(6), in equal proportions, as indicated by ¹³C labelling. The necessary skeletal rearrangement of the butyl chain is interpreted in terms of a 1,2-[enol-olefin] ⁺˙ shift. The results and the mechanisms concerning the minor eliminations of C₂H₄, C₂H₅˙, C₃H₅˙ and C₃H₆ neutrals are also discussed.     

Structural requirements in chiral diphosphine-rhodium complexes. X asymmetric homogeneous hydrogenation of z-N-acetyldehydroamino acids and esters with (1R,2R)-trans-1,2-bis(diphenylphosphinomethyl)cyclobutane/rhodium(I) complexes.

Z--acetamidocinnamate esters were hydrogenated with neutral rhodium(I) complexes containing (1R,2R)-trans-1,2-bis(diphenylphosphinomethyl)cyclobutane. Increasing the steric bulk of the alcohol moiety in the unsaturated esters had little influence upon the optical purity of the N-acetylphanylalanine ester products. In the series Me, Et, i-Pr, and t-Bu the optical purity decreased from 44 % ee-(R) [Me] to 40 % ee-(R) [t-Bu]. The chiral cyclobutane diphosphine appears to be only slightly more effective than the heterocyclic DIOP when ring-substituted Z--acetamidocinnamic acids are hydrogenated with neutral rhodium(I) complexes without the addition of triethylamine. Addition of triethylamine to the solvent blend seems to be more beneficial to the cyclobutane analogue than to DIOP.     

Spectroscopic and electrochemical study of the adsorption of [Co(en)2Cl2]Cl on gamma-alumina: influence of the alumina ligand on Co(III)/(II) redox potential

UV-visible and Raman spectroscopies as well as electrochemical techniques have been used to characterize cis- and trans-[Co(III)(en)2Cl2]Cl (en=ethylenediamine) complexes and the gamma-alumina-supported cis-Co((III)) complex. It is shown that the electrochemical reduction of these complexes occurs according to a multistage mechanism involving two electrochemical steps, with the formation of a dimer that was characterized by UV-visible spectroscopy (intervalence band at 670 nm). The apparent standard redox potential for each step has been determined, and experimental results reveal that cis and trans complexes present similar electrochemical characteristics. It is also shown that the deposition of trans-[Co(III)(en)2Cl2]+ on gamma-alumina leads to an inner-sphere complex (ISC) in a cis configuration in which Cl- ligands are substituted by OH or O- surface groups of alumina. These changes in the coordination sphere of the complex induce a substantial decrease of its apparent redox potential since it is -0.63 V/SCE (saturated calomel electrode) for the gamma-alumina-supported cis-Co(III) complex, whereas values of -0.17 and -0.35 V/SCE were determined in dimethyl sulfoxide (DMSO) for the trans and cis precursor complexes, respectively.