A photoelectron spectroscopic and theoretical study of B16- and B16(2-): an all-boron naphthalene

The structure and chemical bonding of B16- were studied using ab initio calculations and photoelectron spectroscopy. Its global minimum is found to be a quasi-planar and elongated structure (C2h). Addition of an electron to B16- resulted in a perfectly planar and closed shell B16(2-) (D2h), which is shown to possess 10 pi electrons with a pi-bonding pattern similar to that of naphthalene and can thus be considered as an "all-boron naphthalene", a new member in the growing family of hydrocarbon analogues of boron clusters.     

On studying protein phosphorylation patterns using bottom-up LC-MS/MS: the case of human alpha-casein

Most proteomics studies involving mapping post-translational modifications, such as the phosphorylation of serine and threonine, are performed today using the 'bottom-up' approach. This approach involves enzymatic cleavage of proteins, most often by trypsin, with subsequent nano-LC-MS/MS. The occupancy rates of phosphosites in proteins may differ by orders of magnitude, and thus the occupancy rate must be reported for each occupied phosphosite. To highlight potential pitfalls in quantifying the occupancy rates, alpha(s1)-casein from human milk was selected as a model molecule representing moderately phosphorylated proteins. For this purpose, human milk from one Caucasian woman in the eighth month of lactation was used. The phosphorylation level of caseins is believed to have major implications for the formation of micelles that are involved in delivering valuable calcium phosphate and other minerals to the new-born. Human alpha(s1)-casein has been reported to be much less phosphorylated than ruminant caseins, which may indicate a different function of caseins in humans. Revealing the phosphorylation pattern in human casein can thus shed light on its function. The current study found that the sequence region between the residues Ser70 and Ser76 in human alpha(s1)-casein is in fact phosphorylated, contrary to previous knowledge. The site of the most abundant phosphorylation is Ser75, in agreement with the known action of the mammary gland casein kinase. There is evidence for the second phosphorylation in that region, possibly at Ser73. Earlier reported positions of phosphorylations at Ser18 and Ser26 are also confirmed, but not the dominance of Ser18 phosphorylation. The occupancy rates at Ser18, Ser26 and Ser75 are estimated to be (7 +/- 2), (20 +/- 6) and (27 +/- 9)%, respectively. Owing to differences in the ionization efficiency between phosphorylated and unphosphorylated peptides a 30% error margin is added to the occupancy rates. The highlighted pitfalls of the bottom-up strategy include the sensitivity of enzymes to proximal acidic and phosphorylated residues and the presence of multiple isoforms, including unexpected ones, of the tryptic peptides. The utility of the earlier introduced PhosTS_hunter and ModifiComb approaches for evading the latter pitfall is demonstrated.     

Hydrogen rearrangement to and from radical z fragments in electron capture dissociation of peptides

Hydrogen rearrangement is an important process in radical chemistry. A high degree of H. rearrangement to and from z. ionic fragments (combined occurrence frequency 47% compared with that of z.) is confirmed in analysis of 15,000 tandem mass spectra of tryptic peptides obtained with electron capture dissociation (ECD), including previously unreported double H. losses. Consistent with the radical character of H. abstraction, the residue determining the formation rate of z' = z. + H. species is found to be the N-terminal residue in z. species. The size of the complementary c(m)' fragment turned out to be another important factor, with z' species dominating over z. ions for m < or = 6. The H. atom was found to be abstracted from the side chains as well as from alpha-carbon groups of residues composing the c' species, with Gln and His in the c' fragment promoting H. donation and Asp and Ala opposing it. Ab initio calculations of formation energies of .A radicals (A is an amino acid) confirmed that the main driving force for H. abstraction by z. is the process exothermicity. No valid correlation was found between the NC(alpha) bond strength and the frequency of this bond cleavage, indicating that other factors than thermochemistry are responsible for directing the site of ECD cleavage. Understanding hydrogen attachment to and loss from ECD fragments should facilitate automatic interpretation ECD mass spectra in protein identification and characterization, including de novo sequencing.     

A direct comparison of protein structure in the gas and solution phase: the Trp-cage

Molecular dynamics simulations of zwitterions of the Trp-cage protein in the gas phase show that the most stable ion in vacuo has preserved the charge locations acquired in solution. A direct comparison of the gas and solution-phase structures reveals that, despite the similarity in charge location, there is significant difference in the structures, with a substantial increase in hydrogen bonds and exposure of hydrophobic parts in the gas phase. The structure of the salt bridge in the gas phase is also much more stable than in the (experimental) solution structure.     

Fluorination of aromatic compounds with xenon difluoride in the presence of boron trifluoride etherate

Fluorination of benzene with the XeF₂—BF₃?Et₂O system in acetonitrile at low temperatures affords fluorobenzene in 18% yield, the conversion of benzene being 92%. The rest products are di-, tri-, tetra-, and polyphenyls with different fluorination pattern. Toluene and chloro- and bromobenzenes are fluorinated predominantly at the ortho and para positions. Fluorination of 4-nitroanisole affords 2-fluoro-4-nitroanisole in 73% yield.     

Structurization of ferrofluids in the absence of an external magnetic field

Structural transformations in a model ferrofluid in the absence of an external magnetic field have been theoretically studied. The results agree with well-known laboratory experiments and computer simulations in showing that, if the concentration of particles and their magnetic interaction energy are below certain critical values, most particles form separate linear chains. If these parameters exceed the critical values, most particles concentrate so as to form branched network structures. The passage from chains to network has a continuous character rather than represents a discontinuous first-order phase transition.     

Kinetics aggregation of magnetic suspensions

We present results of theoretical and computer studies of the kinetics of chain-like aggregate formation in suspensions of non-Brownian magnetizable particles. An analytical model for calculation of the time-dependent function of distribution over chain size is suggested. This model describes the evolution of the chain structure due to the chain-chain aggregation. In order to verify this model we have compared it with the results of computer simulations of a two-dimensional model of this suspension. Results of computer simulations and of the analytical model are in reasonable agreement up to 5% of the surface concentration of the particles.