QSAR modeling of endpoints for peptides which is based on representation of the molecular structure by a sequence of amino acids

The representation of the molecular structure by a system (sequence) of amino acids has been used to establish quantitative structure–property/activity relationships (QSPR/QSAR) which can be used for (i) bioactivities of epitope-peptides, (ii) antibacterial potencies of polypeptides, and (iii) the binding affinity of peptides that bind to the class I major histocompatibility complex molecule HLA-A*0201. The representation of the peptide structure has been done via 1-letter abbreviations of amino acids, i.e., A (alanine), C (cysteine), D (aspartic), etc. This approach allows classifying amino acids according to their function in a biochemical process (promoters of increase or decrease of an endpoint).     

Deca-heterosubstituted corannulenes

The Cu(I)-catalyzed Ullmann condensation reaction between aliphatic alcohols and sym-pentachlorocorannulene provides a convenient entry to 1,3,5,7,9-pentaalkoxycorannulenes. The latter are easily converted to novel deca-heterosubstituted derivatives, such as 1,3,5,7,9-penta-X-2,4,6,8,10-penta-Y-corannulenes by electrophilic aromatic substitution.     

Dielectric response of imidazolium-based room-temperature ionic liquids

We have used microwave dielectric relaxation spectroscopy to study the picosecond dynamics of five low-viscosity, highly conductive room temperature ionic liquids based on 1-alkyl-3-methylimidazolium cations paired with the bis((trifluoromethyl)sulfonyl)imide anion. Up to 20 GHz the dielectric response is bimodal. The longest relaxation component at the time scale of several 100 ps reveals strongly nonexponential dynamics and correlates with the viscosity in a manner consistent with hydrodynamic predictions for the diffusive reorientation of dipolar ions. Methyl substitution at the C2 position destroys this correlation. The time constants of the weak second process at the 20 ps time scale are practically the same for each salt. This intermediate process seems to correlate with similar modes in optical Kerr effect spectra, but its physical origin is unclear. The missing high-frequency portion of the spectra indicates relaxation beyond the upper cutoff frequency of 20 GHz, presumably due to subpicosecond translational and librational displacements of ions in the cage of their counterions. There is no evidence for orientational relaxation of long-lived ion pairs.     

Synthesis of some new spiro naphtho[2,3‐d][1,3]dithiole‐4,9‐dione derivatives

2(1‐Acetyl‐2‐oxopropylidene)naphtho[2,3‐d][1,3]dithiole‐4,9‐dione 1 reacts with a variety of bidentates reagents to give some new functionally substituted spiro naphthodithiole‐4,9‐dione derivatives.     

Efficient Synthesis of 4-Amino-4-deoxy-L-arabinose and Spacer-equipped 4-Amino-4-deoxy-L-arabinopyranosides by Transglycosylation Reactions

Methyl 4-azido-4-deoxy-β-L-arabinopyranoside has been synthesized in five steps starting from methyl β-D-xylopyranoside in a multigram scale without chromatographic purification in 78% overall yield. The transformation relied on selective tosylation/nosylation at O-4 followed by acylation, S(N)2 displacement with sodium azide and subsequent deprotection. The methyl 4-azido-4-deoxy-arabinoside was then converted into allyl, propenyl, ω-bromohexyl and chlorethoxyethyl spacer glycosides by transglycosylation with the respective alcohols in good yields and fair anomeric selectivity. Reduction of the azido group and further transformations of the aglycon afforded ω-thiol-containing spacer derivatives. Coupling to maleimide-activated BSA provided a potent immunogen which was used to generate murine and rabbit polyclonal sera binding to LPS-core epitopes containing 4-amino-4-deoxy-arabinose residues.     

Prediction of small molecule binding property of protein domains with Bayesian classifiers based on Markov chains

Accurate computational methods that can help to predict biological function of a protein from its sequence are of great interest to research biologists and pharmaceutical companies. One approach to assume the function of proteins is to predict the interactions between proteins and other molecules. In this work, we propose a machine learning method that uses a primary sequence of a domain to predict its propensity for interaction with small molecules. By curating the Pfam database with respect to the small molecule binding ability of its component domains, we have constructed a dataset of small molecule binding and non-binding domains. This dataset was then used as training set to learn a Bayesian classifier, which should distinguish members of each class. The domain sequences of both classes are modelled with Markov chains. In a Jack-knife test, our classification procedure achieved the predictive accuracies of 77.2% and 66.7% for binding and non-binding classes respectively. We demonstrate the applicability of our classifier by using it to identify previously unknown small molecule binding domains. Our predictions are available as supplementary material and can provide very useful information to drug discovery specialists. Given the ubiquitous and essential role small molecules play in biological processes, our method is important for identifying pharmaceutically relevant components of complete proteomes. The software is available from the author upon request.     

Magnetic field tuning of polaron losses in Fe doped BaTiO(3) single crystals

Artificial tuning of dielectric parameters can result from interface conductivity in polycrystalline materials. In ferroelectric single crystals, it has already been shown that ferroelectric domain walls can be the source of such artificial coupling. We show here that low-temperature dielectric losses can be tuned by a dc magnetic field. Since such losses were previously ascribed to polaron relaxation we suggest this results from the interaction of hopping polarons with the magnetic field. The fact that this loss alteration has no counterpart in the real part of the dielectric permittivity confirms that no interface is involved in this purely dynamical effect. The contribution of mobile charges hopping among Fe-related centers was confirmed by ESR spectroscopy, showing a maximum intensity at ca T?～?40?K.     

The self-organizing vector of atom-pairs proportions: use to develop models for melting points

Structural Chemistry - Atom-pairs proportions are the transparent quality of a molecule: if a molecule has two atoms of oxygen and three atoms of nitrogen, the atom-pair atom1-atom2 can be...