Design and development of a two‐dimensional system based on hydrophilic and reversed‐phase liquid chromatography with on‐line sample treatment for the simultaneous separation of excreted xenobiotics and endogenous metabolites in urine

In the present work we describe a two‐dimensional liquid chromatographic system (2D‐LC) with detection by mass spectrometry (MS) for the simultaneous separation of endogenous metabolites of clinical interest and excreted xenobiotics deriving from exposure to toxic compounds. The 2D‐LC system involves two orthogonal chromatographic modes, hydrophilic interaction liquid chromatography (HILIC) to separate polar endogenous metabolites and reversed‐phase (RP) chromatography to separate excreted xenobiotics of low and intermediate polarity. Additionally, the present proposal has the novelty of incorporating an on‐line sample treatment based on the use of restricted access materials (RAMs), which permits the direct injection of urine samples into the system. The work is focused on the instrumental coupling, studying all possible options and attempting to circumvent the problems of solvent incompatibility between the RAM device and the two chromatographic columns, HILIC and RP. The instrumental configuration developed, RAM‐HILIC‐RPLC‐MS/MS, allows the simultaneous assessment of urinary metabolites of clinical interest and excreted compounds derived from exposure to toxic agents with minimal sample manipulation. Thus, it may be of interest in areas such as occupational and environmental toxicology in order to explore the possible relationship between the two types of compounds. Copyright © 2015 John Wiley & Sons, Ltd.     

Indexing text using the Ziv–Lempel trie

Let a text of u characters over an alphabet of size σ be compressible to n phrases by the LZ78 algorithm. We show how to build a data structure based on the Ziv–Lempel trie, called the LZ-index, that takes 4nlog₂n(1+o(1)) bits of space (that is, 4 times the entropy of the text for ergodic sources) and reports the R occurrences of a pattern of length m in worst case time O(m³logσ+(m+R)logn). We present a practical implementation of the LZ-index, which is faster than current alternatives when we take into consideration the time to report the positions or text contexts of the occurrences found.     

Practical algorithms for transposition-invariant string-matching

We consider the problems of (1) longest common subsequence (LCS) of two given strings in the case where the first may be shifted by some constant (that is, transposed) to match the second, and (2) transposition-invariant text searching using indel distance. These problems have applications in music comparison and retrieval. We introduce two novel techniques to solve these problems efficiently. The first is based on the branch and bound method, the second on bit-parallelism. Our branch and bound algorithm computes the longest common transposition-invariant subsequence (LCTS) in time O((m²+loglogσ)logσ) in the best case and O((m²+logσ)σ) in the worst case, where m and σ, respectively, are the length of the strings and the size of the alphabet. On the other hand, we show that the same problem can be solved by using bit-parallelism and thus obtain a speedup of O(w/logm) over the classical algorithms, where the computer word has w bits. The advantage of this latter algorithm over the present bit-parallel ones is that it allows the use of more complex distances, including general integer weights. Since our branch and bound method is very flexible, it can be further improved by combining it with other efficient algorithms such as our novel bit-parallel algorithm. We experiment on several combination possibilities and discuss which are the best settings for each of those combinations. Our algorithms are easily extended to other musically relevant cases, such as δ-matching and polyphony (where there are several parallel texts to be considered). We also show how our bit-parallel algorithm is adapted to text searching and illustrate its effectiveness in complex cases where the only known competing method is the use of brute force.     

A Method for Clustering and Screening of Long-dimensional Chemical Data Based on Fingerprints and Similarity Measurements

A method for the treatment of long-dimensional chemical data arrays is presented in this work with the aim of maximising classification models. The method is based on the construction of fingerprints and the subsequent generation of a similarity matrix. The similarity calculation has been modified through a scaling process to take into account different significance shown by the variables. The method was applied to spectral measurements of wines and several aspects were studied, namely: threshold considered in the construction of fingerprints and patterns, weighting factor used for scaling, normalisation method, etc. The application of both Principal Components Analysis and Soft-Independent Modelling of Class Analogies to the similarity matrices gave better classifications of the information than those obtained using original data.     

Clustering of chemical databases by means of the projection of maximum overlapping sets similarity measurements onto multidimensional spaces

In this paper, we propose a new method for clustering of chemical databases based on the representation of measurements of structural similarity onto multidimensional spaces. The proposed method permits the tuning of the clustering process through the selection of the dimension of the projection space, the normal vectors and the sensibility of the projection process. The structural similarity of each element regarding to the database elements is projected onto the defined spaces generating clusters that represent the characteristics and diversity of the database and whose size and characteristics can be easily adjusted.     

Carbon dendron nano-chains with π-extended conjugation based on end-capped N,N-dimethylamino in linear 1,4-phenylethynyl or in 1,5-naphthylethynyl subunits: fluorescence analysis

The synthesis of dendrons with the end-capped 5-(N,N-dimethylamino)naphthyl-1-ethynyl unit connected to conjugated naphthylethynyl or p-phenylethynyl chains, as the branches of the 1,3,5-substituted benzene core, have been undertaken by heterocoupling reaction between 1,3,5-triiodobenzene and the convenient end-capped 5-(N,N-dimethylamino)naphthylacetylene or 5-(N,N-dimethylamino)naphthylethynylphenylacetylene in the presence of the palladium-copper catalyst system, in excellent yields. The influence of the alternating naphthylethynyl-phenylethynyl chains on the fluorescence emission radiation, in the dendron structures, has been analyzed.     

Representation of the molecular topology of cyclical structures by means of cycle graphs. 3. Hierarchical model of screening of chemical databases

The increase in the size and complexity of chemical databases necessitates the proposal and development of efficient methods of classification and recovery of information, which supposes proposal of a model of classification of database records and the use of a compatible model of screening for inspection of clusters and recovery of the molecules that satisfy the search criterion. The cycle graphs model based on consideration of all the cycles and chains (and equivalent cycles and chains) present in the molecular structure has been proven appropriate for classification of chemical databases, giving rise to a generation of different classification levels depending on the structural elements (cycles and chains) that are considered. In this paper we propose a screening model, compatible with the cycle graphs model, based on a hierarchy of levels of abstraction. The set of molecules that satisfies a screening model (or selection criterion) diminishes as we advance in the hierarchy of levels of the model, which allows filtering of records and, therefore, an increase in the efficiency of the screening process. In the following work of this series we describe and validate the screening tool developed.     

Alkylation of nitroaromatics with tetraalkylborate ion via electrochemical oxidation

Aromatic nucleophilic substitution reaction (S(N)Ar) is one of the most thoroughly studied reactions. Alkylation of nitroaromatics with Grignard reagents via chemical oxidation of the sigma(H)-complexes is the most general method to introduce an alkyl group into a nitroaromatic compound. This approach has considerable drawbacks, especially when more than one nitro group are present in the aromatic ring. In this article, we present an electrochemical approach, which offers a new very selective methodology for obtaining alkyl polynitroaromatic compounds. Different strategies based on the use of tetralkylborate anion as nucleophiles are used so as to increase efficiency and to reduce the drawbacks associated with this reaction. A wide list of dinitro- and trinitro-aromatic compounds are studied, the range of yields obtained being from fair (40%) to excellent (85%). The key to improvement in the process is the use of electrochemical techniques for the oxidation of the mixture sigma(H)-complexes/tetrabutylborate ion. The electroactive character of the nucleophile, which can be oxidized to an alkyl radical, means that the S(N)Ar of the hydrogen polar mechanism is not the only mechanism operating during the electroxidation process, since the hydrogen radical S(N)Ar mechanism is running at the same time. Electrochemical mechanistic studies allow the participation of each mechanism in the global product yield obtained to be quantified.     

The Reaction of Triplet State Benzophenone with Acetylacetone

Irradiation of benzophenone in acetic acid containing acetylacetone resulted in regiospecific addition to form cis-2,2-dihpenyl-3-hydroxy-3-methyl-4-acetyloxetane and the rearrangement products therefrom. In the co-presence of copper ions, the regiospecificity is scrambled to give these products and a small amount of 1,1-diphenyl-1-buten-3-one, the secondary decomposition product of the other oxetane arising from the alternative orientation of the addition.