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Metabolomics is a rapidly developing branch of science that concentrates on identifying biologically active molecules with potential biomarker properties. To define the best biomarkers for diseases, metabolomics uses both models (in vitro, animals) and human, as well as, various techniques such as mass spectroscopy, gas chromatography, liquid chromatography, infrared and UV–VIS spectroscopy and nuclear magnetic resonance. The last one takes advantage of the magnetic properties of certain nuclei, such as 1H, 13C, 31P, 19F, especially their ability to absorb and emit energy, what is crucial for analyzing samples. Among many spectroscopic NMR techniques not only one-dimensional (1D) techniques are known, but for many years two-dimensional (2D, for example, COSY, DOSY, JRES, HETCORE, HMQS), three-dimensional (3D, DART-MS, HRMAS, HSQC, HMBC) and solid-state NMR have been used. In this paper, authors taking apart fundamental division of nuclear magnetic resonance techniques intend to shown their wide application in metabolomic studies, especially in identifying biomarkers.

In order to verify the previously suggested mechanism of anticancer activity of some dimeric indazole derivatives basing on the adhesion (or intercalation) to DNA, a simulation of the interactions of 5-(3,5-dimethyl-1 H -pyrazol-1-yl)-3-[(4-methylphenyl)sulfonyl]-1 H -indazole with guanosine, adenosine, thymidine, cytidine, and DNA was carried out computationally at the DFT level and analyzed within ONIOM approaches. Moreover, a similar simulation was executed for a DNA fragment containing the above bases. The theoretical studies have shown that the interactions may involve both strong and weak hydrogen bonding arising between the DNA bases nitrogen atoms and the tosyl oxygen and pyrazole nitrogen atoms, as well as aromatic carbons of the studied indazole derivative.

The paper describes a new NMR approach for the determination of interaction sites between a heterocyclic ligand, like indazole, and magnesium ions. The method is based on the comparison of chemical shifts of indazole derivative before and after complexation with magnesium salt and is supported by DFT (B3LYP/6-31G(d,p) level of theory, solvent model PCM, IGLO-II basis set) theoretical calculations.

Long range spin–spin couplings found between two phosphorus atoms are quite rare phenomena. A new example of such a coupling through seven bonds is described for 1-[(diethoxyphosphoryl)butyryloxymethyl]-4-[(diethoxyphosphoryl)hydroxymethyl]benzene and 1,4-bis[phosphorylhydroxymethyl]benzene and through six bonds for tetraethyl phenylene-1,3-(bishydroxymethylphosphonate). Coupling constants in this system are also well predicted by theoretical studies.

Complexation of Mg 2+ , Ca 2+ , Zn 2+ and Cu 2+ with alizarin, characterized by NMR and theoretical studies (DFT, B3LYP/6-31G( d , p ) PCM and NMR GIAO B3LYP/IGLOIII), indicated that the metal ion is attached to two hydroxyl groups in a bidentate mode. The alternative complexation in the bidentate mode, with only one hydroxyl group and a carbonyl oxygen, is less possible as it has a higher energy.

The use of quinine as a chiral solvating agent allows us to determine a tentative absolute configuration at the phosphorus atom of hydroxyphosphinates with two stereogenic centres (at the phosphorus and α-carbon atoms). Two ethyl butyryloxyalkane( P -phenyl)phosphinates were hydrolysed using various lipases. In all cases isomers possessing α-carbon atom with an ( S )-configuration were hydrolysed preferentially. The absolute configuration of both chiral centres of obtained α-hydroxyphosphinates was determined by using ( S )-(+)-MTPA-Cl and quinine. The mode of chiral discrimination of α-hydroxyphosphinates by quinine was studied by means of computational chemistry, which confirmed the experimental findings that the signals in 31 P NMR spectra of compounds with an ( R P )-configuration are situated upfield when compared with the respective ( S P ) isomers.

The phosphoryl group (P═O) is able to form hydrogen bonds with the relatively low acidic atoms like in C═H· · · · O═P system. In this article, we present experimental and theoretical investigations on the C═H· · · · O═P hydrogen bond for the complex of tributylphosphine oxide and chloroform.

The study of spin-spin coupling constants across hydrogen bond provides useful information about configuration of complexes. The interesting case of such interactions was observed as a coupling across an intramolecular hydrogen bond in 8-bromo-2′,3′-O-isopropylideneadenosine between the -CH2OH (at 5″ proton) group and the nitrogen atom of adenine. In this paper we report theoretical investigations on the 4h J NH coupling across the H″-C-O-H···N hydrogen bond in adenosine derivatives in various solvent models.

The changes in NMR spectra of O , O -dimethyl-1,4-oxoazetin-2-ylphosphonate (DMOAP) in polar and non-polar solvents were studied by means of experimental and theoretical approach. The precise chemical shift assignments of DMOAP were obtained by means of 1 H, 1 H{ 31 P}, 13 C{ 1 H}, 31 P{H} NMR and theoretical calculations (DTF, using the IGLO II and IGLO III basis set and solvent model PCM for CHCl 3 , MeOH, H 2 O). An optimized structure, calculated using B3LYP/6-31G( d , p ) solvent model PCM, gives three conformers in their energetic minima with various values of N C P O angle. Distribution of particular conformers, their structural differences and effect of internal or external hydrogen bonds in polar and non-polar solvents were considered as potential causes of the observed diversities in NMR spectra.

Mesoporous silica SBA-15 containing propyl-iron-phosphonate groups were considered to confirm their molecular structure. To detect the iron-containing group configuration the Mössbauer spectroscopy was used. Both mesoporous silica SBA-15 containing propyl-iron-phosphonate groups and pure doping agent (iron acetylacetate) were investigated using Mössbauer spectroscopy. The parameters such as isomer shift, quadrupole splitting, and asymmetry in57Fe Mössbauer spectra were analyzed. The differences in Mössbauer spectra were explained assuming different local surroundings of Fe nuclei. On this base we were able to conclude about activation of phosphonate units by iron ions and determinate the oxidation state of the metal ion. To examine bonding between iron atoms and phosphonic units the resonance Raman spectroscopy was applied. The density functional theory (DFT) approach was used to make adequate calculations. The distribution of active units inside silica matrix was estimated by comparison of calculated vibrational spectra with the experimental ones. Analysis of both Mössbauer and resonance Raman spectra seems to confirm the correctness of the synthesis procedure. Also EDX elemental analysis confirms our conclusions.

Background. Nowadays, the Nuclear Magnetic Resonance (NMR) techniques are tested for metabolomic urine profile in order to detect early damage of kidney. Objectives. The purpose of this investigation was the initial assessment of two-dimensional J-resolved NMR urine spectra analysis usability for early kidney injuries detection. The amino acids (AA) and acids profile change after the exposure to nephrotoxic agent (the cisplatin infusion) was examined. Material and Methods. The material was the urine of patients with non-small-cell lung cancer, treated with cisplatin in Pulmonology and Lung Cancers Clinic in Wroclaw. The urine of healthy volunteers was also examined. The identification of metabolites in urine was based on two-dimensional JRES signals in spectra, described in Human Metabolites Database (HMD). The molar concentration of metabolites was calculated from the volume under the signals. The analysis was focused on amino acids and organic acids (lactid acid and pyruvic acid) profiles. Results. Any specific amino acids were identified after cisplatin infusion in comparison to the state before infusion. However, the differences in concentration were observed over 2-fold increase in valine, isoleucine and leucine, over 3-fold in alanine. Also, the concentration of pyruvic and lactic acids increased significantly (p ≤ 0.05, p ≤ 0.01). Conclusions. There were no specific amino acids identified in response to the infusion of cisplatin; however, some changes in the concentrations of amino acids and other small molecules were found. The analysis of two-dimensional JRES spectra showed an increase of alanine, leucine, isoleucine and valine concentration after the application of cisplatin. It seems that it is worth developing the JRES method based on special computer program (Adv Clin Exp Med 2015, 24, 4, 629–635).

Structures, electron ionization and excitation energies, and electron density distribution are studied for carbazole and fluorene derivatives substituted symmetrically by thiophene, ethylenodioxythiophene, furane, or pyrrole. The calculated properties of the molecules directly or indirectly mimic molecular parameters that are important for the design of processes of polymerization or for modeling the final polymer. The studies have been focused on the variation in the properties as a function of the chemical composition of the central fragment and the external rings. The calculated properties of consecutive oligomers indicate their fast convergence to values characterizing polymers.

Because cerebrospinal fluid (CSF) is the biofluid which interacts most closely with the central nervous system, it holds promise as a reporter of neurological disease, for example multiple sclerosis (MScl). To characterize the metabolomics profile of neuroinflammatory aspects of this disease we studied an animal model of MScl—experimental autoimmune/allergic encephalomyelitis (EAE). Because CSF also exchanges metabolites with blood via the blood–brain barrier, malfunctions occurring in the CNS may be reflected in the biochemical composition of blood plasma. The combination of blood plasma and CSF provides more complete information about the disease. Both biofluids can be studied by use of NMR spectroscopy. It is then necessary to perform combined analysis of the two different datasets. Mid-level data fusion was therefore applied to blood plasma and CSF datasets. First, relevant information was extracted from each biofluid dataset by use of linear support vector machine recursive feature elimination. The selected variables from each dataset were concatenated for joint analysis by partial least squares discriminant analysis (PLS-DA). The combined metabolomics information from plasma and CSF enables more efficient and reliable discrimination of the onset of EAE. Second, we introduced hierarchical models fusion, in which previously developed PLS-DA models are hierarchically combined. We show that this approach enables neuroinflamed rats (even on the day of onset) to be distinguished from either healthy or peripherally inflamed rats. Moreover, progression of EAE can be investigated because the model separates the onset and peak of the disease. Figure Graphical representation of Hierarchical Models Fusion applied to concatenated plasma and CSF datasets. Electronic supplementary material The online version of this article (doi:10.1007/s00216-012-5871-4) contains supplementary material, which is available to authorized users.

Aminophosphine oxides and aminophosphonates are, in general, very stable compounds. However, following phosphorus-carbon bond cleavage in aqueous acidic media these compounds sometimes decompose to phosphonic acids derivatives (P(III)). Despite some controversy in the literature, careful analysis supported by theoretical studies leads to the conclusion that decomposition to P(III) derivatives proceeds via an elimination reaction.

Various reaction paths of the P-C bond cleavage of alpha-aminophosphonates in acidic media, resulting in the derivatives of phosphonic acid, has been investigated using density functional level of theories in the gas phase as well as in aqueous medium. Dimethyl (alpha-anilinobenzyl)phosphonate has been used as the model molecule and our investigation confirms a three steps process including protonation, P-C bond cleavage, and the transformation of the products from the final transition state (imine cation and H-phosphonate) through hydrolysis. The most favorable reaction path starts from the amino group protonation, followed by a proton transfer through N-H...O(P) hydrogen bond, and the P-C bond cleavage from the resulting protonated structure. Explicit inclusion of water molecules indicated that two waters are needed for the P-C bond cleavage, and the calculated mechanistic paths in this hydrated model are similar to those of the aqueous solvation model.