Annion binding affinities studied by 1H-NMR

  • chem-select“Synthesis, Selectivity and Structural Study of New C3-Symmetric Tripodal Amides as Anion Receptors. An Experimental and Theoretical Approach”

    Celis, S.; Pi-Boleda, B.; Nolis, P.; Illa, O.; Branchadell, V.; Ortuño, R. Chemistry Select. doi: 10.1002/slct.201600560

Several new nitrilotriacetic acid (NTA) based C3-symmetric tripodal amides have been synthesized. The NTA branches are alkyl chains or esters derived from amino acids of different length, namely glycine, β-alanine and γ-aminobutyric acid. The behavior of these compounds to entrap different monoanions has been tested revealing that they are good ligands able to form host-guest complexes with the following affinity order: H2PO4 > CH3CO2 > PhCO2 > Cl, in DMSO. It was found that, while the end-group effect (CH3, methyl or benzyl ester) was irrelevant, the length of the branches played a role in the selectivity of the receptors considered and, in special, the glycine derivative has shown remarkably high recognition of H2PO4. The 1:1 stoichiometry of the complexes has been experimentally determined based on NMR titration and justified by theoretical calculations that also allowed their structure to be predicted for selected instances. Otherwise, formation of bifluoride anion (HF2) has been experimentally observed by NMR and this fact rends difficult the reliability of the affinity constants determined for fluoride complexes.



Chloroperoxidase-catalyzed amino alcohol oxidation: Substrate specificity and novel strategy for the synthesis of N-Cbz-3-aminopropanal


“Chloroperoxidase-catalyzed amino alcohol oxidation: Substrate specificity and novel strategy for the synthesis of N-Cbz-3-aminopropanal” by G. Masdeu,  M. Pérez-Trujillo, J. López-Santín and Gregorio Álvaro. Process Biochemistry 2016; DOI:10.1016/j.procbio.2016.05.022

The ability of chloroperoxidase (CPO) to catalyze amino alcohol oxidations was investigated. The oxidations of compounds with different configurations with respect to the amine position towards hydroxyl – using H2O2 and tert-butyl hydroperoxide (t-BuOOH) – were analyzed in terms of the initial reaction rate, substrate conversion, and CPO operational stability. It was observed that the further the amino group from the hydroxyl, the lower the initial reaction rate. The effect of the amino-protecting group and other substituents (i.e., methyl and hydroxyl) was also examined, revealing an increase in steric hindrance due to the effect of bulky substituents. The observed reaction rates were higher with t-BuOOH, whereas CPO was more stable with H2O2. Moreover, CPO stability had to be determined case by case as the enzyme activity was modulated by the substrate. The oxidation of N-Cbz-3-aminopropanol (Cbz, carboxybenzyl) to N-Cbz-3-aminopropanal was investigated. Main operational conditions such as the reaction medium, initial amino alcohol concentration, and peroxide nature were studied. The reaction kinetics was determined, and no substrate inhibition was observed. By-products from a chemical reaction between the formed amino aldehyde and the peroxide were identified, and a novel reaction mechanism was proposed. Finally, the biotransformation was achieved by reducing side reactions and identifying the key factors to be addressed to further optimize the product yield.

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Shifts in plant foliar and floral metabolomes in response to the suppression of the associated microbiota


“Shifts in plant foliar and floral metabolomes in response to the suppression of the associated microbiota” by A. Gargallo-Garriga, J. Sardans, M. Pérez-Trujillo, A. Guenther, J. Llusià, L. Rico, J. Terradas, G. Farré-Armengol, I. Filella, T. Parella and J. Peñuelas. BMC Plant Biology 2016; 16:78. DOI: 10.1186/s12870-016-0767-7

The significance of microbial populations to the health and physiology of human and animal hosts has become a burgeoning and increasingly newsworthy topic. Of course, plants are also hosts for microbial life, and our metabolomics new study in BMC Plant Biology suggests that microbial influence on plant biology is more complex than we currently appreciate. When elderflower plants were treated with antibiotics, metabolic changes occurred not only at the sites of microbial colonization – the leaf and flower – but also in internal organs. These results demonstrate key contributions to local metabolic activity of microbes on elderflower leaves and flowers, and suggest that – as seen in other organisms – microbial activity can have a systemic impact host biology.


Optimized polarization build-up times in dissolution DNP-NMR using a benzyl amino derivative of BDPA


“Optimized polarization build-up times in dissolution DNP-NMR using a benzyl amino derivative of BDPA” by José Luis. Muñoz Gómez, Eva Monteagudo, Vega LLoveras, Teodor Parella, Jaume Veciana and José Vidal Gancedo. RSC Advances, 2016, 6, 27077. DOI: 10.1039/c6ra00635c


The synthesis of two novel BDPA-like radicals, a benzyl amino (BAm-BDPA, 7) and a cyano (CN-BDPA, 5) derivative, is reported and their behaviour as polarizing agents for fast dissolution Dynamic Nuclear Polarization (DNP) is evaluated. The radical 7 is a promising candidate for DNP studies since it is soluble in neat [1-13C]pyruvic acid (PA), and therefore the use of an additional glassing agent for sample homogeneity is avoided. In addition, a 60 mM sample of 7 offers optimum 13C NMR signal enhancements using fairly short polarization times (about 1800 s). It is shown that DNP-NMR measurements using 7 can be performed much more efficiently in terms of the signal enhancement per polarization build-up time unit than when using the reference OX63 or BDPA radicals. These enhanced features are translated to a substantial reduction of polarization times that represents an optimum temporary use of the DNP polarizer and allow economized liquid helium consumption.


Exploring the use of Generalized Indirect Covariance to Reconstruct Pure shift NMR Spectra: Current Pros and Cons.


Title: Exploring the use of Generalized Indirect Covariance to Reconstruct Pure shift NMR Spectra: Current Pros and Cons.
Authors: André Fredi, Pau Nolis, Carlos Cobas, Gary E. Martin and Teodor Parella.
DOI: 10.1016/j.jmr.2016.03.003

ABSTRACT: The current pros and cons of a processing protocol to generate pure chemical shift NMR spectra using Generalized Indirect Covariance are presented and discussed. The
transformation of any standard 2D homonuclear and heteronuclear spectrum to its pure shift counterpart by using a reference DIAG spectrum is described. Reconstructed pure shift NMR spectra of NOESY, HSQC, HSQC-TOCSY and HSQMBC experiments are reported
for the target molecule strychnine.graphical abstract




Visiting PhD Student Yaoyao Wang

Blog2Today we are saying goodbye to our dear Yaoyao, though we hope to see her very soon again.

Yaoyao is currently finishing her PhD on metabonomics applied to clinical biomarkers in the Legido-Quigley Lab at King’s College London (KCL).

She has been visiting us for the last two months, during which we have been working together in two metabonomics projects related to drug misuse biomarkers and chiral metabonomics. It has been a great pleasure for us to spend this time with her and continue with this collaboration from now on.

Seminar: Biomarker and metabolomics, a novel approach to detect drug misuse

Yaoyao Wang, visiting PhD student from King’s College London, will be giving a talk on  December the 18th at 10:00 h in the SeRMN. Her talk is entitled “Biomarker and metabolomics: a novel approach to detect drug misuse”.


Yaoyao is from Clinical Biomarkers Lab of the Institute of Pharmaceutical Science, King’s College London (KCL). Her PhD project focuses on developing metabolomics approach to identify biomarkers for drug misuse through the analysis of human biofluids samples and the development of data treatment methods, using R (XCMS) and other bioinformatics tools. She has been collaborating intensively with the Drug Control Centre of KCL using LC-MS.

Her talk will include the metabolomics biomarker discovery of low dose salbutamol in urine collected for anti-doping tests and preliminary longitudinal metabolomics study of “date-rape” drug GHB, as well as a glance of the other on-going projects in Clinical Biomarkers Lab.

All interested people are welcome to attend this seminar.

SeRMN gets a visit of Gustavo G. Simamoto from UNICAMP-Brazil

AvMmMO19F-_NOP6OnHN_BVnx8QEv3yIaDjCf-B76l4EEWe received a visit from Gustavo Giraldi Shimamoto who is PhD student and technical NMR at University of Campinas (UNICAMP-Brazil). Gustavo was one month (November 2015) in our laboratory learning a little about how our NMR service works, the type of service we provide both to universities and to companies and some of our routine work. In addition, Gustavo learned about pulse sequence, modern NMR experiments as pure-shift and HSQMBC. For us it was a great pleasure to receive and meet Gustavo.

SeRMN at the SMASH NMR 2015 Conference

Some of our last research works has been presented at the annual meeting of the SmallMolecule NMR Conference (SMASH) that has been taken place in Baveno (Italy) from 20thto 24thSeptember 2015.

Find below a summary of our contributions.

Núria Marcó presented two posters.


Poster nº 25: “Ultra high-resolution HSQC: application to the efficient and accurate measurement of heteronuclear coupling constants”. Núria Marcó, Andre Fredi and Teodor Parella.

Abstract: Digital resolution and signal resolution are two important concepts in multidimensional NMR spectroscopy. One of the more critical parameters defining the total acquisition time of a 2D NMR experiment is the number of variable t1evolution times required to achieve a satisfactory digital resolution in its indirect F1 dimension. In this study, the success of implementing spectral aliasing along the indirect F1 dimension of HSQC experiments is demonstrated by the easy measurement of heteronuclear coupling constants from the indirect dimension of 2D HSQC spectra, without any significant increase of the experimental time. It is also shown that the gains of introducing aliasing are further improved with the large signal resolution achieved by the collapse of the J(HH) multiplet structure by broadband 1H homodecoupling in the F2 dimension. The resulting 2D cross-peaks exhibit ultra simplified multiplet patterns from which the measurement of the active J values is determined in a straightforward manner. Experimental data will be provided for the simultaneous determination of the magnitude and the sign of J(CX) and J(HX) coupling constants (X = 19F, 31P or 2H).

Poster nº 26: “Extending long-range heteronuclear NMR connectivities by modified HSQMBC experiments”. Josep Saurí, Núria Marcó, R. Thomas Williamson, Gary E. Martin and Teodor Parella.

Abstract: The detection of long-range heteronuclear correlations associated with J(CH) coupling values smaller than 1-2 Hz is a challenge in the structural analysis of small molecules and natural products. LR-HSQMBC, HSQMBC-COSY and HSQMBC-TOCSY pulse schemes are evaluated as complementary NMR methods to standard HMBC/HSQMBC experiments. The re-optimization of the interpulse delay and the incorporation of an additional J(HH) transfer step in the HSQMBC pulse scheme can favor the sensitive observation of traditionally missing or very weak correlations and, in addition, facilitates the detection of a significant number of still longer-range connectivities to both protonated and non-protonated carbons under optimal sensitivity conditions. A comparative 1H-13C study is performed using strychnine as a model compound and several examples are also provided including 1H-15N applications.


PhD Thesis Defense: Metabolomics and stoichiometry adapted to the study of environmental impacts on plants. PhD Thesis by Albert Gargallo Garriga


I am defending my PhD thesis next Thursday (September 10, 2015) at 11.30am in the Sala d´Actes “Carles Miravitlles” of the Institut de Ciències de Materials de Barcelona (ICMAB), Campus UAB. The title of my thesis is “Metabolomics and stoichiometry adapted to the study of environmental impacts on plants” and below you can find an abstract of the work. If you are interested you are very welcome.




Metabolomics has allowed significant advances in biological sciences. An increasing number of ecological studies have applied a metabolomic approach to answer ecological questions (ecometabolomics) during the last few years. The work developed throughout this PhD thesis means a further step in the field of ecometabolomics.

The first chapter of results of this thesis is dedicated to the adaptation of a previously described protocol to conduct metabolomics in ecological studies. It describes in detail the procedures to follow, in the field and in the laboratory, to perform metabolomic analyses using nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) coupled to stoichiometric analysis. This improvement allowed combining the study of ecological stoichiometry and metabolomics in a single protocol and obtaining a wider overview of what is happing to the organism.

In the second and third chapters, the described protocol is applied to study how some climate change factors (drought, warming and irrigation) affect different organs of the plant (shoots and roots of Holcus lanatus and Alopecurus pratensis) at two different seasons. The results show a relationship between the metabolic variation observed in roots and the observed in shoots. The simultaneous metabolomic analysis of both organs of these grasses provide a complete view of the entire plant; including the response of different organs to environmental changes, the global phenotypic response and the metabolic mechanisms underlying these responses.

The fourth chapter is dedicated to the study of the simulated attack to Quercus Ilex leaves by an herbivore. The results show differences in the 1H NMR metabolic profiles of the leaf before and after the wound. A marked increase in C-rich secondary metabolites, quinic acid and quercitol, which are related to the shikimic metabolic pathway, was observed. The results also confirm that quinic acid and quercitol are present in great content in the genus Quercus and they are involved in mechanisms against biotic stress.

In the fifth chapter a study of the relationship between the epiphytic microorganisms and the plant host is described. This study highlights the large complexity of the episphere, the existence of internal microbial communities and the strong relationships between the structure and function of the internal and external plant metabolomes. These results warrant further study of the specific relationships between plants and the microbial communities living on and in them.