Call for applications: Predoctoral 4-year fellowship in NMR Methodology

Applications are welcome for a four-year PhD position in the field of high-resolution NMR spectroscopy at the NMR Service (SeRMN) of the Universitat Autònoma of Barcelona (UAB).

The researcher will investigate the subject “Analysis of complex mixtures by NMR spectroscopy” under the joint supervision of  Dr. Teodor Parella and Dr. Míriam Pérez-Trujillo, as part of the project “Design and Application of New Methodologies in Nuclear Magnetic Resonance” (Diseño y aplicación de nuevas metodologías en resonancia magnética nuclear, CTQ2015-64436-P, 2016-2018) awarded to Dr. Teodor Parella.

This scholarship is awarded by the Spanish Ministry of Economy and Competitiveness (MINECO), through the Predoctoral Research Fellowship Program (*) and it is co-funded by the European Social Fund (ESF).

The call for applications begins September 13th, 2016, and the deadline for submissions is September 27th, 2016 at 15:00.

All information relating to the call for applications is available at the MINECO web site and at the Database of Spanish National Funding. For details or questions about the research project, contact Dr. Teodor Parella.

(*) Convocatoria de Ayudas para contratos predoctorales para la formación de doctores 2016. Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016. Programa Estatal de Promoción del Talento y su Empleabilidad, Subprograma Estatal de Formación.

SeRMN at the SMASH NMR 2016 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 La Jolla (USA) from 11thto 14thSeptember 2016.

Teodor Parella presented two posters.
“In situ determination of 1DCH and 2DHH RDCs from a single 1JCH/2JHH -resolved NMR measurement” of Núria Marcó García, Roberto R. Gil and Teodor Parella.

Abstract: A fast RDC-assisted strategy involving the simultaneous determination of isotropic (scalar) and anisotropic (total) interactions is reported. The concerted use of individual 1DCH for all CHn multiplicities and 2DHH obtained from a single 1JCH/2JHH-resolved NMR spectrum offers an unambiguous assignment of diastereotopic protons and an efficient discrimination between all eight possible diastereoisomeric structures of strychnine which contains six stereocenters.

Figure: 500.13MHz JCH/JHH-Resolved spectra of 1 in A) isotropic CDCl3 and B) anisotropic PMMA-CDCl3 (2H nQ(CDCl3)=26 Hz) conditions. The projections along the F2 dimension are the conventional 1H spectrum in isotropic conditions and the 1H-CPMG spectrum in anisotropic conditions, respectively.

“Pure shift NMR covariance” of André Fredi, Pau Nolis, Carlos Cobas, Gary E. Martin, Teodor Parella.

Abstract: The development of novel experimental strategies to significantly enhance signal resolution by broadband homodecoupling is a current topic of high interest in 1H NMR spectroscopy . A number of different building blocks have been implemented into 1D and 2D homo- and heteronuclear experiments in order to provide resolution-enhanced pure chemical shift 1H NMR spectra, where signals appear collapsed to singlets. On the other hand, Covariance processing methods have been used to generate challenging NMR spectral representations . We present here the first attempts towards a general solution to generate Pure Shift NMR spectra by using Generalized Indirect Covariance (psGIC) co-processing3,4 . The current strategy is based on the calculation of a new 2D psGIC spectrum from the combination of a parent homo- or heteronuclear spectrum and a reference 2D F1-homodecoupled 1H- 1H correlation spectrum only showing diagonal cross-peaks (DIAG), which share a common 1H frequency dimension. Using psGIC, the F1 dimension in the DIAG spectrum is transferred to the F2 dimension of the parent spectrum, thus generating a new pure shift 2D spectrum

Figure: Generation of Pure Shift NMR spectra by using Generalized Indirect Covariance (psGIC)

PhD Thesis by Albert Gargallo Garriga: Publications and Data Sets

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The links below point to the research articles and Mass Spectrometry and NMR Spectroscopy raw datasets that were part of my thesis work. The last link points to my Ph.D. Thesis in pdf format.

Chapter 1

MEE“Ecometabolomics: Optimized NMR-based method” by Albert Rivas-Ubach, Miriam Pérez-Trujillo, Jordi Sardans, Albert Gargallo-Garriga, Teodor Parella, Josep Peñuelas. Methods in Ecology and Evolution, February 2013. DOI: 10.1111/2041-210X.12028

Chapter 4

scireportsOpposite metabolic responses of shoots and roots to drought by Albert Gargallo-Garriga, Jordi Sardans, Míriam Pérez-Trujillo, Albert Rivas-Ubach, Michal Oravec, Teodor Parella and Josep Peñuelas. Scientific reports 4, Article number: 6829, October 2014. DOI: 10.1038/srep06829

Chapter 5

Warming differentially influences the effects of drought on stoichiometry and metabolomics in shoots and roots” by Albert Gargallo-Garriga, Jordi Sardans, Míriam Pérez-Trujillo, Michal Oravec,Otmar Urban, Anke Jentsch, Juergen Kreyling, Carl Beierkuhnlein Teodor Parellaand Josep Peñuelas. New Phytologist. March 2015. DOI: 10.1111/nph.13377

Chapter 6

Plant Biology“Metabolomic responses of Quercus ilex seedlings to wounding simulating herbivory” By Jordi Sardans, Albert Gargallo-Garriga,Míriam Pérez-Trujillo, Teodor Parella, Roger Seco, Iolanda Filella, Josep  Peñuelas. Plant biology. April 2013. DOI: 10.1111/plb.12032

Chapter 7

Ph.D. Thesis

New Book Release: MORPHOLOGICAL MOUSE PHENOTYPING

“MORPHOLOGICAL MOUSE PHENOTYPING: Anatomy, Histology and Imaging” by Jesús Ruberte París, Ana Carretero Romay, and Marc Navarro Beltrán (2016). Editorial Médica Panamericana.

Morphologial Mouse Phenotypiong_BOOKAn extraordinary atlas of mouse anatomy which includes more than 2,200 original images over 600 pages to show the anatomy, histology and cellular structure of mouse organs. This book attempts to provide an overview of the different levels of morphology of the mouse, ranging from gross anatomy and topographical anatomy (to explain the relative position of the organs and structures of a particular body region) down to the microscopic anatomy. Imaging technologies used for that include magnetic resonance imaging (MRI), computed tomography (CT), ultrasonography, angiography, X-ray, and electron microscopy. Also, classical anatomical techniques such as conventional dissection, skeletal preparations, vascular injections, histology and immunohistochemistry have been employed to characterize the mouse morphology.

All MRI images included in this book were acquired at our NMR facility (SeRMN, Universitat Autònoma de Barcelona) in a 7 Tesla Bruker BioSpec spectrometer.

André Fredi’s oral presentation at 8th GERMN / 5th Iberian NMR Meeting

André Fredi did an oral presentaion at 8th GERMN / 5th Iberian NMR Meeting (GERMN 2016) held in Valencia, Spain from 27th to 29th June 2016.

In his presentaion, tha was titled  Exploring the use of Generalized Indirect Covariance to reconstruct Pure Shift NMR spectra: Current Pros and Cons”,IMG-20160628-WA0028

André explained how to make pure spectra shift from Generalized Indirect Covariance processing (psGIC). This new method is basically a new way to get “synthetic” pure shift spectra without the need to purchase a pure shift spectrum in the spectrometer and without the penalties that pure-shift experiments cause.

André has been working as a Ph.D. candidate at the Department of Chemistry and SeRMN under the direction of Dr. Teodor Parella and Dr. Pau Nolis since November 2014, when he enrolled in the Department of Chemistry doctoral program at Universitat Autònoma de Barcelona with a fellowship from CNPq-Brazil. He is currently in his second year and expects to defend the doctoral thesis on 2017/2018.

 

Presentations at the EUROMAR 2016 Conference

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André Fredi (PhD student) and Teodor Parella presented our last research works at the annual meeting of the European magnetic resonance community EUROMAR 2016 Conference that was celebrated on days 3th to 7th July in Aarhus, Denmark. Find below a summary of our contributions.

Teodor Parella presented two posters.

One of them entitled  Selecting the Most Appropriate NMR Experiment to Access Weak and/or Very Long-Range Heteronuclear Correlations”  Josep Saurí, Yizhou Liu, Teodor Parella, R. Thomas Williamson and Gary E. Martin.

Abstract: Heteronuclear long-range NMR experiments are well established as essential NMR techniques for the structure elucidation of unknown natural products and small molecules. It is generally accepted that the absence of a given n JXH correlation in an HMBC or HSQMBC spectra, would automatically place the proton at least four bonds away from the carbon in question. This assumption can, however, be misleading in the case of a mismatch between the actual coupling constant and the delay used to optimize the experiment, which can lead to structural misassignments. Another scenario arises when an investigator, for whatever reason, needs to have access to very long-range correlations to confirm or refute a structure. In such cases, a conventional HMBC experiment will most likely fail to provide the requisite correlation, regardless of the delay optimization. Two recent methods for visualizing extremely weak or very long-range connectivities are the LR-HSQMBC1 and the HSQMBC-TOCSY2 experiments. Although they are intended to provide similar structural information they utilize different transfer mechanisms, which differentiates the experiments making each better suited for specific classes of compounds. Here we have sought to examine the considerations implicit in choosing the best experiment to access weak or very long-range correlations for different types of molecules.
teodor 1

 

The other poster was titled  Optimizing J-modulated ADEQUATE experiments through homonuclear decoupling (HD) and non-uniform sampling (NUS)” Josep Saurí, Teodor Parella, R. Thomas Williamson and Gary E. Martin.

Abstract: Homonuclear 13C–13C couplings at natural abundance can be measured using the J-modulated ADEQUATE experiment. To somewhat ameliorate F1 digitization requirements, a scaling factor was incorporated into the original ADEQUATE pulse sequence1,2. We have introduced BIRDbased homonuclear decoupling (HD) analogous to that described for the 1,1-HD-ADEQUATE and 1,n-HD-ADEQUATE experiments3 and evaluated the combination of NUS and HD on the measurement of both 1 JCC and n JCC homonuclear 13C–13C coupling constants. A significant improvement in the measurement of n JCC coupling constants, and time savings, were realized with the modified experiment.2 teodor 2

André Fredi also presented a poster entitled “Exploring the use of Generalized Indirect Covariance to reconstruct pure shift NMR spectra” André Fredi, Pau Nolis, Carlos Cobas, Gary E. Martin, Teodor Parella.

Abstrac: The development of novel experimental strategies to significantly enhance signal resolution by broadband homodecoupling is a current topic of high interest in 1 H NMR spectroscopy1,2,3. The original Zangger-Sterk experiment has been modified and improved in several ways. All of these novel building blocks have been implemented in a number of 1D and 2D homo- and heteronuclear pulse schemes to provide resolution-enhanced pure chemical shift 1 H NMR spectra, where signals appear collapsed to singlet. On the other hand, covariance processing methods have been used to generate challenging NMR spectral representations4 . We present here the first attempts towards a general solution to generate Pure Shift NMR spectra by using Generalized Indirect Covariance (psGIC). The current strategy is based on the calculation of a new 2D psGIC spectrum from the combination of a parent homo- or heteronuclear spectrum and a reference 2D F1-homodecoupled 1 H- 1 H correlation spectrum only showing diagonal cross-peaks (DIAG), which share a common 1 H frequency dimension. Using psGIC, the F1 dimension in the DIAG spectrum can be transferred to the F2 dimension of the parent spectrum, thus generating a new pure shift 2D spectrum. Examples are provided for a set of 2D NMR spectra of the alkaloid strychnine.3 Andre poster

11B-MQMAS Solid State NMR experiment performed on polyaminoborane derivatives

no spine minimum. half size. Editor: Tamara Hanna JEM: Esther RTP: Bryan NolteAmmonia Borane Dehydrogenation Promoted by a Pincer-Square-Planar Rhodium(I) Monohydride: A Stepwise Hydrogen Transfer from the Substrate to the Catalyst
Esteruelas, M.A.; Nolis, P.; Oliván, M.; Oñate, M.; Vallribera, A.; Vélez, A. DOI: 10.1021/acs.inorgchem.6b01216

The pincer d8-monohydride complex RhH-{xant(PiPr2)2} (xant(PiPr2)2 = 9,9-dimethyl-4,5-bis-(diisopropylphosphino)xanthene) promotes the release of 1 equiv of hydrogen from H3BNH3 and H3BNHMe2 with TOF50% values of 3150 and 1725 h−1, to afford [BH2NH2]n and [BH2NMe2]2 and the tandem ammonia borane dehydrogenation−cyclohexene hydrogenation. DFT calculations on the ammonia borane dehydrogenation suggest that the process takes place by means of cis-κ2-PP-species, through four stages including: (i) Shimoi-type coordination of ammonia borane, (ii) homolytic addition of the coordinated H−B bond to afford a five-coordinate dihydride-boryl-rhodium(III) intermediate, (iii) reductive intramolecular proton transfer from the NH3 group to one of the hydride ligands, and (iv) release of H2 from the resulting square-planar hydride dihydrogen rhodium(I) intermediate.

11B_MQMAS

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.

titrationtripodal

 

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

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“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

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“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.

Fig1_BMCPB_AGG