Dr. Shidong Chen – thesis on the organic residue analysis

Shidong Chen, successfully defended his PhD dissertation entitled “Unravelling prehistoric plant exploitation in eastern Baltic: organic residue analysis of plant-based materials by multi-method approach” on the 12th of September. We were honored to have Dr. Shinya Shoda from Nara National Research Institute for Cultural Properties, Japan as Shidong’s opponent.

From left to right: opponent Dr. Shinya Shoda, Dr. Shidong Chen, supervisors Dr. Ester Oras and Prof. Ivo Leito

Shidong’s PhD work is aimed at discovering plant exploitation in the ancient eastern Baltic area with a focus on two types of plant-derived materials: resinous materials and dietary plants. The main innovations are developing multi-methodological approaches and interpreting multi-proxy datasets with chemometric and statistical methods.

For identifying the composition of resinous adhesives, ATR-FT-IR analysis was conducted in combination with a PCA-based DA classification model for further compositional and spatial/temporal classification. This method can help simplify IR spectra interpretation and reduce the need for GC-MS analysis.

For identifying dietary plants, a multi-method approach was applied by plant micro fossil analysis and EA-IRMS combined with ORA. EA-IRMS can provide preliminary origins of samples with plant and/or animal bases. Plant micro fossil analysis and ORA in complementary can identify the species of plant remains. Correspondence analysis further compares and indicates the agreement of the three methods and visualizes the correlations between the multi-proxy data.

Dr. Shidong Chen moments before the presentation

The plant exploitation in prehistoric easter Baltic shows different patterns with dedicated multi-method case studies on several Stone Age, Bronze Age, and Iron Age sites. In the Stone Age, plant exploitation was more technological (adhesives and resinous compounds) than dietary-related. The plant consumption for dietary purposes became more abundant in the Bronze Age. The major changes happened with the Iron Age displaying a more diverse plant-based diet with more inclusion of C3 cereals (e.g., wheat and barley), yet the spread and cultivation of C4 millet may not have emerged in this region.

Shidong is currently working at ARCHEMY lab as a lab technician at the University of Tartu. He will continue his journey discovering ancient food ways from pots and bones.

Dr. Ernesto de Jesus Zapata Flores – PhD thesis on LC-MS derivatization reagents

Last Wednesday, August 30th, 2023, a moment that marks the culmination of years of hard work and determination of Ernesto de Jesus Zapata Flores – an AMS alumnus. He successfully defended his PhD thesis titled Derivatization Reagents used in negative mode electrospray LC-MS. The opponent was Associate Professor Jeffrey Hawkes from the University of Uppsala, Sweden.

In the vast application of derivatization reagents in RPLC-UV and RPLC-MS positive mode, Ernesto’s thesis delved into the question: What about LC-MS negative mode? Why don’t we compare both modes and see the best of both worlds?

Firstly, the thesis has been inspired by DEEMM – a commercial reagent – which also was one of the earliest reagents studied in our department. The comparison of the ionization mode in the determination of free amino acids in beers showed that (1) the matrix effects were less severe in the negative mode.

Later on, the method applying two azobenzene-based reagents, which were called AzoB and AzoC  (synthesized in our lab), has been fully developed specifically for LC-QqQ. The “gourmet” part that Ernesto has brought to the table of the analytical chemistry community was the study of (2) MS/MS fragmentations of all three reagents with different amino compounds in both ionization modes.

Moreover, his thesis has demonstrated comprehensive research about (3) optimization for the derivatization process and the ion source, (4) the confirmation of reaction yields, and (5) the correlation between ionization efficiency and LOD/LOQ of derivatives. Finally, applications of the validated method (7) for real-world samples (different beverages: beers, Kali, juices) and (8) neutral loss scan have been showcased.

Alongside the road, (9) side reactions managed to be worth some of his sweat and tears. At the end of his PhD journey, he (10) evaluated an identification tool using the transition of derivatives in both MS polarities.

10 out of 10 – that should be given for Ernesto’s dedication on the road to becoming an expert in LC-MS derivatization. Congratulations, Ernesto! We eagerly await your next academic steps. Hopefully, all your goals will be achieved.

Dr. Andre Leesment – PhD thesis on the acidity in biphasic systems and gas-phase

Last Friday, June 9th, 2023, Andre Leesment successfully defended his PhD thesis titled Quantitative studies of Brønsted acidity in biphasic systems and gas-phase. The opponent was Prof. Kiyohiko Sugano from the Ritsumeikan University, Japan.

Dr. Andre Leesment (on the right) after his PhD defence with his supervisor Prof. Ivo Leito (on the left).

Experiments for measuring acidity of medicines, catalysts, and other chemicals are almost always performed under monophasic conditions. However, many of them are lipophilic compounds, and in biphasic systems they prefer the nonpolar organic phase, where their properties are much different from their properties in an aqueous phase. Yet the interactions with the organic phase are completely ignored in a typical acidity measurement. It’s like seeing only half of the picture. Why is such an incomplete approach being used for something this important?

Until recently, there was no theoretical basis or experimental method to conduct measurements of acidity under more relevant conditions. Andre’s PhD thesis focuses on providing the tools to measure acidity, and by extension, many other properties of molecules in biphasic systems in a more realistic and accurate way. Hopefully, these tools lead to a more effective drug development, catalyst research, etc.

Congratulations to you, Andre!  

 

From anion receptor design to real sensor prototypes – PhD thesis of Alo Rüütel

On the 18th of November, 2022, Alo Rüütel successfully defended his PhD thesis titled Design principles of synthetic molecular receptors for anion-selective electrodes.

Alo’s thesis starts by expanding a fundamental question asked by Otto S. Wolfbeis back in 2013: when so much research is done on binding anions with various molecular receptors, why do we see so few real sensors that could be used in real-life applications?

 

 

In response to this, Alo has outlined a sensor development strategy flowchart and identified a “dead zone” – space between receptor evaluation and prototype fabrication stages – on the sensor development pathway where the research most often gets stuck. Alo’s dissertation connects the research fields of receptor design and sensor preparation. The thesis demonstrates the challenges of creating new ion-selective electrodes for carboxylate sensing. This process is accompanied by several scientific challenges at the fundamental level of supramolecular chemistry. To address these problems, influencing factors are explored, such as improving binding, lipophilicity, biphasic binding environments etc. A big outcome of the thesis was a compilation of accurate binding constants of one hundred (!) anion receptors. Perhaps the most tangible result of the thesis were real sensor prototypes, capable of sensing carboxylate anions (e.g. benzoate).

Alo’s performance at the defence was one of the best we have seen. He single-handedly and seemingly effortlessly answered all the (numerous!) questions from the opponent, as well as from the committee.

Please accept our big congratulations, Alo!

Dr. Merit Oss, PhD thesis on the ionization efficiency in ESI

On the 24th of August, 2021, Merit Oss successfully defended her PhD thesis titled “Ionization efficiency in electrospray ionization source and its relations to compounds’ physico-chemical properties” 

The thesis by Merit revolves around ionization efficiency in electrospray ionization (ESI) MS. The main aim was to gain a better understanding of the relations between different molecular properties of compounds and the signal intensities of their ions in ESI-MS. During this study, a large number of ionization efficiency values were obtained. Eleven molecular parameters were taken into account for estimating their importance for evaluating the compound’s ionization efficiency in ESI. It was concluded that in the studied solvent system, a compound’s ionization in the ESI source is determined by its basicity, molecular size, and hydrophobicity/lipophilicity. The results showed that the obtained models for estimating compounds’ ionization efficiency can be used for approximate prediction. 

Congratulations, Merit! We wish you all the best for your future. 

 

Dr. Eliise Tammekivi – PhD thesis on the quantitative analysis of oils

Last Friday, on August 27, 2021, Eliise Tammekivi successfully defended her PhD thesis titled Derivatization and quantitative gas-chromatographic analysis of oils.

In the PhD thesis by Eliise, four derivatization procedures that are widely used for the analysis of oils in cultural heritage or archaeology were compared based on quantitative gas-chromatographic (GC) analysis. It was seen that the TMTFTH derivatization was the most suitable one for the GC analysis of fresh oils. An in-depth uncertainty estimation was performed for one of the derivatization procedures using the ISO GUM approach and the Monte Carlo method. Another one of the improved procedures was applied for the analysis of self-made artificially aged paint samples that had varying pigment to linseed oil ratio to see if the pigment concentration had an effect on the drying of the paint samples.

Additionally, small samples from two paint case study samples relevant to the history of Estonia – crucifix from Karja church and cupboard from Ruhnu island – were analyzed to obtain information about the materials in the paint samples. Finally, the improved quantitative method was used to quantify fatty acids present in yeast cells. 

Congratulations to you, Eliise!  

 

Dr. Astrid Darnell – PhD thesis on the study of anion receptors

On the 20th of May, 2021, Astrid Darnell defended her PhD thesis titled “Computational design of anion receptors and evaluation of host-guest binding“. 

In the thesis by Astrid, the main aim was to study possible new receptor molecule candidates with computational methods. This could improve the design of receptors used for the detection of various important anions (including glyphosate dianion and small monocarboxylate anions). 

The suitability of the COSMO-RS method was tested for studying receptor molecule and anion binding. It was also demonstrated that COSMO-RS was shown to predict correctly the most stable conformers of the majority of the studied molecules. 

The effects of receptor and complex geometries and the spatial matching between host and guest species on the binding affinity of large, structurally complex receptors was investigated towards a selection of analytically interesting carboxylate anions. A number of these receptor structures are now being investigated for practical applications as real carboxylate anion sensors in the form of SC-ISEs.

The final part of the study investigated the applicability of isothermal titration calorimetry (ITC) experiments for the determination of the thermodynamic parameters (e.g. reaction entalphy ΔH) of host-guest binding reactions. Low-volume ITC experiments were found to be applicable for the study of low-affinity host-guest binding reactions and the combined standard uncertainty for reaction entalphy determination for these experiments is in the range of 1-2kJ/mol.

Congratulations to you, Astrid!

We are happy to introduce – Dr. Ruta Hecht and Dr. Max Hecht

Today, on August 28, 2020, Ruta Hecht and Max Hecht defended successfully their PhD theses!

The dissertation by Ruta was titled “Novel eluent additives for LC-MS based bioanalytical methods”. In this thesis, novel fluoroalcoholic eluent additives that showed to have a positive influence on analyte ionisation in the MS source were studied. Additionally, two practical applications employing novel eluent additives were developed and validated for several pharmaceuticals. The two bioanalytical methods were used to obtain data for pharmacokinetic and pharmacodynamic studies in paediatric patients. Both methods reached exceptionally low limits of quantification, with minimal sample amount used due to the positive influence of novel eluent additives on analyte ionisation.

The PhD thesis by Max titled “Advances in the development of a point-of-care mass spectrometer test“. In this work, an on-site testing method was developed and evaluated for medical examination. For example, this method enabled to determine the concentration of an antibiotic and an opioid directly in blood, plasma, or urine in as little as 5 minutes.  Furthermore, traditional laboratory-based methods were developed. These included the diagnose of the rare MNGIE-disease and a 36-second test for the analysis of ecstasy tablets. To investigate potentially harmful drugs added to ecstasy tablets, a large panel of over 100 drugs was measured within a single analysis run on a miniaturised mass spectrometer. 

Congratulations to you both! We wish you all the best for the future!

Dr. Artur Gornischeff – PhD thesis on the study of ionization efficiencies and standard free quantification

On the 18th of August, 2020, Artur Gornischeff defended his PhD thesis titled Study of ionization efficiencies for derivatized compounds in LC/ESI/MS and their application for targeted analysis

In the thesis by Artur, a method that allowed to measure and evaluate the ionization efficiencies of important constituents (amino acids, biogenic amines) in different foodstuffs and beverages was developed. The developed useful method was used to estimate analyte concentrations without standard substances in different matrices (beer, wine, and tea). In addition, the effect of derivatization on ionization efficiencies and the problem of how to choose the suitable ion source and eluent components were addressed. One benefit of the overall results is the possibility to help with distinguishing counterfeit drinks from the original ones. 

Congratulations, Artur! We wish you all the best for your future.  

 

 

 

 

 

Dr. Pilleriin Peets – PhD thesis on the analysis of textile fibres and dyes

Today, on August 25, 2020, Pilleriin Peets successfully defended her PhD thesis titled Development of instrumental methods for the analysis of textile fibres and dyes.

In the thesis by Pilleriin Peets, analytical methods using FT-IR spectroscopy in ATR and reflectance modes were developed for the determination of 16 different fibre types. Additionally, classification methods (discriminant analysis and random forest) were used for the classification of unknown fibres. For the dye analysis, analytical methods using various instrumental sets (HPLC with different mass analysers, MALDI- and ESI-FT-ICR-MS) were developed based on the analysis of seven natural red dyes

Based on these results, a large collection of standard spectra and chromatograms was collected and made available for scientists. The advantageous developed methods were used to analyse several cultural heritage samples from the University of Tartu Art Museum, Estonian National Museum, Conservation and Digitization Centre Kanut (Estonia) and private collections. 

Well done, Pilleriin! We wish you all the best for the future!