New Article in Journal of Biomolecular NMR

Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes

Alexandra Shchukina, Thomas C. Schwarz, Michał Nowakowski, Robert Konrat, Krzysztof Kazimierczuk

figure 10

The accelerated acquisition of multidimensional NMR spectra using sparse non-uniform sampling (NUS) has been widely adopted in recent years. The key concept in NUS is that a major part of the data is omitted during measurement, and then reconstructed using, for example, compressed sensing (CS) methods. CS requires spectra to be compressible, that is, they should contain relatively few “significant” points. The more compressible the spectrum, the fewer experimental NUS points needed in order for it to be accurately reconstructed. In this paper we show that the CS processing of similar spectra can be enhanced by reconstructing only the differences between them. Accurate reconstruction can be obtained at lower sampling levels as the difference is sparser than the spectrum itself. In many situations this method is superior to “conventional” compressed sensing. We exemplify the concept of “difference CS” with one such case—the study of alpha-synuclein binding to liposomes and its dependence on temperature. To obtain information on temperature-dependent transitions between different states, we need to acquire several dozen spectra at various temperatures, with and without the presence of liposomes. Our detailed investigation reveals that changes in the binding modes of the alpha-synuclein ensemble are not only temperature-dependent but also show non-linear behavior in their transitions. Our proposed CS processing approach dramatically reduces the number of NUS points required and thus significantly shortens the experimental time.

New Article in Materials Today Communications

The new Morin – based three-dimensional carbon nanostructures with metal oxides deposits. From synthesis to electro- and photocatalytic applicationsRadon peak-picker based on a neural network

Gisya Abdi, Anna Filip, Krzysztof Kazimierczuk , Tomasz Jaroń, Rafał Jurczakowski, Juan Carlos Colmenares, Andrzej Szczurek


Morin is a natural polyphenolic compound best known for its bioactive properties. Due to its flavonoid structure, Morin may also be considered as a potential precursor of diverse functional materials. Sadly, its poor solubility in water altered its application in this field till now. In this work, by applying simple but effective sol-gel reactions, organic and carbon nanostructures were synthesized and described for the first time. We succeeded in porous materials (BET: 50–600 m2/g) with an original 3D morphology, e.g., hollow hexagonal nanopipes, nanobars, or nanofoams. All received carbons contained metal oxides traces (Co, Zn, Mg, Al), originated from corresponding Lewis acids used as catalysts, and formed after the pyrolysis. The CM-Co samples, having around 7 wt. % of cobalt deposits, were chosen to investigate their suitability for electrochemical conversion of CO2 and photochemical oxidation of benzyl alcohol (BnOH). The CM-Co successfully converted CO2 to CH4 with faradic efficiency (FE) of 12 %, wherein the yield of the reaction was correlated with the applied potential of electrolysis. Furthermore, the CO2 reduction was carried out in ambient conditions. The photochemical oxidation of benzyl alcohol to benzaldehyde yielded 14 % efficiency, while the BnOH oxidation process was realized with a sunlight (UV+VIS) simulator.

New Book Chapter

Chapter 5: The Non-uniform Sampling of 2D NMR Data

Alexandra Shchukina, Paweł Kasprzak, Mateusz UrbańczykKrzysztof Kazimierczuk

Conventional acquisition of two-dimensional (2D) NMR signals is based on an equidistant sampling in both time dimensions. The expected signal bandwidth determines the minimum sampling rate; the desired spectral resolution determines the maximum sampling time. Together, these two principles contribute to a minimum number of sampling points required for satisfactory spectrum quality. Additionally, it takes a few seconds for nuclei to relax between the acquisition of consecutive FID signals in a 2D interferogram. These three requirements cause 2D NMR experiments to last even tens of hours, in extreme cases. One of the standard methods to avoid lengthy data collection is to omit a significant proportion of sampling points during acquisition and reconstruct them later using dedicated algorithms. Such an approach to data acquisition is known as non-uniform sampling (NUS). The reconstruction algorithms exploit specific features of the measured signal, usually some form of compressibility. In this chapter, we will discuss the fundamentals of NUS methods including (a) motivation to use NUS in 2D NMR; (b) basic math behind the reconstruction algorithms; (c) commonly used distributions of sampling points; and (d) the use of related approaches in diffusometry, relaxometry, serial experiments and pure-shift NMR.

New Book Chapter

Chapter 10: Fast 2D NMR to Investigate Dynamic Events in Biomolecules

F. Bruno, E. Luchinat, Krzysztof Kazimierczuk, E. Ravera

Interactions among biological macromolecules are often transient in nature, and NMR offers a seat in the front row for observing such events under physiological conditions, thanks to its intrinsic atomic resolution and non-destructive nature. In this chapter, we describe the multidimensional methods that can be applied to monitor biologically relevant events in real time. This includes the combination of rapid pulsing methods and the development of bioreactors for monitoring interactions and reactions in vivo, the use of non-uniform sampling for methods to monitor variations in the state of a protein, and an outlook on the use of paramagnetism to increase the time resolution of NMR acquisition.

New Article in Dalton Transactions

Towards hydrogen-rich ionic (NH4)(BH3NH2BH2NH2BH3) and related molecular NH3BH2NH2BH2NH2BH3

Rafał Owarzany, Tomasz Jaroń, Krzysztof Kazimierczuk,  Przemysław J. Malinowski, Wojciech Grochala and Karol J. Fijalkowski

Graphical abstract: Towards hydrogen-rich ionic (NH4)(BH3NH2BH2NH2BH3) and related molecular NH3BH2NH2BH2NH2BH3

Attempts of the synthesis of ionic (NH4)(BH3NH2BH2NH2BH3via a metathetical approach resulted in a mixture of the target compound and partly dehydrogenated molecular NH3BH2NH2BH2NH2BH3 product. The mixed specimen was characterised by NMR and vibrational spectroscopies, and the cocrystal structure was analyzed from powder X-ray diffraction data supported by theoretical density functional theory calculations. The compound crystallises in a P21/c unit cell with the lattice parameters of a = 13.401(11) Å, b = 13.196(8) Å, c = 17.828(12) Å, β = 128.83(4)°, V = 2556(3) Å3 and Z = 16. Despite their impressive hydrogen content, similar to ammonia borane, both title compounds release hydrogen substantially polluted with borazine and traces of ammonia and diborane.

New Article in Journal of Physical Chemistry C

Biphasic NMR of Hyperpolarized Suspensions─Real-Time Monitoring of Solute-to-Solid Conversion to Watch Materials Grow

Ertan Turhan, Christopher Pötzl, Waldemar Keil, Mattia Negroni, Karel Kouřil, Benno Meier, Javier Agustin Romero, Krzysztof Kazimierczuk, Ieva Goldberga, Thierry Azaïs, and Dennis Kurzbach

Nuclear magnetic resonance (NMR) spectroscopy is a key method for the determination of molecular structures. Due to its intrinsically high (i.e., atomistic) resolution and versatility, it has found numerous applications for investigating gases, liquids, and solids. However, liquid-state NMR has found little application for suspensions of solid particles as the resonances of such systems are excessively broadened, typically beyond the detection threshold. Herein, we propose a route to overcoming this critical limitation by enhancing the signals of particle suspensions by >3.000-fold using dissolution dynamic nuclear polarization (d-DNP) coupled with rapid solid precipitation. For the proof-of-concept series of experiments, we employed calcium phosphate (CaP) as a model system. By d-DNP, we boosted the signals of phosphate 31P spins before rapid CaP precipitation inside the NMR spectrometer, leading to the inclusion of the hyperpolarized phosphate into CaP-nucleated solid particles within milliseconds. With our approach, within only 1 s of acquisition time, we obtained spectra of biphasic systems, i.e., micrometer-sized dilute solid CaP particles coexisting with their solution-state precursors. Thus, this work is a step toward real-time characterization of the solid–solution equilibrium. Finally, integrating the hyperpolarized data with molecular dynamics simulations and electron microscopy enabled us to shed light on the CaP formation mechanism in atomistic detail.

New Article in Organic Chemistry Frontiers

Redox-induced Diels–Alder revisited: impact of diene’s oxidation on demanding cycloadditions

Michał J. Jadwiszczak, Piotr J. Leszczyński, Zoran Mazej, Przemysław J. Malinowski, Ewa K. Nawrocka,  Krzysztof Kazimierczuk, Piotr Kwiatkowski, Piotr Połczyński, Magdalena Grochowska-Tatarczak,a Karol J. Fijalkowski, Jarosław Sadło and Wojciech Grochala

Graphical abstract: Redox-induced Diels–Alder revisited: impact of diene's oxidation on demanding cycloadditions

This work presents the joint experimental and computational analysis of Diels–Alder (DA) reactions initiated by one-electron oxidation of dienes: anthracene and buta-1,3-diene derivatives. The use of AgSO4 – a very strong one-electron oxidizer – results in reactions proceeding via radical cationic intermediates rather than neutral species. In the case of anthracenes, yields of reactions are significantly enhanced compared to those for their neutral variants. Importantly, this includes also 9-halogenated anthracenes for which DA reactions reported in the literature are scarce. Surprisingly, diene oxidation has only a limited effect on derivatives of buta-1,3-diene. DFT modelling indicates that radical cations of dienes undergo DA reactions with dienophiles more readily than the corresponding neutral species. For anthracene derivatives, calculated barriers are in qualitative agreement with experimental findings. Careful analysis of the whole catalytic cycle allows us to point out various bottlenecks which are responsible for the poor performance of diene oxidation in reactions involving butadienes.

New Book Chapter

Data Processing Methods: Fourier and Beyond

Vladislav Orekhov, Paweł Kasprzak, Krzysztof Kazimierczuk

This chapter presents a compact overview of both practical and rigorously mathematical aspects of modern NMR signal processing. It discusses the properties of the Fourier transform (FT), which will be later useful to explain the effects of the experimental imperfections and signal processing procedures. The fast FT algorithm, used to calculate the discrete FT requires the same number of points in the input and output. However, one can increase the number of spectral points to any desired value by zero filling , that is, extending the free induction decay by adding artificial data points equal to zero at the end. The quadrature detection in one-dimensional spectra is realized through the acquisition of the two modulations, interpreted as real and imaginary parts of a complex NMR signal. The Projection Theorem is a powerful tool, useful in accelerating NMR experiments of dimensionality three and more.

New article in Magnetic Resonance in Chemistry

The assignment of 11B and 1H resonances in the post-reaction mixture from the dry synthesis of Li(BH3NH2BH2NH2BH3)

Ewa K. Nawrocka,  Agnieszka Prus, Rafał Owarzany, Wiktor Koźmiński, Krzysztof Kazimierczuk, Karol J. Fijalkowski

We report a detailed 1H NMR and 11B NMR study of as synthesised Li(BH3NH2BH2NH2BH3) obtained in a novel dry-synthesis method. A combination of 1D and 2D single- and triple quantum techniques was used for the assignment of all observed signals. Minor side-products and reactants were detected in the product: NH3BH3, Li(NH2BH3), Li(BH4) and two yet unknown salts containing 7-membered chain anions: (BH3NH2BH2NH2BH2NH2BH3)– and (BH(NH2BH3)_3)-. We believe the assignment provided within this study might be helpful when analysing the mixtures containing numerous ammonia borane derivatives which often give overlapping signals which are hard to distinguish.

New article in Journal of Magnetic Resonance Open

Radon peak-picker based on a neural network

Ewa K. Nawrocka,  Daniel Dahan, Krzysztof Kazimierczuk, Przemysław Olbratowski

Serial acquisition of one-dimensional NMR spectra appears in many contexts, e.g. in variable-temperature studies or reaction monitoring. In a conventional approach, the spectra are processed separately, and standard peak-picking is performed in each of them. Yet, when chemical shifts change linearly between spectra, the Radon transform (RT) is more effective than conventional data processing, since it provides sensitivity and resolution gains. RT results in a two-dimensional (2D) spectrum with one dimension corresponding to resonance frequencies and the other to their rates of change. However, the lineshapes in 2D RT spectra are not 2D lorentzians, and thus available spectral peak-pickers cannot effectively deal with them. We propose a solution to this problem — a peak-picker dedicated to 2D RT spectra and based on a U-Net neural network. The software contains a user-friendly graphical interface. We test the program on three challenging serial data sets to demonstrate the robustness to peak overlap, complex multiplet structures and low signal-to-noise ratio.