New article in Analytical Chemistry

Enhanced Nuclear Magnetic Resonance Spectroscopy with Isotropic Mixing as a Pseudodimension

Dariusz Gołowicz, Alexandra Shchukina, Krzysztof Kazimierczuk

Chemical analysis based on liquid-state nuclear magnetic resonance spectroscopy exploits numerous observables, mainly chemical shifts, relaxation rates, and internuclear coupling constants. Regarding the latter, the efficiencies of internuclear coherence transfers may be encoded in spectral peak intensities. The dependencies of these intensities on the experimental parameter that influences the transfer, for example, mixing time, are an important source of structural information. Yet, they are costly to measure and difficult to analyze. Here, we show that peak intensity build-up curves in two-dimensional total correlation spectroscopy (2D TOCSY) experiments may be quickly measured by employing nonuniform sampling and that their analysis can be effective if supported by quantum mechanical calculations. Thus, such curves can be used to form a new, third pseudodimension of the TOCSY spectrum. Similarly to the other two frequency dimensions, this one also resolves ambiguities and provides characteristic information. We show how the approach supports the analysis of a fragment of protein Tau Repeat-4 domain. Yet, its potential applications are far broader, including the analysis of complex mixtures or other polymers.

 

New article in Dalton Transactions

Design of a D3h-symmetry prismatic tris-(ferrocene-1,1′-diyl) molecular cage bearing boronate ester linkages

Maurycy Krzyżanowski, Anna M. Nowicka, Krzysztof Kazimierczuk, Krzysztof Durka, Sergiusz Luliński and Artur Kasprzak

Graphical abstract: Design of a D3h-symmetry prismatic tris-(ferrocene-1,1′-diyl) molecular cage bearing boronate ester linkages

This paper presents a simple, highly selective, and efficient (isolated yield of 68%) synthesis of a novel D3h-symmetry prismatic tris-(ferrocene-1,1′-diyl) organic cage (FcB-cage) by incorporating a boronate ester as a linkage motif. 1,1′-Diboronated derivatives of ferrocene and 2,3,6,7,10,11-hexahydroxytriphenylene (HHTP) were used as the starting materials. The synthesized cage was comprehensively characterized by spectroscopic and microscopic methods, powder X-ray diffraction, thermogravimetry and voltammetry. Cyclic voltammetry analysis revealed the electronic communication between the ferrocene units of the FcB-cage. In addition, to better understand the mechanism behind the synthesis of such a cage, as well as its geometric properties, we performed DFT calculations.

New article in Microporous and Mesoporous Materials

Dipole-dipole interactions of sulfone groups as a tool for self-assembly of a 2D Covalent Organic Framework derived from a non-linear diboronic acid

Krzysztof Durka, Krzysztof Kazimierczuk, Sergiusz Luliński

The utility of the nonlinear diboronic acid 2, obtained from 3,7-dibromodibenzo[b,d]thiophene 5,5-dioxide 1, for the preparation of Covalent Organic Frameworks was investigated. Despite significant deviation of boronic groups in 2 from the colinear arrangement, a highly crystalline porous material DBSO-COF was obtained by dehydrative polycondensation with 2,3,6,7,10,11-hexahydroxytriphenylene (HHTP) using a solvothermal approach. Subsequent PXRD studies supported by periodic DFT modelling revealed the formation of the 2D honeycomb-type lattice with eclipsed stacking model. The antiparallel orientation of neighboured layers is strongly favoured owing to dipole-dipole and CH⋯O interactions of sulfone moieties. This gives the net stabilization energy of 45 kJ mol−1 per single sulfone motif, being primarily responsible for the effective formation of the ordered network and strongly contributing to its thermodynamic stability. The morphology was analyzed by SEM which revealed that the material forms uniform in size ca. 40 × 150 nm rod-like nano-crystallites. The Grand Canonical Monte Carlo (GCMC) simulation performed on a single nanoparticle of DBSO-COF allowed to reproduce the experimental isotherm. It also showed that N2 molecules are mostly located close to the CH bonds, while they are repulsed by sulfone groups. Apart from increasing the scope of useful boronic linkers beyond centrosymmetric structures, it was demonstrated that the presence of guest molecules in a porous network should be taken into account in order to obtain a more accurate prediction of porosity parameters.

New Article in Chemistry of Materials

Diazonium-Based Covalent Molecular Wiring of Single-Layer Graphene Leads to Enhanced Unidirectional Photocurrent Generation through the p-doping Effect

Margot Jacquet, Silvio Osella, Ersan Harputlu, Barbara Pałys, Monika Kaczmarek, Ewa K. Nawrocka, Adam A. Rajkiewicz, Marcin Kalek, Paweł P. Michałowski, Bartosz Trzaskowski, C. Gokhan Unlu, Wojciech Lisowski, Marcin Pisarek, Krzysztof Kazimierczuk, Kasim Ocakoglu, Agnieszka Więckowska, and Joanna Kargul

 

Development of robust and cost-effective smart materials requires rational chemical nanoengineering to provide viable technological solutions for a wide range of applications. Recently, a powerful approach based on the electrografting of diazonium salts has attracted a great deal of attention due to its numerous technological advantages. Several studies on graphene-based materials reveal that the covalent attachment of aryl groups via the above approach could lead to additional beneficial properties of this versatile material. Here, we developed the covalently linked metalorganic wires on two transparent, cheap, and conductive materials: fluorine-doped tin oxide (FTO) and FTO/single-layer graphene (FTO/SLG). The wires are terminated with nitrilotriacetic acid metal complexes, which are universal molecular anchors to immobilize His6-tagged proteins, such as biophotocatalysts and other types of redox-active proteins of great interest in biotechnology, optoelectronics, and artificial photosynthesis. We show for the first time that the covalent grafting of a diazonium salt precursor on two different electron-rich surfaces leads to the formation of the molecular wires that promote p-doping of SLG concomitantly with a significantly enhanced unidirectional cathodic photocurrent up to 1 μA cm–2. Density functional theory modeling reveals that the exceptionally high photocurrent values are due to two distinct mechanisms of electron transfer originating from different orbitals/bands of the diazonium-derived wires depending on the nature of the chelating metal redox center. Importantly, the novel metalorganic interfaces reported here exhibit minimized back electron transfer, which is essential for the maximization of solar conversion efficiency.

New Article in Microporous and Mesoporous Materials

Dipole-dipole interactions of sulfone groups as a tool for self-assembly of a 2D Covalent Organic Framework derived from a non-linear diboronic acid

Krzysztof Durka, Krzysztof Kazimierczuk, Sergiusz Luliński

 

The utility of the nonlinear diboronic acid 2, obtained from 3,7-dibromodibenzo[b,d]thiophene 5,5-dioxide 1, for the preparation of Covalent Organic Frameworks was investigated. Despite significant deviation of boronic groups in 2 from the colinear arrangement, a highly crystalline porous material DBSO-COF was obtained by dehydrative polycondensation with 2,3,6,7,10,11-hexahydroxytriphenylene (HHTP) using a solvothermal approach. Subsequent PXRD studies supported by periodic DFT modelling revealed the formation of the 2D honeycomb-type lattice with eclipsed stacking model. The antiparallel orientation of neighboured layers is strongly favoured owing to dipole-dipole and CH⋯O interactions of sulfone moieties. This gives the net stabilization energy of 45 kJ mol−1 per single sulfone motif, being primarily responsible for the effective formation of the ordered network and strongly contributing to its thermodynamic stability. The morphology was analyzed by SEM which revealed that the material forms uniform in size ca. 40 × 150 nm rod-like nano-crystallites. The Grand Canonical Monte Carlo (GCMC) simulation performed on a single nanoparticle of DBSO-COF allowed to reproduce the experimental isotherm. It also showed that N2 molecules are mostly located close to the CH bonds, while they are repulsed by sulfone groups. Apart from increasing the scope of useful boronic linkers beyond centrosymmetric structures, it was demonstrated that the presence of guest molecules in a porous network should be taken into account in order to obtain a more accurate prediction of porosity parameters.

New Article in Magnetic Resonance

NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR

Yulia Pustovalova, Frank Delaglio, D. Levi Craft, Haribabu Arthanari, Ad Bax, Martin Billeter, Mark J. Bostock, Hesam Dashti, D. Flemming Hansen, Sven G. Hyberts, Bruce A. Johnson, Krzysztof Kazimierczuk, Hengfa Lu, Mark Maciejewski, Tomas M. Miljenović, Mehdi Mobli, Daniel Nietlispach, Vladislav Orekhov, Robert Powers, Xiaobo Qu, Scott Anthony Robson, David Rovnyak, Gerhard Wagner, Jinfa Ying, Matthew Zambrello, Jeffrey C. Hoch, David L. Donoho, and Adam D. Schuyler

 

Although the concepts of nonuniform sampling (NUS​​​​​​​) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge 4 decades ago (Bodenhausen and Ernst1981; Barna and Laue1987), it is only relatively recently that NUS has become more commonplace. Advantages of NUS include the ability to tailor experiments to reduce data collection time and to improve spectral quality, whether through detection of closely spaced peaks (i.e., “resolution”) or peaks of weak intensity (i.e., “sensitivity”). Wider adoption of these methods is the result of improvements in computational performance, a growing abundance and flexibility of software, support from NMR spectrometer vendors, and the increased data sampling demands imposed by higher magnetic fields. However, the identification of best practices still remains a significant and unmet challenge. Unlike the discrete Fourier transform, non-Fourier methods used to reconstruct spectra from NUS data are nonlinear, depend on the complexity and nature of the signals, and lack quantitative or formal theory describing their performance. Seemingly subtle algorithmic differences may lead to significant variabilities in spectral qualities and artifacts. A community-based critical assessment of NUS challenge problems has been initiated, called the “Nonuniform Sampling Contest” (NUScon), with the objective of determining best practices for processing and analyzing NUS experiments. We address this objective by constructing challenges from NMR experiments that we inject with synthetic signals, and we process these challenges using workflows submitted by the community. In the initial rounds of NUScon our aim is to establish objective criteria for evaluating the quality of spectral reconstructions. We present here a software package for performing the quantitative analyses, and we present the results from the first two rounds of NUScon. We discuss the challenges that remain and present a roadmap for continued community-driven development with the ultimate aim of providing best practices in this rapidly evolving field. The NUScon software package and all data from evaluating the challenge problems are hosted on the NMRbox platform.

New Article in Journal of Biomolecular NMR

Clustered sparsity and Poisson-gap sampling

Paweł Kasprzak, Mateusz Urbańczyk, Krzysztof Kazimierczuk

figure 1

Non-uniform sampling (NUS) is a popular way of reducing the amount of time taken by multidimensional NMR experiments. Among the various non-uniform sampling schemes that exist, the Poisson-gap (PG) schedules are particularly popular, especially when combined with compressed-sensing (CS) reconstruction of missing data points. However, the use of PG is based mainly on practical experience and has not, as yet, been explained in terms of CS theory. Moreover, an apparent contradiction exists between the reported effectiveness of PG and CS theory, which states that a “flat” pseudo-random generator is the best way to generate sampling schedules in order to reconstruct sparse spectra. In this paper we explain how, and in what situations, PG reveals its superior features in NMR spectroscopy. We support our theoretical considerations with simulations and analyses of experimental data from the Biological Magnetic Resonance Bank (BMRB). Our analyses reveal a previously unnoticed feature of many NMR spectra that explains the success of ”blue-noise” schedules, such as PG. We call this feature “clustered sparsity”. This refers to the fact that the peaks in NMR spectra are not just sparse but often form clusters in the indirect dimension, and PG is particularly suited to deal with such situations. Additionally, we discuss why denser sampling in the initial and final parts of the clustered signal may be useful.

New article in RSC Advances

Variable-temperature NMR spectroscopy for metabolite identification in biological materials

Ewa K. Nawrocka, Mateusz Urbańczyk, Kamil Koziński, Krzysztof Kazimierczuk

Nuclear magnetic resonance is a “workhorse technique” used in metabolomics, complementary to mass spectrometry. Unfortunately, only the most basic NMR methods are sensitive enough to allow fast medical screening. The most common of them, a simple 1H NMR, suffers from low dispersion of resonance frequencies, which often hampers the identification of metabolites. In this article we show that 1H NMR spectra contain previously overlooked parameters potentially helpful in metabolite identification, namely the rates of temperature-induced changes of chemical shifts. We prove that they are reproducible between various metabolite mixtures and can be determined quickly when Radon transform is used to process the data.

New article in Nanoscale

Development of a universal conductive platform for anchoring photo- and electroactive proteins using organometallic terpyridine molecular wiresResolution enhancement in NMR spectra by deconvolution with compressed sensing reconstruction

Margot Jacquet, Miriam Izzo, Silvio Osella, Sylwia Kozdra, Paweł P. Michałowski, Dariusz Gołowicz, Krzysztof Kazimierczuk, Maciej T. Gorzkowski, Adam Lewera, Marian Teodorczyk, Bartosz Trzaskowski, Rafał Jurczakowski, Daniel T. Gryko ORCID and Joanna Kargul

Graphical abstract: Development of a universal conductive platform for anchoring photo- and electroactive proteins using organometallic terpyridine molecular wires

The construction of an efficient conductive interface between electrodes and electroactive proteins is a major challenge in the biosensor and bioelectrochemistry fields to achieve the desired nanodevice performance. Concomitantly, metallo-organic terpyridine wires have been extensively studied for their great ability to mediate electron transfer over a long-range distance. In this study, we report a novel stepwise bottom-up approach for assembling bioelectrodes based on a genetically modified model electroactive protein, cytochrome c553 (cyt c553) and an organometallic terpyridine (TPY) molecular wire self-assembled monolayer (SAM). Efficient anchoring of the TPY derivative (TPY-PO(OH)2) onto the ITO surface was achieved by optimising solvent composition. Uniform surface coverage with the electroactive protein was achieved by binding the cyt c553 molecules via the C-terminal His6-tag to the modified TPY macromolecules containing Earth abundant metallic redox centres. Photoelectrochemical characterisation demonstrates the crucial importance of the metal redox centre for the determination of the desired electron transfer properties between cyt and the ITO electrode. Even without the cyt protein, the ITO-TPY nanosystem reported here generates photocurrents whose densities are 2-fold higher that those reported earlier for ITO electrodes functionalised with the photoactive proteins such as photosystem I in the presence of an external mediator, and 30-fold higher than that of the pristine ITO. The universal chemical platform for anchoring and nanostructuring of (photo)electroactive proteins reported in this study provides a major advancement for the construction of efficient (bio)molecular systems requiring a high degree of precise supramolecular organisation as well as efficient charge transfer between (photo)redox-active molecular components and various types of electrode materials.