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Proton detection in solid state NMR is continuously developing and allows one to gain new insights in structural biology. Overall, this progress is a result of the synergy between hardware development, new NMR methodology and new isotope labeling strategies, to name a few factors. Even though current developments are rapid, it is worthwhile to summarize what can currently be achieved employing proton detection in biological solids. We illustrate this by analysing the signal-to-noise ratio (SNR) for spectra obtained for a microcrystalline α-spectrin SH3 domain protein sample by (i) employing different degrees of chemical dilution to replace protons by incorporating deuterons in different sites, by (ii) variation of the magic angle spinning (MAS) frequencies between 20 and 110 kHz, and by (iii) variation of the static magnetic field B0. The experimental SNR values are validated with numerical simulations employing up to 9 proton spins. Although in reality a protein would contain far more than 9 protons, in a deuterated environment this is a sufficient number to achieve satisfactory simulations consistent with the experimental data. The key results of this analysis are (i) with current hardware, deuteration is still necessary to record spectra of optimum quality; (ii) 13CH3 isotopomers for methyl groups yield the best SNR when MAS frequencies above 100 kHz are available; and (iii) sensitivity increases with a factor beyond B0 3/2 with the static magnetic field due to a transition of proton-proton dipolar interactions from a strong to a weak coupling limit.

In this manuscript, we provide an analytical description of the performance of the cross-polarization experiment, including linear ramp and adiabatic tangential sweep modifications, using effective Hamiltonians and simple rotations in 3D space. It is shown that radiofrequency field inhomogeneity induces a reduction of the transfer efficiency at increasing MAS frequencies for both the ramp and the adiabatic CP experiments. The effect depends on the ratio of the dipolar coupling constant and the sample rotation frequency. In particular, our simulations show that for small dipolar couplings (1 kHz) and ultrafast MAS (above 100 kHz) the transfer efficiency is below 40 % when extended contact times up to 20 ms are used and relaxation losses are ignored. New recoupling and magnetization transfer techniques that are designed explicitly to account for inhomogeneous RF fields are needed.

Solid state (ss-) 27Al NMR is one of the most valuable tools for experimental characterization of zeolites, owing to its high sensitivity and the detailed structural information which can be extracted from the spectra. Unfortunately, the interpretation of ss-NMR is complex, and the determination of aluminum distributions remains generally unfeasible. As a result, computational modelling of 27Al ss-NMR spectra has grown increasingly popular as a means to support experimental characterization. However, a number of simplifying assumptions are commonly made in NMR modelling, several of which are not fully justified. In this work, we systematically evaluate the effects of various common models on the prediction of 27Al NMR chemical shifts in zeolites CHA and MOR. We demonstrate the necessity of operando modelling; in particular, taking into account the effects of water loading, temperature and the character of the charge-compensating cation. We observe that conclusions drawn from simple, high symmetry model systems such as CHA do not transfer well to more complex zeolites and can lead to qualitatively wrong interpretations of peak positions, Al assignment and even the number of signals. We use machine learning regression to develop a simple yet robust relationship between chemical shift and local structural parameters in Al-zeolites. This work highlights the need for sophisticated models and high-quality sampling in the field of NMR modelling and provides correlations which allow for the accurate prediction of chemical shifts from dynamical simulations.

2D-to-3D transformation of layered zeolite precursors (e.g., MCM-22P, IPC-1P, pre-FER) into three-dimensional frameworks in combination with metal encapsulation has been recently shown as efficient synthetic strategy to stabilize metal clusters in a zeolite matrix. Even though, tailoring the number of acid sites in a zeolite support and its effect on the properties of thus prepared metal@zeolite materials (e.g., metal dispersion and catalytic activity) remained unrevealed. Herein, we report on the synthesis of Pd@MCM-22 catalysts via modified 2D-to-3D transformation method, which allows to achieve close to nominal loading of noble metal (e.g., 0.1, 0.3, 0.8 wt.%) by time-separation of swelling of MCM-22P layered zeolite precursor and subsequent incorporation with metal. In turn, alternating Si/Al ratio of MCM-22P (e.g., Si/Al = 15, 20, 30) enabled the preparation of Pd@MCM-22 catalysts with variable concentration of acid sites (0.28 – 0.55 mmol/g), while not affecting the Pd dispersion. Decrease in Pd dispersion with increasing metal loading was accompanied with declining catalytic activity in a model reaction of selective hydrogenation of nitro-group in 3-nitrotoluene: 0.1 wt. % Pd (dispersion = 52.6%, reaction rate = 21.2 mol·g-1Pd·h-1) > 0.3 wt. % Pd (9.6 mol·g-1Pd·h-1) > 0.8 wt. % Pd (23.2%, 3.7 mol·g-1Pd·h-1). The results of this study reveal that the reported synthesis strategy can be successfully used to confine small metal nanoparticles in a zeolite matrix while tuning its acidic characteristics for designing bifunctional metal-acidic catalysts.

The model of counterion-induced metallacarborane aggregation in water was verified on sodium bis(1,2-dicarbollide), one of the most studied examples of metallacarboranes. This case study introduces a novel approach in anionic boron cluster self-assembly that resembles the behavior of polyoxometalate nanoions. The key prerequisite of the counterion binding to the aggregates is the strongly uneven charge distribution of cobalt bis(dicarbollide) clusters. Simultaneously, the size of the counterion should fit into the void between the metallacarborane clusters within the aggregate. In consequence, compact pentamers with two bound sodium cations via Coulombic-driven assembly are formed. This behavior cannot be explained solely by the hydrophobic effect─the paradigm of metallacarborane aggregation in the current literature. The pentamers can merge into bigger nanostructures via the second aggregation mechanism that sheds light on the complex behavior of metallacarboranes in water. The proof-of-concept of counterion-induced metallacarborane aggregation and the proposed total description of the self-assembly via the two-process model are results of calorimetry modeling, quantum chemistry calculations, and molecular dynamics simulations.

Hydrophobic blocks of amphiphilic block copolymers often form glassy micellar cores at room temperature with a rigid structure that limits their applications as nanocapsules for targeted delivery. Nevertheless, we prepared and analyzed core/shell micelles with a soft core, formed by a self-assembled block copolymer consisting of a hydrophobic block and a polycation block, poly(lauryl acrylate)-block-poly(trimethyl-aminoethyl acrylate) (PLA-QPDMAEA), in aqueous solution. By light and small-angle neutron scattering, by transmission electron microscopy and by fluorescence spectroscopy, we showed that these core/shell micelles are spherical and cylindrical with a fluid-like PLA core and a positively charged outer shell and that they can encapsulate and release hydrophobic solutes. Moreover, after mixing these PLA-QPDMAEA core/shell micelles with another diblock copolymer, consisting of a hydrophilic block and a polyanion block, namely poly(ethylene oxide)-block-poly(methacrylic acid) (PEO-PMAA), we observed the formation of novel vesicle-like multicompartment structures containing both soft hydrophobic and interpolyelectrolyte (IPEC) layers. By combining small-angle neutron scattering with self-consistent field modeling, we confirmed the formation of these complex vesicle-like structures with a swollen PEO core, an IPEC inner layer, a PLA soft layer, an IPEC outer layer and a loose PEO corona. Thus, these multicompartment micelles with fluid and IPEC layers and a hydrophilic corona may be used as nanocapsules with several tunable properties, including the ability to control the thickness of each layer, the charge of the IPEC layers and the stability of the micelles, to deliver both hydrophobic and multivalent solutes.

Recently, proton-detected magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) spectroscopy has become an attractive tool to study the structure and dynamics of insoluble proteins at atomic resolution. The sensitivity of the employed multidimensional experiments can be systematically improved when both transversal components of the magnetization are transferred simultaneously after an evolution period. The method of preservation of equivalent pathways has been explored in solution-state NMR; however, it does not find widespread application due to relaxation issues connected with increased molecular size. We present here for the first time heteronuclear transverse mixing sequences for correlation experiments at moderate and fast MAS frequencies. Optimal control allows to boost the signal-to-noise ratio (SNR) beyond the expected factor of 2 for each indirect dimension. In addition to the carbon-detected sensitivity-enhanced 2D NCA experiment, we present a novel proton-detected, doubly sensitivity-enhanced 3D hCANH pulse sequence for which we observe a 3-fold improvement in SNR compared to the conventional experimental implementation. The sensitivity gain turned out to be essential to unambiguously characterize a minor fibril polymorph of a human lambda-III immunoglobulin light chain protein that escaped detection so far.

The application of the Assembly–Disassembly–Organization–Reassembly (ADOR) protocol to the synthesis of germanosilicate zeolites has become a major milestone in material design by enabling the prep...

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their charge regulation and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Our model predicts differences in the charge states between oligopeptides and monomeric amino acids, showing that conformational flexibility and electrostatic interactions between weak acid and base side chains play a key role in the charge regulation. By comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the charge state of various peptide sequences. Ultimately, our model is the first step towards understanding the charge regualtion in flexible disordered proteins, and towards using predictive bottom-up design of responsive ampholytes to tailor theirproperties as a function of charge and pH.

Naphthoquinones isolated from Quambalaria cyanescens (quambalarines) are natural pigments possessing significant cytotoxic and antimicrobial properties. Determining the structure of naphthoquinone compounds is important for the understanding of their biological activities and the informed synthesis of related analogues. Identifying quambalarines is challenging, because they contain a hydroxylated naphthoquinone scaffold and have limited solubility. Here, we report a detailed structural study of quambalarine derivatives, which form strong intramolecular hydrogen bonds (IMHBs) that enable the formation of several tautomers; these tautomers may complicate structural investigation due to their fast interconversion. To investigate tautomeric equilibria and identify new quambalarines, we complemented the experimental NMR spectroscopy data with density functional theory (DFT) calculations.

Zeolites with particles of nm-scale size and restricted aggregation propensity were designed by decoration of zeolite surface with specific functional groups to address the problem of irreversible aggregation of respective nanoparticles. Highly crystalline MFI nano zeolites synthesized using hydrothermal method were functionalized with silanes of different nature (monodentate vs. polydentate, hydrophobic vs. hydrophilic) to investigate the influence of the type of surface functional groups on the stability of zeolite nanoparticles against aggregation in solution, accessibility of acid sites located in zeolite framework, and catalytic properties of resulting hybrid materials. The as-prepared materials were characterized by XRD, DLS, nitrogen adsorption, and adsorption of acetonitrile followed by FTIR, solid state 29Si and 27Al NMR, ICP-OES, TEM. Finally, we investigated the catalytic performance of designed materials in acylation of p-xylene to demonstrate that surface functionalization does not lead to deterioration of catalytic activity of the zeolite nanoparticles. Characterization data and catalytic results confirmed the improved stability of prepared nanoparticles with reasonable accessibility of acid sites. This finding can be used for preparation of aggregation-resistant zeolites dispersible in liquid-phase reaction mixtures in order to mimic homogeneous catalytic systems.

A first series of fluorinated [n]helical compounds (n=5 and 6) with the dihydroindenofluorene scaffold was prepared in 5 or 9 (octafluorinated dihydroindenofluorene) steps and their photophysical properties were determined. Rh-catalyzed intramolecular [2+2+2] cyclotrimerization of triyndiols, which were prepared in a modular fashion from simple starting material such as fluorinated haloarylcarbaldehydes, to the intermediate [n]helical dihydroindeno[2,1-c]fluorene-5,8-diols was the crucial synthetic step and proceeded with high efficacy. Their further transformation gave the desired selectively fluorinated bispirodihydroindeno[2,1-c]fluorenes. Their absorption and emission spectra were recorded. The fluorescence quantum yields were up to 92 % and the emission maxima were red-shifted in comparison with their non-fluorinated counterparts (386-413 nm).

Radio-frequency (rf) field inhomogeneity is a common problem in NMR which leads to non-ideal rotations of spins in parts of the sample. Often, a physical volume restriction of the sample is used to reduce the effects of rf-field inhomogeneity, especially in solid-state NMR where spacers are inserted to reduce the sample volume to the centre of the coil. We show that band-selective pulses in the spin-lock frame can be used to apply B1-field selective inversions to spins that experience selected parts of the rf-field distribution. Any frequency band-selective pulse can be used for this purpose, but we chose the family of I-BURP pulses (Geen and Freeman, 1991) for the measurements demonstrated here. As an example, we show that the implementation of such pulses improves homonuclear frequency-switched Lee–Goldburg decoupling in solid-state NMR., Magnetic Resonance, 1 (2), ISSN:2699-0016

Radio-frequency field inhomogeneity is one of the most common imperfections in NMR experiments. They can lead to imperfect flip angles of applied radio-frequency (rf) pulses or to a mismatch of resonance conditions, resulting in artefacts or degraded performance of experiments. In solid-state NMR under magic angle spinning (MAS), the radial component becomes time-dependent because the rf irradiation amplitude and phase is modulated with integer multiples of the spinning frequency. We analyse the influence of such time-dependent MAS-modulated rf fields on the performance of some commonly used building blocks of solid-state NMR experiments. This analysis is based on analytical Floquet calculations and numerical simulations, taking into account the time dependence of the rf field. We find that, compared to the static part of the rf field inhomogeneity, such time-dependent modulations play a very minor role in the performance degradation of the investigated typical solid-state NMR experiments., Magnetic Resonance, 2 (1), ISSN:2699-0016

Peptides containing amino acids with ionisable side chains represent a typical example of weak ampholytes, that is, molecules with multiple titratable acid and base groups, which generally exhibit charge regulating properties upon changes in pH. Charged groups on an ampholyte interact electrostatically with each other, and their interaction is coupled to conformation of the (macro)molecule, resulting in a complex feedback loop. Their charge-regulating properties are primarily determined by the pKA of individual ionisable side-chains, modulated by electrostatic interactions between the charged groups. The latter is determined by the amino acid sequence in the peptide chain. In our previous work we introduced a simple coarse-grained model of a flexible peptide. We validated it against experiments, demonstrating its ability to quantitatively predict charge on various peptides in a broad range of pH. In the current work, we investigated two types of peptide sequences: diblock and alternating, each of them consisting of an equal number of amino acids with acid and base side-chains. We showed that changing the sequence while keeping the same overall composition has a profound effect on the conformation, whereas it practically does not affect total charge on the peptide. Nevertheless, the sequence significantly affects the charge state of individual groups, showing that the zero net effect on the total charge is a consequence of unexpected cancellation of effects. Furthermore, we investigated how the difference between the pKA of acid and base side chains affects the charge and conformation of the peptide, showing that it is possible to tune the charge-regulating properties by following simple guiding principles based on the pKA and on the amino acid sequence. Our current results provide a theoretical basis for understanding of the complex coupling between the ionisation and conformation in flexible polyampholytes, including synthetic polymers, biomimetic materials and biological molecules, such as intrinsically disordered proteins, whose function can be regulated by changes in the pH.

Naphthoquinones isolated from

Peptides containing amino acids with ionisable side chains represent a typical example of weak ampholytes, that is, molecules with multiple titratable acid and base groups, which generally exhibit charge regulating properties upon changes in pH. Charged groups on an ampholyte interact electrostatically with each other, and their interaction is coupled to conformation of the (macro)molecule, resulting in a complex feedback loop. Their charge-regulating properties are primarily determined by the pKA of individual ionisable side-chains, modulated by electrostatic interactions between the charged groups. The latter is determined by the amino acid sequence in the peptide chain. In our previous work we introduced a simple coarse-grained model of a flexible peptide. We validated it against experiments, demonstrating its ability to quantitatively predict charge on various peptides in a broad range of pH. In the current work, we investigated two types of peptide sequences: diblock and alternating, each of them consisting of an equal number of amino acids with acid and base side-chains. We showed that changing the sequence while keeping the same overall composition has a profound effect on the conformation, whereas it practically does not affect total charge on the peptide. Nevertheless, the sequence significantly affects the charge state of individual groups, showing that the zero net effect on the total charge is a consequence of unexpected cancellation of effects. Furthermore, we investigated how the difference between the pKA of acid and base side chains affects the charge and conformation of the peptide, showing that it is possible to tune the charge-regulating properties by following simple guiding principles based on the pKA and on the amino acid sequence. Our current results provide a theoretical basis for understanding of the complex coupling between the ionisation and conformation in flexible polyampholytes, including synthetic polymers, biomimetic materials and biological molecules, such as intrinsically disordered proteins, whose function can be regulated by changes in the pH.

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their ionisation response and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Differences in ionisation response between oligopeptides and monomeric amino acids showed that electrostatic interactions between weak acid and base side chains play a key role in oligopeptide ionisation, as predicted by our model. Moreover, by comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the ionisation response and electrophoretic mobilities of various peptide sequences. Ultimately, our model is the first step towards using predictive bottom-up design of responsive ampholytes to tailor their properties as a function of charge and pH.

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their ionisation response and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Differences in ionisation response between oligopeptides and monomeric amino acids showed that electrostatic interactions between weak acid and base side chains play a key role in oligopeptide ionisation, as predicted by our model. Moreover, by comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the ionisation response and electrophoretic mobilities of various peptide sequences. Ultimately, our model is the first step towards using predictive bottom-up design of responsive ampholytes to tailor their properties as a function of charge and pH.

Boron-rich particles with the boron fraction ca.10-20 wt % of controllable shape and size that can be easily prepared via simple ion co-assembly are promising material for tumor treatment by boron neutron capture therapy. Electroneutral, dynamic core-shell polymeric nanoparticles were prepared by co-assembly of cationic PEO-block-PGEA diblock copolymer with sodium closo-dodecaborate, Na2 [B12 H12 ]. This is the first example of polymer nanoparticles based on [B12 H12 ]2- nano-ion pairing. The high [B12 H12 ]2- loading is proven by calorimetry at physiological salt concentration. As a result of rational design, rod-, worm- and sphere-like particles were produced and further tested using human glioblastoma and cervical carcinoma cell lines. Rod-like particles yielded the highest internalization capability in all tested cell lines.

This chapter provides a number of examples of numerical simulations in NMR. Main focus is on advanced simulations in solid-state NMR using the widely used SIMPSON simulation package. The chapter starts with introductory examples providing a gentle introduction to SIMPSON and various concepts of solid-state NMR. Following the introduction is a demonstration on how SIMPSON can interact with SIMMOL for setting up spin systems of protein spin systems. Finally, we demonstrate how the versatile Tcl interface of SIMPSON can be used to expand the capabilities of SIMPSON, here exemplified by simulations of chemical exchange. The examples demonstrate that SIMPSON may be regarded a ‘virtual NMR spectrometer’.

The shape of nanoparticles is a key factor for efficient delivery of a cargo to cells. We prepared nanogels of controllable shape suitable for boron delivery from cationic triblock terpolymers poly(ethylene oxide)-b-poly(2-(N, N, N’, N’-tetramethyl guanidium) ethyl acrylate)-b-poly(2-(dimethylamino)ethyl acrylate), PEO-b-PGEA-b-PDMAEA, and closo-dodecaborate nano-ions. The physical crosslinking based on ion pairing of closo-dodecaborate with PGEA blocks led to preassembled nanogels of spherical and wormlike shape. PDMAEA blocks were later chemically crosslinked with 1,2-bis(2-iodoethoxy)ethane, BIEE, to maximize the boron loadings and the nanogels stability. Depending on the blocks lengths, a shape transition was observed after the chemical crosslinking. As confirmed by flow cytometry and confocal microscopy in cervical carcinoma cell lines in vitro, the wormlike chemically crosslinked nanogels were internalized the most efficiently.

[Abstract] The solution dynamics of the Eu(III) complexes of H4dota (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetracarboxylic acid) and H5do3ap (1,4,7,10-tetraazacyclododecane-4,7,10-tris(carboxymethyl)-1-methylphosphonic acid, bound in both monoprotonated and fully deprotonated forms) were investigated by using a combination of NMR measurements and DFT calculations. In solution, an equilibrium between the square antiprismatic (SAP) and twisted-square antiprismatic isomers (TSAP) of these complexes is present. These two isomers interconvert by rotation of the pendant arms or inversion of the cyclen chelate rings. 1D EXSY NMR spectra were used to determine these exchange rates with unprecedented accuracy. It was found that the two processes occur at different rates. Additional variable-temperature measurements allowed determination of the corresponding activation parameters for the two processes. DFT calculations were then used to obtain mechanistic information at the molecular level. The results show that the cyclen inversion pathway involves stepwise inversion of the four chelate rings formed upon metal ion coordination. However, the arm rotation process may operate through a synchronous rotation of the pendant arms or a stepwise mechanism depending on the system. A mixed cluster-continuum approach was required to improve the agreement between experimental and calculated activation parameters for the arm rotation process. The obtained results will aid the design of MRI contrast agents. Furthermore, the methodology developed in this work can be further applied for the investigation of other dynamic paramagnetic systems, e.g. peptides with Ln(III) probes or natively paramagnetic metalloproteins. Czech Science Foundation; 16-03156S Charles University; 1076016 Czech Republic. Ministry of Education; LTC 170607 Ministerio de Economía y Competitividad; CTQ2013-43243-P

Seasonal changes in the contents of water-soluble carbon (WSC) and hot water-extractable carbon (HWC) were investigated in the organic and underlying mineral horizons of soils in a common garden experiment at 40 years old post-mining sites. The sites were planted with alder, oak, or spruce or overgrown by a spontaneous succession dominated by willow. Sampling was performed at 2-month intervals from April 2013 until March 2014. Two major peaks in WSC in the mineral horizons were evident: one in early summer and another in late autumn or winter. The peaks were more pronounced at sites with deciduous trees than with spruce. According to liquid-state 1 H NMR spectroscopy, hot-water extracts (HWE) from the mineral horizons had a higher relative content of aliphatic components in summer, while the winter samples had a larger relative abundance of carbohydrates. The results suggest that the peaks had different sources of carbon. RDA with variation partitioning showed that both tree species and season significantly affected the composition of HWE, but that tree species was most important, explaining 67.3% of data variability. However, the trends in temporal variation in concentrations and chemical composition were remarkably similar at the studied sites suggesting the changes were mainly induced by seasons.

This is the first experimental evidence that both self-assembly and surface activity are common features of all water-soluble boron cluster compounds. The solution behavior of anionic polyhedral boranes (sodium decaborate, sodium dodecaborate, and sodium mercaptododecaborate), carboranes (potassium 1-carba-dodecaborate), and metallacarboranes {sodium [cobalt bis(1,2-dicarbollide)]} was extensively studied, and it is evident that all the anionic boron clusters form multimolecular aggregates in water. However, the mechanism of aggregation is dependent on size and polarity. The series of studied clusters spans from a small hydrophilic decaborate-resembling hydrotrope to a bulky hydrophobic cobalt bis(dicarbollide) behaving like a classical surfactant. Despite their pristine structure resembling Platonic solids, the nature of anionic boron cluster compounds is inherently amphiphilic-they are stealth amphiphiles.

Isothermal titration calorimetry (ITC) is an apt tool for a total thermodynamic description of self-assembly of atypical amphiphiles such as anionic boron cluster compounds (COSAN) in water. Global fitting of ITC enthalpograms reveals remarkable features that differentiate COSAN from classical amphiphiles: (i) strong enthalpy and weak entropy contribution to the free energy of aggregation, (ii) low degree of counterion binding, and (iii) very low aggregation number, leading to deviations from the ideal closed association model. The counterion condensation obtained from the thermodynamic model was compared with the results of 7Li DOSY NMR of Li[COSAN] micelles, which allows direct tracking of Li cations. The basic thermodynamic study of COSAN alkaline salt aggregation was complemented by NMR and ITC experiments in dilute Li/NaCl and acetonitrile aqueous solutions of COSAN. The strong affinity of acetonitrile molecules to COSAN clusters was microscopically investigated by all-atomic molecular dynamics simulations. The impact of ionic strength on COSAN self-assembling was comparable to the behavior of classical amphiphiles, whereas even a small amount of acetonitrile cosolvent has a pronounced nonclassical character of COSAN aggregation. It demonstrates that large self-assembling changes are triggered by traces of organic solvents.

The hyaluronate receptor CD44 plays role in cell adhesion and migration and is involved in tumor metastasis. The extracellular domain of CD44 comprises the hyaluronate-binding domain (HABD) and the membrane-proximal stem region; the short intracellular portion interacts with adaptor proteins and triggers signaling pathways. Binding of hyaluronate to CD44 HABD induces an allosteric conformational change, which results in CD44 shedding. A poorly characterized epitope in human CD44 HABD is recognized by the murine monoclonal antibody MEM-85, which cross-blocks hyaluronate binding to CD44 and also induces CD44 shedding. MEM-85 is of therapeutic interest, as it inhibits growth of lung cancer cells in murine models. In this work, we employed a combination of biophysical methods to determine the MEM-85 binding epitope in CD44 HABD and to provide detailed insight into the mechanism of MEM-85 action. In particular, we constructed a single-chain variable fragment (scFv) of MEM-85 as a tool for detailed characterization of the CD44 HABD–antibody complex and identified residues within CD44 HABD involved in the interaction with scFv MEM-85 by NMR spectroscopy and mutational analysis. In addition, we built a rigid body model of the CD44 HABD–scFv MEM-85 complex using a low-resolution structure obtained by small-angle X-ray scattering. The MEM-85 epitope is situated in the C-terminal part of CD44 HABD, rather than the hyaluronate-binding groove, and the binding of MEM-85 induces a structural reorganization similar to that induced by hyaluronate. Therefore, the mechanism of MEM-85 cross-blocking of hyaluronate binding is likely of an allosteric, relay-like nature.

Numerical simulations are finding an increasing use as means to design optimal experiments for NMR and MRI applications. This is ascribed to increasing challenges in designing experiments by analytic means due to increasing complexity in the involved nuclear spin systems (including anisotropic nuclear spin interactions) and the wish to exploit advanced instrumentation optimally under the consideration of sample geometry, sample rotation, gradient fields, and inhomogeneities in radio-frequency and static fields. This chapter describes how to set up the objective function as well as different optimization methods operating on levels of Bloch equations, density operators, and propagators with particular focus on optimal control theory. Examples are given within liquid- and solid-state NMR spectroscopy and MRI.

In this study, we present a method for the detection of n-3 fatty acid (n-3 FA) signals using MRS in adipose tissue in vivo. This method (called oMEGA-PRESS) is based on the selective detection of the CH3 signal of n-3 FA using the MEGA-PRESS (MEshcher–GArwood Point-RESolved Spectroscopy) J-difference editing technique. We optimized the envelope shape and frequency of spectral editing pulses to minimize the spurious co-editing and incomplete subtraction of the CH3 signal of other FAs, which normally obscure the n-3 FA CH3 signal in MR spectra acquired using standard PRESS techniques. The post-processing of the individual data scans with the phase and frequency correction before data subtraction and averaging was implemented to further improve the quality of in vivo spectra. The technique was optimized in vitro on lipid phantoms using various concentrations of n-3 FA and examined in vivo at 3 T on 15 healthy volunteers. The proportion of n-3 FA estimated by the oMEGA-PRESS method in phantoms showed a highly significant linear correlation with the n-3 FA content determined by gas chromatography. The signal attributed to n-3 FA was observed in all subjects. Comparisons with the standard PRESS technique revealed an enhanced identification of the n-3 FA signal using oMEGA-PRESS. The presented method may be useful for the non-invasive quantification of n-3 FA in adipose tissue, and could aid in obtaining a better understanding of various aspects of n-3 FA metabolism. Copyright © 2014 John Wiley & Sons, Ltd.

The synthesis of a series of star-shaped C 3 -symmetric amines and their inclusion complexation properties toward α-, β-, γ-cyclodextrins and their permethylated derivatives has been described. The star molecules comprise of 1,3,5-trisubstited benzene core and the points formed by (alkylamino)methyl or 4-((alkylamino)methyl)phenyl groups. The modes of host–guest interaction were studied by UV–Vis spectroscopy, ITC, 1H NMR and 2D-NMR (NOESY). It was found that star molecules containing (tert-butylamino)methyl, (adamantan-1-ylamino)methyl, 4-((isopropylamino)methyl)phenyl, 4-((tert-butylamino)methyl)phenyl and protonated 4-((adamantan-1-ylamino)methyl)phenyl points form strong host–guest complexes with β-cyclodextrin. It was also proved that the largest C 3 -symmetric guest can form complexes with β-cyclodextrin with stoichiometry 3 which is required for construction of dendrimer supramolecular structures. None of the investigated amines forms a strong complex with permethylated cyclodextrins.

Cytosolic dNT-1 nucleotidase plays a key role in the homeostasis of pyrimidine deoxyribonucleotides in mammalian cells. The enzyme is responsible for the dephosphorylation of physiological substrates as well as nucleoside analogues that are used in antiviral and anticancer therapies, therefore selective inhibition of the dNT-1 nucleotidase activity may lead to an increase in efficacy of this type of therapeutic compounds. Here, we report the backbone ¹H, ¹³C and ¹⁵N assignments for the 47 kDa dNT-1 dimer, which will be used for structural characterisation of dNT-1 complexes with small molecule inhibitors obtained through modification of pyrimidine nucleotide scaffolds or optimisation of successful binders obtained from the screening of fragment libraries.

Preparation of two benzylic bis(phosphonic acids) modified with primary amine or carboxylic acid groups on the benzene ring is described. These compounds were prepared and characterized in the form of both bis(phosphonate) tetraesters and corresponding free acids. The phosphonic acid esters are suitable for further derivation, mainly for conjugation through the amide bond. Mild conversion of the bis(phosphonate) esters to free acids using trimethylsilylbromide allowed to work with functional groups sensitive to conditions of acidic and/or alkaline hydrolysis. Three bis(phosphonate)-containing fluorescent probes were prepared from the building blocks, utilizing amide and sulfamide bonds as spacers. Dyes containing the dansyl group, rhodamine B, and fluorescein were chosen due to their common availability and low cost. The prepared bis(phosphonate)-building blocks and modified fluorescent probes were used for adsorption studies with hydroxyapatite, the commonly used model of bone tissue. Sorption ability of the prepared bis(phosphonate) compounds was similar to that of pamidronate.

Kinetically inert Ni(ii) complexes of N(1),N(8)-bis(2,2,2-trifluoroethyl)cyclams with hydrogen atoms or phosphonic acid groups in the N(4),N(11)-positions show significant (19)F NMR relaxation rate enhancement useful for 19-fluorine MRI imaging.

Multiple-spin-echo experiments have found wide use in nuclear magnetic resonance spectroscopy. In particular, the Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence is used to determine transverse relaxation times T(2). Herein it is demonstrated, both theoretically and experimentally, that for a pair of almost identical spins-1/2 the experimental setup can have a profound effect on the observed spin dynamics. It is shown that, in the case of dipolar relaxation, the measured T(2) values can roughly vary between the limits of identical and unlike spins, just depending on the repetition rate of pi pulses with respect to chemical shift separation. Such an effect can, in the extreme narrowing regime, amount to a 50% difference.

The self-assembly of metallacarboranes, a peculiar family of compounds exhibiting surface activity and resembling molecular-scale Pickering stabilizers, has been investigated by comparison to the micellization of sodium dodecylsulfate (SDS). These studies have shown that molecules without classical amphiphilic topology but with an inherent amphiphilic nature can behave similarly to classical surfactants. As shown by NMR techniques, the self-assembly of both metallacarboranes and SDS obey a closed association model. However, the aggregation of metallacarboranes is found to be enthalpy-driven, which is very unusual for classical surfactants. Possible explanations of this fact are outlined.

In this Letter, we demonstrate the use of separated local-field NMR spectroscopy under magic-angle spinning conditions as a means of studying molecular reorientation in solid inclusion compounds. S ...

This thesis discusses several different methods offered by solution and solid state nuclear magnetic resonance for investigation of host-guest complexes and their constituents. The presented methods were used especially (but not exclusively) to address rotational dynamics of the bound guest in different molecular systems.The main part of this thesis presents results of a project that combines and compares solution and solid state NMR investigations of inclusion complexes of a spherical, cage-like molecule of cryptophane-E with small neutral guest molecules like chlorinated methanes. Strong and weak bonding of these host--guest systems is studied in solution using C-13 NMR relaxation and in the crystalline form, using advanced dipolar recoupling methods as well as deuterium NMR lineshape and spin relaxation analysis. Comparison of the results from all the techniques suggests very similar guest behaviour regardless of the physical state of the system. Residing inside the cavity, CHCl3 behaves almost as an integral part of cryptophane-E, whereas the reorientation of CH2Cl2 is influenced only slightly by weak interactions with its host. Molecular flexibility of thiacalix[4]arenes, a new class of the very popular calixarene family, was also studied by C-13 NMR relaxation in solution. Calixarenes are widely used in supramolecular chemistry as building blocks of receptors to many guest molecules.The thesis is completed with examination of a β-cyclodextrin (β-CD) inclusion complex with adamantanecarboxylic acid (AdCA) where changes of translational and rotational diffusion properties of the guest were monitored during complexation with the host. By means of C-13 NMR relaxation it was found that despite the high association constant (which suggests strong interactions between the two molecules) AdCA rotates fast around the β-CD symmetry axis inside the cavity. This motion is made possible by the spherical shape of the adamantyl moiety and the whole system resembles to a "molecular bearing".