Crystal‐Structure Determination of Powdered Paramagnetic Lanthanide Complexes by Proton NMR Spectroscopy

Shifts for crystals : Solid‐state NMR spectroscopy can be used for structure determination of microcrystalline paramagnetic solids at natural isotopic abundance. The protocol makes use of paramagnetic effects, measured on suitably recorded ¹H NMR spectra, to define the conformation of a molecule in the lattice and the intermolecular packing in the solid phase. The method is illustrated with a family of lanthanide compounds (see picture).

     

Noncovalent Interactions at Lanthanide Complexes

Lanthanide complexes have attracted a widespread attention due to their structural diversity, as well as multifunctional and tunable properties. The development of lanthanide based functional materials has often relied on the design of the secondary coordination sphere of the corresponding lanthanide complexes. For instance, usually simple lanthanide salts (solvento complexes) do not catalyze effectively organic reactions or provide low yield of the expected product, whereas the presence of a suitable organic ligand with a noncovalent bond donor or acceptor centre (secondary coordination sphere) modifies the symmetry around the metal centre in lanthanide complexes which then successfully can act as catalysts in both homogenous and heterogenous catalysis. In this minireview, we discuss several relevant examples, based on X-ray crystal structure analyses, in which the hydrogen, halogen, chalcogen, pnictogen, tetrel and rare-earth bonds, as well as cation-π, anion-π, lone pair-π, π–π and pancake interactions, are used as a synthon in the decoration of the secondary coordination sphere of lanthanide complexes.     

Bioconjugation of Proteins with a Paramagnetic NMR and Fluorescent Tag

Site‐specific labeling of proteins with lanthanide ions offers great opportunities for investigating the structure, function, and dynamics of proteins by virtue of the unique properties of lanthanides. Lanthanide‐tagged proteins can be studied by NMR, X‐ray, fluorescence, and EPR spectroscopy. However, the rigidity of a lanthanide tag in labeling of proteins plays a key role in the determination of protein structures and interactions. Pseudocontact shift (PCS) and paramagnetic relaxation enhancement (PRE) are valuable long‐range structure restraints in structural‐biology NMR spectroscopy. Generation of these paramagnetic restraints generally relies on site‐specific tagging of the target proteins with paramagnetic species. To avoid nonspecific interaction between the target protein and paramagnetic tag and achieve reliable paramagnetic effects, the rigidity, stability, and size of lanthanide tag is highly important in paramagnetic labeling of proteins. Here 4′‐mercapto‐2,2′: 6′,2′′‐terpyridine‐6,6′′‐dicarboxylic acid (4MTDA) is introduced as a a rigid paramagnetic and fluorescent tag which can be site‐specifically attached to a protein by formation of a disulfide bond. 4MTDA can be readily immobilized by coordination of the protein side chain to the lanthanide ion. Large PCSs and RDCs were observed for 4MTDA‐tagged proteins in complexes with paramagnetic lanthanide ions. At an excitation wavelength of 340 nm, the complex formed by protein–4MTDA and Tb³⁺ produces high fluorescence with the main emission at 545 nm. These interesting features of 4MTDA make it a very promising tag that can be exploited in NMR, fluorescence, and EPR spectroscopic studies on protein structure, interaction, and dynamics.     

Paramagnetic DOSY: An Accurate Tool for the Analysis of the Supramolecular Interactions between Lanthanide Complexes and Proteins

Diffusion ordered NMR is implemented to determine accurately the mobility of paramagnetic tris‐dipicolinate lanthanide complexes that are versatile probes of protein structure. It is shown that diffusion coefficient ratios can be measured with an accuracy of 1 % using a standard BPPLED pulse sequence, which allows for observing significant, though weak, variations when different species are interacting with the paramagnetic compound. We demonstrate that this approach is complementary to classical chemical shift titration experiments, and that it can be applied successfully to probe the supramolecular dynamic interactions between lanthanide complexes and small molecules on the one hand, or to determine rapidly their affinity for a targeted protein.     

Noncovalent Synthesis of Protein Dendrimers

The covalent synthesis of complex biomolecular systems such as multivalent protein dendrimers often proceeds with low efficiency, thereby making alternative strategies based on noncovalent chemistry of high interest. Here, the synthesis of protein dendrimers using a strong but noncovalent interaction between a peptide and complementary protein is proposed as an efficient strategy to arrive at dendrimers fully functionalized with protein domains. The association of S‐peptide to S‐protein results in the formation of an active enzyme (ribonuclease S) and therefore serves as an ideal system to explore this synthetic approach. Native chemical ligation was used to couple four S‐peptides by means of their C‐terminal thioester to a cysteine‐functionalized dendritic scaffold, thus yielding a tetravalent S‐peptide wedge. A fully functional ribonuclease S tetramer was prepared by addition of four equivalents of S‐protein. Biophysical techniques (isothermal titration calorimetry (ITC), surface plasmon resonance (SPR), and mass spectrometry) and an enzymatic activity assay were used to verify the formation of the multivalent complex. The noncovalent synthetic strategy presented here provides access to well‐defined, dynamic, semisynthetic protein assemblies in high yield and is therefore of interest to the field of nanomedicine as well as biomaterials.     

Design Principles and Theory of Paramagnetic Fluorine‐Labelled Lanthanide Complexes as Probes for 19F Magnetic Resonance: A Proof‐of‐Concept Study

The synthesis and spectroscopic properties of a series of CF₃‐labelled lanthanide(III) complexes (Ln=Gd, Tb, Dy, Ho, Er, Tm) with amide‐substituted ligands based on 1,4,7,10‐tetraazacyclododecane are described. The theoretical contributions of the ¹⁹F magnetic relaxation processes in these systems are critically assessed and selected volumetric plots are presented. These plots allow an accurate estimation of the increase in the rates of longitudinal and transverse relaxation as a function of the distance between the Ln^III ion and the fluorine nucleus, the applied magnetic field, and the re‐rotational correlation time of the complex, for a given Ln^III ion. Selected complexes exhibit pH‐dependent chemical shift behaviour, and a pK_a of 7.0 was determined in one example based on the holmium complex of an ortho‐cyano DO3A‐monoamide ligand, which allowed the pH to be assessed by measuring the difference in chemical shift (varying by over 14 ppm) between two ¹⁹F resonances. Relaxation analyses of variable‐temperature and variable‐field ¹⁹F, ¹⁷O and ¹H NMR spectroscopy experiments are reported, aided by identification of salient low‐energy conformers by using density functional theory. The study of fluorine relaxation rates, over a field range of 4.7 to 16.5 T allowed precise computation of the distance between the Ln^III ion and the CF₃ reporter group by using global fitting methods. The sensitivity benefits of using such paramagnetic fluorinated probes in ¹⁹F NMR spectroscopic studies are quantified in preliminary spectroscopic and imaging experiments with respect to a diamagnetic yttrium(III) analogue.     

Insight of the Metal–Ligand Interaction in f-Element Complexes by Paramagnetic NMR Spectroscopy

The magnetic properties of Ln^III and An^III complexes formed with dipicolinate ligands have been studied by NMR spectroscopy. To know precisely the geometries of these complexes, a crystallographic study by single-crystal X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) in solution was performed. Several methods to separate the paramagnetic shifts observed in the NMR spectra were applied to these complexes. Methods using a number of nuclei of the dipicolinate ligands revealed an abrupt change in the geometries of the complexes and a metal–ligand interaction in the middle of the lanthanide series. A study of the variation of the paramagnetic shifts with temperature demonstrated that higher-order terms of the dipolar and contact contributions are required, especially for the lightest Ln^III and almost all the studied An^III. Bleaney's parameters <S_z>_a and relating to the contact and dipolar terms, respectively, were deduced from experimental data and compared with the results of ab initio calculations. Quite a good agreement was found for the temperature dependencies of <S_z>_a and . However, the values obtained from cation magnetic anisotropy calculations showed some discrepancies with the values derived from Bleaney's equation defined for Ln^III. Other parameters, such as the crystal field parameter and the hyperfine constants F_i obtained from the experimental data of the [An(ethyl-dpa)₃]³⁻ complexes (ethyl-dpa=4-ethyl-2,6-dipicolinic acid), are at odds with the assumptions underlying Bleaney's theory.     

Discriminating Halogen‐Bonding from Other Noncovalent Interactions by a Combined NOE NMR/DFT Approach

Herein a combined NOE NMR/DFT methodology to discriminate between adducts held together by halogen bonding (XB) and other noncovalent interactions (non‐XB, such as lone pair/π), based on the determination of the XB donors′ and acceptors′ relative orientation, is proposed. In particular, ¹⁹F,¹H HOESY NMR spectroscopy experiments and DFT calculations on different XB donors, such as perfluorohexyl iodide ( I1 ), iodopentafluorobenzene ( I2 ) and bromopentafluorobenzene ( Br ), combined with different Lewis bases, such as 1,4‐diazabicyclo[2.2.2]octane ( DABCO ) and 2,4,6‐trimethylpyridine ( Me₃Py ), were performed. The results clearly show that in the case DABCO / I1 the XB adduct is practically the only one present in solution, whereas for the other pairs a certain amount of non‐XB adduct is present. Combining DFT and HOESY results, the amount of non‐XB adducts can be roughly quantified under our experimental conditions as 4 % for DABCO / I2 , between 10 and 20 % for Me₃Py / I1 and Me₃Py / I2 , and 44 % for DABCO / Br.     

Lanthanide(III) Complexes with Two Hexapeptides Incorporating Unnatural Chelating Amino Acids: Secondary Structure and Stability

Unnatural metal‐chelating amino acids bearing aminodiacetate side‐chains have been introduced into two hexapeptides to obtain efficient lanthanide‐binding peptides. The synthesis of the enantiopure Fmoc‐Ada_n(tBu)₂‐OH synthons is described with overall yields of 32 and 50 % for n=2 and n=3 side‐chain carbon atoms, respectively. The two peptides AcWAda_nPGAda_nGNH₂ ( P ⁿ ) were synthesized from the protected synthons by standard solid‐phase peptide synthesis. Studies of the lanthanide complexes of the two peptides P ⁿ by luminescence titrations, mass spectrometry, circular dichroism, and solution NMR spectroscopy demonstrate that the Ada_n chain length has a dramatic effect on the complexation properties. Indeed, the flexible compound P³ forms a mononuclear complex of moderate stability (β₁₁=10^9.9), which tends to transform into a binuclear species in the presence of excess of the metal ion. Interestingly, the more compact peptide P² provides stable Ln³⁺ complexes with the exclusive formation of the mononuclear Ln P² adduct. The stability constant of Tb P² is two orders of magnitude higher (β₁₁=10^12.1) than that measured for P³ . The 800 MHz NMR spectrum of the La³⁺ complex of P² evidences a well‐defined type II β‐turn as well as a hydrophobic Trp(indole)–Pro interaction. These interactions exemplify the non‐innocent character of the peptide spacer in the complex La P² as well as the role of a peptide secondary structure in the stabilization of metal complexes.     

Binding Motifs in the Naked Complexes of Target Amino Acids with an Excerpt of Antitumor Active Biomolecule: An Ion Vibrational Spectroscopy Assay

The structures of proton-bound complexes of 5,7-dimethoxy-4H-chromen-4-one ( 1 ) and basic amino acids (AAs), namely, histidine (His) and lysine (Lys), have been examined by means of mass spectrometry coupled with IR ion spectroscopy and quantum chemical calculations. This selection of systems is based on the fact that 1 represents a portion of glabrescione B, a natural small molecule of promising antitumor activity, while His and Lys are protein residues lining the cavity of the alleged receptor binding site. These species are thus a model of the bioactive adduct, although clearly the isolated state of the present study bears little resemblance to the complex biological environment. A common feature of [ 1 +AA+H]⁺ complexes is the presence of a protonated AA bound to neutral 1 , in spite of the fact that the gas-phase basicity of 1 is comparable to those of Lys and His. The carbonyl group of 1 acts as a powerful hydrogen-bond acceptor. Within [ 1 +AA+H]⁺ the side-chain substituents (imidazole group for His and terminal amino group for Lys) present comparable basic properties to those of the α-amino group, taking part to a cooperative hydrogen-bond network. Structural assignment, relying on the comparative analysis of the infrared multiple photon dissociation (IRMPD) spectrum and calculated IR spectra for the candidate geometries, derives from an examination over two frequency ranges: 900–1800 and 2900–3700 cm⁻¹. Information gained from the latter one proved especially valuable, for example, pointing to the contribution of species characterized by an unperturbed carboxylic OH or imidazole NH stretching mode.     

Site‐Specific Labeling of Proteins with a Chemically Stable,High‐Affinity Tag for Protein Study

Site‐specific labeling of proteins with paramagnetic lanthanides offers unique opportunities by virtue of NMR spectroscopy in structural biology. In particular, these paramagnetic data, generated by the anisotropic paramagnetism including pseudocontact shifts (PCS), residual dipolar couplings (RDC), and paramagnetic relaxation enhancement (PRE), are highly valuable in structure determination and mobility studies of proteins and protein–ligand complexes. Herein, we present a new way to label proteins in a site‐specific manner with a high‐affinity and chemically stable tag, 4‐vinyl(pyridine‐2,6‐diyl)bismethylenenitrilo tetrakis(acetic acid) (4VPyMTA), through thiol alkylation. Its performance has been demonstrated in G47C and E64C mutants of human ubiquitin both in vitro and in a crowded environment. In comparison with the published tags, 4VPyMTA has several interesting features: 1) it has a very high binding affinity for lanthanides (higher than EDTA), 2) there is no heterogeneity in complexes with lanthanides, 3) the derivatized protein is stable and potentially applicable to the in situ analysis of proteins.     

Increasing the Chemical‐Shift Dispersion of Unstructured Proteins with a Covalent Lanthanide Shift Reagent

The study of intrinsically disordered proteins (IDPs) by NMR often suffers from highly overlapped resonances that prevent unambiguous chemical‐shift assignments, and data analysis that relies on well‐separated resonances. We present a covalent paramagnetic lanthanide‐binding tag (LBT) for increasing the chemical‐shift dispersion and facilitating the chemical‐shift assignment of challenging, repeat‐containing IDPs. Linkage of the DOTA‐based LBT to a cysteine residue induces pseudo‐contact shifts (PCS) for resonances more than 20 residues from the spin‐labeling site. This leads to increased chemical‐shift dispersion and decreased signal overlap, thereby greatly facilitating chemical‐shift assignment. This approach is applicable to IDPs of varying sizes and complexity, and is particularly helpful for repeat‐containing IDPs and low‐complexity regions. This results in improved efficiency for IDP analysis and binding studies.     

NMR Spectroscopy of Paramagnetic Complexes

Serviceable NMR spectra can, with a few exceptions^[1,6], be recorded for paramagnetic complexes in solution. These spectra provide information about the structure of the complexes and the distribution of the unpaired electrons, and hence also about reactive centers in the molecule. The elucidation of intermolecular and intramolecular exchange phenomena, e.g. the determination of ligand exchange rate constants, the determination of rotation barriers, and the detection of contact complexes in solution, or even of occupation equilibria of the electrons, is possible in this way. It can be seen, therefore, that NMR studies on paramagnetic complexes can be a rich source of information.     

Magnetic Resonance of Paramagnetic Complexes

The line width of the ESR and NMR signals of paramagnetic transition metal complexes is determined mainly by the electron spin-lattice relaxation time τ_e. Values of τ_e greater than 10^?9 lead to ESR spectra that are readily resolved, while values smaller than 10^?11 give NMR spectra having small line widths. Since fast relaxation processes are effective in nearly all transition metal complexes with several unpaired electrons and in all complexes having an orbitally degenerate ground state, the NMR method has a wider scope. The sign and magnitude of the electron-nucleus coupling can be determined with great sensitivity from the NMR spectra, whereas only the magnitude of this interaction can be determined from the ESR spectra. Free spin densities can be found very accurately from the NMR shifts, and the method can therefore be advantageously applied to kinetic measurements, e.g. on short-lived contact complexes.     

Exclusively Heteronuclear NMR Experiments to Obtain Structural and Dynamic Information on Proteins

Provided that ¹³C‐detected NMR experiments are either preferable or complementary to ¹H detection, we report here tools to determine C^α? C′, C′? N, and C^α? H^α residual dipolar couplings on the basis of the CON experiment. The coupling constants determined on ubiquitin are consistent with the subset measured with the ¹H‐detected HNCO sequences. Since the utilization of residual dipolar couplings may depend on the mobility of the involved nuclei, we also provide tools to measure longitudinal and transverse relaxation rates of N and C′. This new set of experiments is a further development of a whole strategy based on ¹³C direct‐detection NMR spectroscopy for the study of biological macromolecules.