Chemical Shift Changes Research Articles

Plant defensins as a model to study the thermostability of surface hydrophobic clusters: The Pisum sativum defensin 2 (Psd2)

Plant defensins (PDs) display a CSαβ-fold that lacks a canonical hydrophobic core. They display almost all hydrophobic residues on the protein surface. The exposed hydrophobic residues form surface clusters stabilized by the vicinity of hydrophilic residues and the hydration shell. Here, we used Psd2 as a model to study the formation and stabilization of these local foldons named surface hydrophobic clusters (SHC). We characterized the temperature dependence of 15N CPMG relaxation dispersion profiles to describe the complex dynamics of Psd2 and indirectly study the thermodynamics of SHCs in PDs. We show a correlation between residues undergoing conformational exchange and the SHCs. Chemical shift changes between the native ground state and the first thermally accessible excited state enabled us to map the major conformational changes in Psd2 conformational equilibrium. The observation of a cold-driven excited state revealed that SHCs are stabilized by hydrophobic contacts, which are exposed at low temperatures, leading to a favorable decrease in enthalpy compensated by an unfavorable entropy reduction. At higher temperatures, we detected another excited conformer that may play a role in membrane-specific interaction, as previously described for other defensins.

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Nuclear magnetic resonance (NMR) spectroscopy is a versatile method for studying folding in peptides, proteins, and their mimetics. In natural entities, the straightforward to obtain metric of proton chemical shift provides residue‐level insights into folded structure as well as dynamics. Rao et al. report the expansion of such methods to protein‐like chains with non‐canonical backbone compositions. Comparison of the NMR properties of a library of artificial residues in random coil and helical contexts reveals systematic chemical shift changes associated with certain residues adopting a helical folded conformation. (doi: 10.1002/pep2.24297) image

Templated Enzymatic Synthesis of δ-Cyclodextrin.

While α-, β-, and γ-cyclodextrin (CD) are ubiquitous hosts employed by supramolecular chemists, δ-CD (formed from nine α-1,4-linked glucopyranose units) has received very little attention. α-, β-, and γ-CD are the major products of the enzymatic breakdown of starch by cyclodextrin glucanotransferase (CGTase), but δ-CD forms only transiently in this reaction, as a minor component of a complex mixture of linear and cyclic glucans. In this work, we show how δ-CD can be synthesized in unprecedented yields by employing a bolaamphiphile template in an enzyme-mediated dynamic combinatorial library of cyclodextrins. NMR spectroscopy studies revealed that δ-CD can thread up to three bolaamphiphiles forming [2]-, [3]-, or [4]-pseudorotaxanes, depending on the size of the hydrophilic headgroup and the length of the alkyl chain axle. Threading of the first bolaamphiphile occurs in fast exchange on the NMR chemical shift time scale, while subsequent threading occurs in slow exchange. To extract quantitative information for 1:2 and 1:3 binding events occurring in mixed exchange regimes, we derived equations for nonlinear curve fitting that take into consideration both the chemical shift changes for species in fast exchange and the integrals for species in slow exchange to determine Ka1, Ka2, and Ka3. Template T1 could be used to direct the enzymatic synthesis of δ-CD due to the cooperative formation of a 1:2 complex─the [3]-pseudorotaxane δ-CD·T12. Importantly, T1 is recyclable. It can be readily recovered from the enzymatic reaction by precipitation and reused in subsequent syntheses enabling preparative-scale synthesis of δ-CD.

Niobium incorporation into rare-earth doped aluminophosphate glasses: Structural characterization, optical properties, and luminescence

Luminescent Rare Earth (RE3+) doped phosphate glasses with molar composition (1-x)(60P2O5 – 15ZnO – 5Al2O3 – 10BaO – 10PbO)-xNb2O5 (x = 0, 10, 20 and 30 wt%) doped with 1.0, 1.2 and 0.3 wt% of Eu2O3, Yb2O3 and Er2O3, respectively, were prepared by conventional melt cooling. The glasses were characterized by optical reflectance, Raman scattering, and multinuclear (31P, 27Al, and 93Nb) solid-state NMR spectroscopy. Monotonic 31P chemical shift changes as a function of Nb2O5 content are consistent with the successive formation of Nb-O-P linkages. Aluminum is found in four-, five-, and six-coordination, with a successive decrease in average coordination number with increasing niobium content, while 93Nb NMR indicates three distinct niobium environments in these glasses. Incorporation of Nb2O5 has the expected effects on refractive index values, optical basicity, optical electronegativity, Urbach Energy, and the indirect bandgap, while RE3+ emission properties are only slightly modified. Under UV excitation, narrow emission bands are observed arising from 5D0→7FJ (J = 0, 1, 2, 3, and 4) transitions of Eu3+. At least two distinct Eu3+ lifetime values are observed, suggesting a spread of different ionic environments within the glass structure. Co-doping with Er3+/Yb3+ promotes emission in the infrared region, with a emission band maximum near 1535 nm and a width of 30.65 nm under excitation at 980 nm. Based on the results, these glasses may be potential candidates for energy conversion from infrared or UV region to the visible region and also infrared solid-state emitters.

Solvent Effects Used for Optimal Simultaneous Analysis of Amino Acids via 19F NMR Spectroscopy.

19F NMR has been extensively used in simultaneous analysis of multicomponent due to its 100% natural isotope abundance, high NMR-sensitivity, and wide-range chemical shifts. The solvent effects are usually observed in NMR spectroscopy and cause large changes in 19F chemical shifts. Herein, we propose that the simultaneous analysis of a complex mixture can be achieved using solvent effects via 19F NMR spectroscopy, such as a mixture solution of amino acids (AAs). AAs are not only cell-signaling molecules, but are also considered as biomarkers of some diseases. Hence, the analysis of AAs is important for human health and the diagnosis of diseases. In this work, the key to the success of sensing 19 biogenic AAs is the use of 2-fluorobenzaldehyde (2FBA) as a highly sensitive derivatizing agent and solvent effects to produce distinguishable 19F NMR signals. As a result, the resolution of 19F NMR spectroscopy of multiple 2FBA-labeled AAs is obviously higher than other methods based on 19F NMR. Moreover, 14 and 18 AAs can be satisfactorily differentiated and unambiguously identified in different complicated media supporting the growth of mammalian cells. Furthermore, quantification of the concentration of AAs can be made, and the limit of detection reaches 10 μM. Our work provides new insights into the simultaneous analysis of a multicomponent mixture based on solvent effects by 19F NMR spectroscopy.

Unravelling the mechanisms of drugs partitioning phenomena in micellar systems via NMR spectroscopy

Despite extensive use of micelles in materials and colloidal science, their supramolecular organization as well as host–guest interactions within these dynamic assemblies are poorly understood. Small guest molecules in the presence of micelles undergo constant exchange between a micellar aggregate and the surrounding solution, posing a considerable challenge for their molecular level characterisation. In this work we reveal the interaction maps between small guest molecules and surfactants forming micelles via novel applications of NMR techniques supported with state-of-the-art analytical methods used in colloidal science. Model micelles composed of structurally distinct surfactants (block non-ionic polymer Pluronic® F-127, non-ionic surfactant Tween 20 or Tween 80, and ionic surfactant sodium lauryl sulphate, SLS) were selected and loaded with model small molecules of biological relevance (i.e. the drugs fluconazole, FLU or indomethacin, IMC) known to have different partition coefficients. Molecular level organization of FLU or IMC within hydrophilic and hydrophobic domains of micellar aggregates was established using the combination of NMR methods (1D 1H NMR, 1D 19F NMR, 2D 1H–1H NOESY and 2D 1H-19F HOESY, and the multifrequency-STD NMR) and corroborated with molecular dynamics (MD) simulations. This is the first application of multifrequency-STD NMR to colloidal systems, enabling us to elucidate intricately detailed patterns of drug/micelle interactions in a single NMR experiment within minutes. Importantly, our results indicate that flexible surfactants, such as block copolymers and polysorbates, form micellar aggregates with a surface composed of both hydrophilic and hydrophobic domains and do not follow the classical core–shell model of the micelle. We propose that the magnitude of changes in 1H chemical shifts corroborated with interaction maps obtained from DEEP-STD NMR and 2D NMR experiments can be used as an indicator of the strength of the guest-surfactant interactions. This NMR toolbox can be adopted for the analysis of broad range of colloidal host–guest systems from soft materials to biological systems.

New organic ionic plastic crystals based on pyrrolidinium dication for a solid‐phase electrolyte

AbstractA series of 1,4‐bis(N‐alkylpyrrolidinium)butane salts combined with Br−, I−, PF6−, and Tf2N− anions were newly designed and synthesized. In nonpolar CDCl3 solution, the axial and equatorial proton peaks of the bis‐pyrrolidinium cation ring are distinguished in 1H NMR. Also, the strengths of ion paring could be estimated from the 1H NMR chemical shift changes of the bridge and pyrrolidinium proton peaks. 1,4‐Bis(N‐hepthylpyrrolidinium)butane I− is an organic ionic plastic crystal showing the lowest fusion entropy value (ΔSf = 3.4 J K·mol−1). Softer crystalline morphologies were found by polarized optical microscope images at plastic crystal phase of each sample and the results were corresponding to differential scanning calorimetry results. 1,4‐Bis(N‐ethylpyrrolidinium)butane Tf2N− showed the softest crystal phase. Ionic conductivity changes and electrochemical stabilities of the bis‐pyrrolidinium PF6− and Tf2N− salts were also measured, and they were stable up to 4.3 V (vs. Li/Li+) and expected to be applied as an electrolyte component.

Crystal growth, phase transition, and nuclear magnetic resonance of organic-inorganic hybrid perovskite NH2(CH3)2CdCl3.

Understanding the physicochemical properties of organic-inorganic hybrid materials is essential to promote their applications. In this study, a single crystal of NH2(CH3)2CdCl3 was grown, and it exhibited a monoclinic structure. Its phase transition temperatures were 460 and 470 K, and it showed sufficient thermal stability. The changes in the NMR chemical shifts of each atom in the crystal with increasing temperature were determined; the chemical shift of 1H of NH2 in the NH2(CH3)2 cation changed with temperature, which was correlated to the changes in the chemical shift of 14N in NH2. The change in 113Cd chemical shifts indicate the change of six Cl atoms around Cd in CdCl6. Therefore, the change in the coordination geometry of CdCl6 is attributed to the change in the N-H⋯Cl hydrogen bond between the NH2(CH3)2 cation and CdCl6 anion. In addition, the 13C activation energies Ea obtained from the spin-lattice relaxation time T1ρ values are smaller than those of the 1H Ea values, suggesting that is free compared to 1H in the cation. We believe that this study furthers our fundamental understanding of organic-inorganic hybrid materials to promote their practical solar cell applications.

Diorganotin(IV) complexes with hydroxamic acids derivatives of some histone deacetylases inhibitors

Organotin(IV) compounds show great potential as antitumor metallodrugs with lower toxicity and higher antiproliferative activity. Histone deacetylases (HDAC) inhibitors are characterised by high bioavailability and low toxicity. In this research, the two novel octahedral organotin(IV) complexes of physiologically active hydroxamate-based ligands, N-hydroxy-4-phenylbutanamide (HL1) and N-hydroxy-2-propylpentanamide (HL2), have been prepared and characterized using FTIR, 1H-, 13C- and 119Sn-NMR spectroscopy. Particular emphasis was put on the binding characteristics of ligands. The structures were additionally analysed by the density functional theory at B3LYP-D3BJ/6- -311++G(d,p)(H,C,N,O)/LanL2DZ(Sn) level. The theoretical IR and NMR spectra were compared to the spectroscopic data, and it was concluded that the predicted structures described well the experimental ones. The stability of different isomers of HL1 and HL2 was assessed by the natural bond orbital analysis, and the importance of intramolecular hydrogen bond was outlined. The interactions between donor atoms and Sn were investigated and correlated with the changes in chemical shift and the wavenumbers of characteristic vibrations.

Processing on crystal growth, structure, thermal property, and nuclear magnetic resonance of organic-inorganic hybrid perovskite type [NH3(CH2)6NH3]ZnCl4 crystal.

Organic-inorganic hybrid compounds have recently gained significant attention in recent years due to their diverse applications. Herein, [NH3(CH2)6NH3]ZnCl4 crystals were grown, and their triclinic structure, phase transition temperature (TC = 408 K), and high thermal stability (Td = 584 K) was determined using X-ray diffraction (XRD), differential scanning calorimetry, and thermogravimetry measurements. By analyzing the chemical in response to temperature changes, we observed that the coordination geometry around 1H and 13C were highly symmetric below TC, whereas their symmetry was lowered above TC. The change of N-H⋯Cl hydrogen bond from XRD results and the change of 14N NMR chemical shifts was due to the changes to the coordination geometry of Cl- around Zn2+ in the ZnCl4 anion. The activation energy of 1H was three times greater than that of 13C, and this result indicates that the energy transfer of 13C was easier than those of 1H. We compared the results for [NH3(CH2)nNH3]ZnCl4 (n = 6) studied here with those for n = 2, 3, 4, and 5 obtained from previous studies. The characteristics of the length of CH2 in the methylene chain are expected to be used for potential applications in the near future.

Preparation, characterization, and structural studies of new sodium gallium tungstate phosphate glasses

A new glass forming region in the quaternary system Na2O-P2O5-WO3-Ga2O3 along the composition line (NaPO3)80-x(Ga2O3)20(Na2WO4)x (x = 0, 5, 10, 15, 20 and 25 mol%) has been prepared and characterized by X-ray diffraction, Differential Scanning Calorimetry (DSC), Raman scattering and 31P, 23Na and 71Ga nuclear magnetic single and double resonance NMR techniques. The partial substitution of the NaPO3 component by Na2WO4 produces a significant increase of molar volume (decreased oxygen packing density), whereas the glass transition temperatures Tg pass through a shallow maximum near x = 10 to 15. While in the x = 0 sample the structure is dominated by Q1 units linked to gallium in four-, five- and six-coordination, the gradual substitution of phosphate by tungstate significantly affects network reconstruction, eliminating P-O-P linkages, the concentration of which is found to be greatly diminished above the x = 10 level. While the structure of these glasses is dominated by Q0 units, connected to both gallium and tungstate species, 71Ga{31P} REDOR data suggest significant decreases in the extent of gallium-phosphorus connectivity with increasing Na2WO4 content. Finally, monotonic changes in both 23Na chemical shifts and 23Na-31P second moment values, M2(Na-P), indicate that the anionic surroundings of the sodium ions evolve from a pure phosphate to a mixed phosphate/tungstate environment.

Structural Parameters of the Interaction between Ciprofloxacin and Human Topoisomerase-II β Enzyme: Toward New 19F NMR Chemical Shift Probes

New tools for cancer diagnosis are being studied since early diagnosis can be crucial for a successful treatment. In this context, the use of NMR probes constitutes an efficient method of diagnosis. In this study, we investigated the use of ciprofloxacin to indirectly label the overexpression of topoisomerase-II enzymes by changes in 19F NMR chemical shifts of ciprofloxacin. Increased topoisomerase-II expression has been associated with cancer occurrence, mainly with aggressive forms of breast cancer, thus constituting a promising molecular target for new tumor cell identifiers. Using DFT calculations, we performed a spectroscopy analysis of ciprofloxacin in different chemical environments and evaluated the solvent and enzymatic effects. Our results show that ciprofloxacin forms a stable complex with the enzyme, and the main intermolecular interactions between ciprofloxacin and human topoisomerase-IIβ are hydrogen bonds, followed by π-π stacking and electrostatic interactions. Additionally, a shift of 6.04 ppm occurs in the 19F NMR signal when ciprofloxacin interacts with the human topoisomerase-IIβ enzyme, and this parameter may be an indirect marker indicating the overexpression of these enzymes in the body.

Nanobody GPS by PCS: An Efficient New NMR Analysis Method for G Protein Coupled Receptors and Other Large Proteins.

NMR chemical shift changes can report on the functional dynamics of biomacromolecules in solution with sizes >1 MDa. However, their interpretation requires chemical shift assignments to individual nuclei, which for large molecules often can only be obtained by tedious point mutations that may interfere with function. We present here an efficient pseudocontact shift NMR method to assign biomacromolecules using bound antibodies tagged with lanthanoid DOTA chelators. The stability of the antibody allows positioning the DOTA tag at many surface sites, providing triangulation of the macromolecule nuclei at distances >60 Å. The method provides complete assignments of valine and tyrosine 1H-15N resonances of the β1-adrenergic receptor in various functional forms. The detected chemical shift changes reveal strong forces exerted onto the backbone of transmembrane helix 3 during signal transmission, which are absorbed by its electronic structure. The assignment method is applicable to any soluble biomacromolecule for which suitable complementary binders exist.

Chemical Shifts of Artificial Monomers Used to Construct Heterogeneous-Backbone Protein Mimetics in Random Coil and Folded States.

The construction of protein-sized synthetic chains that blend natural amino acids with artificial monomers to create so-called heterogeneous-backbones is a powerful approach to generate complex folds and functions from bio-inspired agents. A variety of techniques from structural biology commonly used to study natural proteins have been adapted to investigate folding in these entities. In NMR characterization of proteins, proton chemical shift is a straightforward to acquire, information-rich metric that bears directly on a variety of properties related to folding. Leveraging chemical shift to gain insight into folding requires a set of reference chemical shift values corresponding to each building block type (i.e., the 20 canonical amino acids in the case of natural proteins) in a random coil state and knowledge of systematic changes in chemical shift associated with particular folded conformations. Although well documented for natural proteins, these issues remain unexplored in the context of protein mimetics. Here, we report random coil chemical shift values for a library of artificial amino acid monomers frequently used to construct heterogeneous-backbone protein analogues as well as a spectroscopic signature associated with one monomer class, β3-residues bearing proteinogenic side chains, adopting a helical folded conformation. Collectively, these results will facilitate the continued utilization of NMR for the study of structure and dynamics in protein-like artificial backbones.

Intra-ring proton transfer effect on the Structure-NLO property relationships of phthalocyanine derivatives

Based on the phthalocyanine, four models (1–4) are designed to explore the intra-ring proton transfer effect on structure–property relationships. The results show that small differences in structure bring fascinating changes in nucleus-independent chemical shifts (NICS) values, anisotropy of the induced current density (AICD), natural population analysis (NPA) charge, electrostatic potential (ESP), UV–vis absorption spectrum as well as unit sphere representation (USR). Significantly, the largest static first hyperpolarizability βtot value (1.47 × 104) of 4 is approximately 15 times larger than that (8.98 × 102 au) of 1 due to the intra-ring proton transfer regulating conjugation degree of the conjugation section. Furthermore, the dynamic first hyperpolarizability βHRS at the wavelengths λ = 1907, 1460 nm is elaborated in detail. We hope that the present work may evoke the possibility to probe into a promising field for nonlinear optics (NLO) application.

Growth, structure, phase transition, thermal properties, and structural dynamics of organic–inorganic hybrid [NH3(CH2)5NH3]ZnCl4 crystal

In this study, the physicochemical properties of [NH3(CH2)5NH3]ZnCl4 crystals were investigated using X-ray diffraction (XRD), Fourier transform infrared spectroscopy, differential scanning calorimetry (DSC), thermogravimetric analysis, and nuclear magnetic resonance (NMR). The crystals at 300 K had a monoclinic structure with C2/c space group and lattice constants are a = 21.4175 Å, b = 7.3574 Å, c = 19.1079 Å, β = 120.5190°, and Z = 8. Three endothermic peaks at 256, 390, and 481 K were observed in the DSC curve. From the single-crystal XRD patterns, powder XRD patterns, and optical microscopy results based on the temperature change, the phase transition and melting temperatures were determined to be 390 and 481 K, respectively. NMR studies indicated no change in 1H chemical shifts, but a change in the chemical shifts for C2, located between C1 and C3 of the cation at 340 K. Increase in molecular motion caused an increase in the spin–lattice relaxation time, T1ρ, at low spinning rates, under magic-angle spinning rate conditions. This crystal showed a minor change in the N−H···Cl hydrogen bond, related to the coordination geometry of the ZnCl4 anion.

Absolute thermometry using hyperpolarized 129 Xe free-induction decay and spin-echo chemical-shift imaging in rats.

To implement and test variants of chemical shift imaging (CSI) acquiring both free induction decays (FIDs) showing all dissolved-phase compartments and spin echoes for specifically assessing Xe in lipids in order to perform precise lipid-dissolved Xe MR thermometry in a rat model of general hypothermia. Imaging was performed at 2.89 T. of Xe in lipids was determined in one rat by fitting exponentials to decaying signals of global spin-echo spectra. Four rats (conventional CSI) and six rats (turbo spectroscopic imaging) were scanned at three time points with core body temperature 37/34/37 C. Lorentzian functions were fit to spectra from regions of interest to determine the water-referenced chemical shift of lipid-dissolved Xe in the abdomen. Absolute Xe-derived temperature was compared to values from a rectal probe. Global of Xe in lipids was determined as . Friedman tests showed significant changes of chemical shift with time for both sequence variants and both FID and spin-echo acquisitions. Mean and SD of Xe and rectal probe temperature differences were found to be (FID) and (spin echo) for conventional CSI as well as (FID) and (spin echo) for turbo spectroscopic imaging. Xe MRI using conventional CSI and turbo spectroscopic imaging of lipid-dissolved Xe enables precise temperature measurements in the rat's abdomen using both FID and spin-echo acquisitions with acquisition of spin echoes enabling most precise temperature measurements.

Formulating Ternary Inclusion Complex of Sorafenib Tosylate Using β-Cyclodextrin and Hydrophilic Polymers: Physicochemical Characterization and In Vitro Assessment.

Sorafenib tosylate (SFNT) is the first-line drug for hepatocellular carcinoma. It exhibits poor solubility leading to low oral bioavailability subsequently requiring intake of large quantities of drug to exhibit desired efficacy. The present investigation was aimed at enhancing the solubility and dissolution rate of SFNT using complexation method. The binary inclusion complex was prepared with β-cyclodextrin (β-CD). The molecular docking studies confirmed the hosting of SFNT into hydrophobic cavity of β-CD, while the phase solubility studies revealed the stoichiometry of complexation with a stability constant of 735.8M-1. Theternary complex was prepared by combining the SFNT-β-CD complex with PEG-6000 and HPMC polymers.The results from ATR-IR studies revealed no interaction between drug and excipients. The decreased intensities in ATR-IR peaks and changes in chemical shifts from NMR of SFNT in complexes indicate the possibility of SFNT hosting into the hydrophobic cavity of β-CD.The disappearance of SFNT peak in DSC and XRD studies revealed the amorphization upon complexation.The ternary complexes exhibited improved in vitro solubility (17.54µg/mL) compared to pure SFNT (0.19µg/mL) and binary inclusion complex (1.52µg/mL). The dissolution profile of ternary inclusion complex in 0.1 N HCl was significantly higher compared to binary inclusion complex and pure drug. In cytotoxicity studies, the ternary inclusion complex has shown remarkable effect than the binary inclusion complex and pure drug on HepG2 cell lines.

Structures and Oxidation Properties of Phenylene-Bridged Diazacycloalkanes: Ring Size Effects on Structures and Properties.

Phenylenediamine derivatives have been investigated as functional molecules because of their characteristic oxidation properties. In this study, phenylene-bridged diazacycloalkanes, that is, C10, C12, and C14, in which numbers indicate the lengths of a side chain, were synthesized, and the effects of the macroring size on their structures and oxidation properties were investigated. X-ray crystallography revealed that the structures around the nitrogen atoms were remarkably dependent on the chain lengths. The benzene plane of C10 is arranged almost perpendicular to the macroring to avoid steric contact. However, the benzene plane of C14 and alkyl frame were co-planar. Stabilization resulting from conjugation was comparable to destabilization caused by macroring strain according to DFT calculations. Structural differences between C10 and C14 caused changes in the NMR chemical shifts of the inner methylene protons and first oxidation potentials in solution. Notably, the properties of C12 can be analyzed as those of distributed structures, which is of interest with respect to exploiting the metastable structure of the molecules. The observed relationships between the steric structures and properties can facilitate the design of functional molecules containing phenylenediamine moieties.

The measurement of binding affinities by NMR chemical shift perturbation

We have carried out chemical shift perturbation titrations on three contrasting proteins. The resulting chemical shifts have been analysed to determine the best way to fit the data, and it is concluded that a simultaneous fitting of all raw shift data to a single dissociation constant is both the most accurate and the most precise method. It is shown that the optimal weighting of 15N chemical shifts to 1H chemical shifts is protein dependent, but is around the consensus value of 0.14. We show that chemical shift changes of individual residues can be fit to give residue-specific affinities. Residues with affinities significantly stronger than average are found in close contact with the ligand and are suggested to form a rigid contact surface, but only when the binding involves little conformational change. This observation may be of value in analysing binding and conformational change.