Lanthanide triple-stranded helical complexes with a substituted 2,6-pyridinedicarboxylateElectronic supplementary information (ESI) available: analytical, IR and luminescence data, contact and dipolar shifts, calculated Cartesian co-ordinate for the EuIII complex, plots of chemical shifts for protons H8, H9 versus the chemical shift of proton H2. See http://www.rsc.org/suppdata/dt/b1/b104448f/

2001 ◽  
pp. 3084-3091 ◽  
Author(s):  
Carlos Platas-Iglesias ◽  
Claude Piguet ◽  
Nicolas André ◽  
Jean-Claude G. Bünzli
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Supplementary Information

scholarly journals Structure of Nanobody Nb23

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3567
Author(s):  
Mathias Percipalle ◽  
Yamanappa Hunashal ◽  
Jan Steyaert ◽  
Federico Fogolari ◽  
Gennaro Esposito
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Solution Structure ◽  
Chemical Shifts ◽  
Molecular Size ◽  
Side Chain ◽  
3D Nmr ◽  
Target Antigen ◽  
Internuclear Distances ◽  
2D And 3D

Background: Nanobodies, or VHHs, are derived from heavy chain-only antibodies (hcAbs) found in camelids. They overcome some of the inherent limitations of monoclonal antibodies (mAbs) and derivatives thereof, due to their smaller molecular size and higher stability, and thus present an alternative to mAbs for therapeutic use. Two nanobodies, Nb23 and Nb24, have been shown to similarly inhibit the self-aggregation of very amyloidogenic variants of β2-microglobulin. Here, the structure of Nb23 was modeled with the Chemical-Shift (CS)-Rosetta server using chemical shift assignments from nuclear magnetic resonance (NMR) spectroscopy experiments, and used as prior knowledge in PONDEROSA restrained modeling based on experimentally assessed internuclear distances. Further validation was comparatively obtained with the results of molecular dynamics trajectories calculated from the resulting best energy-minimized Nb23 conformers. Methods: 2D and 3D NMR spectroscopy experiments were carried out to determine the assignment of the backbone and side chain hydrogen, nitrogen and carbon resonances to extract chemical shifts and interproton separations for restrained modeling. Results: The solution structure of isolated Nb23 nanobody was determined. Conclusions: The structural analysis indicated that isolated Nb23 has a dynamic CDR3 loop distributed over different orientations with respect to Nb24, which could determine differences in target antigen affinity or complex lability.

Circular dichroism spectra of tetraamminecobalt(III) complexes of amino alcohols

1978 ◽  
Vol 31 (11) ◽  
pp. 2399 ◽  
Author(s):  
CJ Hawkins ◽  
GA Lawrance ◽  
JA Palmer
Keyword(s):  
Circular Dichroism ◽  
Chemical Shift ◽  
Chemical Shifts ◽  
Amino Alcohols ◽  
Circular Dichroism Spectra ◽  
Chemical Shift Difference ◽  
Solvent Dependence ◽  
Cotton Effects ◽  
Circular Dichroïsm ◽  
Chiral Amino Alcohols

The circular dichroism spectra are reported for tetraamminecobalt(III) complexes with the chiral amino alcohols 2-aminopropan-1-ol, 2- aminobutan-1-ol, 1-aminopropan-2-ol, 2-amino-1-phenyl-ethanol, ψ- ephedrine and ephedrine with the alcohol groups protonated (OH) and deprotonated (O-). The solvent dependence of the chemical shifts of the NH protons was investigated to determine the effects of stereoselective solvation on the circular dichroism, but, in contrast to some other related systems, the chemical shift difference between the two NH2 protons was relatively insensitive to solvent. Consistent with this, the circular dichroism spectra of the tetraphenylborate salts of the deprotonated complexes were found not to be markedly dependent on solvent. Tetraammine-{(-)-ψ-ephedrine)cobalt(III) and tetraammine{(-)- ephedrine}cobalt(III) were found to have the same signs of Cotton effects for the various d-d transitions, whereas bis{(-)-ψ- ephedrine}copper(II) and bis{(-)-ephedrine}copper(II) had opposite signs. This has been explained in terms of different conformer populations in the cobalt(III) and copper(II) systems.

NMR studies of tandem WW domains of Nedd4 in complex with a PY motif-containing region of the epithelial sodium channel

1998 ◽  
Vol 76 (2-3) ◽  
pp. 341-350 ◽  
Author(s):  
Voula Kanelis ◽  
Neil A Farrow ◽  
Lewis E Kay ◽  
Daniela Rotin ◽  
Julie D Forman-Kay
Keyword(s):  
Chemical Shift ◽  
Sodium Channel ◽  
Chemical Shifts ◽  
Epithelial Sodium Channel ◽  
Chemical Shift Assignment ◽  
Nmr Studies ◽  
Ww Domains ◽  
Ww Ii ◽  
Py Motif ◽  
Shift Assignment

Nedd4 (neuronal precursor cell-expressed developmentally down-regulated 4) is a ubiquitin-protein ligase containing multiple WW domains. We have previously demonstrated the association between the WW domains of Nedd4 and PPxY (PY) motifs of the epithelial sodium channel (ENaC). In this paper, we report the assignment of backbone 1Hα, 1HN, 15N, 13C', 13Cα, and aliphatic 13C resonances of a fragment of rat Nedd4 (rNedd4) containing the two C-terminal WW domains, WW(II+III), complexed to a PY motif-containing peptide derived from the β subunit of rat ENaC, the βP2 peptide. The secondary structures of these two WW domains, determined from chemical shifts of 13Cα and 13Cβ resonances, are virtually identical to those of the WW domains of the Yes-associated protein YAP65 and the peptidyl-prolyl isomerase Pin1. Triple resonance experiments that detect the 1Hα chemical shift were necessary to complete the chemical shift assignment, owing to the large number of proline residues in this fragment of rNedd4. A new experiment, which correlates sequential residues via their 15N nuclei and also detects 1Hα chemical shifts, is introduced and its utility for the chemical shift assignment of sequential proline residues is discussed. Data collected on the WW(II+III)-βP2 complex indicate that these WW domains have different affinities for the βP2 peptide.Key words: WW domain, PY motif, Nedd4, ENaC, NMR.

Determination of chemical shifts in 6-condensed syringylic lignin model compounds

Holzforschung ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Lucas Lagerquist ◽  
Jani Rahkila ◽  
Patrik Eklund
Keyword(s):  
Chemical Shift ◽  
Methoxy Group ◽  
Chemical Shifts ◽  
Model Compounds ◽  
Correlation Peak ◽  
Lignin Model Compounds ◽  
Benzylic Alcohols ◽  
Lignin Model ◽  
C Nmr

Abstract A small library of 6-substituted syringyl model compounds with aliphatic, carboxylic, phenylic, benzylic alcohols and brominated substituents were prepared. The influence of the substituents on the chemical shifts of the compounds was analyzed. All of model compounds showed a characteristic increase in the 13C NMR chemical shift of the methoxy group vicinal to the substitution. This 13C NMR peak and its corresponding correlation peak in HSQC could potentially be used to identify 6-condensation in syringylic lignin samples.

scholarly journals XPS Investigations on Solid and Vacuum Deposited, Oxidized and Non-oxidized Palladium

1995 ◽  
Vol 50 (4-5) ◽  
pp. 381-387 ◽  
Author(s):  
Jürgen Kintrup ◽  
Harald Züchner
Keyword(s):  
Chemical Shift ◽  
Curve Fitting ◽  
Photoelectron Spectroscopy ◽  
Chemical Shifts ◽  
Atmospheric Oxygen ◽  
Hydrogen Permeability ◽  
Photoelectric Effect ◽  
High Accuracy ◽  
X Ray ◽  
Charging Effect

Abstract X-ray photoelectron spectroscopy (XPS) has been carried out to study the reaction of differently prepared palladium samples (solid and film Pd) with atmospheric oxygen. A careful curve fitting of the measured Pd-3d5/2 peak allows to separate the Pd-3d5/2 peak for Pd in surface PdO from the dominant Pd-3d5/2 peak of the non-oxidized bulk palladium and to determine the chemical shift of the "oxidized" Pa line with high accuracy. Differences in the chemical shifts for the surface PdO on solid and film palladium are explained by a different charging caused by the photoelectric effect in XPS measurements. The smaller charging effect observed for film palladium as compared to solid palladium indicates a stronger oxygen bonding to the (rougher) film palladium. The strong Pd-O bonding seems to be an essential reason for the reduced hydrogen-permeability of film palladium compared to solid palladium

Are the amide bonds in N-acyl imidazoles twisted? A combined solid-state 17O NMR, crystallographic, and computational study

2015 ◽  
Vol 93 (4) ◽  
pp. 451-458 ◽  
Author(s):  
Xianqi Kong ◽  
Aaron Tang ◽  
Ruiyao Wang ◽  
Eric Ye ◽  
Victor Terskikh ◽  
...  
Keyword(s):  
Solid State ◽  
Chemical Shift ◽  
Crystal Structures ◽  
Computational Study ◽  
Chemical Shifts ◽  
Amide Bond ◽  
Chemical Shift Tensors ◽  
Amide Bonds ◽  
Bond Rotation ◽  
Quadrupole Coupling

We report synthesis of 17O-labeling and solid-state 17O NMR measurements of three N-acyl imidazoles of the type R-C(17O)-Im: R = p-methoxycinnamoyl (MCA-Im), R = 4-(dimethylamino)benzoyl (DAB-Im), and R = 2,4,6-trimethylbenzoyl (TMB-Im). Solid-state 17O NMR experiments allowed us to determine for the first time the 17O quadrupole coupling and chemical shift tensors in this class of organic compounds. We also determined the crystal structures of these compounds using single-crystal X-ray diffraction. The crystal structures show that, while the C(O)–N amide bond in DAB-Im exhibits a small twist, those in MCA-Im and TMB-Im are essentially planar. We found that, in these N-acyl imidazoles, the 17O quadrupole coupling and chemical shift tensors depend critically on the torsion angle between the conjugated acyl group and the C(O)–N amide plane. The computational results from a plane-wave DFT approach, which takes into consideration the entire crystal lattice, are in excellent agreement with the experimental solid-state 17O NMR results. Quantum chemical computations also show that the dependence of 17O NMR parameters on the Ar–C(O) bond rotation is very similar to that previously observed for the C(O)–N bond rotation in twisted amides. We conclude that one should be cautious in linking the observed NMR chemical shifts only to the twist of the C(O)–N amide bond.

scholarly journals Following excited-state chemical shifts in molecular ultrafast x-ray photoelectron spectroscopy

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
D. Mayer ◽  
F. Lever ◽  
D. Picconi ◽  
J. Metje ◽  
S. Alisauskas ◽  
...  
Keyword(s):  
Excited State ◽  
Chemical Shift ◽  
Photoelectron Spectroscopy ◽  
Chemical Shifts ◽  
Excited Molecule ◽  
Charge Motion ◽  
Core Electron ◽  
Xps Spectra ◽  
X Ray ◽  
State Chemical

AbstractThe conversion of photon energy into other energetic forms in molecules is accompanied by charge moving on ultrafast timescales. We directly observe the charge motion at a specific site in an electronically excited molecule using time-resolved x-ray photoelectron spectroscopy (TR-XPS). We extend the concept of static chemical shift from conventional XPS by the excited-state chemical shift (ESCS), which is connected to the charge in the framework of a potential model. This allows us to invert TR-XPS spectra to the dynamic charge at a specific atom. We demonstrate the power of TR-XPS by using sulphur 2p-core-electron-emission probing to study the UV-excited dynamics of 2-thiouracil. The method allows us to discover that a major part of the population relaxes to the molecular ground state within 220–250 fs. In addition, a 250-fs oscillation, visible in the kinetic energy of the TR-XPS, reveals a coherent exchange of population among electronic states.

scholarly journals Protein structure refinement using a quantum mechanics-based chemical shielding predictor

2016 ◽  
Author(s):  
Lars A. Bratholm ◽  
Jan H. Jensen
Keyword(s):  
Quantum Mechanics ◽  
Simulated Annealing ◽  
Chemical Shift ◽  
Force Field ◽  
Chemical Shifts ◽  
Protein Structures ◽  
Empirical Methods ◽  
Structural Refinement ◽  
Chemical Shielding ◽  
Chemical Shift Prediction

The accurate prediction of protein chemical shifts using quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of protein backbone and CB chemical shifts (ProCS15, PeerJ 2016, 3:e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: Simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1 - 0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If a residue-specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiment that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differs in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift.

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