Proton N.M.R. of the muramyl dipeptide adjuvant in dimethyl sulfoxide

1982 ◽  
Vol 35 (3) ◽  
pp. 489 ◽  
Author(s):  
BE Chapman ◽  
M Batley ◽  
JW Redmond
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Chemical Shift ◽  
Dimethyl Sulfoxide ◽  
Chemical Shifts ◽  
Muramyl Dipeptide ◽  
Side Chain ◽  
Active Principle ◽  
Temperature Dependences ◽  
Amide Protons

The active principle of complete Freund's adjuvant, N-acetylmuramyl-L-alanyl-D-isoglutamine, was studied in the α-anomeric form in dimethyl sulfoxide solutions by 1H n.m.r, at 200 MHz. All resonances except those of the nonanomeric sugar protons were assigned. Temperature dependences of the chemical shifts of the amide protons indicated that the alanyl NH is involved in hydrogen bonding. The isoglutamine β-CH2 protons showed large chemical-shift nonequivalence, an effect consistent with a hydrogen bond to the side chain carboxyl of this residue.

The interaction of dimethyl sulfoxide with N-benzoyl amino acids

1981 ◽  
Vol 34 (9) ◽  
pp. 1869 ◽  
Author(s):  
CW Fong ◽  
HG Grant
Keyword(s):  
Amino Acids ◽  
Hydrogen Bonding ◽  
Dimethyl Sulfoxide ◽  
Benzene Ring ◽  
Chemical Shifts ◽  
Side Chain ◽  
Torsional Angle ◽  
Intermolecular Hydrogen Bonding ◽  
Atom Increase ◽  
Self Association

The interaction of dimethyl sulfoxide with N-benzoyl amino acids in deuterochloroform has been investigated by 13C n.m.r. spectroscopy. Examination of the chemical shifts of the benzene ring reveals that intermolecular hydrogen bonding between dimethyl sulfoxide and the amido-hydrogen atom increase the effective steric size of the amino hydrogen, resulting in an increase in the torsional angle between the benzene ring and the C(O)NHCH(R)COOH side chain. Self-association of N- benzoyl amino acids in deuterochloroform occurs largely through two COOH...O=C hydrogen bonds and does not involve intermolecular hydrogen bonding to the N-H proton.

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.

N—H...S and N—H...O hydrogen bonds: `pure' and `mixed'R22(8) patterns in the crystal structures of eight 2-thiouracil derivatives

2014 ◽  
Vol 70 (2) ◽  
pp. 241-249 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Ernst Egert
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Dimethyl Sulfoxide ◽  
Crystal Structures ◽  
Thiouracil Derivatives ◽  
Bonding Patterns

The preferred hydrogen-bonding patterns in the crystal structures of 5-propyl-2-thiouracil, C7H10N2OS, (I), 5-methoxy-2-thiouracil, C5H6N2O2S, (II), 5-methoxy-2-thiouracil–N,N-dimethylacetamide (1/1), C5H6N2O2S·C4H9NO, (IIa), 5,6-dimethyl-2-thiouracil, C6H8N2OS, (III), 5,6-dimethyl-2-thiouracil–1-methylpyrrolidin-2-one (1/1), C6H8N2OS·C5H9NO, (IIIa), 5,6-dimethyl-2-thiouracil–N,N-dimethylformamide (2/1), 2C6H8N2OS·C3H7NO, (IIIb), 5,6-dimethyl-2-thiouracil–N,N-dimethylacetamide (2/1), 2C6H8N2OS·C4H9NO, (IIIc), and 5,6-dimethyl-2-thiouracil–dimethyl sulfoxide (2/1), 2C6H8N2OS·C2H6OS, (IIId), were analysed. All eight structures containR22(8) patterns. In (II), (IIa), (III) and (IIIa), they are formed by two N—H...S hydrogen bonds, and in (I) by alternating pairs of N—H...S and N—H...O hydrogen bonds. In contrast, the structures of (IIIb), (IIIc) and (IIId) contain `mixed'R22(8) patterns with one N—H...S and one N—H...O hydrogen bond, as well asR22(8) motifs with two N—H...O hydrogen bonds.

Proton Magnetic Resonance Spectra of Some Amphetamines and Related Compounds and Observations on Rotamer Populations

1971 ◽  
Vol 49 (19) ◽  
pp. 3143-3151 ◽  
Author(s):  
K. Bailey ◽  
A. W. By ◽  
K. C. Graham ◽  
D. Verner
Keyword(s):  
Hydrogen Bonding ◽  
Phenyl Ring ◽  
Proton Magnetic Resonance ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Side Chain ◽  
Amino Group ◽  
Ortho Position ◽  
Electronic Effects ◽  
Related Compounds

Data from the p.m.r. spectra of β-amino-, β-aminohydrochloride-, β-hydroxy-, and β-nitro-α-phenyl-propanes having methyl or methoxy substituants on the phenyl ring (37 compounds in all) are presented. The α and β protons of the side-chain give a pattern usually analyzable as ABX. The data are discussed in terms of correlations of coupling constants and chemical shifts with electronegativity of the substituent groups, steric and electronic effects, and apparent changes in rotamer populations. Hydrogen-bonding between the amino group of amphetamines and a methoxyl function at the ortho position in the phenyl ring is indicated for the salts but not the free bases.

109Ag NMR-Study of the Selective Solvation of the Ag+ Ion in Solvent Mixtures of Water and the Organic Solvents: Pyridine, Acetonitrile, and Dimethyl Sulfoxide

1984 ◽  
Vol 39 (1) ◽  
pp. 83-94 ◽  
Author(s):  
L. Guinand. K. L. Hobt. E. Mittermaier ◽  
E. Rößler ◽  
A. Schwenk ◽  
H. Schneider
Keyword(s):  
Chemical Shift ◽  
Dimethyl Sulfoxide ◽  
Organic Solvents ◽  
Mole Fraction ◽  
Chemical Exchange ◽  
Chemical Shifts ◽  
Equilibrium Constants ◽  
Solvent Mixtures ◽  
Nmr Study ◽  
Solvent Molecules

In mixtures of water (W) and one of the organic solvents pyridine, acetonitrile, and dimethyl sulfoxide (O), the silver ion forms the following solvate complexes: AgW2, AgWO, and Ag02. The chemical shift of 109Ag is strongly affected by the ligating solvent molecules, and replacing the ligand W by one of the three organic ligands yields a higher Larmor frequency. In solvent mixtures, only a single resonance line has been observed because of rapid chemical exchange. The measured chemical shifts in the range up to 400 ppm are mean values of the chemical shifts of the different solvate species in a given mixture, weighted with their relative concentrations. The 109Ag chemical shifts were determined for 0.05 to 0.15 molal solutions of AgNO3, as functions of the mole fractions of the solvent components. Using a Gaussian least squares fitting routine, the individual chemical shifts of the Ag+ solvate complexes and the corresponding equilibrium constants were determined. This fit was successful for the whole mole fraction range of DMSO, while in the solvent systems with acetonitrile and with pyridine at higher concentrations of the organic component the chemical shift is influenced by more than two solvent molecules. In these cases equilibrium constants were calculated from chemical shift data for solutions of low mole fraction of acetonitrile and pyridine.

Temperature dependence of chemical shifts of protons in hydrogen bonds. Experimental evidence on an intramolecular hydrogen bond

1968 ◽  
Vol 46 (17) ◽  
pp. 2865-2868 ◽  
Author(s):  
T. Schaefer ◽  
G. Kotowycz
Keyword(s):  
Hydrogen Bond ◽  
Carbon Tetrachloride ◽  
Chemical Shift ◽  
Hydrogen Bonds ◽  
Temperature Dependence ◽  
Intramolecular Hydrogen Bond ◽  
Chemical Shifts ◽  
Hydroxyl Proton ◽  
Intramolecular Hydrogen ◽  
Strong Intramolecular Hydrogen Bond

A temperature dependence of the chemical shift of the hydroxyl proton in the strong intramolecular hydrogen bond in 3,5-dichlorosalicylaldehyde is observed in carbon tetrachloride and benzene-d6 solutions. Its magnitude of 0.25 to 0.30 × 10−2 p.p.m. per ° C over a range of 100 °C is in agreement with the model described by Muller and Reiter (1).

scholarly journals ProCS15: A DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

2015 ◽  
Author(s):  
Anders S Larsen ◽  
Lars A Bratholm ◽  
Anders S Christensen ◽  
Maher Jan Channir ◽  
Jan H. Jensen
Keyword(s):  
Hydrogen Bonding ◽  
Chemical Shift ◽  
Chemical Shifts ◽  
Structural Models ◽  
Protein G ◽  
Chemical Shielding ◽  
The Third ◽  
Entire Structure ◽  
Igg Binding ◽  
Structural Ensembles

We present ProCS15: A program that computes the isotropic chemical shielding values of backbone and C β atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7 - 1.1, 0.2 - 0.4, and 1.8 - 2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively.

Correspondence: Hydrogen Bond to Gold? 1H NMR is Not a Proof of Hydrogen Bonds in Transition Metal Complexes

2018 ◽  
Author(s):  
Jan Vícha ◽  
Cina Foroutan-Nejad ◽  
Michal Straka
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Chemical Shifts ◽  
X Ray ◽  
Structure And Dynamics ◽  
Hydrogen Bonding Interactions ◽  
Overall Stability ◽  
Gold Compounds ◽  
C Nmr

Illusive Au<sup>I/III</sup>···H hydrogen bonds and their effect on structure and dynamics of molecules have been a matter of debate. While a number of X-ray studies reported gold compounds with short Au<sup>I/III</sup>···H contacts, a solid spectroscopic evidence for Au<sup>I/III</sup>···H bonding has been missing. Recently<a></a><a>, Bakar <i>et al.</i></a> (NATURE COMMUNICATIONS 8:576) reported compound with four short Au···H contacts (2.61­–2.66 Å; X-ray determined). Assuming the central cluster be [Au<sub>6</sub>]<sup>2+</sup>and observing the <sup>1</sup>H (<sup>13</sup>C) NMR resonances at relevant H(C) nuclei deshielded with respect to precursor compound, the authors concluded with reservations that <i>“the present Au···H–C interaction is a kind of “hydrogen bond”, where the [Au<sub>6</sub>]<sup>2+</sup>serves as an acceptor”</i>. Here, we show that the Au<sub>6</sub>cluster in their compound bears negative charge and the Au···H contacts lead to a weak (~1 kcal/mol) auride···hydrogen bonding interactions, though unimportant for the overall stability of<b></b>the molecule. Additionally, computational analysis of NMR chemical shifts reveals that the deshielding effects at respective hydrogen nuclei are not directly related to Au···H–C hydrogen bonding .

scholarly journals The role of nitro groups in the binding of nitroaromatics to protein MOPC 315

1978 ◽  
Vol 173 (3) ◽  
pp. 713-722 ◽  
Author(s):  
P Gettins ◽  
D Givol ◽  
R A Dwek
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
High Resolution ◽  
Hydrogen Bonds ◽  
Fluorescence Quenching ◽  
Nitro Group ◽  
Protein Interactions ◽  
Chemical Shifts ◽  
Binding Constants

Two series of dinitrophenyl haptens, in which chlorine replaces one or both nitro groups, were used to investigate, by a combination of high-resolution 1H n.m.r. and fluorescence quenching, the presence of groups in the combining site of protein MOPC 315, which form hydrogen bonds to the aromatic-ring substituents of the hapten. The large differences in binding constants on successive replacement of nitro groups were shown to be due to specific hapten-substituent-protein interactions by (a) showing that there was little difference in the interaction between these haptens and 3-methylindole (a model for the residue tryptophan-93L with which the hapten stacks in protein MOPC 315), (b) proving by 1H n.m.r. that the mode of hapten binding is constant and (c) showing that the differences in Kd were consistent with the relative hydrogen-bonding capacities of chlorine and the nitro moiety. In this way it was established that each nitro group forms a hydrogen bond. Furthermore, from consideration of the 1H n.m.r. chemical shifts of several dinitrophenyl haptens and their trinitrophenyl analogues, it was shown that there is no distortion of the o-nitro group on binding to the variable fragment of protein MOPC 315.

NUCLEAR SHIELDING PARAMETERS FOR PROTONS IN HYDROGEN BONDS: II. CORRELATION OF CHEMICAL SHIFTS IN INTRAMOLECULAR HYDROGEN BONDS WITH INFRARED STRETCHING FREQUENCIES

1960 ◽  
Vol 38 (8) ◽  
pp. 1249-1254 ◽  
Author(s):  
L. W. Reeves ◽  
E. A. Allan ◽  
K. O. Strømme
Keyword(s):  
Hydrogen Bond ◽  
Chemical Shift ◽  
Hydrogen Bonds ◽  
Infinite Dilution ◽  
Chemical Shifts ◽  
Intramolecular Hydrogen Bonds ◽  
A Value ◽  
Nuclear Shielding ◽  
Intramolecular Hydrogen ◽  
Hydrogen Bonded

Nuclear shielding parameters have been obtained for 24 intramolecularly hydrogen-bonded phenols and naphthols. The shielding parameters are corrected for large diamagnetic anisotropies and a value ΔσOH obtained which represents the change in shielding parameter in parts per million with reference to the infinite dilution chemical shift of phenol, α-naphthol, or β-naphthol. These values of ΔσOH are approximately proportional to the change ΔvOH in the OH stretching frequency on formation of the hydrogen bond.

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