Fast-pulsing NMR techniques for the detection of weak interactions: successful natural abundance probe of hydrogen bonds in peptides

2013 ◽  
Vol 11 (43) ◽  
pp. 7611 ◽  
Author(s):  
Amandine Altmayer-Henzien ◽  
Valérie Declerck ◽  
David J. Aitken ◽  
Ewen Lescop ◽  
Denis Merlet ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Weak Interactions ◽  
Natural Abundance ◽  
Nmr Techniques

Distinguishment of Weak Interactions of Hydrogen Atoms Bound to Carbon Atoms: X-Ray Crystal Structural and Hirshfeld Surface Analyses of 2-Hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene with the 2-Methoxylated Homologue

2021 ◽  
Vol 19 ◽  
Author(s):  
Kikuko Iida ◽  
Toyokazu Muto ◽  
Miyuki Kobayashi ◽  
Hiroaki Iitsuka ◽  
Kun Li ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Molecular Conformation ◽  
Weak Interactions ◽  
Carbonyl Oxygen ◽  
Hirshfeld Surface ◽  
Molecular Surface ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Classical Hydrogen Bond

Abstract: X-ray crystal and Hirshfeld surface analyses of 2-hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene and its 2-methoxylated homologue show quantitatively and visually distinct molecular contacts in crystals and minute differences in the weak intermolecular interactions. The title compound has a helical tubular packing, where molecules are piled in a two-folded head-to-tail fashion. The homologue has a tight zigzag molecular string lined up behind each other via nonclassical intermolecular hydrogen bonds between the carbonyl oxygen atom and the hydrogen atom of the naphthalene ring. The dnorm index obtained from the Hirshfeld surface analysis quantitatively demonstrates stronger molecular contacts in the homologue, an ethereal compound, than in the title compound, an alcohol, which is consistent with the higher melting temperature of the former than the latter. Stabilization through the significantly weak intermolecular nonclassical hydrogen bonding interactions in the homologue surpasses the stability imparted by the intramolecular C=O…H–O classical hydrogen bonds in the title compound. The classical hydrogen bond places the six-membered ring in the concave of the title molecule. The hydroxy group opposingly disturbs the molecular aggregation of the title compound, as demonstrated by the distorted H…H interactions covering the molecular surface, owing to the rigid molecular conformation. The position of effective interactions predominate over the strength of the classical/nonclassical hydrogen bonds in the two compounds.

[N,N′-Bis(diphenylphosphino)pyridine-2,6-diamine-κ3 P,N 1,P′]chloropalladium(II) chloride monohydrate 1,2-dichloroethane solvate

2006 ◽  
Vol 62 (5) ◽  
pp. m1106-m1108 ◽  
Author(s):  
Julia Wiedermann ◽  
David Benito-Garagorri ◽  
Karl Kirchner ◽  
Kurt Mereiter
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Weak Interactions ◽  
Water Molecules ◽  
Square Planar ◽  
Chloride Monohydrate

The title compound, [PdCl(C29H25N3P2)]Cl·H2O·C2H4Cl2, contains a cationic pincer-type PNP complex with Pd in a square-planar coordination. The complexes form dimers which are π–π stacked via their pyridine rings and linked into chains via hydrogen bonds via four-membered rings of two chloride anions and two water molecules. Pairs of 1,2-dichloroethane molecules are entrapped in pockets of the structure and show weak interactions with palladium.

Syntheses and structures of two novel fluorescent metal–organic frameworks generated from a tridentate donor–acceptor motif ligand

2020 ◽  
Vol 76 (6) ◽  
pp. 605-615
Author(s):  
Yong-Jin Zhao ◽  
Jian-Ping Ma ◽  
Jianzhong Fan ◽  
Yan Geng ◽  
Yu-Bin Dong
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Weak Interactions ◽  
Metal Organic Frameworks ◽  
3D Structure ◽  
Organic Ligand ◽  
Bidentate Ligand ◽  
Donor Acceptor ◽  
Metal Organic ◽  
3D Networks

The tridentate organic ligand 4,4′,4′′-(4,4,8,8,12,12-hexamethyl-8,12-dihydro-4H-benzo[9,1]quinolizino[3,4,5,6,7-defg]acridine-2,6,10-triyl)tribenzoic acid (H3L) has been synthesized (as the methanol 1.25-solvate, C48H39NO6·1.25CH3OH). As a donor–acceptor motif molecule, H3L possess strong intramolecular charge transfer (ICT) fluorescence. Through hydrogen bonds, H3L molecules construct a two-dimensional (2D) network, which pack together into three-dimensional (3D) networks with an ABC stacking pattern in the crystalline state. Based on H3L and M(NO3)2 salts (M = Cd and Zn) under solvothermal conditions, two metal–organic frameworks (MOFs), namely, catena-poly[[triaquacadmium(II)]-μ-10-(4-carboxyphenyl)-4,4′-(4,4,8,8,12,12-hexamethyl-8,12-dihydro-4H-benzo[9,1]quinolizino[3,4,5,6,7-defg]acridine-2,6-diyl)dibenzoato], [Cd(C48H37NO6)(H2O)3] n , I, and poly[[μ3-4,4′,4′′-(4,4,8,8,12,12-hexamethyl-8,12-dihydro-4H-benzo[9,1]quinolizino[3,4,5,6,7-defg]acridine-2,6,10-triyl)tribenzoato](μ3-hydroxido)zinc(II)], [Zn2(C48H36NO6)(OH)] n , II, were synthesized. Single-crystal analysis revealed that both MOFs adopt a 3D structure. In I, partly deprotonated HL 2− behaves as a bidentate ligand to link a CdII ion to form a one-dimensional chain. In the solid state of I, the existence of weak interactions, such as O—H...O hydrogen bonds and π–π interactions, plays an essential role in aligning 2D nets and 3D networks with AB packing patterns for I. The deprotonated ligand L 3− in II is utilized as a tridentate building block to bind ZnII ions to construct 3D networks, where unusual Zn4O14 clusters act as connection nodes. As a donor–acceptor molecule, H3L exhibits fluorescence with a photoluminescence quantum yield (PLQY) of 70% in the solid state. In comparison, the PL of both MOFs is red-shifted with even higher PLQYs of 79 and 85% for I and II, respectively.

Weak interactions in chain polymers [M(μ-X)2 L 2]∞ (M = Zn, Cd; X = Cl, Br; L = substituted pyridine) – an electron density study

2009 ◽  
Vol 65 (5) ◽  
pp. 600-611 ◽  
Author(s):  
Ruimin Wang ◽  
Christian W. Lehmann ◽  
Ulli Englert
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Critical Points ◽  
Weak Interactions ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Density Distributions ◽  
The One ◽  
Experimental Electron Density ◽  
Density Study

The experimental electron-density distributions in crystals of five chain polymers [M(μ-X)2(py)2] (M = Zn, Cd; X = Cl, Br; py = 3,5-substituted pyridine) have been obtained from high-resolution X-ray diffraction data sets (sin θ/λ > 1.1 Å−1) at 100 K. Topological analyses following Bader's `Atoms in Molecules' approach not only confirmed the existence of (3, −1) critical points for the chemically reasonable and presumably strong covalent and coordinative bonds, but also for four different secondary interactions which are expected to play a role in stabilizing the polymeric structures which are unusual for Zn as the metal center. These weaker contacts comprise intra- and inter-strand C—H...X—M hydrogen bonds on the one hand and C—X...X—C interhalogen contacts on the other hand. According to the experimental electron-density studies, the non-classical hydrogen bonds are associated with higher electron density in the (3, −1) critical points than the halogen bonds and hence are the dominant interactions both with respect to intra- and inter-chain contacts.

Introducing new half-integer quadrupolar nuclei for solid state NMR of inclusion compounds

2015 ◽  
Vol 93 (9) ◽  
pp. 1014-1024
Author(s):  
Igor L. Moudrakovski ◽  
Christopher I. Ratcliffe ◽  
John A. Ripmeester
Keyword(s):  
Solid State ◽  
Gas Hydrates ◽  
Inclusion Compounds ◽  
Chemical Shift Anisotropy ◽  
Natural Abundance ◽  
Quadrupolar Nuclei ◽  
Guest Molecules ◽  
Quadrupolar Coupling ◽  
Nmr Techniques ◽  
The Impact

Broad developments in experimental NMR techniques have opened new and exciting opportunities for application of solid state nuclear magnetic resonance (SS NMR) in studies of gas hydrates and inclusion compounds in general. Perhaps the most important advance of the last 10 years was the extension into very high magnetic fields beyond 20 T. This progress is especially significant in studies concerned with low-γ, low natural abundance, and quadrupolar nuclei. This work reports our recent exploration of clathrate hydrates and other inclusion compounds (β-quinol, tert-Bu-Calix[4], and dodecasil-3C) with SS NMR of nuclei that were not so long ago completely out of reach for NMR, namely 131Xe, 83Kr, and 33S. Although 129Xe is a widely used NMR probe, applications of the low-γ isotope 131Xe were very scarce. Being a quadrupolar spin 3/2 nucleus, 131Xe provides an additional probe for sampling the electric field gradients in inclusion compounds. Another nucleus that has been seriously under-explored is 83Kr, with its very low γ being the main obstacle, and along with quadrupolar coupling we report the first detection of the chemical shift anisotropy in krypton. The relative values of the Sternheimer antishielding factors for 131Xe and 83Kr, obtained by comparison of the spectra of the two in identical cage environments, are also discussed. Though 33S NMR of solids is notoriously difficult due to its low γ, low natural abundance, and relatively large quadrupolar moment, working at the field of 21.1 T it was possible to acquire, in a reasonable time, natural abundance 33S SS NMR spectra of various H2S and SO2 gas hydrates and inclusion compounds. In most cases the spectra are dominated by the quadrupolar interactions, providing information on the symmetry of the cages encapsulating the guest molecules, and also show the effects of very rapid reorientation of the encaged H2S and SO2. The impact of the introduction of new NMR nuclei on hydrate research is discussed.

Weak C—H...O and C—H...π hydrogen bonds and π–π stacking interactions in a series of fourN′-[(E)-(aryl)methylidene]-N-methyl-2-oxo-1,3-oxazolidine-4-carbohydrazides

2015 ◽  
Vol 71 (8) ◽  
pp. 647-652 ◽  
Author(s):  
Thais C. M. Nogueira ◽  
Alessandra C. Pinheiro ◽  
James L. Wardell ◽  
Marcus V. N. de Souza ◽  
Jordan P. Abberley ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Weak Interactions ◽  
The Other ◽  
Stacking Interactions ◽  
Screw Axis ◽  
Chiral Structure ◽  
Π Stacking ◽  
Unit Form ◽  
Protective Groups ◽  
Local Inversion

Oxazolidin-2-ones are widely used as protective groups for 1,2-amino alcohols and chiral derivatives are employed as chiral auxiliaries. The crystal structures of four differently substituted oxazolidinecarbohydrazides, namelyN′-[(E)-benzylidene]-N-methyl-2-oxo-1,3-oxazolidine-4-carbohydrazide, C12H12N3O3, (I),N′-[(E)-2-chlorobenzylidene]-N-methyl-2-oxo-1,3-oxazolidine-4-carbohydrazide, C12H12ClN3O3, (II), (4S)-N′-[(E)-4-chlorobenzylidene]-N-methyl-2-oxo-1,3-oxazolidine-4-carbohydrazide, C12H12ClN3O3, (III), and (4S)-N′-[(E)-2,6-dichlorobenzylidene]-N,3-dimethyl-2-oxo-1,3-oxazolidine-4-carbohydrazide, C13H13Cl2N3O3, (IV), show that an unexpected mild-condition racemization from the chiral starting materials has occurred in (I) and (II). In the extended structures, the centrosymmetric phases, which each crystallize with two molecules (AandB) in the asymmetric unit, formA+Bdimers linked by pairs of N—H...O hydrogen bonds, albeit with different O-atom acceptors. One dimer is composed of one molecule with anSconfiguration for its stereogenic centre and the other with anRconfiguration, and possesses approximate local inversion symmetry. The other dimer consists of eitherR,RorS,Spairs and possesses approximate local twofold symmetry. In the chiral structure, N—H...O hydrogen bonds link the molecules intoC(5) chains, with adjacent molecules related by a 21screw axis. A wide variety of weak interactions, including C—H...O, C—H...Cl, C—H...π and π–π stacking interactions, occur in these structures, but there is little conformity between them.

scholarly journals Bonding in Group 1 Citrate Salts

2014 ◽  
Vol 70 (a1) ◽  
pp. C655-C655
Author(s):  
James Kaduk ◽  
Alagappa Rammohan
Keyword(s):  
Hydrogen Bonds ◽  
Alkali Metal ◽  
Weak Interactions ◽  
Alkali Metal Cation ◽  
Quantitative Measure ◽  
Electrostatic Energy ◽  
Hydroxyl Groups ◽  
Local Environments ◽  
The Stability ◽  
Cation Size

Computational studies of > 15 new crystal structures and the 10 previously-reported structures of alkali metal citrates provide insight into why the atoms are where they are. The metal-citrate bonding is predominantly ionic, with very little covalent character, which decreases as the cation size increases. Bond valence calculations indicate that most cations are crowded, and that the crowding decreases as the cation size increases. Although most oxygen atoms coordinate to the metals, a few do not, and they tend to be the least-negative oxygens. Both the citrate hydroxyl groups and water molecules tend to bridge two cations, and the carboxylate coordination is more varied. The solid state energy differences are dominated by differences in van der Waals and electrostatic energy contributions. In the Li and Na salts, the citrate anion occurs predominantly in a higher-energy "kinked" conformation, rather than the extended lowest-energy conformation observed in salts of the larger cations. Detailed conformational analysis of the citrate anions enables quantification of the conformational energy costs in these solids. Hydrogen bonding is important to the stability of these salts. The Mulliken overlap population in the hydrogen bonds provides a quantitative measure of their strength, and permits identification of long (weak) interactions which are significant in some of these compounds. Patterns in both the local environments of the hydrogen bonds and the more-extended features (graph sets) are noted. Polymorphs and sets of isostructural compounds permit more-detailed analysis of the structures and energetics in these compounds. The order of ionization of the three carboxylic acid groups is in general central/terminal/terminal, but there are two exceptions. While we have concentrated on salts containing a single alkali metal cation (and hydrogen), the structures of NaK2C6H5O7 and NaKHC6H5O7 provide an exciting window on a larger universe of mixed salts.

3D Heteronuclear NMR techniques for carbon-13 in natural abundance

1990 ◽  
Vol 112 (23) ◽  
pp. 8599-8600 ◽  
Author(s):  
Horst Kessler ◽  
P. Schmieder ◽  
H. Oschkinat
Keyword(s):  
Heteronuclear Nmr ◽  
Natural Abundance ◽  
Nmr Techniques ◽  
3D Heteronuclear Nmr
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