Comparative Study of Weak Interactions in Molecular Crystals:  H−H Bonds vs Hydrogen Bonds†

2006 ◽  
Vol 110 (28) ◽  
pp. 8970-8978 ◽  
Author(s):  
David J. Wolstenholme ◽  
T. Stanley Cameron
Keyword(s):  
Hydrogen Bonds ◽  
Comparative Study ◽  
Weak Interactions ◽  
Molecular Crystals

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.

Associations of squaric acid and its anions as multiform building blocks of hydrogen-bonded molecular crystals

2001 ◽  
Vol 57 (6) ◽  
pp. 859-865 ◽  
Author(s):  
Gastone Gilli ◽  
Valerio Bertolasi ◽  
Paola Gilli ◽  
Valeria Ferretti
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Negative Charge ◽  
Three Dimensional ◽  
Molecular Crystals ◽  
Building Blocks ◽  
Squaric Acid ◽  
Orthosilicic Acid ◽  
Molecular Plane ◽  
Dimensional Crystal

Squaric acid, H2C4O4 (H2SQ), is a completely flat diprotic acid that can crystallize as such, as well as in three different anionic forms, i.e. H2SQ·HSQ−, HSQ− and SQ2−. Its interest for crystal engineering studies arises from three notable factors: (i) its ability of donating and accepting hydrogen bonds strictly confined to the molecular plane; (ii) the remarkable strength of the O—H...O bonds it may form with itself which are either of resonance-assisted (RAHB) or negative-charge-assisted [(−)CAHB] types; (iii) the ease with which it may donate a proton to an aromatic base which, in turn, back-links to the anion by strong low-barrier N—H+...O1/2− charge-assisted hydrogen bonds. Analysis of all the structures so far known shows that, while H2SQ can only crystallize in an extended RAHB-linked planar arrangement and SQ2− tends to behave much as a monomeric dianion, the monoanion HSQ− displays a number of different supramolecular patterns that are classifiable as β-chains, α-chains, α-dimers and α-tetramers. Partial protonation of these motifs leads to H2SQ·HSQ− anions whose supramolecular patterns include ribbons of dimerized β-chains and chains of emiprotonated α-dimers. The topological similarities between the three-dimensional crystal chemistry of orthosilicic acid, H4SiO4, and the two-dimensional one of squaric acid, H2C4O4, are finally stressed.

Theoretical Modeling of the N-H and N-D Stretching Bands of Hydrogen-Bonded 1-Methylthymine Crystal and Its Deuterated Form

2006 ◽  
Vol 2 (4) ◽  
pp. 205-219
Author(s):  
Marek Boczar ◽  
Łukasz Boda ◽  
Marek J. Wójcik
Keyword(s):  
Hydrogen Bonds ◽  
High Frequency ◽  
Molecular Crystals ◽  
Low Frequency ◽  
Unit Cell ◽  
Fermi Resonance ◽  
Bending Vibrations ◽  
Theoretical Simulation ◽  
Stretching Vibrations ◽  
Centrosymmetric Dimers

Theoretical model for vibrational interactions in the hydrogen bonds in molecular crystals with four molecules forming two centrosymmetric dimers in the unit cell is presented. The model takes into account anharmonic-type couplings between the high-frequency N-H(D) and the low-frequency N•••O stretching vibrations in each hydrogen bond, resonance interactions (Davydov coupling) between equivalent hydrogen bonds in each dimer, resonance interdimer interactions within an unit cell and Fermi resonance between the N-H(D) stretching fundamental and the first overtone of the N-H(D) in-plane bending vibrations. The vibrational Hamiltonian, selection rules, and expressions for the integral properties of an absorption spectrum are derived. The model is used for theoretical simulation of the νs stretching bands of 1-methylthymine and its ND derivative at 300 K. The effect of deuteration is successfully reproduced by our model.

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.

Sign in / Sign up

Export Citation Format

Share Document