Theory of nematic ordering driven by hydrogen bonding between rods and solvent molecules

The role of more than one binding site on a nitroxide free radical in magnetic resonance determinations of the properties of the complex formed with a hydrogen donor is examined. The expression that relates observed hyperfine couplings in EPR spectra to complex formation constants and concentrations of each species in solution becomes much more complex when multiple binding sites are present, but reduces to a simpler form when binding at the two sites occurs independently and the binding at the non-nitroxide site does not produce significant differences in the hyperfine coupling constant in the complexed radical. Effects on studies of hydrogen bonding between multiple binding site nitroxides and hydrogen donor solvent molecules by other magnetic resonance methods are potentially more extreme.

Download Full-text

Relevance of Hydrogen Bonds for the Histamine H2 Receptor-Ligand Interactions: A Lesson from Deuteration

Biomolecules ◽

10.3390/biom10020196 ◽

2020 ◽

Vol 10 (2) ◽

pp. 196 ◽

Cited By ~ 4

Author(s):

Mojca Kržan ◽

Jan Keuschler ◽

Janez Mavri ◽

Robert Vianello

Keyword(s):

Hydrogen Bonding ◽

Active Sites ◽

Density Functional ◽

Receptor Activation ◽

Histamine H2 Receptor ◽

Therapeutic Practice ◽

H2 Receptor ◽

Ligand Interactions ◽

Solvent Molecules ◽

Near Future

We used a combination of density functional theory (DFT) calculations and the implicit quantization of the acidic N–H and O–H bonds to assess the effect of deuteration on the binding of agonists (2-methylhistamine and 4-methylhistamine) and antagonists (cimetidine and famotidine) to the histamine H2 receptor. The results show that deuteration significantly increases the affinity for 4-methylhistamine and reduces it for 2-methylhistamine, while leaving it unchanged for both antagonists, which is found in excellent agreement with experiments. The revealed trends are interpreted in the light of the altered strength of the hydrogen bonding upon deuteration, known as the Ubbelohde effect, which affects ligand interactions with both active sites residues and solvent molecules preceding the binding, thus providing strong evidence for the relevance of hydrogen bonding for this process. In addition, computations further underline an important role of the Tyr250 residue for the binding. The obtained insight is relevant for the therapy in the context of (per)deuterated drugs that are expected to enter therapeutic practice in the near future, while this approach may contribute towards understanding receptor activation and its discrimination between agonists and antagonists.

Download Full-text

Tris(biimidazolato)chromium(III) as a building block for hydrogen-bonded supramolecular assemblies

Canadian Journal of Chemistry ◽

10.1139/v06-110 ◽

2006 ◽

Vol 84 (7) ◽

pp. 949-959 ◽

Cited By ~ 10

Author(s):

Letitia M Gruia ◽

Fernande D Rochon ◽

André L Beauchamp

Keyword(s):

Crystal Structure ◽

Hydrogen Bonding ◽

Porous Material ◽

Intermolecular Interactions ◽

Long Range ◽

Building Block ◽

Benzene Molecule ◽

Methanol Solution ◽

Solvent Molecules ◽

Free Material

The trischelate [Cr(H2biim)3](NO3)3 complex of 2,2′-biimidazole (H2biim) was obtained by reacting CrCl3·3THF with [Ag(H2biim)](NO3) in methanol. In the solvent-free material, each ligand forms two N-H···O bonds to a nitrate ion and generates locally neutral [Cr(H2biim)3](NO3)3 units. A methanol solvate was also obtained in which intermolecular interactions involve optimal use of the hydrogen-bonding ability of the [Cr(H2biim)3]3+ cations, NO3– anions, and methanol molecules. In both cases, there is no long-range regular organization of the complex units. Deprotonation of [Cr(H2biim)3](NO3)3 with NaOCH3 yielded neutral Cr(Hbiim)3. Its powder pattern is similar to that of Ru(Hbiim)3, suggesting that it also consists of mutually perpendicular interlocked honeycomb sheets. Recrystallization by slow diffusion of diisopropyl ether into a methanol solution yielded a porous material of composition Cr(Hbiim)3·2.6C6H14O in which superposed honeycomb sheets create infinite channels (~13 Å diameter) filled with disordered solvent molecules. A totally different structure is adopted by the solvate Cr(Hbiim)3·C6H6·2H2O, where the benzene molecule is encapsulated in a cavity created by five complex molecules.Key words: chromium, biimidazole, supramolecular, crystal structure, hydrogen bonding.

Download Full-text

THE STUDY OF HYDROGEN BONDING AND RELATED PHENOMENA BY ULTRAVIOLET LIGHT ABSORPTION: PART IV. INTERMOLECULAR HYDROGEN BONDING IN ANILINES AND PHENOLS

Canadian Journal of Chemistry ◽

10.1139/v60-127 ◽

1960 ◽

Vol 38 (6) ◽

pp. 896-910 ◽

Cited By ~ 38

Author(s):

J. C. Dearden ◽

W. F. Forbes

Keyword(s):

Hydrogen Bonding ◽

Ultraviolet Light ◽

Light Absorption ◽

Intermolecular Hydrogen Bonding ◽

Solvent Molecules

Intermolecular hydrogen bonding in anilines and phenols can be subdivided into bonding involving solute molecules only, and into bonding involving both solute and solvent molecules. Interactions which do not involve hydrogen bonding are also possible between solute and solvent molecules. Spectral effects which may be associated with each of these interactions are described and discussed for anilines and phenols. By noting the effects of substituents on the various interactions, tentative conclusions can be deduced concerning the nature of these interactions.

Download Full-text

Chlorido(dimethyl 2,2′-bipyridine-4,4′-dicarboxylate-κ2N,N′)(η5-pentamethylcyclopentadienyl)rhodium(III) chloride 1-hydroxypyrrolidine-2,5-dione disolvate

Acta Crystallographica Section C Crystal Structure Communications ◽

10.1107/s0108270113009633 ◽

2013 ◽

Vol 69 (6) ◽

pp. 584-587

Author(s):

Dharmalingam Sivanesan ◽

Hyung Min Kim ◽

Yoon Sungho

Keyword(s):

Hydrogen Bonding ◽

Hydrogen Bonds ◽

Substitution Reaction ◽

Three Dimensional ◽

Title Complex ◽

Rhodium Complex ◽

Synthetic Route ◽

Dimensional Network ◽

Weak Hydrogen Bonds ◽

Solvent Molecules

The title complex, [Rh(C10H15)Cl(C14H12N2O4)]Cl·2C4H5NO3, has been synthesized by a substitution reaction of the precursor [bis(2,5-dioxopyrrolidin-1-yl) 2,2′-bipyridine-4,4′-dicarboxylate]chlorido(pentamethylcyclopentadienyl)rhodium(III) chloride with NaOCH3. The RhIIIcation is located in an RhC5N2Cl eight-coordinated environment. In the crystal, 1-hydroxypyrrolidine-2,5-dione (NHS) solvent molecules form strong hydrogen bonds with the Cl−counter-anions in the lattice and weak hydrogen bonds with the pentamethylcyclopentadienyl (Cp*) ligands. Hydrogen bonding between the Cp* ligands, the NHS solvent molecules and the Cl−counter-anions form links in a V-shaped chain of RhIIIcomplex cations along thecaxis. Weak hydrogen bonds between the dimethyl 2,2′-bipyridine-4,4′-dicarboxylate ligands and the Cl−counter-anions connect the components into a supramolecular three-dimensional network. The synthetic route to the dimethyl 2,2′-bipyridine-4,4′-dicarboxylate-containing rhodium complex from the [bis(2,5-dioxopyrrolidin-1-yl) 2,2′-bipyridine-4,4′-dicarboxylate]rhodium(III) precursor may be applied to link Rh catalysts to the surface of electrodes.

Download Full-text

How many solvent molecules are required to solvate chiral 1,2-diols with hydrogen bonding solvents? A VCD spectroscopic study

Physical Chemistry Chemical Physics ◽

10.1039/c9cp06030h ◽

2020 ◽

Vol 22 (3) ◽

pp. 1525-1533 ◽

Cited By ~ 5

Author(s):

Luisa Weirich ◽

Juliana Magalhães de Oliveira ◽

Christian Merten

Keyword(s):

Hydrogen Bonding ◽

Spectroscopic Study ◽

Spectroscopic Analysis ◽

Model Systems ◽

Solvent Interactions ◽

Solvent Molecules

A VCD spectroscopic analysis of selected model systems for solute–solvent interactions of chiral diols with hydrogen bonding solvents DMSO and ACN.

Download Full-text

Synthesis and crystal structures of some bis(3-methyl-1H-indol-2-yl)(salicyl)methanes

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229618017758 ◽

2019 ◽

Vol 75 (1) ◽

pp. 65-69

Author(s):

Wyatt Cole ◽

Stephanie L. Hemmingson ◽

Audrey C. Eisenberg ◽

Catherine A. Ulman ◽

Joseph M. Tanski ◽

...

Keyword(s):

Hydrogen Bonding ◽

Dimethyl Sulfoxide ◽

Crystal Structures ◽

Double Layer ◽

Acid Catalysis ◽

Double Layers ◽

One Dimensional ◽

Salicylaldehyde Derivatives ◽

Central Carbon ◽

Solvent Molecules

Four 2,2′-bisindolylmethanes (BIMs), a useful class of polyindolyl species joined to a central carbon, were synthesized using salicylaldehyde derivatives and simple acid catalysis; these are 2-[bis(3-methyl-1H-indol-2-yl)methyl]-6-methylphenol, (IIa), 2-[bis(3-methyl-1H-indol-2-yl)methyl]-4,6-dichlorophenol, (IIb), 2-[bis(3-methyl-1H-indol-2-yl)methyl]-4-nitrophenol, (IIc), and 2-[bis(3-methyl-1H-indol-2-yl)methyl]-4,6-di-tert-butylphenol, (IId). BIMs (IIa) and (IIb) were characterized crystallographically as the dimethyl sulfoxide (DMSO) disolvates, i.e. C26H24N2O·2C2H6OS and C25H20Cl2N2O·2C2H6OS, respectively. Both form strikingly similar one-dimensional hydrogen-bonding chain motifs with the DMSO solvent molecules. BIM (IIa) packs into double layers of chains whose orientations alternate every double layer, while (IIb) forms more simply packed chains along the a axis. BIM (IIa) has a remarkably long c axis.

Download Full-text

Crystal structure of chlorido(5,10,15,20-tetraphenylporphyrinato-κ4N)manganese(III) 2-aminopyridine disolvate

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s205698901500050x ◽

2015 ◽

Vol 71 (2) ◽

pp. 165-167 ◽

Cited By ~ 1

Author(s):

Wafa Harhouri ◽

Salma Dhifaoui ◽

Shabir Najmudin ◽

Cecilia Bonifácio ◽

Habib Nasri

Keyword(s):

Crystal Structure ◽

Hydrogen Bonding ◽

Hydrogen Bonds ◽

Title Compound ◽

Axial Ligand ◽

Pyramidal Geometry ◽

Porphyrin Macrocycle ◽

Planar Conformation ◽

Solvent Molecules ◽

Square Pyramidal Geometry

In the title compound, [Mn(C44H28N4)Cl]·2C5H6N2, the MnIIIcentre is coordinated by four pyrrole N atoms [averaged Mn—N = 2.012 (4) Å] of the tetraphenylporphyrin molecule and one chloride axial ligand [Mn—Cl = 2.4315 (7) Å] in a square-pyramidal geometry. The porphyrin macrocycle exhibits a non-planar conformation with majorrufflingandsaddlingdistortions. In the crystal, two independent solvent molecules form dimers through N—H...N hydrogen bonding. In these dimers, one amino N atom has a short Mn...N contact of 2.642 (1) Å thus completing the Mn environment in the form of a distorted octahedron, and another amino atom generates weak N—H...Cl hydrogen bonds, which link further all molecules into chains along theaaxis.

Download Full-text

Hydrogen-bond patterns in 1,4-dihydro-2,3-quinoxalinediones: ligands for the glycine modulatory site on the NMDA receptor

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768195011773 ◽

1996 ◽

Vol 52 (3) ◽

pp. 487-499 ◽

Cited By ~ 11

Author(s):

M. Kubicki ◽

T. W. Kindopp ◽

M. V. Capparelli ◽

P. W. Codding

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonding ◽

Binding Site ◽

Three Dimensional ◽

Hydrogen Bonding Pattern ◽

Wide Range ◽

Show Evidence ◽

Additional Hydrogen Bond ◽

Hydrogen Bond Patterns ◽

Solvent Molecules

The crystal structures of five 1,4-dihydro-2,3-quinoxalinediones, antagonists of the NMDA modulatory glycine binding site on the excitary amino acid (EAA) receptor complex, have been determined: (I) 6,7-dinitro-1,4-dihydro-2,3-quinoxalinedione (DNQX); (II) 5,7-dinitro-1,4-dihydro-2,3-quinoxalinedione (MNQX); (III) 6-nitro-1,4-dihydro-2,3-quinoxalinedione hydrate; (IV) 6,7-dichloro-1,4-dihydro-2,3-quinoxalinedione; (V) 5,7-dichloro-1,4-dihydro-2,3-quinoxalinedione dimethylformamide. The crystal structure of the most active compound (II) contains a unique intramolecular N—H...O(NO2) hydrogen bond, which may be important for activity, as semiempirical calculations show that this bond is stable over a wide range of dihedral angles between the planes of the molecule and of the nitro group. In the other compounds the intermolecular hydrogen bonds connect molecules into three-dimensional networks. In compounds (I), (III) and (IV) head-to-tail: π-stacking is found between molecules connected by a center of symmetry. The geometries of the hydrogen-bonded —NH—C=O fragments show evidence of π-cooperativity or resonance-assisted hydrogen bonding. Graph-set analysis of the hydrogen-bond patterns of quinoxalinedione derivatives shows a tendency to form two types of hydrogen-bonding motifs: a centrosymmetric dimeric ring and an infinite chain. Even though this pattern may be modified by the presence of additional hydrogen-bond acceptors and/or donors, as well as by solvent molecules, general similarities have been found. Comparison of all quinoxalinedione structures suggests that the hydrogen-bonding pattern necessary for the biological activity at the glycine binding site contains one donor and two acceptors.

Download Full-text

The effect of the coordination orientation of N atoms on polymeric structures: synthesis and characterization of one- and two-dimensional CuII coordination polymers based on 4-amino-3-(pyridin-2-yl)-5-[(pyridin-3-ylmethyl)sulfanyl]-1,2,4-triazole

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229619003747 ◽

2019 ◽

Vol 75 (4) ◽

pp. 443-450

Author(s):

Guiying Zhu ◽

Yang Lu ◽

Guoxia Jin ◽

Xuan Ji ◽

Jianping Ma

Keyword(s):

Hydrogen Bonding ◽

Coordination Polymers ◽

3D Structure ◽

Three Dimensional ◽

Great Influence ◽

Two Dimensional ◽

3D Network ◽

Solvent Molecules ◽

Bonding Systems ◽

Polymeric Structures

Three new one- (1D) and two-dimensional (2D) CuII coordination polymers, namely poly[[bis{μ2-4-amino-3-(pyridin-2-yl)-5-[(pyridin-3-ylmethyl)sulfanyl]-1,2,4-triazole}copper(II)] bis(methanesulfonate) tetrahydrate], {[Cu(C13H12N5S)2](CH3SO3)2·4H2O} n (1), catena-poly[[copper(II)-bis{μ2-4-amino-3-(pyridin-2-yl)-5-[(pyridin-4-ylmethyl)sulfanyl]-1,2,4-triazole}] dinitrate methanol disolvate], {[Cu(C13H12N5S)2](NO3)2·2CH3OH} n (2), and catena-poly[[copper(II)-bis{μ2-4-amino-3-(pyridin-2-yl)-5-[(pyridin-4-ylmethyl)sulfanyl]-1,2,4-triazole}] bis(perchlorate) monohydrate], {[Cu(C13H12N5S)2](ClO4)2·H2O} n (3), were obtained from 4-amino-3-(pyridin-2-yl)-5-[(pyridin-3-ylmethyl)sulfanyl]-1,2,4-triazole with pyridin-3-yl terminal groups and from 4-amino-3-(pyridin-2-yl)-5-[(pyridin-4-ylmethyl)sulfanyl]-1,2,4-triazole with pyridin-4-yl terminal groups. Compound 1 displays a 2D net-like structure. The 2D layers are further linked through hydrogen bonds between methanesulfonate anions and amino groups on the framework and guest H2O molecules in the lattice to form a three-dimensional (3D) structure. Compound 2 and 3 exhibit 1D chain structures, in which the complicated hydrogen-bonding interactions play an important role in the formation of the 3D network. These experimental results indicate that the coordination orientation of the heteroatoms on the ligands has a great influence on the polymeric structures. Moreover, the selection of different counter-anions, together with the inclusion of different guest solvent molecules, would also have a great effect on the hydrogen-bonding systems in the crystal structures.

Download Full-text