Hydrogen bond

About: Hydrogen bond is a research topic. Over the lifetime, 57701 publications have been published within this topic receiving 1306326 citations.

Cryptates: inclusion complexes of macropolycyclic receptor molecules

Abstract: Molecular receptors use intermolecular interactions for the selective binding of substrates. Macropolycyclic molecules containing appropriate binding sites and cavities of suitable size and shape, may be designed so as to display molecular recognition in the formation of selective inclusion complexes, cryptates, with metal cations, anions and molecules. Macrocyclic receptors which form stable and selective complexes with primary ammonium and guanidinium groups are discussed; they display central and lateral discrimination. Enhanced rates of intramolecular thiolysis and hydrogen transfer have been observed when suitable reactive groups are attached to the receptor. Macrobicyclic ligands form very stable and selective cryptates with alkali and alkaline-earth cations; they may be modified so as to selectively complex toxic heavy metal cations. Binuclear cryptates of two types have been synthesized: macrobicyclic complexes of an ellipsoidal Bis-Tren ligand and cylindrical macrotricyclic complexes. They display interesting properties (like cation-cation interactions, copper protein type spectral parameters etc.) and are suitable for formation of “cascade complexes” by interaction of substrates with the bound cations. Spherical macrotricyclic receptors form cryptates with cations, anions and small inorganic species. They display tetrahedral recognition and may be considered as topologically optimal receptors for the ammonium ion, the water molecule, the halide ions, with which they form cryptates where the substrate is held in the intramolecular cavity by a tetrahedral array of hydrogen bonds. Finally, the macrobicyclic Bis-Tren system in its protonated form, complexes triatomic species like the azide anion. It represents a further step in the design of abiotic molecular receptors for polyatomic molecules or ions. The main lines of further developments in the chemistry of macropolycycles comprise the design of receptors for other important groups (carboxylate, phosphate), of polynuclear complexes and cascade complexes of potential use in polynuclear catalysis, of molecular catalysts as enzyme models and new chemical reagents.

Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N‐methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases

Abstract: We have developed a methodology to derive RESP charges for molecular mechanical models that include “lone pairs” on lone-pair donor sites and atom-centered polarizabilities. This approach uses a very high level ab initio cc-pVTZ basis set,1 where the multipole moments of the molecules are as accurate as possible. The partial charges are derived self-consistently so that the model, whose electrostatic potential comes from both partial charges and induced dipoles, reproduces the quantum mechanical electrostatic potential. We then study the ability of such models to reproduce the aqueous solvation free energy of methanol and N-methyl acetamide (NMA), the base pair hydrogen bonding of the 26 base pairs analyzed by Hobza et al. and the chloroform/water partition coefficients of the five N-methyl substituted nucleic acid bases. The base pair H-bond energies are described as well as the atom centered additive model, after modifying the van der Waals parameter on the NH to give reasonable base pair H-bond distances. The experimental solvation free energies (gas→water) of methanol and NMA are well described, and the water/CHCl3 partition coefficients are improved over the additive model, without any parameter changes. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1048–1057, 2001