A series of methylated and non-methylated β-cyclodextrin (β-CD) structures in three macrocyclic configurations (a-c) were studied with molecular dynamics (MD) simulations to elucidate the dynamic behavior of the different CD structures using a continuum water model with the AMBER* force field. A set of parameters were defined to describe the geometric dimensions of the CD, such as its cavity shape, the upper and lower rim sizes, and the tilting of each of the glucose rings. Correlation analyses between the different parameters were carried out, and they have provided insights into the different dynamic behaviors for the different CD structures. Detailed analyses on the crystal structures of the different methylated and non-methylated β-CD complexes were also carried out using the defined parameters. Correlation of parameters from crystal structures and MD simulations has allowed us to identify the effect that crystal packing/guest inclusion has on the CD geometries. The overall analysis approach can be a useful tool for other related macrocyclic structures, such as modified α-, β-CDs or even calixarenes.
A quantitative description of chemical bonds in bis(diiminosuccinonitrilo)nickel, Ni(disn) 2 , is made in terms of topological properties of electron densities. These properties are obtained both from an X-ray diffraction experiment and from molecular orbital calculations. The asphericity in electron density around the Ni ion is surely observable from the Laplacian of the electron density with density accumulation in the d π direction but density depletion along the d σ (Ni-N) direction. On the basis of the topological properties at bond critical points, the bonding between Ni and the imino nitrogen atom is classified as mainly a closed-shell interaction but with some covalent character. The bonds within the ligand, disn, are all shared interactions, and the bond order is reflected clearly from the density at the critical point, F(r c ). The π-delocalization of the molecule is precisely indicated by the bond ellipticity and is illustrated by Fermi-hole distribution. Atom domains in the molecule are demonstrated. Molecular electrostatic potential is derived both from experiment and from MO calculations. For all the properties, the agreement between experiment and theory is reasonable.
Hydrogen bonding and charge interactions are both essential for molecular recognition and the self-assembly of biological macromolecules. They are also employed heavily in the design of new systems for fundamental, biological, and materials research. The influence of a charge-bearing functional group on pK a values [1] and chemical reactivity [2] has been well documented in the form of Hammett-type substituent constants in physical organic studies. Changes in the hydrogen-bonding behavior of ligands upon complexation with cationic transition metal centers have been indicated by theoretical calculations. [3] Such calculations also indicated that anions could induce a large cooperative effect in the hydrogen-bonding network of peptides. [4] Enhancement was observed experimentally in urea´carboxylate binding when the carbonyl group of the urea molecule was coordinated to a Lewis acid. [5] The optical property of [Ru(bpy) 3 ] 2 (bpy bipyridine) in a phosphodiester sensor was changed when the hydrogen-bonding sites were bound. [6] Although both hydrogen-bonding and charge-bearing sites are important in molecular recognition, interestingly, it is not common to find examples in supramolecular chemistry in which hydrogenbonding sites are designed to be controlled by a covalently bound charge-bearing substituent. Charge-assisted CÀH´´´X hydrogen bonds have been recognized in recent years [7] and metallocene complexes have been used to achieve redoxswitched binding. [8] Nevertheless, the binding sites are basically adjacent to the charged centers, and we felt that charge centers can have a more far-reaching influence on a binding site.If a charged group and a binding site can communicate with each other, one can use a three-component system (a charged group, a linker, and a binding site) as a signal transducer. The charge-bearing group can be viewed as a reaction site, whose charge state can be altered by reactions such as protonation, metalation, oxidation, reduction, or chemical transformation of a functional group. On the basis of this concept we designed test compounds 1 a ± d and 2 a ± d, and calculated the energies N X X N H H N X X N H H H n n 1a: X = CH, n = 1 1b: X = CH, n = 2 1c: X = CH, n = 3 1d: X = CH, n = 4 2a: X = CH, n = 1 2b: X = CH, n = 2 2c: X = CH, n = 3 2d: X = CH, n = 4 3a: X = N, n = 1 3b: X = N, n = 2 3c: X = N, n = 3 3d: X = N, n = 4 4a: X = N, n = 1 4b: X = N, n = 2 4c: X = N, n = 3 4d: X = N, n = 4of formation of a hydrogen bond (binding energies) to find out how efficiently the reaction and binding centers can communicate with each other. In these compounds the reaction center is an imine group and the binding center is pyrrole; compounds 1 a ± d are neutral imines and 2 a ± d are cationic iminium compounds. Ammonia was chosen as the hydrogen-bonding partner of the NÀH group of pyrrole for the sake of geometric simplicity, since it only has one lone pair of electrons. The ammonia binding energy of 2 a (À 13.17 kcal mol À1 ) at the HF/6-31G* level is double that of cationic 1 a (À 6.84 kcal mo...
Density functional theory (DFT) at the B3LYP/6–31 + G(d,p)//B3LYP/6–31G(d) level was used to calculate 17O and 13C NMR chemical shifts of the carbonyl group of aromatic acyl chlorides 1a–n. The aryl groups included substituted phenyl, furyl, thienyl and naphthyl. The calculated 17O chemical shifts correlated well with the experimental values and with Hammett‐type σ+ constants. Therefore, in many cases it is possible to deduce σ+ constants of substituted aryl groups via gas‐phase calculation of 17O chemical shifts of the carbonyl groups. The σ+ values obtained in the gas‐phase calculation show the intrinsic property of substituents, so they provide a good reference set for systematic comparison to evaluate the effect of the environment. Furthermore, the concept of n–π* mixing can be used to understand the sensitivity of the O and Cl atoms and the insensitivity of the C atom towards substituent effects in aromatic acyl chlorides. Copyright © 2001 John Wiley & Sons, Ltd.
Signal enhancement from a reaction center to a hydogen‐bonding site occurs when they are separated by an azo linker (see schematic representation). A computational study has shown that the binding of ammonia to a pyrrole unit in an iminium compound increases as the length of the azo group between the two sites increases. This surprising result is explained in terms of resonance effects and the larger electron‐withdrawing power of longer azo linkers.
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