Binding neutral guests to concave surfaces of molecular hosts. Directional association of water and methylene chloride with hosts containing only cyclic urea binding sites

This paper is concerned with studies of weak intermolecular interactions in molecular inclusion type systems involving uncharged host and guest entities. Three new complexes of synthetic organic ligands with water and methylene chloride have been characterized by single-crystal X-ray diffraction. The hosts are composed of three cyclic urea units whose carbonyl groups are held in convergent positions by bonding their attached nitrogens to one another through two (noncyclic ligand) or three (macrocyclic ligand) rigid spacer units. Conformational organization is further enforced by an aliphatic bridge between two of the phenylene spacers in the macrocyclic hosts and an additional dimerization of the open-chain ligand. The host species were found to be particularly suitable to interact with proton donating H₂O and CH₂Cl₂ guest moieties, as their molecular surface contains appropriately sized polar cavities lined with the carbonyl functions. Association between the interacting components in these complexes is stabilized by O–HO and C–HO hydrogen bonds. In the corresponding crystal structures additional molecules of the solvent are located between units of the complex. The significance of preorganization of the host structure to an efficient guest binding is emphasized by an observation that no stable complexes of a similar but unbridged macrocyclic ligand could be crystallized from the same solvent. The structural features of the inclusion compounds are described in detail, and the host-guest interaction scheme is compared to that observed in complexes of 18-crown-6 with neutral guests. Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82039 (98 pages)     

Comparison of potential energy maps and molecular shape invariance maps for two-dimensional conformational problems

Summary It is well known that many molecular properties are strongly dependent on internal nuclear arrangements. Two possible, independent approaches can be followed while studying changes in molecular characteristics as functions of the nuclear geometry. These are the analysis of potential energy surfaces and the analysis of molecular shape. In this work, we seek to establish relationships between potential energy maps and shape invariance region maps, where each point of these maps represents a nuclear configuration. The study is performed by analyzing the occurrence and lack of certain symmetries in both types of maps. As illustrative examples, we consider the three structural isomers of the dihydroxybenzene molecule. Potential energy is computed at the STO-3G ab initio level, while the shape is described by the shape group method as applied to fused-sphere van der Waals surfaces. It is shown that the symmetry of the shape invariance maps follows closely, but not exactly, the symmetry of potential energy surfaces. The molecular surface is thus blind to some small changes of the potential (a feature to be expected to hold also for molecular surfaces defined in terms of electronic charge density). Our findings suggest that a crude fused-sphere model may suffice to describe some of the structural changes in molecular surfaces, as well as their relationships to the electronic energy.     

A rapid method for molecular shape comparison of medium-sized molecules. Conformational calculations on sandalwood odor,IV

Summary A fast method of a surface comparison of two or more molecules to be matched is presented. The Van der Waals surfaces of molecules are described by points calculated as the intersection of grid lines with the molecular surface. The mean surface of various molecules with the same biological activity can be constructed. It is used for further comparisons with similar molecules lacking this activity. Deviations of any molecular surface from the mean surface can be mapped onto the surface. The method was tested on a distinct group of sandalwood odor molecules and it was shown that such matching and comparison procedures are useful in the investigation of odor structure-activity relationships proposed as CAFD (computer aided fragrance design).Dedicated to Prof. Dr. W. Fleischhacker, on occasion of his 60th anniversary     

Potential energy surfaces for van der waals complexes of rare gases with H2S and H2S2: Extension to xenon interactions and hyperspherical harmonics representation

This article is an account and extension of a series of recent investigations, which using extensive quantum chemical methods provide analytical hyperspherical representations of the potential energy surfaces for the interactions of rare gases with H₂S as a rigid molecule, and H₂S₂, considered as a floppy molecule with respect to torsional mode. For the H₂S‐rare gas systems, the representation is based on a minimal model, here introduced and discussed. For H₂S₂, the study of the interaction with Xe, not considered previously, completes the series. The results are discussed with reference to the properties and trends expected for interactions of van der Waals type. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Crystal and molecular structure of a crown-bridgedp-t-butyl-calix[4]arene (1:1) pyridine complex. Host-guest interaction model based on molecular mechanics analysis [1]

The crystal and molecular structure of a crownedp-t-butyl-calix[4]arene (1:1) pyridine complex is reported. Colourless transparent prismatic crystals (obtained from pyridine) C₅₄H₇₄O₈·C₅H₅N,a=13.486(4),b=15.193(4),c=16.432(5) Å, =116.44(4)°, space groupP2₁,Z=2,D _calc=1.02g cm^–3, CuK radiation =1.5418 Å (CuK )=4.99 cm^–1. Refinement was carried out using 1702 reflections withI>3(I) toR 0.12. The macrocycle shows a distorted cone conformation which defines an intramolecular apolar cavity whose elliptical aperture is 11.5×8.6 Å calculated as distances between the two opposite central C atoms of the Bu ^t groups. A molecule of pyridine is included in this cavity, whereas the intermolecular cavities of the host lattice remain empty. The influence of the guest molecule on the conformation of the calixarene-crown is discussed. Potential energy calculations are performed in order to understand the nature of the host-guest interactions responsible for the stabilisation of the complex. Evidence for stabilizing CH₃- interactions are obtained from the calculations. Supplementary Data relevant to this article have been deposited with the British Library as supplementary Publication No. SUP 82068 (9 pages).     

Thermodynamic analysis of equilibria between binary liquid and solid solutions in ternary systems. Application to systems in which two guests compete for sites in the same host,tetrakis(4-methylpyridine)nickel(II) isothiocyanate

A thermodynamic analysis is presented of the equilibria between liquid solutions of guest A in guest B and solid solutions of HA in HB, where HA and HB are isomorphous 1:1 compounds of these guests with the host H. (The treatment is applicable whether or not HA and HB are inclusion compounds.) The mole ratio of A to B in the liquid,R ₁, is generally different from the same ratio in the solid,R _s. Data on many systems have indicated a linear relation between InR ₁, and InR _s, but to date no theoretical basis has been forthcoming. The present analysis shows that this relation is usually sigmoidal in shape but, with certain restrictions, is nearly linear. The slope and intercept are interpreted in terms of the equilibrium constant for the displacement of A from HA by B and the deviations from ideality in the liquid and solid phases. If the deviations from ideality in the liquid phase are known or can be estimated, those for the solid phase can be determined, and thermodynamic equilibrium constants and standard free energy changes for the displacement of A by B calculated. These methods were applied to available data for the following pairs of guests with the host Ni(4-mepy)₄(NCS)₂:p-xylene with each ofp-dibromobenzenp-xylene-d₆,p-xylene-d ₁₀,p-bromotoluene,p-chlorotoluene,p-dichlorobenzene,p-fluorotoluene, ethylbenzene, toluene, and benzene, and the pairsp-dichlorobenzene/p-chlorotoluene and ethylbenzene/ toluene.