Ligand close packing, molecular compactness, the methyl tilt, molecular conformations, and a new model for the anomeric effect.

All the atoms in a molecule attract each other until they reach their equilibrium positions at which point the repulsive forces between the atoms just balance the attractive forces and there are no resultant forces acting on any of the atoms in the molecule. Thus, we can consider that in the equilibrium geometry the atoms in a molecule are arranged as compactly as possible. This is the basis of the ligand close packing (LCP) model according to which three or four monatomic ligands X, such as F, Cl or O (formally =O or O(-)) pack as closely as possible around a small central atom such as a boron or carbon atom giving a truly close-packed equilateral triangular AX(3) molecule or a tetrahedral AX(4) molecules. Such monatomic ligands can, to a good approximation, be described as having a spherical shape with a single ligand radius r(X). In contrast, ligands with donor atoms with lone pairs such as the oxygen atom in an OX group have a less symmetrical electron density requiring two ligand radii, r(O(lp)) in the lone pair direction, and r(O(b)) in the bonding direction, where r(O(lp)) < r(O(b)) for an approximate description. On this basis we propose an explanation for the "methyl tilt", in methanol and many related molecules, and in conjunction with the concept of compactness, a model for explaining the relative energies of the conformations of molecules containing OH and OMe ligands, including molecules that exhibit the anomeric effect. We compare our model for the anomeric effect with the widely accepted "hyperconjugation" model. We also discuss the relationship between the concept of compactness and the concept of hardness.

A topological study of the geometry of AF6E molecules: weak and inactive lone pairs.

The geometries of AF6E molecules, which may have either an O(h) or a C(3v) geometry, have been studied by means of the electron localization function. Our results show that when the molecule has a C(3v) geometry, there is a valence-shell monosynaptic V(A) basin corresponding to the presence of a lone pair in the valence shell of the central atom A. The population of this basin is, however, extensively delocalized so that the electron density has a core-valence basin character, which is consistent with an earlier suggestion of a weakly active lone pair that gives a C(3v) distorted octahedral molecule rather than the valence-shell electron-pair repulsion predicted pentagonal-pyramid geometry. In contrast, the molecules with O(h) geometry do not have a monosynaptic valence-shell basin, but they have a larger core. These results provide confirmation of a previous suggestion that in AX6E (X = Cl, Br, I) molecules with the O(h) geometry the ligands X are sufficiently closely packed around the central atom A so as to leave no space in the valence shell for the lone pair E, which remains part of the core. Among the corresponding fluorides, only BrF6- has the O(h) geometry, while the others have the C(3v) geometry because there is sufficient space in the valence shell to accommodate the lone pair, the presence of which distorts the O(h) geometry to C(3v). The energies of the O(h) and C(3v) geometries have been shown to be very similar so the observed geometries are a consequence of a very fine balance between ligand-ligand repulsions and the energy gained by the expansion of the two nonbonding electrons into the valence shell.

Models of molecular geometry.

Although the structure of almost any molecule can now be obtained by ab initio calculations chemists still look for simple answers to the question "What determines the geometry of a given molecule?" For this purpose they make use of various models such as the VSEPR model and qualitative quantum mechanical models such as those based on the valence bond theory. The present state of such models, and the support for them provided by recently developed methods for analyzing calculated electron densities, are reviewed and discussed in this tutorial review.

Continuous real-time monitoring of phosphine concentrations in air using electrochemical detectors interfaced by radio telemetry.

This work involves the novel use of a radio telemetry-based system that continuously monitors phosphine using two different types of electrochemical detectors (ECD/RT). The ECD/RT units were used to monitor phosphine inside and at varying distances from large tobacco storage warehouses. A master controller unit transferred the data to a personal computer that received and displayed the data. Supervisory control and data acquisition software assimilated the data from each ECD/RT unit, displayed and updated it as new transmissions were received, and stored the data in secure databases. Phosphine concentrations outside five warehouses simultaneously under fumigation and at the facility boundaries were <0.3 parts per million (ppm). Phosphine levels ranged from 0 to 580 ppm inside sealed warehouses. A comparison was made between the data collected at an ECD/RT unit approximately 4 m downwind of a sealed warehouse and a colorimetric tube at the same location. The final phosphine concentration from the colorimetric method was 0.05 ppm and the average over the 20-minute collection period for the ECD/RT was 0.13 ppm. This system allows for continuous, remote monitoring around warehouses under fumigation and superior time resolution allowing timely response to fugitive emissions of phosphine.

Bond Lengths and Bond Angles in Oxo, Hydroxo, and Alkoxo Molecules of Be, B, and C: A Close-Packed Nearly Ionic Model.

We have surveyed the experimental data for oxo, hydroxo, and alkoxo molecules of Be, B, and C and have shown that the intramolecular interligand distances for a given central atom are remarkably constant and independent of coordination number and of the presence of other ligands. Atomic charges obtained from the analysis of the calculated electron densities for a large selection of molecules of this type have shown that these molecules are predominately ionic. On the basis of these results we suggest that the bond lengths and geometries of these molecules can be best understood in terms of a model in which anion-like ligands are close-packed around a cation-like central atom. Values of the interligand radius of each ligand obtained from the intramolecular interligand contact distances are smaller than the crystal ionic radii and decrease as expected with decreasing ligand charge. This model provides a simple quantitative explanation of the decrease in the bond lengths in these molecules with decrease in the coordination number from four to three and of the changes in bond length caused by the presence of other ligands with different ligand radii. With decreasing bond length the electron density at the bond critical point increases correspondingly for Be-O, B-O, and C-O bonds. The nontetrahedral angles found in all A(OX)(4) molecule are explained on the basis of a noncylindrically symmetrical charge distribution around oxygen.

Bonding and Geometry of OCF(3)(-), ONF(3), and Related Molecules in Terms of the Ligand Close Packing Model.

The nature of the bonding in OCF(3)(-) and the isoelectronic molecule ONF(3) has been the subject of much discussion for many years, because these species appear to have unusual bond lengths and angles. We have reinvestigated the nature of the bonding in these and some related molecules by analyzing their calculated electron density distributions. The results show that the bonding in the series OBF(3)(2)(-), OCF(3)(-), ONF(3) ranges from predominately ionic in OBF(3)(2)(-) to predominately covalent in ONF(3) and that the interligand distances are consistent with the close packing of the ligands around the central atom. The AO bonds (A = B, C, N) are double bonds ranging in nature from a very ionic B=O bond to a predominately covalent N=O double bond, but all three are strong and short so that, in accordance with the ligand close packing (LCP) model, the AF bonds are correspondingly long. Also consistent with this model the bonds in a three-coordinated AOF(2) molecule are shorter than those in the corresponding AOF(3) molecule. Protonation of the doubly bonded oxygen, which converts the A=O bond to a single A-OH bond in each case, considerably lengthens the A-O bond, and the bond angles accordingly adopt values much closer to the tetrahedral angle. The difficulties of trying to describe the bonding in these molecules in terms of Lewis structures are discussed.

Reinterpretation of the Lengths of Bonds to Fluorine in Terms of an Almost Ionic Model.

We have calculated the electron density distributions, electron densities at the bond critical point, and atomic charges in the period 2 and 3 fluorides and a number of their cations and anions. On the basis of this information and an analysis of X-F bond lengths, we have examined the factors that determine the lengths of these bonds. We have shown that all the molecules except NF(3), OF(2), and F(2) have considerable ionic character. The bond lengths of the fluorides reach a minimum value at BF(3) in period 2 and at SiF(4) in period 3 when the product of the charges on the central atom and a fluorine reaches a maximum, consistent with a predominately ionic model for these fluorides. The length of a given A-F bond decreases with decreasing coordination number, and we show that it is determined primarily by packing considerations. This provides an alternative to the previously proposed back-bonding model explanation, for which our work provides no convincing evidence. There is also no evidence to support the Schomaker-Stevenson equation which has been widely used to correct A-F bond lengths calculated from the sum of the covalent radii of A and F for the difference in the electronegativities of A and F. We propose a new value for the covalent radius of fluorine and point out the limitations of its use.