Bond Bundles and the Origins of Functionality

Abstract

We briefly review the method by which the electron charge density of atomic systems is decomposed into unique volumes called bond bundles, which are characterized by well-defined and additive properties. We then show that boundaries of bond bundles topologically constrain their chemical reactivity. To illustrate this fact, we model the response of the bond bundles of ethane and ethene to electrophilic attack and from the results of these models posit that functional group properties can be inferred from the shapes of their bond bundles. By relating functionality to bond bundle shape, it is possible to see subtle changes in chemical reactivity that are otherwise difficult to explain, as is illustrated by comparing bond bundles through a series of impact sensitive polynitroaromatic molecules.

Predictive methods for computational metalloenzyme redesign – a test case with carboxypeptidase A

“…The change in r(r) between the ring-bond CPs is only 0.0392 e Bohr À3 in the native enzyme while it is 0.0467 e Bohr À3 in V243R_FpepD. In accordance with the electron-preceding picture, [92][93][94][95] it should be less energy intensive for the native enzyme ring CP to annihilate the bond CP than in the mutant enzyme, which agrees with our mechanistic study, and QTAIM predictions based on the reactant states. The observed correspondence between values of r(r) at bond and ring CPs in the reacting region combined with bond bundle analysis and the energetic barrier to the reaction outlines a potential strategy for predicting enzyme reactivity.…”

“…67,68 The shape, size, and valence electron count of bond bundles have been used to understand chemical reactivity and stability. 69,70 The electronic charge densities of the native enzyme and V243R, hippuryl-L-aspartate mutant with the bound substrates (in the ES, TS, and EI states) were calculated using the Amsterdam Density Functional Package (ADF) version 2014.01 66,71-73 using similar computational parameters as in the QM mechanistic study. Single point calculations were performed on the reactant, transition state, and intermediate complexes using the nuclear coordinates from the stationary states obtained in the mechanistic study described below.…”

In search of an intrinsic chemical bond

“…In an open system-a molecule or a solid with a free surface-all four types of CPs need not be present, in which case some of the 1-ridges will be of infinite length and some of the 2-ridges will have infinite area [12,15]. In such systems the 2-ridges form a set of open tetrahedra [16,17].…”

A Full Topological Analysis of Unstable and Metastable Bond Critical Points

“…Compared to the H 2 bond bundle, the HÀH bond bundle of the phenyl complex is small in both total volume and electron count (0.6 e À AE 0.3 e À ) and possesses a structure that has been associated with incipient instability. [31,32] It is precisely the bond bundle interaction that points to Pauli repulsion as the mechanism destabilizing the phenyl complex. The bond CP between the hydrogen atoms necessitates a HÀH bond bundle that competes for the same space as the CÀH bond bundle, thereby displacing its boundary, as shown in Figure 4.…”