Bond Bundle Analysis of Ketosteroid Isomerase.

Bond bundle analysis is used to investigate enzymatic catalysis in the ketosteroid isomerase (KSI) active site. We identify the unique bonding regions in five KSI systems, including those exposed to applied oriented electric fields and those with amino acid mutations, and calculate the precise redistribution of electron density and other regional properties that accompanies either enhancement or inhibition of KSI catalytic activity. We find that catalytic enhancement results from promoting both inter- and intra-molecular electron density redistribution, between bond bundles and bond wedges within the KSI-docked substrate molecule, in the forward direction of the catalyzed reaction. Though the redistribution applies to both types of perturbed systems and is thus suggestive of a general catalytic role, we observe that bond properties (e.g., volume vs energy vs electron count) can respond independently and disproportionately depending on the type of perturbation. We conclude that the resulting catalytic enhancement/inhibition proceeds via different mechanisms, where some bond properties are utilized more by one type of perturbation than the other. Additionally, we find that the correlations between bond wedge properties and catalyzed reaction barrier energies are additive to predict those of bond bundles and atomic basins, providing a rigorous grounding for connecting changes in local charge density to resulting shifts in reaction barrier energy.

Neighborhoods and functionality in metals.

The fundamental construct of organic chemistry involves understanding molecular behavior through functional groups. Much of computational chemistry focuses on this very principle, but metallic materials are rarely analyzed using these techniques owing to the assumption that they are delocalized and do not possess inherent functionality. In this paper, we propose a methodology that recovers functional groups in metallic materials from an energy perspective. We characterize neighborhoods associated with functional groups in metals by observing the evolution of Bader energy of the central cluster as a function of cluster size. This approach can be used to conceptually decompose metallic structure into meaningful chemical neighborhoods allowing for localization of energy-dependent properties. The generalizability of this approach is assessed by determining neighborhoods for crystalline materials of different structure types, and significant structural defects such as grain boundaries and dislocations. In all cases, we observe that the neighborhood size may be universal-around 2-3 atomic diameters. In its practical sense, this approach opens the door to the application of chemical concepts, e.g., orbital methods, to investigate a broad range of metallurgical phenomena, one neighborhood at a time.

Electron Density Geometry and the Quantum Theory of Atoms in Molecules.

A novel form of charge density analysis, that of isosurface curvature redistribution, is formulated and applied to the toy problem of carbonyl oxygen activation in formaldehyde. The isosurface representation of the electron charge density allows us to incorporate the rigorous geometric constraints of closed surfaces toward the analysis and chemical interpretation of the charge density response to perturbations. Visual inspection of 2D isosurface motion resulting from applied external electric fields reveals how the isosurface curvature flows within and between atoms and that a molecule can be uniquely and completely partitioned into chemically significant regions of positive and negative curvatures. These concepts reveal that carbonyl oxygen activation proceeds primarily through curvature and charge redistribution within rather than between Bader atoms. Using gradient bundle analysis─the partitioning of formaldehyde into infinitesimal volume elements bounded by QTAIM zero-flux surfaces─the observations from visual isosurface inspection are verified. The results of the formaldehyde carbonyl analysis are then shown to be transferable to the substrate carbonyl in the ketosteroid isomerase enzyme, laying the groundwork for extending this approach to the problems of enzymatic catalysis.

Predicting Chemical Reactivity from the Charge Density through Gradient Bundle Analysis: Moving beyond Fukui Functions.

Predicting chemical reactivity is a major goal of chemistry. Toward this end, atom condensed Fukui functions of conceptual density functional theory have been used to predict which atom is most likely to undergo electrophilic or nucleophilic attack, providing regioselectivity information. We show that the most probable regions for electrophilic attack within each atom can be predicted through analysis of gradient bundle volumes, a property that depends only on the charge density of the neutral molecules. We also introduce gradient bundle condensed Fukui functions to compare the stereoselectivity information obtained from gradient bundle volume analysis. We demonstrate this method using the test set of molecular fluorine, oxygen, nitrogen, carbon monoxide, and hydrogen cyanide.

The influence of zero-flux surface motion on chemical reactivity.

Visualizing and predicting the response of the electron density, ρ(r), to an external perturbation provides a portion of the insight necessary to understand chemical reactivity. One strategy used to portray electron response is the electron pushing formalism commonly utilized in organic chemistry, where electrons are pictured as flowing between atoms and bonds. Electron pushing is a powerful tool, but does not give a complete picture of electron response. We propose using the motion of zero-flux surfaces (ZFSs) in the gradient of the charge density, ∇ρ(r), as an adjunct to electron pushing. Here we derive an equation rooted in conceptual density functional theory showing that the movement of ZFSs contributes to energetic changes in a molecule undergoing a chemical reaction. Using a substituted acetylene, 1-iodo-2-fluoroethyne, as an example, we show the importance of both the boundary motion and the change in electron counts within the atomic basins of the quantum theory of atoms in molecules for chemical reactivity. This method can be extended to study the ZFS motion between smaller gradient bundles in ρ(r) in addition to larger atomic basins. Finally, we show that the behavior of ∇ρ(r) within atomic basins contains information about electron response and can be used to predict chemical reactivity.

An electronic criterion for assessing intrinsic brittleness of metallic glasses.

Bulk metallic glasses (BMGs) are characterized by a number of remarkable physical and mechanical properties. Unfortunately, these same materials are often intrinsically brittle, which limits their utility. Consequently, considerable effort has been expended searching for correlations between the phenomenologically complex mechanical properties of metallic glasses and more basic properties, such correlations might provide insight into the structure and bonding controlling the deformation properties of BMGs. While conducting such a search, we uncovered a weak correlation between a BMG's work function and its susceptibility to brittle behavior. We argue that the basis for this correlation is a consequence of a component of the work function - the surface dipole - and a fundamental bond property related to the shape of the charge density at a bond critical point. Together these observations suggest that simple first principle calculations might be useful in the search for tougher BMGs.

Looking for design in materials design.

Despite great advances in computation, materials design is still science fiction. The construction of structure-property relations on the quantum scale will turn computational empiricism into true design.

Topology of electronic charge density and energetics of planar faults in fcc metals.

Using ab initio calculations we have studied the energetics and the evolution of the electronic charge density with shear in three fcc metals exhibiting different deformation properties, aluminum, silver, and iridium. The charge redistribution described by the change in character of specific charge density critical points (cps), is ascertained from the values of the charge density, rho(0), and its three principal curvatures, rho( parallel parallel), rho(hh), and rho(vv), respectively. The change in character of cps correlates with the energetics. For all three metals, rho(hh) vanishes near the unstable stacking configuration. The symmetry or asymmetry of the charge redistribution, measured by rho(hh)/rho(vv), may be an important factor determining stacking fault energies.