Samantha Jenkins

Pointing the way to the products? Comparison of the stress tensor and the second-derivative tensor of the electron density

The eigenvectors of the electronic stress tensor can be used to identify where new bond paths form in a chemical reaction. In cases where the eigenvectors of the stress tensor are not available, the gradient-expansion-approximation suggests using the eigenvalues of the second derivative tensor of the electron density instead; this approximation can be made quantitatively accurate by scaling and shifting the second-derivative tensor, but it has a weaker physical basis and less predictive power for chemical reactivity than the stress tensor. These tools provide an extension of the quantum theory of atoms and molecules from the characterization of molecular electronic structure to the prediction of chemical reactivity.

Information theory-based software metrics and obfuscation

Abstract A new approach to software metrics using concepts from information theory, data compression, complexity theory and analogies with real physical systems is described. A novel application of software obfuscation allows an existing software package to be analysed in terms of the effects of perturbations caused by the obfuscator. Parallels are drawn between the results of the software analysis and the behaviour of physical systems as described by classical thermodynamics.

Structures, energies and bonding in neutral and charged Li microclusters

Structural and chemical properties of charged and neutral Lithium microclusters are investigated for

The Ehrenfest force topology: a physically intuitive approach for analyzing chemical interactions

{\text{Li}}_n^q(n = {5} - {1}0,q = 0,\pm {1})

Hydrophobic meddling in small water clusters

. A total of 18 quantum conformational spaces are randomly walked to produce candidate structures for local minima. Very rich potential energy surfaces are produced, with the largest structural complexity predicted for anionic clusters. Analysis of the electron charge distributions using the quantum theory of atoms in molecules (QTAIM) predicts major stabilizing roles of Non–nuclear attractors (NNAs) via NNA···Li interactions with virtually no direct Li···Li interactions, except in the least stable configurations. A transition in behavior for clusters containing more than seven nuclei is observed by using the recently introduced quantum topology to determine in a quantum mechanically consistent fashion the number of spatial dimensions each cluster has. We experiment with a novel scheme for extracting persistent structural motifs with increase in cluster size. The new structural motifs correlate well with the energetic stability, particularly in highlighting the least stable structures. Quantifying the degree of covalent character in Lithium bonding independently agrees with the observation in the transition in cluster behavior for lithium clusters containing more than seven nuclei. Good correlation with available experimental data is obtained for all properties reported in this work.

Tiling for Performance Tuning on Different Models of GPUs

Structural and chemical properties of the building block of silica nanowires, (SiO(2))(6), are investigated with the theory of atoms and molecules (QTAIM). Twenty-five conformers have been analyzed, ten of which have not been reported before. We extend the silica (SiO(2))(6) topology phase space using QTAIM; the Poincaré-Hopf topological sum rules are applied and used to identify the spanning set of topologies, and this includes finding eight new distinct topologies that satisfy the Poincaré-Hopf relation. A simple phase diagram of the solutions of the Poincaré-Hopf relation is created with the aid of a new classification scheme to determine the boundary between topological stability and instability. Sum rules are then found to be applicable to any set of isomers. We determine that O-O bonding interactions exist for the silica (SiO(2))(6) conformers in regions where the energy surface is flattest. In addition, we identify unstable local minima in the topology of the charge density in order to further compare conformer instabilities. We quantify the dimensionality of a molecule using the Poincaré-Hopf relation instead of Euclidean geometry. This quantum topological definition of geometry shows that the four most energetically stable (SiO(2))(6) conformers are quantified as two-dimensional within the new quantum topology.

A bond, ring and cage resolved Poincaré–Hopf relationship for isomerisation reaction pathways

Modified ANO-RCC basis sets are used to determine twelve molecular graphs of the Ehrenfest force for H2, CH4, CH2O, CH3NO, C2H2, C2H4, C3H3NO, N4H4, H2O, (H2O)2, (H2O)4 and (H2O)6. The molecular graphs include all types of topological critical points and a mix of bonding types is chosen to include sigma-, π- and hydrogen-bonding. We then compare a wide range of point properties: charge density, trace of the Hessian, eigenvalues, ellipticity, stiffness, total local energy and the eigenvectors are calculated at the bond critical points (BCPs) and compared for the Ehrenfest, QTAIM and stress tensor schemes. QTAIM is found to be the only partitioning scheme that can differentiate between shared- and closed-shell chemical bond types. Only the results from the Ehrenfest force partitioning, however, are demonstrated to be physically intuitive. This is demonstrated for the water molecule, the water-dimer and the water clusters (H2O)4 and (H2O)6. In particular, both the stiffness and the trace of the Hessians of the appropriate quantities of the sigma-bond BCPs for the water clusters are found to depend on the quantum topology dimension of the molecular graph. The behavior of all the stress tensor point properties is found to be erratic. This is explained by the ambiguity in the theoretical definition of the stress tensor. As a complementary approach the Ehrenfest force provides a new indicator of the mixed chemical character of the hydrogen-bond BCP, which arises from the collinear donor sigma-bond donating a degree of covalent character to the hydrogen-bond. This indicator takes the form of the relative orientation of the shallowest direction of the Ehrenfest potential of the hydrogen-bond BCPs and the corresponding direction for the collinear sigma-bond BCP.

Distinguishing and quantifying the torquoselectivity in competitive ring-opening reactions using the stress tensor and QTAIM

AbstractExcited state intramolecular proton transfer (ESIPT) reaction along the O-H⋅⋅⋅⋅O hydrogen bond of o-hydroxy benzaldehyde (OHBA), methyl salicylate (MS) and salicylic acid (SA) was investigated by ab-initio quantum chemical calculation and theory of atoms and molecules (QTAIM) for the first time. Variation in several geometric as well as QTAIM parameters along the reaction coordinate was monitored in the fully relaxed excited state potential energy curve (PEC) obtained from intrinsic reaction coordinate (IRC) analysis. Although, the excited state barrier height for the forward reaction (∆E0#) reduces substantially in all the systems, MS and SA do not show any obvious asymmetry for proton transfer. For MS and SA, the crossover of the bond index as well as the lengths of the participating bonds at the saddle point is assigned due to this symmetry in accordance with bond energy – bond order (BEBO) model, which does not hold true in OHBA both in the ground and excited states. Bond ellipticity, covalent and metallic character were examined for different structures along the reaction path within the QTAIM framework. The QTAIM analysis was found to be able to uniquely distinguish between the ground and excited states of the OHBA molecule as well as both determining the effects on the bonding character of adding different substituent groups and differentiating between the ESIPT reactions in the SA and MS molecules. FigureIn this paper, we report the dynamics and charge density topology of excited state intramolecular proton transfer (ESIPT) process in model systems like o-hydroxy benzaldehyde, salicylic acid and methyl salicylate using ab-initio quantum chemical calculation and also quantum theory of atoms and molecules (QTAIM) using fully relaxed excited state potential energy surface. The later technique has been used for the first time to explore the excited state process