Spanning Set of Silica Cluster Isomer Topologies from QTAIM

The effect of adsorption and grafting on the acidity of [(HSO3)C3C1im]+[Cl]- on the surface of (SiO2)4O2H4 clusters

Both adsorption and graft of active components on the surface of the silica are paramount methods for preparing heterogeneous catalysts. In this paper, the acidity of [(HSO₃)C3C1im]⁺[Cl]^- adsorbed and grafted on the surface of silica clusters was calculated at the level of B3LYP-d3/6-311++g(d, p). The results showed that both methods can enhance the acidity of the ionic liquids (ILs). The hydroxyl group on the carrier surface can increase the acidity, and moreover the acidity increases with the number of hydroxyl group. Besides, geometric parameters, ESP, topology and NBO analysis proved that the ILs acidity on the hydroxyl-free surface was mainly influenced by the interaction between -SO₃ group and cluster surface. And yet the ILs acidity on the hydroxylated surface changes followed with the moderate strength hydrogen bond between the ILs and cluster surface.

3-D bond-paths of QTAIM and the stress tensor in neutral lithium clusters, Lim (m = 2-5), presented on the Ehrenfest force molecular graph

In this investigation we set out to understand the origins of non-nuclear attractors (NNAs) found for neutral lithium clusters Lim (m = 2-5) on the QTAIM molecular graph but not on the Ehrenfest force F(r) molecular graph. Therefore, we pursued the stress tensor σ(r) without using the dependency on the QTAIM partitioning, since previously σ(r) was only calculated within the QTAIM partitioning, to see if any indication of NNA character can be determined. Because the stress tensor σ(r) lacks an associated scalar- or vector-field as is the case for QTAIM and the Ehrenfest F(r) partitioning schemes respectively, a stress tensor σ(r) partitioning scheme cannot be constructed. Therefore, to overcome this difficulty we use next generation QTAIM, constructed from the most preferred directions of electronic charge density accumulation, to calculate the stress tensor σ(r) 3-D bond-paths on the Ehrenfest force F(r) molecular graph. Using next generation 3-D bond-paths within the Ehrenfest force F(r) partitioning, we can classify the degree of NNA character in the absence of NNAs. A much higher degree of NNA character is found to be present for the stress tensor σ(r) 3-D bond-paths than for the corresponding QTAIM or Ehrenfest force F(r) 3-D bond-paths. The stabilizing effect of the NNA is demonstrated by undertaking Li2 bond-path compression and stretching distortions sufficient to cause the annihilation of the NNA. The compression and stretching distortions also lead to a large increase in the 3-D bond-path asymmetry and persistent bond-path torsion respectively.

Non-nuclear attractors in small charged lithium clusters, Limq (m = 2-5, q = ±1), with QTAIM and the Ehrenfest force partitioning

In this investigation we explore the function and existence of the non-nuclear attractor (NNA) for a series of small charged lithium clusters Limq (m = 2-5, q = ±1) using QTAIM and the Ehrenfest force F(r) partitioning schemes. The NNAs were found to be present in all of the Limq (m = 2-5, q = ±1) clusters for QTAIM, in contrast none were found for F(r). We discovered that the anionic and cationic lithium dimers are limiting cases for minimal and maximal impact of the NNA related to the relative sparseness of total charge density ρ(r) distributions respectively. Evidence is found that the NNA in the anionic dimer is in the process of being annihilated by two neighboring BCPs. We provide a measure of the size of the NNA and find for Limq (m = 2-5, q = ±1) that larger NNAs correlate with increased Li-Li separations. The NNA was determined to be a persistent feature by varying the Li separations for the cationic and anionic dimers. Very large Li separations failed to induce an NNA in the F(r) anionic dimer and therefore we conclude that F(r) is unable to detect NNAs. The metallicity ξ(rb) was also used to measure the sparseness of the distribution of ρ(r) and significant metallic character, on the basis of ξ(rb) > 1, was present for QTAIM but not for F(r), providing further evidence that F(r) cannot detect NNAs. Advantages of the use of Ehrenfest force F(r) partitioning scheme are discussed that include the design of nano-devices through tuning of the Ehrenfest potential VF(b) by the application of external forces such as a constant electric or strain field.

Exploration of the forbidden regions of the Ramachandran plot (ϕ-ψ) with QTAIM

A new QTAIM interpretation of the Ramachandran plot is formulated from the most and least facile eigenvectors of the second-derivative matrix of the electron density with a set of 29 magainin-2 peptide conformers. The presence of QTAIM eigenvectors associated with the most and least preferred directions of electronic charge density explained the role of hydrogen bonding, HH contacts and the glycine amino acid monomer in peptide folding. The highest degree of occupation of the QTAIM interpreted Ramachandran plot was found for the glycine amino acid monomer compared with the remaining backbone peptide bonds. The mobility of the QTAIM eigenvectors of the glycine amino acid monomer was higher than for the other amino acids and was comparable to that of the hydrogen bonding, explaining the flexibility of the magainin-2 backbone. We experimented with a variety of hybrid QTAIM-Ramachandran plots to highlight and explain why the glycine amino acid monomer largely occupies the 'forbidden' region on the Ramachandran plot. In addition, the new hybrid QTAIM-Ramachandran plots contained recognizable regions that can be associated with concepts familiar from the conventional Ramachandran plot whilst retaining the character of the QTAIM most and least preferred regions.

Curly arrows, electron flow, and reaction mechanisms from the perspective of the bonding evolution theory

Despite the usefulness of curly arrows in chemistry, their relationship with real electron density flows is still imprecise, and even their direct connection to quantum chemistry is still controversial. The paradigmatic description - from first principles - of the mechanistic aspects of a given chemical process is based mainly on the relative energies and geometrical changes at the stationary points of the potential energy surface along the reaction pathway; however, it is not sufficient to describe chemical systems in terms of bonding aspects. Probing the electron density distribution during a chemical reaction can provide important insights, enabling us to understand and control chemical reactions. This aim has required an extension of the relationships between the concepts of traditional chemistry and those of quantum mechanics. Bonding evolution theory (BET), which combines the topological analysis of the electron localization function (ELF) and Thom's catastrophe theory (CT), provides a powerful method that offers insight into the molecular mechanism of chemical rearrangements. In agreement with the laws of physical and aspects of quantum theory, BET can be considered an appropriate tool to tackle chemical reactivity with a wide range of possible applications. In this work, BET is applied to address a long-standing problem: the ability to monitor the flow of electron density. BET analysis shows a connection between quantum mechanics and bond making/forming processes. Likewise, the present approach retrieves the classical curly arrows used to describe the rearrangements of chemical bonds and provides detailed physical grounds for this type of representation. We demonstrate this procedure using the test set of prototypical examples of thermal ring apertures, and the degenerated Cope rearrangement of semibullvalene.

QTAIM and Stress Tensor Characterization of Intramolecular Interactions Along Dynamics Trajectories of a Light-Driven Rotary Molecular Motor

A quantum theory of atoms in molecules (QTAIM) and stress tensor analysis was applied to analyze intramolecular interactions influencing the photoisomerization dynamics of a light-driven rotary molecular motor. For selected nonadiabatic molecular dynamics trajectories characterized by markedly different S₁ state lifetimes, the electron densities were obtained using the ensemble density functional theory method. The analysis revealed that torsional motion of the molecular motor blades from the Franck-Condon point to the S₁ energy minimum and the S₁/S₀ conical intersection is controlled by two factors: greater numbers of intramolecular bonds before the hop-time and unusually strongly coupled bonds between the atoms of the rotor and the stator blades. This results in the effective stalling of the progress along the torsional path for an extended period of time. This finding suggests a possibility of chemical tuning of the speed of photoisomerization of molecular motors and related molecular switches by reshaping their molecular backbones to decrease or increase the degree of coupling and numbers of intramolecular bond critical points as revealed by the QTAIM/stress tensor analysis of the electron density. Additionally, the stress tensor scalar and vector analysis was found to provide new methods to follow the trajectories, and from this, new insight was gained into the behavior of the S₁ state in the vicinity of the conical intersection.

A QTAIM and stress tensor investigation of the torsion path of a light-driven fluorene molecular rotary motor

The utility of the QTAIM/stress tensor analysis method for characterizing the photoisomerization of light driven molecular rotary machines is investigated on the example of the torsion path in fluorene molecular motor. The scalar and vector descriptors of QTAIM/stress tensor reveal additional information on the bonding interactions between the rotating units of the motor, which cannot be obtained from the analysis of the ground and excited state potential energy surfaces. The topological features of the fluorene motor molecular graph display that, upon the photoexcitation a certain increase in the torsional stiffness of the rotating bond can be attributed to the increasing topological stability of the rotor carbon atom attached to the rotation axle. The established variations in the torsional stiffness of the rotating bond may cause transfer of certain fraction of the torsional energy to other internal degrees of freedom, such as the pyramidalization distortion. © 2016 Wiley Periodicals, Inc.

A topological assessment of the electronic structure of mesoionic compounds

Mesoionic compounds belonging to the 1,3-oxazol-5-one, 1,3-diazole-4-thione and 1,3-thiazole-5-thione rings have been evaluated by a combination of Density Functional Theory, Quantum Theory of Atoms in Molecules, Electron Localization Function, Natural Bond Orbitals and Geodesic Electrostatic Potential Charge calculations. Atomic, bond, and ring properties have been considered to describe the electronic structure of mesoionic compounds. The results show that not only the ring type, but also the substituent groups have great influence on these properties. In addition, there is a significant and heterogeneous π-bonding contribution throughout the mesoionic rings. Finally, we conclude that some classical conceptions of charge localization and π-bonding contribution in these compounds are misleading or incomplete. © 2015 Wiley Periodicals, Inc.

Intriguing properties of unusual silicon nanocrystals

Optimized structures of A: empty Si₁₈H₁₂Si; B: Si₁₉H₁₂, the 19^th Si atom situated in the center of the lattice structure, C: Si₁₈GeH₁₂, Ge atom situated in the center of the lattice structure.

Hybrid QTAIM and electrostatic potential-based quantum topology phase diagrams for water clusters

The topological diversity of sets of isomers of water clusters (W = H₂O)_n, 7 ≤ n ≤ 10, is analyzed employing the scalar fields of total electronic charge density ρ(r) and the molecular electrostatic potential (MESP).

Structure, stability, and dissociation of small ionic silicon oxide clusters [SiO(n)+ (n = 3, 4)]: insight from density functional and topological exploration

The structures, energies, isomerization, and decomposition pathways of small ionic silicon oxide clusters, SiO(n)(+) (n = 3, 4), on doublet and quartet energy surfaces are investigated by density functional theory. New structural isomers of these ionic clusters have been obtained with this systematic study. The energy ordering of the isomeric cluster ions on doublet spin surface is found to follow the same general trend as that of the neutral ones, while it differs on the quartet surface. Our computational results reveal the energetically most preferred decomposition pathways of the ionic clusters on both spin surfaces. To comprehend the reaction mechanism, bonding evolution theory has also been employed using atoms in molecules formalism. The possible reasons behind the structural deformation of some isomers on quartet surface have also been addressed. Our results are expected to provide important insight into the decomposition mechanism and relative stability of the SiO(n)(+) clusters on both the energy surfaces.