Flip rearrangement in the water pentamer: Analysis of electronic structure

Tunneling pathways of the flip rearrangement between permutation-inversion isomers corresponding to the energetically degenerate global energy minima of (H2O)5 are analyzed in terms of the electronic structure. We demonstrate that charge density-based scalar measures quantify the responses of the bonding to the flip rearrangement and we discovered a high degree of continuity of the values that depend on the presence of the sliding motion of the bond critical point relative to the oxygen atom. The scalar measures can distinguish the pairs of permutation-inversion isomers everywhere except at the transition state due to the asymmetrical energy barrier; however, they cannot determine the most and least facile directions of the flip rearrangement. The vector or directional character of the two sides of the pathway is captured by the stress tensor trajectories constructed in a non-Cartesian space, defined by the variation of the position of the bond critical point. The stress tensor trajectories are presented in terms that enable bond-flexing, bond-twist, and bond-anharmonicity of the flip rearrangement between permutation-inversion isomers to be quantified. The stress tensor trajectories can distinguish the isomers at the transition state and demonstrate that the clockwise and counter-clockwise directions of the flip rearrangement are the most and least facile respectively

Mixed Chiral and Achiral Character in Substituted Ethane: A Next Generation QTAIM Perspective

We use the newly introduced spanning stress tensor trajectory $U_{\sigma}$-space construction within next generation quantum theory of atoms in molecules (NG-QTAIM) for a chirality investigation of singly and doubly substituted ethane with halogen substituents: F, Cl, Br. A lack of achiral character in $U_{\sigma}$-space was discovered for singly substituted ethane. The resultant axial bond critical point (BCP) sliding responded more strongly to the increase in atomic number of the substituted halogen than the chirality. The presence of the very light F atom was found responsible for a very high degree of achiral character of the doubly substituted ethane.Comment: arXiv admin note: substantial text overlap with arXiv:2203.0975

Chirality reversal with the carrier-envelope phase : A next generation QTAIM interpretation

Funding: The Hunan Natural Science Foundation of China project gratefully acknowledged approval number: 2022JJ30029. The One Hundred Talents Foundation of Hunan Province is also gratefully acknowledged for the support of S.J. and S.R.K. MJP thanks the EPSRC for funding through grants EP/T021675 and EP/V006746.Simulated circularly-polarized 10 femtosecond laser pulses that induce a mixture of excited states are applied to ethane. Additionally, the carrier-envelope phase (CEP) angle ϕ, that quantifies the relationship between the time-varying direction of electric (E)-field and the amplitude envelope was used to manipulate the mechanical and chiral properties of ethane using Next Generation Quantum Theory of Atoms in Molecules (NG-QTAIM). The chirality assignments were reversed from S to R as the CEP angle ϕ was increased from ϕ = 0.0° to ϕ = 180°. A one-to-one mapping between the CEP angle ϕ and NGQTAIM trajectories was discovered.Peer reviewe

The cis-effect explained using next generation QTAIM

The National Natural Science Foundation of China is gratefully acknowledged, project approval number: 21673071. The One Hundred Talents Foundation of Hunan Province is also gratefully acknowledged for the support of S.J. and S.R.K. H.F. and T.v.M. gratefully acknowledge computational support via the EaStCHEM Research Computing Facility.We used next-generation QTAIM (NG-QTAIM) to explain the cis-effect for two families of molecules: C2X2 (X = H, F, Cl) and N2X2 (X = H, F, Cl). We explained why the cis-effect is the exception rather than the rule. This was undertaken by tracking the motion of the bond critical point (BCP) of the stress tensor trajectories Tσ(s) used to sample the Uσ-space cis- and trans-characteristics. The Tσ(s) were constructed by subjecting the C1-C2 BCP and N1-N2 BCP to torsions ± θ and summing all possible Tσ(s) from the bonding environment. During this process, care was taken to fully account for multi-reference effects. We associated bond-bending and bond-twisting components of the Tσ(s) with cis- and trans-characteristics, respectively, based on the relative ease of motion of the electronic charge density ρ(rb). Qualitative agreement is found with existing experimental data and predictions are made where experimental data is not available.Publisher PDFPeer reviewe

Intramolecular Hydrogen Bonding 2021

This book describes the results of both theoretical and experimental research on many topical issues in intramolecular hydrogen bonding. Its great advantage is that the presented research results have been obtained using many different techniques. Therefore, it is an excellent review of these methods, while showing their applicability to the current scientific issues regarding intramolecular hydrogen bonds. The experimental techniques used include X-ray diffraction, infrared and Raman spectroscopy (IR), nuclear magnetic resonance spectroscopy (NMR), nuclear quadrupole resonance spectroscopy (NQR), incoherent inelastic neutron scattering (IINS), and differential scanning calorimetry (DSC). The solvatochromic and luminescent studies are also described. On the other hand, theoretical research is based on ab initio calculations and the Car–Parrinello Molecular Dynamics (CPMD). In the latter case, a description of nuclear quantum effects (NQE) is also possible. This book also demonstrates the use of theoretical methods such as Quantum Theory of Atoms in Molecules (QTAIM), Interacting Quantum Atoms (IQA), Natural Bond Orbital (NBO), Non-Covalent Interactions (NCI) index, Molecular Tailoring Approach (MTA), and many others

TOPOLOGICAL DESCRIPTORS ENABLING NOVEL DISSECTIONS OF ELECTRON POSITION AND SPIN PROPERTIES IN COMPLEX MOLECULAR SYSTEMS

Macroscopic and microscopic properties of molecular and solid-state systems are intimately related to the their electronic structure. The electron position and spin densities, which represent the probability distributions to find all or unpaired electrons in the space, contain information concerning several chemical-relevant properties, such as the chemical bonding and the magnetic behaviour. Understanding the fine atomic-level mechanism behind these properties is a key step to design chemical modifications to properly tune and develop materials or molecules with specific features. Topological descriptors can be used to extract information from these electron distributions. In this work, novel applications of the source function descriptor have been developed to gain further insights on the electron and spin density-related properties. These developments, together with other topological descriptors, were used to get further insights on relevant chemical systems. Firstly, the source function reconstruction was enlarged to a multi-dimensional grid of points with a particular focus on the two-dimensional maps. This analysis allows to see the ability of chosen subsets of atoms to reconstruct the density in the selected area within a cause-effect relationship and to rationalise the chemical or magnetic behaviours. The source function partial reconstructed maps depict if in a molecular region the atomic contributions are important, modest or negligible. Besides, they may also be useful for a proper selection of the reference points and for a full understanding of the source function percentages analysis. In fact, the choice of the reference point where to reconstruct the studied density is neither easy nor objective for non-standard situations, such as for the spin density. This novel application was applied to the study of the spin density on a couple of azido Cu complexes. The source function partial reconstructed maps allow to unravel the different role played by the paramagnetic centre Cu and the ligand atoms and to explain the spin transmission mechanism at a molecular level. Moreover, they enable to highlight the nature of the spin density differences between the two complexes and among adopted computational approaches. DFT functionals tend to over-delocalise the spin density towards the ligand atoms introducing a biased spin-polarization mechanism between the Cu and the ligand atoms. The same descriptor was then applied to the study of the hydrogen bonds in the DNA base pairs. The source function reveals the delocalised nature of these interactions, highlighting that distant groups and rings have non-negligible effects on the reconstruction of the electron density in the intermolecular region. Besides, the analysis demonstrates that the purine and pyrimidine bases equally contribute to the reconstruction of the electron density at the hydrogen bond critical points. The source function also reveals that subtle variations of the atomic source contributions occur when the pairs are ionized, revealing that sources and sinks effects redistribution plays an important role in the stabilization of the DNA base pairs. The source function was also used to develop a method to extract full population matrices purely based on the electron density distribution and then amenable to experimental determination. The peculiar features of this descriptor, in particular the cause-effect relationship, assign a profound chemical meaning to the matrix elements in contrast with other population analyses such as the Mulliken's one, where the matrix elements are associated to orbital overlaps. The latest breakthroughs on the development of this method are shown together with some numerical examples on very simple compounds. The full population matrices obtained using the source function descriptor are able to retrieve the major chemical features. A detailed analysis on the intermolecular interactions involved in the in vivo molecular recognition of the antimalarial drug chloroquine with the heme moiety has been carried out using a combined topological-energetic analysis. This work reveals that charged-assisted hydrogen bonds set up between the lateral chains of the chloroquine and the propionate group of the heme are the most important interactions in the drug:substrate recognition process

Computational investigations of some molecular properties, their perturbation by external electric fields, and their use in quantitative structure-to-activity relationships

217 leaves : ill. (chiefly col.) ; 29 cm.Includes abstract and appendix.Includes bibliographical references.This thesis consists of three quantum chemical investigations. The first investigates the changes in the chemical bond in strong electric fields, a necessary first step for understanding the behaviour of a substrates or drugs in enzyme active sites where such fields are ubiquitous. The second study traces the atomic origins of the sharp peaks in the dipole moment near the transition states of chemical laser reactions. The Quantum Theory of Atoms in Molecules is used to decompose the dipole moment surfaces into atomic contributions. Since these peaks can be exploited in the laser control, this knowledge adds another layer of control on tuneable reactions through the choice of reactants maximizing the laser-molecule interaction. The last study outlines a quantitative structure-to-activity study relating the observed anti-carcinogenic and anti-inflammatory activities of 150 molecules to calculated electronic properties, reducing the cost, time, and effort in the design of anticancer and anti-inflammatory drugs

Prediction of structures and properties of high-pressure solid materials using first principles methods

The purpose of the research contained in this thesis is to allow for the prediction of new structures and properties of crystalline structures due to the application of external pressure by using first-principles numerical computations. The body of the thesis is separated into two primary research projects. The properties of cupric oxide (CuO) have been studied at pressures below 70 GPa, and it has been suggested that it may show room-temperature multiferroics at pressure of 20 to 40 GPa. However, at pressures above these ranges, the properties of CuO have yet to be examined thoroughly. The changes in crystal structure of CuO were examined in these high-pressure ranges. It was predicted that the ambient pressure monoclinic structure changes to a rocksalt structure and CsCl structure at high pressure. Changes in the magnetic ordering were also suggested to occur due to superexchange interactions and Jahn-Teller instabilities arising from the d-orbital electrons. Barium chloride (BaCl) has also been observed, which undergoes a similar structural change due to an s – d transition, and whose structural changes can offer further insight into the transitions observed in CuO. Ammonia borane (NH3BH3) is known to have a crystal structure which contains the molecules in staggered conformation at low pressure. The crystalline structure of NH3BH3 was examined at high pressure, which revealed that the staggered configuration transforms to an eclipsed conformation stabilized by homopolar B–Hδ-∙∙∙ δ-H–B dihydrogen bonds. These bonds are shown to be covalent in nature, comparable in bond strength to conventional hydrogen bonds, and may allow for easier molecular hydrogen formation in hydrogen fuel storage