Where are the lone pairs? QC and QCT.

The article by Guzmán-Hernández & Jancik [(2024). Acta Cryst. C80, 766-774] is an excellent example of how QC-QCT (quantum crystallography-quantum chemical topology) methodology can extract structural information from a crystal.

Quantum Topological Atomic Properties of 44K molecules.

We present a data set of quantum topological properties of atoms of 44K randomly selected molecules from the GDB-9 data set. These atomic properties were obtained as defined by the quantum theory of atoms in molecules (QTAIM) within an atomic basin, a region of real space bounded by zero-flux surfaces in the electron density gradient vector field. The wave function files were generated through DFT static calculations (B3LYP/6-31G), and the atomic properties were calculated using QTAIM.

Spin Energy Contributions of the Kinetic Energy Density in the Stabilization of the Metal-Ligand Interactions.

The kinetic energy (KE) density plays an essential role in the stabilization mechanism of covalent, polar covalent, and ionic bondings; however, its role in metal-ligand bindings remains unclear. In a recent work, the energetic contributions of the spin densities α and β were studied to explain the geometrical characteristics of a series of metal-ligand complexes. Notably, the KE density was found to modulate/stabilize the spin components of the intra-atomic nucleus-electron interactions within the metal in the complex.

Stereoelectronic interactions are too weak to explain the molecular conformation in solid state of -2--butyl-5-(-butylsulfonyl)-1,3-dioxane.

-2--Butyl-5-(-butylsulfonyl)-1,3-dioxane (-1) exhibits a high degree of eclipsing in the H-C5-S-C segment in the solid state, the origin of which remains unexplained. The eclipsed conformation that corresponds to an energetic minimum in the solid state practically corresponds to a rotational transition state in solution, which allows an approach to understand transitions states. The difference in the enthalpy of sublimation Δ between -1 and the more stable -1 is 8.

Hydrolysis of ester phosphates mediated by a copper complex.

Phosphate ester hydrolysis is an important reaction that plays a major role in both enzymatic and non-enzymatic processes, including DNA and pesticide breaking. Although it is a widely studied reaction, the precise mechanistic details, especially for copper complexes, remain under discussion. To contribute to the debate, we present the catalyzed hydrolysis of phosphomono-, di- and tri-esters mediated by the [Cu(1,10-phenanthroline)] complex.

DNA recognition site of anticancer tinidazole copper(II) complexes.

This paper describes the recognition process of tetrahedral [Cu(tnz)X] (X = Cl, Br) complexes by a DNA chain, analyzing the specific interaction between the DNA bases and backbone with the metal and the tinidazole (tnz) ligand. We identified the coordination of the copper metal center with one or two phosphates as the first recognition site for the tinidazole copper(II) complexes, while the ligands present partial intercalation into the minor groove. Also, we discuss a novel trigonal copper(I) tnz bromide complex, obtained by reducing the previously reported [Cu(tnz)Br].

How do density functionals affect the Hirshfeld atom refinement?

In this work, the effect of mixing different amounts of Hartree-Fock (HF) exchange with hybrid density functionals applied to the Hirshfeld atom refinement (HAR) of urea and oxalic acid dihydrate is explored. Together, the influence of using different basis sets, methods (including MP2 and HF) and cluster sizes (to model bulk effects) is studied. The results show that changing the amount of HF exchange, no matter the level of theory, has an impact almost exclusively on the H atom refinement parameters.

How solvent determines the molecular reactive conformation and the selectivity: Solvation spheres and energy.

In solution, the solvent determines the molecular conformation and the chemical reaction viability and selectivity. When solvent-solute and solvent-solvent interactions present similar strengths, explicit salvation is the best way to describe a system. The problem to solve is how big the explicit shell should be.

Excited state dynamics and photochemistry of nitroaromatic compounds.

Nitrated aromatic molecules have unique photoinduced channels. Due to the presence of oxygen-centered non-bonding orbitals, they can undergo sub-picosecond intersystem crossing showing one of the strongest couplings between the singlet and triplet manifolds among organic molecules. Several nitroaromatic compounds also have a distinctive nitric oxide photodissociation channel which occurs through a complex sequence of atom rearrangements and state changes.

Intermediate Detection in the Casiopeina-Cysteine Interaction Ending in the Disulfide Bond Formation and Copper Reduction.

A strategy to improve the cancer therapies involves agents that cause the depletion of the endogenous antioxidant glutathione (GSH), increasing its efflux out of cells and inducing apoptosis in tumoral cells due to the presence of reactive oxygen species. It has been shown that Casiopeina copper complexes caused a dramatic intracellular GSH drop, forming disulfide bonds and reducing Cu to Cu. Herein, through the determination of the [Cu]-SH bond before reduction, we present evidence of the adduct between cysteine and one Casiopeina as an intermediate in the cystine formation and as a model to understand the anticancer activity of copper complexes.

Ancillary Ligand in Ternary Cu Complexes Guides Binding Selectivity toward Minor-Groove DNA.

Copper-containing compounds known as Casiopeı́nas are biologically active molecules which show promising antineoplastic effects against several cancer types. Two possible hypotheses regarding the mode of action of the Casiopeı́nas have emerged from the experimental evidence: the generation of reactive oxygen species or the ability of the compounds to bind and interact with nucleic acids. Using robust molecular dynamics simulations, we investigate the interaction of four different Casiopeı́nas with the DNA duplex d(GCACGAACGAACGAACGC).

Do weak interactions affect the biological behavior of DNA? A DFT study of CpG island-like chains.

The origin, stability, and contribution to the formation of noncovalent interactions, such as hydrogen bonds and π - π stacking, have been already widely discussed. However, there are few discussions about the relevance of these weak interactions in DNA performance. In this work, we seek to shed light on the effect of hydrogen bonds and π - π stacking interactions on the biological behavior of DNA through the description of these intermolecular forces in CpG island-like (GC-rich) chains.

From the Linnett-Gillespie model to the polarization of the spin valence shells of metals in complexes.

In this paper, we present a novel approach to track the origin of the metal complex structure from the topology of the α and β spin densities as an extension of the Linnett-Gillespie model. Usually, the theories that explain the metal-ligand interactions consider the disposition and the relative energies of the empty or occupied set of d orbitals, ignoring the spin contribution explicitly. Our quantum topological approach considers the spatial distribution of the α and β spin valence shells, and the energy interaction between them.

Predicting reactive sites with quantum chemical topology: carbonyl additions in multicomponent reactions.

Quantum Chemical Topology (QCT) is a well established structural theoretical approach, but the development of its reactivity component is still a challenge. The hypothesis of this work is that the reactivity of an atom within a molecule is a function of its electronic population, its delocalization in the rest of the molecule, and the way it polarizes within an atomic domain. In this paper, we present a topological reactivity predictor for cabonyl additions, κ.

π-Extended push-pull azo-pyrrole photoswitches: synthesis, solvatochromism and optical band gaps.

A new family of push-pull biphenyl-azopyrrole compounds 3b-g and 4b-d was efficiently obtained via a Suzuki cross-coupling reaction between 2-(4'-iodophenyl-azo)-N-methyl pyrrole (1a) or 3-(4'-iodophenyl-azo)-1,2,5-trimethyl pyrrole (2a) and 4'-substituted phenyl boronic acids in excellent yields. The influence of the π-biphenyl backbone and pyrrole pattern substitution was correlated with their optical properties. Solvatochromic studies via UV-visible spectrophotometry revealed that the inclusion of a 4'-nitro-biphenyl fragment favors a red-shift of the main absorption band in these azo compounds compared with their non-substituted analogues.

Laplacian of the Hamiltonian Kinetic Energy Density as an Indicator of Binding and Weak Interactions.

The kinetic energy is the center of a controversy between two opposite points of view about its role in the formation of a chemical bond. One school states that a lowering of the kinetic energy associated with electron delocalization is the key stabilization mechanism of covalent bonding. In contrast, the opposite school holds that a chemical bond is formed by a decrease in the potential energy due to a concentration of electron density within the binding region.

Enhancing Acute Oral Toxicity Predictions by using Consensus Modeling and Algebraic Form-Based 0D-to-2D Molecular Encodes.

Quantitative structure-activity relationships (QSAR) are introduced to predict acute oral toxicity (AOT), by using the QuBiLS-MAS (acronym for quadratic, bilinear and N-Linear maps based on graph-theoretic electronic-density matrices and atomic weightings) framework for the molecular encoding. Three training sets were employed to build the models: EPA training set (5931 compounds), EPA-full training set (7413 compounds), and Zhu training set (10 152 compounds). Additionally, the EPA test set (1482 compounds) was used for the validation of the QSAR models built on the EPA training set, while the ProTox (425 compounds) and T3DB (284 compounds) external sets were employed for the assessment of all the models.

Distribution of toxicity values across different species and modes of action of pesticides from PESTIMEP and PPDB databases.

The continuous use of compounds contained in commodities such as processed food, medicines, and pesticides, demands safety measures, in particular, for those in direct contact with humans and the environment. Safety measures have evolved and regulations are now in place around the globe. In the case of pesticides, attempts have been made to use toxicological data to inform of potentially harmful compounds either across species, on different routes of exposure, or entirely new chemicals.

Reactivity patterns for the activation of CO and CS with alumoxane and aluminum hydrides.

Carbon dioxide is readily fixed when reacting with either alumoxane dihydride [{MeLAl(H)}2(μ-O)] (1) or aluminum dihydride [MeLAlH2] (2) (MeL = HC[(CMe)N(2,4,6-Me3C6H2)]2-) to produce bimetallic aluminum formates [(MeLAl)2(μ-OCHO)2(μ-O)] (3) and [(MeLAl)2(μ-OCHO)2(μ-H)2] (5), respectively. Furthermore, [(MeLAl)2(μ-OCHO)2(μ-OH)2] (4) is easily obtained upon the reaction of 3 or 5 with H2O. The stability of the unusual dialuminum diformate dihydride core observed in 5 stems from the proximity of the Al centers allowing the formation of two Al-HAl bridges and precluding further hydride transfer to the HCO2 moieties.

Self-Assembly of Aluminum- and Gallium-Based meso-Metallaporphyrins.

The molecular meso-metallaporphyrin has been obtained from the reaction of AlMe with the bulky 4,5-(Ph(HO)C)-1,2,3-triazole (1). The presence of Al-Me groups coordinated to the triazole rings creates three different stereoisomers that were identified by single-crystal X-ray diffraction. Further studies revealed that, for steric reasons, only one of the two main stereoisomers is active in the polymerization of ε-caprolactone.

Origin of the Photoinduced Geometrical Change of Copper(I) Complexes from the Quantum Chemical Topology View.

Copper(I) complexes (CICs) are of great interest due to their applications as redox mediators and molecular switches. CICs present drastic geometrical change in their excited states, which interferes with their luminescence properties. The photophysical process has been extensively studied by several time-resolved methods to gain an understanding of the dynamics and mechanism of the torsion, which has been explained in terms of a Jahn-Teller effect.

Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs).

Background: Several topological (2D) and geometric (3D) molecular descriptors (MDs) are calculated from local vertex/edge invariants (LOVIs/LOEIs) by performing an aggregation process. To this end, norm-, mean- and statistic-based (non-fuzzy) operators are used, under the assumption that LOVIs/LOEIs are independent (orthogonal) values of one another. These operators are based on additive and/or linear measures and, consequently, they cannot be used to encode information from interrelated criteria.

The OECD Principles for (Q)SAR Models in the Context of Knowledge Discovery in Databases (KDD).

The steps followed in the knowledge discovery in databases (KDD) process are well documented and are widely used in different areas where exploration of data is used for decision making. In turn, while different workflows for developing quantitative structure-activity relationship (QSAR) models have been proposed, including combinatorial use of QSAR, there is now agreement on common requirements for building trustable predictive models. In this work, we analyze and confront the steps involved in KDD and QSAR and present how they comply with the OECD principles for the validation, for regulatory purposes, of QSAR models.

GOWAWA Aggregation Operator-based Global Molecular Characterizations: Weighting Atom/bond Contributions (LOVIs/LOEIs) According to their Influence in the Molecular Encoding.

A different perspective to compute global weighted definitions of molecular descriptors from the contributions of each atom (LOVIs) or covalent bond (LOEIs) within a molecule is presented, using the generalized ordered weighted averaging - weighted averaging (GOWAWA) aggregation operator. This operator is rather different from the other norm-, mean- and statistic-based operators used up to date for the descriptors calculation from LOVIs/LOEIs. GOWAWA unifies the generalized ordered weighted averaging (GOWA) and the weighted generalized mean (WGM) functions and, in addition, it uses a smoothing parameter to assign different importance values to both functions depending on the problem under study.