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

cis-2-tert-Butyl-5-(tert-butylsulfonyl)-1,3-dioxane (cis-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 ΔsubH between cis-1 and the more stable trans-1 is 8.40 kcal mol-1, lets to consider that the intermolecular interactions in the crystalline structure must be responsible for the conformational effect observed in the solid state. The study of the experimental electron density of cis-1 in solid state allowed to establish that CH⋯OS intermolecular interaction is the main contribution to the observed eclipsing. The charge density analysis was also performed using the quantum theory of atoms in molecules to evaluate the nature and relevance of the intermolecular interactions in the crystal structure.

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(II)(1,10-phenanthroline)] complex. The reaction coordinates for several substrates were explored through the metadynamics formalism. Thus, we found that for mono- and di-substituted ester phosphates a concerted mechanism is observed, where a coordinated hydroxyl group attacks the phosphorus atom at the same side as the leaving group, along with a proton transfer. In contrast, tri-substituted phosphate remains coordinated with the metal, and the nucleophile acts independently following an addition-elimination process. That is, the metallic complex achieves a specific nucleophile-phosphate interaction that produces a concerted transition state in the phosphoester hydrolysis process.

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

This paper describes the recognition process of tetrahedral [CuII(tnz)2X2] (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)2Br2]. This complex sheds light on the mechanism of action of tnz metal complexes as one of the most stable DNA-complex adducts depicts a trigonal geometry around the copper ion.

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. In this paper, we want to answer one of the fundamental questions in the implementation of explicit solvation, exactly how many solvent molecules should be added and where they should be placed. Here we determine the first solvent sphere around a molecule and describe how it controls the conformation and selectivity of a selected reaction. NMR experiments were carried out to identify the number of solvent molecules around the solute that constitutes the first solvent sphere, and the interaction between this solvent sphere and the solute was detected using DFT and QTAIM calculations. A new approach to the solvation energy is presented. Finally, we established the role of solvent molecules in the conformation of the solute and in the transition states that produce the two possible products of the reaction.

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. These remarkable processes have stimulated the attention of several research groups over the last few years who have applied modern femtosecond spectroscopies and new computational methods to these topics. Nitroaromatic molecules also have demonstrated their value as case-studies, where they can serve to understand the influence of torsional motions between the nitro substituent and the aromatic system in the conversions between states. In this contribution we highlight several of the recent results in this area. Due to the importance of the atmospheric photochemistry of nitrated compounds and their accumulating applications as nitric oxide release agents, continued research about the effects of the different state orderings, substitution patterns, and solvent effects is central to the development of future applications and for a better understanding of their environmental pathways. From this analysis, several pending issues are highlighted, which include the nature of the dominant singlet state involved in intersystem crossing, the role of the formation of charge-transfer states, the yield of the internal conversion channel to the electronic ground state, and a more generalized understanding of the sequence of steps which lead to nitric oxide dissociation.

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 CuII to CuI. Herein, through the determination of the [CuII]-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. Evidence of such an intermediate has never been presented before.

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 ß 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 ß spin valence shells, and the energy interaction between them. We used the properties of the atomic graph, a topological object that summarises the charge concentrations and depletions on the valence shell of an atom in a molecule, and the interacting quantum atoms (IQA) energy partition scheme. Unlike the Linnett-Gillespie model, which is based on electron-electron repulsion, our approach states that the ligands provoke a redistribution of the electron density to maximize the nuclear-electron interactions in each spin valence shell to bypass the concentration of electron-electron interactions, resulting in a polarization pattern which determines the position of the ligands.

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. It is a measure of the polarization of the electron density with the carbonyl functional group. κ is a model obtained from a QSAR procedure, using quantum-topological atomic descriptors and reported hydration equilibrium constants of carbonyl compounds. To validate the predictive capability of κ, we applied it to organic reactions, including a multicomponent reaction. κ was the only property that predicts the reactivity in each reaction step. The shape of κ can be interpreted as the change between two electrophilic states of a functional group, reactive and non-reactive.

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. In this work, a topographic analysis of the Hamiltonian Kinetic Energy Density (KED) and its laplacian is presented to gain more insight into the role of the kinetic energy within chemical interactions. This study is focused on atoms, diatomic and organic molecules, along with their dimers. In addition, it is shown that the laplacian of the Hamiltonian KED exhibits a shell structure in atoms and that their outermost shell merge when a molecule is formed. A covalent bond is characterized by a concentration of kinetic energy, potential energy and electron densities along the internuclear axis, whereas a charge-shift bond is characterized by a fusion of external concentration shells and a depletion in the bonding region. In the case of weak intermolecular interactions, the external shell of the molecules merge into each other resulting in an intermolecular surface comparable to that obtained by the Non-covalent interaction (NCI) analysis.

Reactivity patterns for the activation of CO2 and CS2 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. Contrary to this behavior, 1 and 2 react with CS2 giving cyclic alumoxane and aluminum sulfides [(MeLAl)2(µ-S)(µ-O)] (6) and [{MeLAl(µ-S)}2] (7), respectively. The molecular structures of 3-7 were characterized by IR, Raman, solution or solid-state (MAS) NMR spectroscopy and mass spectrometry and for 4-7 were characterized by X-ray diffraction studies. NMR kinetic studies and DFT calculations suggest that the mechanisms for the formation of 6 and 7 involve the transfer of a hydride group forming transient aluminum thioformate intermediates which proceed to form Al-S-Al moieties through the cleavage of C-S bonds and insertion of a sulfur atom, followed by the elimination of thioformaldehyde.

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.

The Role of the DNA Backbone in Minor-Groove Ligand Binding.

Molecular recognition between ligands and nucleic acids plays a key role in therapeutic activity. Some molecules interact with DNA in a nonbonded manner through intercalation or through the DNA grooves. The recognition of minor-groove binders is attributed to a set of hydrogen-bonding interactions between the binders and the hydrogen-bond-acceptor groups on the groove floor and walls. It is commonly considered that interactions with the sugar groups of the DNA backbone are insignificant and do not contribute to the binding affinity or the specificity. However, our group has found that the deoxyribose rings have a central function in the recognition and the intercalation of metal complexes into DNA. Herein, we determined the specific interactions between the binder CGP 40215A and the minor-groove atoms, based on the local properties of electron density. We found that specific interactions between the deoxyribose moiety within the backbone of DNA and the binder are essential for molecular recognition, and they are responsible for one third of the interaction energy.

Ultrafast excited state hydrogen atom transfer in salicylideneaniline driven by changes in aromaticity.

We investigated two important unresolved issues on excited state intramolecular proton transfer (ESIPT) reactions, i.e., their driving force and the charge state of the transferred species by means of quantum chemical topology. We related changes in the aromaticity of a molecule after electron excitation to reaction dynamics in an excited state. Additionally, we found that the conveyed particle has a charge intermediate between that of a bare proton and a neutral hydrogen atom. We anticipate that the analysis presented in this communication will yield valuable insights into ESIPT and other similar photochemical reactions.

A C-Glycosylflavone from Piper ossanum, a Compound Conformationally Controlled by CH/π and Other Weak Intramolecular Interactions.

The structure of the known 2''-O-α-rhamnosyl-4''-O-methylvitexin (apigenin-8-C-α-rhamnosyl-(1→2)-ß-4-O-methylglucopyranoside), isolated from the leaves of Piper ossanum, was revised to acacetin-8-C-neohesperidoside (acacetin-8-C-α-rhamnosyl-(1→2)-ß-glucopyranoside or 2''-O-α-rhamnosyl-4'-O-methylvitexin) (1). The NMR data and theoretical calculations established the preferred conformation of 1, which is controlled by CH/π interactions. This phenomenon explains the unusual chemical shifts of some protons in the molecule, besides other weak intramolecular interactions such as the anomeric effect, the Δ2 effect, and several hydrogen bonds.