Toward Efficient and Stereoselective Aromatic and Dearomative Cope Rearrangements: Experimental and Theoretical Investigations of α-Allyl-α'-Aromatic γ-Lactone Derivatives

The aromatic Cope rearrangement is an elusive transformation that has been the subject of a limited number of investigations compared to those seemingly close analogues, namely the Cope and aromatic Claisen rearrangement. Herein we report our investigations inspired by moderate success observed in the course of pioneering works. By careful experimental and theoretical investigations, we demonstrate that key substitutions on 1,5-hexadiene scaffold allow fruitful transformations. Especially, efficient functionalisation of the heteroaromatic rings results from the aromatic Cope rearrangement, while highly stereoselective interrupted aromatic Cope rearrangements highlight the formation of chiral compounds through a dearomative process.

IGMPlot: A program to identify, characterize, and quantify molecular interactions

We describe the development and features of a program called IGMPlot, which is based on the independent gradient model (IGM) and its local descriptor δ g $$ \delta g $$ . The IGM approach analyzes the gradient of the electron density (ED) in a molecular system to identify regions of space where chemical interactions take place. IGMPlot is intended for use by both experimental scientists and theoretical chemists. It is standalone software written in C++, with versions available for multiple platforms. Some key features are: probing and quantifying interactions between two given molecular fragments, determining bond strength (IBSI), estimating the atomic contributions to an intermolecular interaction and preparing data to build 2D and 3D representations of interaction regions. The software has been updated to include new features: critical point analysis of the ED, assessing ED asymmetry of a given bond (PDA) and a new descriptor called q g $$ qg $$ designed to enhance the IGM- δ g $$ \delta g $$ analysis. The program can be found at: http://igmplot.univ-reims.fr.

New insight into atomic-level interpretation of interactions in molecules and reacting systems

We hereby introduce the atomic Degree Of Interaction (DOI), a new concept rooted in the electron density-based Independent Gradient Model (IGM). Capturing any manifestation of electron density sharing around an...

Novel approach to accurately predict bond strength and ligand lability in platinum-based anticancer drugs

Prompted by the antineoplastic properties of cisplatin, a plethora of platinum(ii)-based complexes have been synthesized in the past decades. At present, their rational design is based on a number of structure-activity relationships involving the nature of the ligands initially coordinated to platinum(ii): either non-labile (acting as a carrier) or labile (undergoing substitution). The coordinate bond strength of the labile ligand plays a key role in the first step of the drug mechanism of action, i.e., the hydrolysis process, which is associated to the retention time of the medicine in the body. Therefore, an accurate determination of the metal-ligand bond strength becomes highly relevant as it will help the rational design of novel chemotherapeutic agents. Herein, we challenge the recently developed intrinsic bond strength index (IBSI) as a rapid and practical tool to assess the ligand lability in Pt(ii) complexes. In a first stage, given the importance of the trans-effect in synthetic strategies of cisplatin-based drugs, the effect of eleven trans-directing ligands T is quantified in two sets of complexes [Pt(NH3)2(H2O)T]n+ and [PtCl2(NH3)T]m+ where T = H2O, F-, NH3, Cl-, Br-, I-, SO32-, CH3-, CN-, CO, and H-. An essential outcome of this work is a novel index IBSItrans = IBSIσ + IBSIπ able to rank the directing ligands by their trans-effect according to their σ-donation and π-backbonding electronic contributions. In a second stage, we apply the IBSI score to a panel of eleven case studies, comprising mostly antineoplastic agents, such as cisplatin, carboplatin, lobaplatin etc., in order to quantify the coordinate bond strength of the ligands, providing insights about the hydrolysis process. The obtained results, in good agreement with experimental data and reported theoretical studies, demonstrate that the IBSI score is able to deliver a rapid and reliable picture of the coordinate bond strength, representing a chemically intuitive tool helpful for the development of novel anticancer agents prior to synthetic efforts.

Pyridazinone derivatives as potential anti-inflammatory agents: synthesis and biological evaluation as PDE4 inhibitors

Cyclic nucleotide phosphodiesterase type 4 (PDE4), which controls the intracellular level of cyclic adenosine monophosphate (cAMP), has aroused scientific attention as a suitable target for anti-inflammatory therapy of respiratory diseases. This work describes the development and characterization of pyridazinone derivatives bearing an indole moiety as potential PDE4 inhibitors and their evaluation as anti-inflammatory agents. Among these derivatives, 4-(5-methoxy-1H-indol-3-yl)-6-methylpyridazin-3(2H)-one possesses promising activity, and selectivity towards PDE4B isoenzymes and is able to regulate potent pro-inflammatory cytokine and chemokine production by human primary macrophages.

A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach

The independent gradient model (IGM) is a recent electron density-based computational method that enables to detect and quantify covalent and noncovalent interactions. When applied to large systems, the original version of the technique still relies on promolecular electron densities given by the sum of spherically averaged atomic electron distributions, which leads to approximate evaluations of the inter- and intramolecular interactions occurring in systems of biological interest. To overcome this drawback and perform IGM analyses based on quantum mechanically rigorous electron densities also for macromolecular systems, we coupled the IGM approach with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) that allow fast and reliable reconstructions of polypeptide and protein electron densities. The validation tests performed on small polypeptides and peptide dimers have shown that the novel IGM-ELMO strategy provides results that are systematically closer to the fully quantum mechanical ones and outperforms the IGM method based on the crude promolecular approximation, but still keeping a quite low computational cost. The results of the test calculations carried out on proteins have also confirmed the trends observed for the IGM analyses conducted on small systems. This makes us envisage the future application of the novel IGM-ELMO approach to unravel complicated noncovalent interaction networks (e.g., in protein-protein contacts) or to rationally design new drugs through molecular docking calculations and virtual high-throughput screenings.

Mechanistic insights into Smiles rearrangement. Focus on π-π stacking interactions along the radical cascade

The synthesis of new arene and heteroarene scaffolds of therapeutic interest has generated a renewed interest in the domino radical cyclisation-Smiles. In this work we present a detailed mechanistic investigation of the radical version of a cascade involving a desulfonative Smiles rearrangement on an aromatic ring bearing a sulfonamide linker. Competing routes have been explored to characterize the molecular mechanism of the studied reaction. The knowledge gained from previous experimental observations is explained through the energy profile obtained by means of quantum mechanical calculations. This study answers questions about the rate determining step and the type of mechanism involved (two-step or concerted). Supplementary rate constant calculations as well as quantum molecular dynamics support experimental observations. An IGM-δg analysis performed along the reaction path unveils and quantifies an intramolecular π-π stacking interaction accelerating the reaction. This novel post processing IGM-δg tool based on the electron density, turns out to be useful to monitor and quantify specific intramolecular weak interactions along a reaction path from wave functions. From this mechanistic investigation it turns out that Smiles rearrangement here takes place in two steps rather than in a direct intramolecular radical substitution. Furthermore, we show that chain length effects must be taken into account in the functionalization of new sulfonylated derivatives subjected to this radical cascade, given their influence in the reaction rate.

New Way for Probing Bond Strength

The covalent chemical bond is intimately linked to electron sharing between atoms. The recent independent gradient model (IGM) and its δg descriptor provide a way to quantify locally this electron density interpenetration from wavefunction calculations. Each bond has its own IGM-δg^pair signature. The present work establishes for the first time a strong link between this bond signature and the physically grounded bond force constant concept. Analyzing a large set of compounds and bonds, the intrinsic bond strength index (IBSI) emerges from the IGM formulation. Our study shows that the IBSI does not belong to the class of conventional bond orders (like Mulliken, Wiberg, Mayer, delocalization index, or electron localization function-ELF), but is rather a new complementary index, related to the bond strength. A fundamental outcome of this research is a novel index allowing to range all two-center chemical bonds by their intrinsic strength in molecular situation. We believe that the IBSI is a powerful and robust tool for interpretation accessible to a wide community of chemists (organic, inorganic chemistry, including transition-metal complexes and reaction mechanisms).

The Independent Gradient Model: A New Approach for Probing Strong and Weak Interactions in Molecules from Wave Function Calculations

Extraction of the chemical interaction signature from local descriptors based on electron density (ED) is still a fruitful field of development in chemical interpretation. In a previous work that used promolecular ED (frozen ED), the new descriptor, δg , was defined. It represents the difference between a virtual upper limit of the ED gradient (∇ρIGM , IGM=independent gradient model) that represents a noninteracting system and the true ED gradient (∇ρ ). It can be seen as a measure of electron sharing brought by ED contragradience. A compelling feature of this model is to provide an automatic workflow that extracts the signature of interactions between selected groups of atoms. As with the noncovalent interaction (NCI) approach, it provides chemists with a visual understanding of the interactions present in chemical systems. ∇ρIGM is achieved simply by using absolute values upon summing the individual gradient contributions that make up the total ED gradient. Hereby, we extend this model to relaxed ED calculated from a wave function. To this end, we formulated gradient-based partitioning (GBP) to assess the contribution of each orbital to the total ED gradient. We highlight these new possibilities across two prototypical examples of organic chemistry: the unconventional hexamethylbenzene dication, with a hexa-coordinated carbon atom, and β-thioaminoacrolein. It will be shown how a bond-by-bond picture can be obtained from a wave function, which opens the way to monitor specific interactions along reaction paths.

Synthesis and biological evaluation of pyridazinone derivatives as potential anti-inflammatory agents

Cyclic nucleotide phosphodiesterase type 4 (PDE4), that controls intracellular level of cyclic nucleotide cAMP, has aroused scientific attention as a suitable target for anti-inflammatory therapy in respiratory diseases. Here we describe the development of two families of pyridazinone derivatives as potential PDE4 inhibitors and their evaluation as anti-inflammatory agents. Among these derivatives, 4,5-dihydropyridazinone representatives possess promising activity, selectivity towards PDE4 isoenzymes and are able to reduce IL-8 production by human primary polymorphonuclear cells.

Development of the first model of a phosphorylated, ATP/Mg2+-containing B-Raf monomer by molecular dynamics simulations: a tool for structure-based design

A model of phosphorylated and ATP-containing B-Raf protein kinase is needed as a tool for the structure-based design of new allosteric inhibitors, since no crystal structure of such a system has been resolved. Here, we present the development of such a model as well as a thorough analysis of its structural features. This model was prepared using a systematic molecular dynamics approach considering the presence or absence of both the phosphate group at the Thr599 site and the ATP molecule. Then, different structural features (i.e. DFG motif, Mg²⁺ binding loop, activation loop, phosphorylation site and αC-helix region) were analysed for each trajectory to validate the aimed 2pBRAF_ATP model. Moreover, the structure and activating interactions of this 2pBRAF_ATP model were found to be in agreement with previously reported information. Finally, the model was further validated by means of a molecular docking study with our previously developed lead compound I confirming that this ATP-containing, phosphorylated protein model is suitable for further structure-based design studies.

Accurately extracting the signature of intermolecular interactions present in the NCI plot of the reduced density gradient versus electron density

An electron density (ED)-based methodology is developed for the automatic identification of intermolecular interactions using pro-molecular density. The expression of the ED gradient in terms of atomic components furnishes the basis for the Independent Gradient Model (IGM). This model leads to a density reference for non interacting atoms/fragments where the atomic densities are added whilst their interaction turns off. Founded on this ED reference function that features an exponential decay also in interference regions, IGM model provides a way to identify and quantify the net ED gradient attenuation due to interactions. Using an intra/inter uncoupling scheme, a descriptor (δg^inter) is then derived that uniquely defines intermolecular interaction regions. An attractive feature of the IGM methodology is to provide a workflow that automatically generates data composed solely of intermolecular interactions for drawing the corresponding 3D isosurface representations.

Relationships between Th1 or Th2 iNKT cell activity and structures of CD1d-antigen complexes: meta-analysis of CD1d-glycolipids dynamics simulations

A number of potentially bioactive molecules can be found in nature. In particular, marine organisms are a valuable source of bioactive compounds. The activity of an α-galactosylceramide was first discovered in 1993 via screening of a Japanese marine sponge (Agelas mauritanius). Very rapidly, a synthetic glycololipid analogue of this natural molecule was discovered, called KRN7000. Associated with the CD1d protein, this α-galactosylceramide 1 (KRN7000) interacts with the T-cell antigen receptor to form a ternary complex that yields T helper (Th) 1 and Th2 responses with opposing effects. In our work, we carried out molecular dynamics simulations (11.5 µs in total) involving eight different ligands (conducted in triplicate) in an effort to find out correlation at the molecular level, if any, between chemical modulation of 1 and the orientation of the known biological response, Th1 or Th2. Comparative investigations of human versus mouse and Th1 versus Th2 data have been carried out. A large set of analysis tools was employed including free energy landscapes. One major result is the identification of a specific conformational state of the sugar polar head, which could be correlated, in the present study, to the biological Th2 biased response. These theoretical tools provide a structural basis for predicting the very different dynamical behaviors of α-glycosphingolipids in CD1d and might aid in the future design of new analogues of 1.

Molecular properties affecting the adsorption coefficient of pesticides from various chemical families

Forty pesticides were selected in function of their chemical families and their physico-chemical properties to represent a wide range of pesticide properties. Adsorption of these pesticides was studied on two soils by batch experiments. The two soils differed largely in organic matter and calcite contents. Distribution coefficient Kd was determined for each pesticide on the two soils. Adsorption was higher for the soil having the highest organic matter content and the lowest calcite content. In order to identify pesticide properties governing retention, eight molecular descriptors were determined from three-dimensional (3D) structure of molecules. Class-specific quantitative structure properties relationship (QSPR) soil adsorption models using one and two parameters were developed from experimental Kd. Three properties seemed to influence most retention of pesticides: hydrophobicity, solubility, and polarisability. Models combining these properties were suggested and discussed.

Molecular properties affecting the adsorption coefficient of phenylurea herbicides

The adsorption of 12 pesticides of the phenylurea family was studied by batch experiments in order to determine the adsorption coefficient, K d. The study was conducted in two soils chosen for their differences in organic matter and calcite contents. K d pesticide adsorption coefficients were higher for soil S1 than for soil S2 due to the presence of a higher organic matter content and a lower calcite content in soil S1. To identify pesticide properties governing retention, 18 molecular descriptors were considered. Class-specific quantitative structure-property relationship (QSPR) soil sorption models using one, two, and three descriptors were developed from our experimental data using linear regressions. One of the aims of this work was to check whether QSPR models that did not include literature values of K ow were able to predict K d coefficients in satisfactory agreement with our experimental data. The influence of the level of theory in determining K ow and polarisability predictors on the predictive performance of the model was also examined by comparing quantum chemistry and empirical (QikProp) approaches. The one-descriptor model using "quantum" polarisability α was found to perform almost as well as or better than the other models.

Tunneling in the reaction of acetone with OH

Based on recent detailed quantum mechanical computations of the mechanism of the title reaction and, this paper presents kinetics analysis of the overall rate constant and its temperature dependence, for which ample experimental data are available for comparison. The analysis confirms that the principal channel is the formation of acetonyl radical + H(2)O, while the channel leading to acetic acid is of negligible importance. It is shown that the unusual temperature dependence of the overall rate constant, as observed experimentally, is well accounted for by standard RRKM treatment that includes tunneling. This treatment is applied at the microcanonical level, with chemically activated distribution of entrance species, i.e. using a stationary rather than a thermal distribution that incorporates collisional energy transfer and competition between the redissociation and exit channel. A similar procedure is applied to the isotopic reaction acetone-d6 + OH with equally satisfying results, so that the experimental temperature dependence of the KIE (kinetic isotope effect) is perfectly reproduced. This very good agreement between calculation and experiment is obtained without any fitting to experimental values and without any adjustment of the parameters of calculation.