Exploring isofunctional molecules: Design of a benchmark and evaluation of prediction performance.

Identification of novel chemotypes with biological activity similar to a known active molecule is an important challenge in drug discovery called 'scaffold hopping'. Small-, medium-, and large-step scaffold hopping efforts may lead to increasing degrees of chemical structure novelty with respect to the parent compound. In the present paper, we focus on the problem of large-step scaffold hopping. We assembled a high quality and well characterized dataset of scaffold hopping examples comprising pairs of active molecules and including a variety of protein targets. This dataset was used to build a benchmark corresponding to the setting of real-life applications: one active molecule is known, and the second active is searched among a set of decoys chosen in a way to avoid statistical bias. This allowed us to evaluate the performance of computational methods for solving large-step scaffold hopping problems. In particular, we assessed how difficult these problems are, particularly for classical 2D and 3D ligand-based methods. We also showed that a machine-learning chemogenomic algorithm outperforms classical methods and we provided some useful hints for future improvements.

To bend or not to bend: experimental and computational studies of structural preference in Ln(Tp(iPr)2)2 (Ln = Sm, Tm).

The synthesis and characterization of Ln(Tp(iPr2))2 (Ln = Sm, 3Sm; Tm, 3Tm) are reported. While the simple (1)H NMR spectra of the compounds indicate a symmetrical solution structure, with equivalent pyrazolyl groups, the solid-state structure revealed an unexpected, "bent sandwich-like" geometry. By contrast, the structure of the less sterically congested Tm(Tp(Me2,4Et))2 (4) adopts the expected symmetrical structure with a linear B-Tm-B arrangement. Computational studies to investigate the origin of the unexpected bent structure of the former compounds indicate that steric repulsion between the isopropyl groups forces the Tp ligands apart and permits the development of unusual interligand C-H···N hydrogen-bonding interactions that help stabilize the structure. These results find support in the similar geometry of the Tm(III) analogue [Tm(Tp(iPr2))2]I, 3Tm(+), and confirm that the low symmetry is not the result of a metal-ligand interaction. The relevance of these results to the general question of the coordination geometry of MX2 and M(C5R5)2 (M = heavy alkaline earth and Ln(II), X = halide, and C5R5 = bulky persubstituted cyclopentadienyl) complexes and the importance of secondary H-bonding and nonbonding interactions on the structure are highlighted.

Redox-active phosphines: synthesis and crystal structures of palladium(II) complexes of a metallaphosphine in two different oxidation states.

The redox-active metallaphosphine [Fe(dppe)(η(5)-C5Me5)(C≡C-PPh2)] reacts with [Pd(1,5-cod)Cl2] to give mono- and bis-phosphine coordinated palladium centres as a function of stoichiometry, and these complexes provide a stable redox-active platform which allows reversible one-electron {Fe(II)→Fe(III)(+)} oxidations within the palladium coordination sphere.

Revisiting the molecular roots of a ubiquitously successful synthesis: nickel(0) nanoparticles by reduction of [Ni(acetylacetonate)2].

The widely used preparation of Ni(0) nanoparticles from [Ni(acac)(2)] (acac=acetylacetonate) and oleylamine, often considered to be a thermolysis or a radical reaction, was analyzed anew by using a combination of DFT modeling and designed mechanistic experiments. Firstly, the reaction was followed up by using TGA to evaluate the energy barrier of the limiting step. Secondly, all the byproducts were identified using NMR spectroscopy, mass spectrometry, FTIR, and X-ray crystallography. These methods allowed us to depict both main and side-reaction pathways. Lastly, DFT modeling was utilized to assess the validity of this new scheme by identifying the limiting steps and evaluating the corresponding energy barriers. The oleylamine was shown to reduce the [Ni(acac)(2)] complex not through a one-electron radical mechanism, as often stated, but as an hydride donor through a two-electron chemical reduction route. This finding has strong consequences not only for the design of further nanoparticles syntheses that use long-chain amine as a reactant, but also for advanced understanding of catalytic reactions for which these nanoparticles can be employed.

Insights into the mechanism of reaction of [(C5Me5)2Sm(II)(thf)2] with CO2 and COS by DFT studies.

Reaction mechanisms for the oxidative reactions of CO(2) and COS with [(C(5)Me(5))(2)Sm] have been investigated by means of DFT methods. The experimental formation of oxalate and dithiocarbonate complexes is explained. Their formation involve the samarium(III) bimetallic complexes [(C(5)Me(5))(2)Sm-CO(2)-Sm(C(5)Me(5))(2)] and [(C(5)Me(5))(2)Sm-COS-Sm(C(5)Me(5))(2)] as intermediates, respectively, ruling out radical coupling for the formation of the oxalate complex.

Pd(II) and Ni(II) complexes featuring a "phosphasalen" ligand: synthesis and DFT study.

A phosphorus analog of salen ligands featuring iminophosphorane functionalities in place of the imine groups was synthesised in 2 steps from o-diphenylphosphinophenol via the preparation of the corresponding bis-aminophosphonium salt. This novel tetradentate ligand (1), which we named phosphasalen, was coordinated to Pd(II) and Ni(II) metal centres affording complexes 6 and 7 respectively, which were characterised by multinuclear NMR, elemental and X-ray diffraction analyses. Both neutral complexes adopt a nearly square-planar geometry around the metal with coordination of all iminophosphorane and phenolate moieties. The electronic properties of these new complexes were investigated by cyclic voltammetry and comparison with known salens was made when possible. Moreover, the particular behaviour of the phosphasalen nickel complex 7 was further investigated through magnetic moment measurements and a DFT study.

Theoretical treatment of redox processes involving lanthanide(II) compounds: reactivity of organosamarium(II) and organothulium(II) complexes with CO2 and pyridine.

An effective methodology to deal with the theoretical treatment on the redox chemistry of divalent organolanthanide complexes is reported and has been tested on two representative substrates, pyridine and CO(2), with two different metals (samarium and thulium). An influence of the ancillary ligands, namely, C(5)Me(5) (Cp*) or (2,3,4,5-tetramethylphospholyl) (Tmp), on the one- or two-electron oxidation processes is observed. The theoretical results are in excellent agreement with the experimental observations indicating the efficiency of the method.

Mechanism of the dehydrogenative silylation of alcohols catalyzed by cationic gold complexes: an experimental and theoretical study.

The catalytic activity both of cationic [(XDPP)Au][X] (XDPP = bis-2,5-diphenylphosphole xantphos X = BF(4)) and of the isolated gold hydride complex [(XDPP)(2)Au(2)H][OTf] in the dehydrogenative silylation process is presented. A parallel theoretical study using density functional theory revealed a mechanism involving the counter anion as a co-catalyst, which was experimentally confirmed by testing various counterions (X = OTf, NTf(2), PF(6)). Finally, a "Au(2)H(+)" species was determined as the intermediate during the catalytic cycle, which correlates well with the experimental findings on the first example of catalytic activity of an isolated "Au-H" complex.