Phosphine-Catalyzed Stereoselective Dearomatization of 3-NO2-Indoles with Allenoates.

The stereoselective phosphine-catalyzed (( pMeOC6H4)3P, 10-20 mol %) dearomatization of 3-NO2-indoles with allenoates is described. A range of densely functionalized indolines (18 examples) is obtained in high yields (up to 96%) under mild reaction conditions (rt, air, reagent-grade solvent). Computational simulations and labeling experiments revealed a stepwise [3 + 2]-type mechanism involving a water-assisted hydrogen shift and accounted for the diastereoselection recorded.

Lennard-Jones Intermolecular Potentials for the Description of 6-Membered Aromatic Heterocycles Interacting with the Isoelectronic CO2 and CS2.

We have generated Lennard-Jones potentials for the interaction between CX2 (X = O, S) and 11 nitrogen-doped benzene derivatives in different orientations at the M06-2X/def2-tzvpp level as tools to parametrize accurate force fields and to better understand the interaction of these greenhouse gases with heterocyclic building blocks used in the design of capture and detection systems. We find that the most favorable interactions are found between the carbon in CO2 and the main heterocycle in the ring in a parallel orientation, whereas the preferred interaction mode of CS2 is established between sulfur and the π density of the aromatic ring. The fact that the preferences for interaction sites and orientations of CO2 and CS2 are most of the times opposite helps in terms of ensuring the selectivity of these systems in front of these two isoelectronic compounds. The existence of very good linear correlations ( R2 values very close to one) between the number of nitrogen atoms in the heterocyclic ring and the depth of the interaction potential wells opens the door to the use of these results in generating coarse-grained potentials or models with predictive power for use in the design of larger systems.

Rational Design of Efficient Environmental Sensors: Ring-Shaped Nanostructures Can Capture Quat Herbicides.

The viability of using [n]-cycloparaphenylenes (CPPs) of different sizes to encapsulate diquat (DQ) pesticide molecules has been tested analyzing the origin of the host-guest interactions stabilizing the complex. This analysis provides rational design capabilities to construct ad hoc capturing systems tailored to the desired pollutant. All CPPs considered (n = 7-12) are capable of forming remarkably stable complexes with DQ, though [9]-CPP is the best candidate, where a fine balance is established between the energy penalty due to the deformation + repulsion of the pesticide molecule inside the cavity (larger in smaller CPPs) and the maximization of the favorable dispersion, electrostatic and induction contributions (which also decrease in larger rings). These encouraging results prompted us to evaluate the potential of using Resonance Raman spectroscopy on nanohoop complexes as a tool for DQ sensing. The shifts observed in the vibrational frequencies of DQ upon complexation allow us to determine whether complexation has been achieved. Additionally, a large enhancement of the signals permits a selective identification of the vibrational modes.

Mechanism of the Molybdenum-Mediated Cadogan Reaction.

Oxygen atom transfer reactions are receiving increasing attention because they bring about paramount transformations in the current biomass processing industry. Significant efforts have therefore been made lately in the development of efficient and scalable methods to deoxygenate organic compounds. One recent alternative involves the modification of the Cadogan reaction in which a Mo(VI) core catalyzes the reduction of o-nitrostyrene derivatives to indoles in the presence of PPh3. We have used density functional theory calculations to perform a comprehensive mechanistic study on this transformation, in which we find two clearly defined stages: an associative path from the nitro to the nitroso compound, characterized by the reduction of the catalyst in the first step, and a peculiar mechanism involving oxazaphosphiridine and nitrene intermediates leading to an indole product, where the metal catalyst does not participate.

Lennard-Jones Potentials for the Interaction of CO2 with Five-Membered Aromatic Heterocycles.

We used M06-2X/Def2-TZVPP to calculate a broad set of rigid interaction profiles between CO2 and 30 different aromatic heterocycles, based on pyrrole, furan, and thiophene with ring positions subsituted with up to four nitrogens. For each system, several orientations of the fragments were explored to both find the preferred interaction mode and have information about other interaction modes that can contribute to the binding energy when CO2 is captured by complex systems. From these data, Lennard-Jones potentials were obtained, which can be used for the parametrization of force fields that correctly describe the multipolar and dispersion interactions at play between these kinds of fragments. These results are expected to contribute to the development of new force fields for the study of chemical systems for the capture and sequestration of CO2 and also directly for the design of such systems.

CO2 Complexes with Five-Membered Heterocycles: Structure, Topology, and Spectroscopic Characterization.

In a first step toward the rational design of macrocyclic structures optimized for CO2 capture, we systematically explored the potential of 30 five-membered aromatic heterocycles to establish coordinating complexes with this pollutant. The interactions between the two moieties were studied in several orientations, and the obtained complexes were analyzed in terms of electron density and vibrational fingerprint. The former is an aid to provide an in-depth knowledge of the interaction, whereas the latter should help to select structural motifs that have not only good complexation properties but also diagnostic spectroscopic signals.

[MoO2]2+-Mediated Oxygen Atom Transfer via an Unusual Lewis Acid Mechanism.

Density functional theory is applied to the study of the oxygen atom transfer reaction from sulfoxide (DMSO) to phosphine (PMe3) catalyzed by the [MoO2]2+ active core. In this work, two fundamentally different roles are explored for this dioxometal complex in the first step of the catalytic cycle: as an oxidizing agent and as a Lewis acid. The latter turns out to be the favored pathway for the oxygen atom transfer. This finding may have more general implications for similar reactions catalyzed by the same [MoO2]2+ core.

From Hydrindane to Decalin: A Mild Transformation through a Dyotropic Ring Expansion.

An unexpected ring expansion converting hydrindane cores into decalins has been observed. The process occurs under very mild conditions and with exquisite transfer of chiral information. The ring expansion provides access to decorated decalins with complete stereocontrol. The reaction mechanism is studied in order to gain insight into the underlying causes for the low thermal requirements in this reaction and the nature of the chirality transfer process. Interestingly, both result from an unprecedented dyotropic reaction involving a mesylate group.

Dynamic Effects Responsible for High Selectivity in a [3,3] Sigmatropic Rearrangement Featuring a Bispericyclic Transition State.

Bispericyclic transition states appear when two independent pericyclic transition states merge into one. They are a particular case of the more general ambimodal concept applied to a transition state that connects reactants with two or more products involving reaction path bifurcations through valley-ridge inflections. In the present computational work, the first example of a bifurcating sigmatropic reaction featuring a bispericyclic transition state is reported for a cyclohexane featuring opposing methylene and a vinylidene fragments. Perhalogenation of a C-C bond in this substrate imparts a strong desymmetrization to the bifurcating potential energy surface. These systems undergo the [3,3] sigmatropic rearrangement with high selectivity, with a preferred product that depends on which halogen decorates the C-C bond. We have found that dynamic effects have a paramount role in the selectivity observed for these reactions.

A Radical Mechanism for the Vanadium-Catalyzed Deoxydehydration of Glycols.

We propose a novel mechanism for the deoxydehydration (DODH) reaction of glycols catalyzed by a [Bu4N][VO2(dipic)] complex (dipic = pyridine-2,6-dicarboxylate) using triphenylphosphine as a reducing agent. Using density functional theory, we have confirmed that the preferred sequence of reaction steps involves reduction of the V(V) complex by phosphine, followed by condensation of the glycol into a [VO(dipic)(-O-CH2CH2-O-)] V(III) complex (6), which then evolves to the alkene product, with recovery of the catalyst. In contrast to the usually invoked closed-shell mechanism for the latter steps, where 6 suffers a [3+2] retrocycloaddition, we have found that the homolytic cleavage of one of the C-O bonds in 6 is preferred by 12 kcal/mol. The resulting diradical intermediate then collapses to a metallacycle that evolves to the product through an aromatic [2+2] retrocycloaddition. We use this key change in the mechanism to propose ways to design better catalysts for this transformation. The analysis of the mechanisms in both singlet and triplet potential energy surfaces, together with the location of the MECPs between them, showcases this reaction as an interesting example of two-state reactivity.

Rational Design in Catalysis: A Mechanistic Study of ß-Hydride Eliminations in Gold(I) and Gold(III) Complexes Based on Features of the Reaction Valley.

ß-Hydride eliminations for ethylgold(III) dichloride complexes are identified as reactions with an unusually long prechemical stage corresponding to the conformational preparation of the reaction complex and spanning six phases. The prechemical process is characterized by a geared rotation of the L-Au-L group (L = Cl) driving methyl group rotation and causing a repositioning of the ligands. This requires more than 28 kcal/mol of the total barrier of 34.0 kcal/mol, according to the unified reaction valley approach, which also determines that the energy requirements of the actual chemical process leading to the ß-elimination product are only about 5.5 kcal/mol. A detailed mechanistic analysis was used as a basis for a rational design of substrates (via substituents on the ethyl group) and/or ligands, which can significantly reduce the reaction barrier. This strategy takes advantage of either a higher trans activity of the ligands or a tuned electronic demand of the ethyl group. The ß-hydride elimination of gold(I) was found to suffer from strong Coulomb and exchange repulsion when a positively charged hydrogen atom enforces a coordination position in a d(10)-configured gold atom, thus triggering an unassisted σ-π Au(I)-C conversion.

Solving the Pericyclic-Pseudopericyclic Puzzle in the Ring-Closure Reactions of 1,2,4,6-Heptatetraene Derivatives.

The ongoing controversy whether cyclization reactions of conjugated allenes or ketenes follow a pericyclic or a pseudopericyclic mechanism has triggered dozens of investigations, which have led to new valuable synthetic routes. In this work, the mechanism of 10 representative cyclization reactions of hepta-1,2,4,6-tetraenes with different terminal groups is investigated utilizing the unified reaction valley approach that registers all electronic structure changes of the target molecule along the entire reaction pathway. A clear differentiation between a purely pericyclic and a purely pseudopericyclic mechanism is established. Additionally, it is found that, by using suitable functional groups, a pericyclic mechanism can be converted into a pseudopericyclic one, which is associated with a steady decrease of the reaction barrier and a continuous change from one mechanism to the other. The energetics of the reaction are confirmed by coupled cluster calculations of the CCSD(T) type. The mechanistic insight gained is used to design new pseudopericyclic reactions with low or no barrier, which will open new synthetic avenues.

Accounting for Diradical Character through DFT. The Case of Vinyl Allene Oxide Rearrangement.

The transformation of vinyl allene oxides into cyclopentenones is key to the biosynthesis of a number of hormone-like molecules in plants. Two competitive paths are generally accepted for this transformation: a concerted SN2-like mechanism and a stepwise path with a diradical oxyallyl intermediate. Recently, a new stepwise closed-shell path has been proposed that circumvents the key oxyallyl intermediate. In this work, we conduct a thorough computational investigation, including dynamic effects, to identify the most likely mechanism for this transformation.

Computational approaches to homogeneous gold catalysis.

Homogenous gold catalysis has been exploding for the last decade at an outstanding pace. The best described reactivity of Au(I) and Au(III) species is based on gold's properties as a soft Lewis acid, but new reactivity patterns have recently emerged which further expand the range of transformations achievable using gold catalysis, with examples of dual gold activation, hydrogenation reactions, or Au(I)/Au(III) catalytic cycles.In this scenario, to develop fully all these new possibilities, the use of computational tools to understand at an atomistic level of detail the complete role of gold as a catalyst is unavoidable. In this work we aim to provide a comprehensive review of the available benchmark works on methodological options to study homogenous gold catalysis in the hope that this effort can help guide the choice of method in future mechanistic studies involving gold complexes. This is relevant because a representative number of current mechanistic studies still use methods which have been reported as inappropriate and dangerously inaccurate for this chemistry.Together with this, we describe a number of recent mechanistic studies where computational chemistry has provided relevant insights into non-conventional reaction paths, unexpected selectivities or novel reactivity, which illustrate the complexity behind gold-mediated organic chemistry.

Bis(o-methylserotonin)-containing iridium(III) and ruthenium(II) complexes as new cellular imaging dyes: synthesis, applications, and photophysical and computational studies.

We report the synthesis, characterization, and scope of a new versatile emissive molecular probe functionalized with a 1,10-phenanthroline moiety containing methylserotonin groups as binding sites for metal ion recognition. The synthesis, characterization, and evaluation of the in vitro imaging capability of the iridium(III) and ruthenium(II) complexes [Ir(ppy)2(N-N)](+) and [Ru(bpy)2(N-N)](2+), in which ppy is 2-phenylpyridine, bpy is 2,2'-bipyridine, and N-N is a 1,10-phenanthroline ligand functionalized with two methylserotonin groups to serve as binding sites for metal ion recognition, is reported. The uptake of these compounds by living freshwater fish (Carassius auratus) was studied by fluorescence microscopy, and the cytotoxicity of ligand N-N and [Ru(bpy)2(N-N)](2+) in this species was also investigated.

Computational insights on the mechanism of the catalytic hydrogenation with BINAP-diamine-Ru complexes: the role of base and origin of selectivity.

In this work we show that a base is needed to generate the active catalyst through any of three different paths close in energy. The facial differentiation arises from steric interactions that induce a very asynchronous, non-pericyclic disfavored transition state. Catalyst regeneration takes place through two steps that avoid a forbidden pericyclic mechanism.

Theoretical and experimental exploration of the photochemistry of resveratrol: beyond the simple double bond isomerization.

The photochemical isomerization of resveratrol has been the subject of recent studies in which contradictory results were reported. The photoproduct mixture of this reaction needs to be considered more complex than the coexistence of cis and trans isomers. An unidentified third product, at least, has been detected in various studies although its nature was unknown. In this work, we aim to provide a thorough description of the photochemical course of this reaction through experimental and computational approaches working in a synergetic association.

DFT-based mechanistic insights into noble metal-catalyzed rearrangement of propargylic derivatives: chirality transfer processes.

Cascade transformations of enynes and propargylic acyl derivatives triggered by the π-acid activation of the alkyne by gold or platinum catalysts can afford diverse and complex molecular skeletons under mild conditions in an atom-economical manner. Often the rearrangements benefit from additional roles of the metal, either activating other functional groups and/or organizing the intermediates for further reactions. Mechanistic insights gleaned from kinetic and labeling studies have been complemented by quantum chemical calculations for different substrates and reaction types, which show some common features that can be traced back to the combination of the propargylic system and the noble metal catalyst. Among other results, theoretical studies of the reactivity of some systems revealed the prevalence of very low barriers for the bond-forming/bond-breaking processes along complex multistep mechanistic manifolds. As a consequence, the barriers corresponding to conformational changes (single bond rotations, helix inversions…) of the intermediates acquire unexpected importance. Thus, memory of chirality in reactions of enantiopure substrates is preserved, in some cases, in formally planar intermediates that however do not undergo conformational scrambling. In this chapter we will review how computational chemistry continues to play a key role in our understanding and interpretation of the catalytic cycles of complex transformations catalyzed by gold and platinum, in particular those involving transfer of chirality.

Hg2+ detection by new anthracene pendant-arm derivatives of mixed N/S- and N/S/O-donor macrocycles: fluorescence, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and density functional theory studies.

The optical response of four new anthracenylmethyl pendant-arm derivatives (L1-L4) of the macrocyclic ligands [12]aneNS(3), [12]aneNS(2)O, [15]aneNS(2)O(2), and [12]aneN(2)SO toward the metal ions Zn(2+), Cd(2+), Pb(2+), Cu(2+), Hg(2+), Ag(+), Fe(2+), Co(2+), Ni(2+), Mn(2+), Ca(2+), Na(+), Mg(2+), and K(+) was investigated in 1:1 (v/v) MeCN/H(2)O solutions. A strong chelation enhancement of quenching effect was observed on the fluorescent emission intensity of L2 as a consequence of the host-guest interaction with Hg(2+) and the formation of a 1:2 metal-to-ligand complex. Density functional theory calculations confirmed the formation of a sandwich-type complex between L2 and Hg(2+) as a favorable process. A matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry study using the four ligands as active MALDI probes was also performed. L1-L4 have also been explored as fluorescence chemosensors in microsamples using NANODROP technology.

Cyclization Cascade of Allenyl Azides: Synergy Between Theory and Experiment.

Collaborative work between experimentalists and computational chemists have demonstrated a stong synergy which allowed the rationalization of allenyl azide chemistry and permited the development of an efficient synthetic tool aimed at the preparation of several alkaloids. Saturated allenyl azides undergo a reaction cascade involving key diradical intermediates that follow the Curtin-Hammett model whereas unsaturated allenyl azides form indolidene intermediates that furnish the final indole products via electrocyclic ring closure events taking place out of the Curtin-Hammett regime. The regiochemistry of the reaction cascade with the latter substrates can be manipulated by Cu(I) addition to the reaction mixture.