Allylic and Allenylic Dearomatization of Indoles Promoted by Graphene Oxide by Covalent Grafting Activation Mode.

The site-selective allylative and allenylative dearomatization of indoles with alcohols was performed under carbocatalytic regime in the presence of graphene oxide (GO, 10 wt % loading) as the promoter. Metal-free conditions, absence of stoichiometric additive, environmentally friendly conditions (H2 O/CH3 CN, 55 °C, 6 h), broad substrate scope (33 examples, yield up to 92 %) and excellent site- and stereoselectivity characterize the present methodology. Moreover, a covalent activation model exerted by GO functionalities was corroborated by spectroscopic, experimental and computational evidences. Recovering and regeneration of the GO catalyst through simple acidic treatment was also documented.

Stable and Biocompatible Monodispersion of C60 in Water by Peptides.

The lack of solubility in water and the formation of aggregates hamper many opportunities for technological exploitation of C60. Here, different peptides were designed and synthesized with the aim of monomolecular dispersion of C60 in water. Phenylalanines were used as recognizing moieties, able to interact with C60 through π-π stacking, while a varying number of glycines were used as spacers, to connect the two terminal phenylalanines. The best performance in the dispersion of C60 was obtained with the FGGGF peptidic nanotweezer at a pH of 12. A full characterization of this adduct was carried out. The peptides disperse C60 in water with high efficiency, and the solutions are stable for months both in pure water and in physiological environments. NMR measurements demonstrated the ability of the peptides to interact with C60. AFM measurements showed that C60 is monodispersed. Electrospray ionization mass spectrometry determined a stoichiometry of C60@(FGGGF)4. Molecular dynamics simulations showed that the peptides assemble around the C60 cage, like a candy in its paper wrapper, creating a supramolecular host able to accept C60 in the cavity. The peptide-wrapped C60 is fully biocompatible and the C60 "dark toxicity" is eliminated. C60@(FGGGF)4 shows visible light-induced reactive oxygen species (ROS) generation at physiological saline concentrations and reduction of the HeLa cell viability in response to visible light irradiation.

DNAzymes at Work: A DFT Computational Investigation on the Mechanism of 9DB1.

The 9DB1 DNAzyme follows an addition-elimination (AN+DN) two-step mechanism, involving a phosphorane intermediate, where the 3'-hydroxyl group (nucleophile) of one RNA fragment attacks the 5'-triphosphate of another RNA fragment. This mechanism does not involve a divalent metal cation in agreement with the experimental evidence. The process is assisted by two proton transfers that activate the nucleophile (first step) and the leaving group (second step). The dA13 nucleotide is not directly involved in the reaction. However, it plays an important role in determining the regioselectivity of the process: since the dA13 phosphate forms a strong hydrogen bond with the 2'-hydroxyl, only the 3'-hydroxyl can behave as a nucleophile and form the new 3'-5' bond. In silico mutagenesis, where the dA13 phosphate oxygen involved in the hydrogen contact was replaced by a sulfur atom, causes a significant rearrangement of the A50 ribose position with an increase in the activation barrier and a consequent lower enzymatic activity in agreement with the experimental evidence. A similar effect is determined by the replacement of the 2'-hydroxyl with different groups such as F, H, and OMe.

Aggregation Pathways of Native-Like Ubiquitin Promoted by Single-Point Mutation, Metal Ion Concentration, and Dielectric Constant of the Medium.

Ubiquitin-positive protein aggregates are biomarkers of neurodegeneration, but the molecular mechanism responsible for their formation and accumulation is still unclear. Possible aggregation pathways of human ubiquitin (hUb) promoted by both intrinsic and extrinsic factors, are here investigated. By a computational analysis, two different hUb dimers are indicated as possible precursors of amyloid-like structures, but their formation is disfavored by an electrostatic repulsion involving Glu16 and other carboxylate residues present at the dimer interface. Experimental data on the E16V mutant of hUb shows that this single-point mutation, although not affecting the overall protein conformation, promotes protein aggregation. It is sufficient to shift the same mutation by only two residues (E18V) to regain the behavior of wild-type hUb. The neutralization of Glu16 negative charge by a metal ion and a decrease of the dielectric constant of the medium by addition of trifluoroethanol (TFE), also promote hUb aggregation. The outcomes of this research have important implications for the prediction of physiological parameters that favor aggregate formation.

A Full QM Computational Study of the Catalytic Mechanism of α-1,4-Glucan Lyases.

We investigated the catalytic mechanism of α-1,4-glucan lyases using a full QM DFT approach based on the M06-2X functional. The reaction profile of the whole catalytic process can be divided into three phases: glycosylation, deglycosylation-elimination and tautomerization. Glycosylation is a highly asynchronous SN 1-like process with an energy barrier of 10.2 kcal mol-1 . A proton moves from the Asp665 residue to the glycosidic oxygen. Asp553 acts as a nucleophile and attacks the anomeric carbon causing the cleavage of the glycosidic bond. Deglycosilation-elimination is the rate-determining step of the entire process with an overall barrier of 18.3 kcal mol-1 . The final step (restoring the catalyst and tautomerization) occurs rather easily, since the Asp553 carboxylate group "assists" the proton transfer in the tautomerization process. Our computations clearly indicate that tautomerization must occur inside the enzyme before leaving the active site rather than in the aqueous solution. Outside of the protein environment the enol-AF→keto-AF process "assisted" by a water molecule has a barrier of 35.8 kcal mol-1 .

The Reaction Pathway of Cellulose Pyrolysis to a Multifunctional Chiral Building Block: The Role of Water Unveiled by a DFT Computational Investigation.

LAC (hydroxylactone (1R,5S)-1-hydroxy-3,6-dioxabicyclo[3.2.1]octan-2-one) is one of the most interesting products of the pyrolysis of cellulose and represents a useful chiral building block in organic synthesis. A computational investigation at the DFT level on the mechanism of formation of LAC shows that this species can be obtained following two reaction paths, path A and path B, starting from a well-known pyrolysis product (ascopyrone P). A series of internal rearrangements involving in all cases a proton transfer leads directly to LAC (path B). An alternative path (path A) can be also followed. From this path, via a "gate" connecting the two reaction channels, it is possible to reach path B and form LAC. In both cases, the rate-determining step of the process is the initial keto-enol isomerization. We found that water, which is present in the reaction mixture, "catalyzes" the reaction by assisting the proton transfers present in all the steps of the process. In particular, water lowers the barrier of the rate-determining step that becomes 40.9 kcal mol-1 (79.4 kcal mol-1 in the absence of water). The corresponding computed rate constant is 4.3×10 s-1 at 500 °C, a value which is consistent with the presence of LAC in the absence of metal catalysts. The results of this study on the non-catalyzed process underpin the important role played by water in the formation of pyrolysis products of cellulose where proton transfer is a key mechanistic step.

Computational Evidence for the Catalytic Mechanism of Tyrosylprotein Sulfotransferases: A Density Functional Theory Investigation.

In this paper we have examined the mechanism of tyrosine O-sulfonation catalyzed by human TPST-2. Our computations, in agreement with Teramoto's hypothesis, indicate a concerted SN2-like reaction (with an activation barrier of 18.2 kcal mol(-1)) where the tyrosine oxygen is deprotonated by Glu(99) (base catalyst) and simultaneously attacks as a nucleophile the sulfuryl group. For the first time, using a quantum mechanics protocol of alanine scanning, we identified unequivocally the role of the amino acids involved in the catalysis. Arg(78) acts as a shuttle that "assists" the sulfuryl group moving from the 3'-phosphoadenosine-5'-phosphosulfate molecule to threonine and stabilizes the transition state (TS) by electrostatic interactions. The residue Lys(158) keeps close the residues participating in the overall H-bond network, while Ser(285), Thr(81), and Thr(82) stabilize the TS via strong hydrogen interactions and contribute to lower the activation barrier.

Gold(I)-Catalyzed Dearomative [2+2]-Cycloaddition of Indoles with Activated Allenes: A Combined Experimental-Computational Study.

The gold-catalyzed synthesis of methylidene 2,3-cyclobutane-indoles is documented through a combined experimental/computational investigation. Besides optimizing the racemic synthesis of the tricyclic indole compounds, the enantioselective variant is presented to its full extent. In particular, the scope of the reaction encompasses both aryloxyallenes and allenamides as electrophilic partners providing high yields and excellent stereochemical controls in the desired cycloadducts. The computational (DFT) investigation has fully elucidated the reaction mechanism providing clear evidence for a two-step reaction. Two parallel reaction pathways explain the regioisomeric products obtained under kinetic and thermodynamic conditions. In both cases, the dearomative CC bond-forming event turned out to be the rate-determining step.

Gold(I)-Assisted α-Allylation of Enals and Enones with Alcohols.

The intermolecular α-allylation of enals and enones occurs by the condensation of variously substituted allenamides with allylic alcohols. Cooperative catalysis by [Au(ItBu)NTf2] and AgNTf2 enables the synthesis of a range of densely functionalized α-allylated enals, enones, and acyl silanes in good yield under mild reaction conditions. DFT calculations support the role of an α-gold(I) enal/enone as the active nucleophilic species.

Stacked naphthyls and weak hydrogen-bond interactions govern the conformational behavior of P-resolved cyclic phosphonamides: a combined experimental and computational study.

P-Enantiomerically pure cyclic phosphonamides have been synthesized via a cyclization reaction of (S,S)-aminobenzylnaphthols with chloromethylphosphonic dichloride. The reaction is highly stereoselective and gives almost exclusively (S,S,SP)-cyclic phosphonamides in good yields. Analysis of the X-ray crystal structures shows clearly that the cyclization reaction forces the two naphthyl rings into a stable parallel displaced stacking assembly and indicates also the existence of intramolecular CH···π interactions and weak forms of intermolecular hydrogen bondings, involving the oxygen and the chlorine atoms. QM computations and NMR spectra in solution confirm the stacked molecular assembly as the preferred arrangement of the two naphthyl groups.

Wavepacket splitting and two-pathway deactivation in the photoexcited visual pigment isorhodopsin.

Isorhodopsin is the visual pigment analogue of rhodopsin. It shares the same opsin environment but it embeds 9-cis retinal instead of 11-cis. Its photoisomerization is three times slower and less effective. The mechanistic rationale behind this observation is revealed by combining high-level quantum-mechanical/molecular-mechanical simulations with ultrafast optical spectroscopy with sub-20 fs time resolution and spectral coverage extended to the near-infrared. Whereas in rhodopsin the photoexcited wavepacket has ballistic motion through a single conical intersection seam region between the ground and excited states, in isorhodopsin it branches into two competitive deactivation pathways involving distinct conical intersection funnels. One is rapidly accessed but unreactive. The other is slower, as it features extended steric interactions with the environment, but it is productive as it follows forward bicycle pedal motion.

Conformational selection of ubiquitin quaternary structures driven by zinc ions.

Zinc ions bridging two ubiquitin molecules (with His68 at the interface) contribute to select a subset of conformers from the noncovalent dimer ensemble, thus restricting quaternary structure dynamics, which hampers apo-protein crystallization. The type of selected conformer is shown to determine the crystal packing, which varies from orthorhombic to cubic symmetry.

Mechanistic insights into enantioselective gold-catalyzed allylation of indoles with alcohols: the counterion effect.

Enantioselective gold-catalysis is emerging as a powerful tool in organic synthesis for the stereoselective manipulation of unfunctionalized unsaturated hydrocarbons. Despite the exponential growth, the molecular complexity of common chiral gold complexes generally prevents a complete description of the mechanism steps and activation modes being documented. In this study, we present the results of a combined experimental-computational (DFT) investigation of the mechanism of the enantioselective gold-catalyzed allylic alkylation of indoles with alcohols. A stepwise S(N)2'-process (i.e. anti-auroindolination of the olefin, proton-transfer, and subsequent anti-elimination [Au]-OH) is disclosed, leading to a library of tricyclic-fused indole derivatives. The pivotal role played by the gold counterion, in terms of molecular arrangement (i.e. "folding effect") and proton-shuttling in restoring the catalytic species, is finally documented.

Deciphering the Reactive Pathways of Competitive Reactions inside Carbon Nanotubes.

Nanoscale control of chemical reactivity, manipulation of reaction pathways, and ultimately driving the outcome of chemical reactions are quickly becoming reality. A variety of tools are concurring to establish such capability. The confinement of guest molecules inside nanoreactors, such as the hollow nanostructures of carbon nanotubes (CNTs), is a straightforward and highly fascinating approach. It mechanically hinders some molecular movements but also decreases the free energy of translation of the system with respect to that of a macroscopic solution. Here, we examined, at the quantum mechanics/molecular mechanics (QM/MM) level, the effect of confinement inside CNTs on nucleophilic substitution (SN2) and elimination (syn-E2 and anti-E2) using as a model system the reaction between ethyl chloride and chloride. Our results show that the three reaction mechanisms are kinetically and thermodynamically affected by the CNT host. The size of the nanoreactor, i.e., the CNT diameter, represents the key factor to control the energy profiles of the reactions. A careful analysis of the interactions between the CNTs and the reactive system allowed us to identify the driving force of the catalytic process. The electrostatic term controls the reaction kinetics in the SN2 and syn/anti-E2 reactions. The van der Waals interactions play an important role in the stabilization of the product of the elimination process.

Computational evidence for the substrate-assisted catalytic mechanism of O-GlcNAcase. A DFT investigation.

A DFT computational investigation of the catalytic mechanism of O-GlcNAcase shows the existence of a substrate-assisted reaction pathway similar to that proposed in the literature on the basis of experimental evidence: the carbonyl oxygen of the N-acyl group bonded at C2 of the substrate pyranose ring attacks the anomeric carbon affording a bicyclic oxazoline intermediate and causing the breaking of the glycosidic bond and the expulsion of the aglycon. This occurs in a single kinetic step where the transfer of a proton from Asp-243 (behaving as a general base) to the leaving group is simultaneous to the cycle formation and departure of the aglycon (an activation barrier E(a) of 16.5 kcal mol(-1)). Even if the other component of the catalytic dyad (Asp-242) is not actually involved in a proton transfer (as commonly suggested), it plays an important role in the catalysis through a complex network of hydrogen bonds that contribute to lower the activation barrier. The transition state of the process resembles an oxocarbenium ion (half chair conformation with an approximately planar sp(2) anomeric carbon). Following the lines of previous experiments aimed to demonstrate the existence of a substrate-assisted mechanism, it is found that the computed E(a) increases when the hydrogen atoms of the N-acetyl group are replaced with one, two and three F atoms and that a good linear correlation exists between the activation barrier E(a) and the σ* Taft electronic parameter of the fluoro-substituted N-acetyl groups.

Product formation in rhodopsin by fast hydrogen motions.

The photochemical cis-trans isomerization of retinal in rhodopsin is investigated by structure sampling and excited state QM/MM trajectories with surface hopping. The calculations uncover the motions responsible for photoproduct formation and elucidate the reasons behind the efficient photoisomerization in the primary event of visual transduction.

Asymmetric phase-transfer-catalyzed intramolecular N-alkylation of indoles and pyrroles: a combined experimental and theoretical investigation.

Asymmetric phase-transfer catalysis (PTC) has risen to prominence over the last decade as a straightforward synthetic methodology for the preparation of pharmacologically active compounds in enantiomerically pure form. However, the complex interplay of weak nonbonded interactions (between catalyst and substrate) that could account for the stereoselection in these processes is still unclear, with tentative pictorial mechanistic representations usually proposed. Here we present a full account dealing with the enantioselective phase-transfer-catalyzed intramolecular aza-Michael reaction (IMAMR) of indolyl esters, as a valuable synthetic tool to obtain added-value compounds, such as dihydro-pyrazinoindolinones. A combined computational and experimental investigation has been carried out to elucidate the key mechanistic aspects of this process.

Electron Dynamics with Explicit-Time Density Functional Theory of the [4+2] Diels-Alder Reaction.

The prototype Diels-Alder (DA) reaction between butadiene and ethene (system 1) and the DA reaction involving 1-methoxy-butadiene and cyano-ethylene (system 2) are investigated with an explicit-time-dependent Density Functional Theory approach. Bond orders and atomic net charges obtained in the dynamics at the transition state geometry and along the reaction coordinate toward reactants are used to provide a picture of the process in terms of VB/Lewis resonance structures that contribute to a resonance hybrid. The entire dynamics can be divided into different domains (reactant-like, product-like, and transition state domains) where different Lewis resonance structures contribute with different weights. The relative importance of these three domains varies along the reaction coordinate. In addition to the usual reactant-like and product-like covalent Lewis structures, ionic Lewis structures have non-negligible weights. In system 2, the electron-donor OCH3 on the diene and the electron-acceptor CN on the dienophile make more important the contributions of ionic Lewis structures that stabilize the transition state and determine the decrease of the reaction barrier with respect to system 1.

Electrostatic control of the photoisomerization efficiency and optical properties in visual pigments: on the role of counterion quenching.

Hybrid QM(CASPT2//CASSCF/6-31G*)/MM(Amber) computations have been used to map the photoisomerization path of the retinal chromophore in Rhodopsin and explore the reasons behind the photoactivity efficiency and spectral control in the visual pigments. It is shown that while the electrostatic environment plays a central role in properly tuning the optical properties of the chromophore, it is also critical in biasing the ultrafast photochemical event: it controls the slope of the photoisomerization channel as well as the accessibility of the S(1)/S(0) crossing space triggering the ultrafast decay. The roles of the E113 counterion, the E181 residue, and the other amino acids of the protein pocket are explicitly analyzed: it appears that counterion quenching by the protein environment plays a key role in setting up the chromophore's optical properties and its photochemical efficiency. A unified scenario is presented that discloses the relationship between spectroscopic and mechanistic properties in rhodopsins and allows us to draw a solid mechanism for spectral tuning in color vision pigments: a tunable counterion shielding appears as the elective mechanism for L<-->M spectral modulation, while a retinal conformational control must dictate S absorption. Finally, it is suggested that this model may contribute to shed new light into mutations-related vision deficiencies that opens innovative perspectives for experimental biomolecular investigations in this field.

A combined theoretical and experimental investigation on the enantioselective oxidation of aryl benzyl sulfides in the presence of a chiral titanium catalyst.

An experimental investigation of the enantioselective oxidation of aryl benzyl sulfides by tert-butyl hydroperoxide in the presence of a titanium/hydrobenzoin catalyst has shown that these sulfides are ideal substrates for this catalytic system, with negligible interference by the substituents on the aryl groups. A reaction mechanism based on DFT computations has been proposed. The DFT MPWB1K functional was used in the theoretical investigation to account for weak hydrogen-bonding and pi interactions. The computed reaction profile explains the experimentally observed enantioselectivity, which is determined by the thermodynamics of the first phase of the reaction. A detailed discussion of the hydrogen-bonding and pi interactions that drive the reaction along the observed stereochemical path is given.