Andrea Bottoni

Blocking the passage: C60 geometrically clogs K(+) channels.

Classical molecular dynamics (MD) simulations combined with docking calculations, potential of mean force estimates with the umbrella sampling method, and molecular mechanic/Poisson-Boltzmann surface area (MM-PBSA) energy calculations reveal that C60 may block K(+) channels with two mechanisms: a low affinity blockage from the extracellular side, and an open-channel block from the intracellular side. The presence of a low affinity binding-site at the extracellular entrance of the channel is in agreement with the experimental results showing a fast and reversible block without use-dependence, from the extracellular compartment. Our simulation protocol suggests the existence of another binding site for C60 located in the channel cavity at the intracellular entrance of the selectivity filter. The escape barrier from this binding site is ∼21 kcal/mol making the corresponding kinetic rate of the order of minutes. The analysis of the change in solvent accessible surface area upon C60 binding shows that binding at this site is governed purely by shape complementarity, and that the molecular determinants of binding are conserved in the entire family of K(+) channels. The presence of this high-affinity binding site conserved among different K(+) channels may have serious implications for the toxicity of carbon nanomaterials.

Tuning Cysteine Reactivity and Sulfenic Acid Stability by Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis thaliana.

AIMSnCysteines and H2O2 are fundamental players in redox signaling. Cysteine thiol deprotonation favors the reaction with H2O2 that generates sulfenic acids with dual electrophilic/nucleophilic nature. The protein microenvironment surrounding the target cysteine is believed to control whether sulfenic acid can be reversibly regulated by disulfide formation or irreversibly oxidized to sulfinates/sulfonates. In this study, we present experimental oxidation kinetics and a quantum mechanical/molecular mechanical (QM/MM) investigation to elucidate the reaction of H2O2 with glycolytic and photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana (cytoplasmic AtGAPC1 and chloroplastic AtGAPA, respectively).nnnRESULTSnAlthough AtGAPC1 and AtGAPA have almost identical 3D structure and similar acidity of their catalytic Cys149, AtGAPC1 is more sensitive to H2O2 and prone to irreversible oxidation than AtGAPA. As a result, sulfenic acid is more stable in AtGAPA.nnnINNOVATIONnBased on crystallographic structures of AtGAPC1 and AtGAPA, the reaction potential energy surface for Cys149 oxidation by H2O2 was calculated by QM. In both enzymes, sulfenic acid formation was characterized by a lower energy barrier than sulfinate formation, and sulfonate formation was prevented by very high energy barriers. Activation energies for both oxidation steps were lower in AtGAPC1 than AtGAPA, supporting the higher propensity of AtGAPC1 toward irreversible oxidation.nnnCONCLUSIONSnQM/MM calculations coupled to fingerprinting analyses revealed that two Arg of AtGAPA (substituted by Gly and Val in AtGAPC1), located at 8-15 Å distance from Cys149, are the major factors responsible for sulfenic acid stability, underpinning the importance of long-distance polar interactions in tuning sulfenic acid stability in native protein microenvironments.

DFT Mechanistic Investigation of the Gold(I)-Catalyzed Synthesis of Azepino[1,2-a]indoles

We describe a computational DFT investigation on the mechanism of the one‐pot synthesis of azepino‐indoles catalyzed by [Au(IPr)Cl]/AgOTf (IPr=1,3‐bis(2,6‐diisopropylphenyl‐imidazol‐2‐ylidene) by the simultaneous construction of the pyrrolyl and seven‐membered rings. The mechanism of the final ring‐closing event is elucidated, which reveals the counterion‐assisted nucleophilic trapping of the carbonyl moiety by the alkenyl‐gold species formed inu2005situ. The computational evidence supports the labeling control experiments and highlights the presence of a cyclopropyl‐gold‐carbenoid intermediate in the final intramolecular 1,3‐hydrogen‐shift/skeleton‐rearrangement sequence.

Calcite Single Crystals as Hosts for Atomic‐Scale Entrapment and Slow Release of Drugs

Doxorubicin (DOX)/CaCO3 single crystals act as pH responsive drug carrier. A biomimetic approach demonstrates that calcite single crystals are able, during their growth in the presence of doxorubicin, to entrap drug molecules inside their lattice along specific crystallographic directions. Alterations in lattice dimensions and microstructural parameters are determined by means of high-resolution synchrotron powder diffraction measurements. Confocal microscopy confirms that doxorubicin is uniformly embedded in the crystal and is not simply adsorbed on the crystal surface. A slow release of DOX was obtained preferentially in the proximity of the crystals, targeting cancer cells.

CNT-Confinement Effects on the Menshutkin SN2 Reaction: The Role of Nonbonded Interactions

We investigated the effects of CNT confinement ((6,6) tube) on the model Menshutkin reaction H3N + H3CCl = H3NCH3((+)) + Cl((-)), which is representative of chemical processes involving developing of charge separation along the reaction pathway. We used either a full QM approach or a hybrid QM/MM approach. We found that the CNT significantly lowers the activation barrier with respect to the hypothetical gas-phase reaction: The activation barrier Ea varies from 34.6 to 25.7 kcal mol(-1) (a value similar to that found in a nonpolar solvent) and the endothermicity ΔE from 31.2 to 13.5 kcal mol(-1). A complex interplay between C-H···π, N-H···π, and Cl···π nonbonded interactions of the endohedral system with the CNT wall explains the lower barrier and lower endothermicity. The hybrid QM/MM approach (MM = UFF force field) does not reproduce satisfactorily the QM energy ΔE (18.1 vs 13.5 kcal mol(-1)), while optimum agreement is found in the barrier Ea (25.8 vs 25.7 kcal mol(-1)). These results suggest that the simple Qeq formalism (included in the MM potential) does not describe properly the effect of CNT polarization in the presence of the net charge separation featuring the final product. A more accurate estimate of the tube polarization was obtained with single-point QM/MM computations including PCM corrections (using the benzene dielectric constant) on the QM/MM optimized structures. After PCM corrections, Ea changes slightly (from 25.8 to 24.5 kcal mol(-1)), but a more significant variation is observed for ΔE that becomes 13.1 kcal mol(-1), in rather good agreement with the full QM. This level of theory (QM/MM with PCM correction, MM = UFF) represents a more general approach suitable for describing CNT-confined chemical processes involving significant charge separation. QM/MM computations were extended to CNTs of different radii: (4,4), (5,5), (7,7), (8,8), (9,9), (10,10), (12,12), (14,14) CNTs and, as a limit case, a graphene sheet. The lack of space available in the small tube (4,4) causes a strong structural distortion and a consequent increase in Ea and ΔE (40.8 and 44.0 kcal mol(-1), respectively). These quantities suddenly decrease with the augmented volume inside the (5,5) tube. For larger tubes, different structural arrangements of the endohedral system are possible, and Ea and ΔE remain almost constant until the limiting case of graphene.

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 40.9u2005kcalu2009mol-1 (79.4u2005kcalu2009mol-1 in the absence of water). The corresponding computed rate constant is 4.3×10u2005s-1 at 500u2009°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 Teramotos 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.

Graphene Oxide Promotes Site-Selective Allylic Alkylation of Thiophenes with Alcohols

The graphene oxide (GO) assisted allylic alkylation of thiophenes with alcohols is presented. Mild reaction conditions and a low GO loading enabled the isolation of a range of densely functionalized thienyl and bithienyl compounds in moderate to high yields (up to 90%). The cooperative action of the Brønsted acidity, epoxide moieties, and π-surface of the 2D-promoter is highlighted as crucial in the reaction course of the present Friedel-Crafts-type protocol.

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.

Covalent or Non-Covalent? A Mechanistic Insight into the Enantioselective Brønsted Acid Catalyzed Dearomatization of Indoles with Allenamides

The reaction mechanism of the enantioselective Brønsted acid catalyzed dearomatization of C(2),C(3)‐disubstituted indoles with allenamides is investigated by means of density functional theory (DFT) calculations and ESI‐MS analysis. The first step of the process (rate‐determining step) is the formation of a covalent adduct between allenamide and the chiral organo‐promoter. The resulting chiral α‐amino allylic phosphate undergoes dearomative condensation with indoles. In the first step, the indole moiety remains bonded to the catalyst through strong hydrogen contacts. It can take on two different orientations that make the Re or Si prochiral face available to the subsequent electrophilic attack of allenamide. The attack on the indole faces originates two reaction paths leading to different stereoisomeric products, which differ in the configuration of the new stereocenter at the C3‐indole position.