Passerini-Smiles Reaction of α-Ketophosphonates: Platform for Phospha-Brook/Smiles Embedded Cascades.

The Passerini-Smiles reactions of α-ketophosphonates with nitrophenols has been used as a platform to observe complex cascades involving multiple Smiles transfers coupled with phospha-Brook rearrangement. When using 4-nitrophenols a rare 1,3-Truce-Smiles rearrangement is observed leading to diarylacetamide derivatives. 2-Nitro-derivatives lead to a completely different reactivity pattern that may be explained by a nitro to nitroso conversion followed by a σ-π metathesis. All mechanistic assumptions are confirmed by DFT calculations performed on both families of adducts. The potential of this work has been further demonstrated by the use of N-aryl α-ketoamides as alternative starting materials for these cascades as well as the disclosure of new aza-Nazarov access to hydroxy-indolones.

Palladium-Catalyzed C8-Arylation of Naphthalenes through C-H Activation: A Combined Experimental and Computational Study.

Herein, a direct C8-arylation reaction of 1-amidonaphthalenes is described. By using diaryliodonium salts as arylating agents, the palladium-catalyzed C-H activation reaction showed perfect C8 regioselectivity and a wide functional group tolerance. In most cases, the desired polyaromatic compounds were isolated in good to excellent yields. To explain the observed regioselectivity, DFT calculations were performed and highlighted the crucial role of the amide directing group. Finally, the utility of this method is showcased by the synthesis of benzanthrone derivatives.

Temperature and Pressure Dependent Rate Coefficients for the Reaction of Ketene with Hydroxyl Radical.

The reaction of ketene with hydroxyl radical is drawing growing attention, for it is found to constitute an important step during the combustion of hydrocarbon and oxygenated hydrocarbon fuels, e.g., acetylene, propyne, allene, acetone, gasoline, diesel, jet fuels, and biofuels. We studied the potential energy surface (PES) of this reaction using B2PLYP-D3/cc-PVTZ for geometry optimization and composite methods based on CCSD(T)-F12/cc-PVTZ-F12 for energy calculations. From this PES, temperature- and pressure-dependent rate coefficients and branching ratios at 200-3000 K and 0.01-100 atm were derived using the RRKM/ME approach. The reaction is dominated by four product channels: (i) OH addition on the olefinic carbon of ketene to form CH2OH + CO, which is the most dominant under all conditions; (ii) H abstraction producing HCCO + H2O, which is favored at high temperatures; (iii) OH addition on the carbonyl carbon to form CH3 + CO2, which is favored at low pressures and high temperatures; and (iv) collisional stabilization of CH2COOH, which is favored at high pressures and low temperatures. With increasing temperatures, the overall rate constant koverall exhibit first negative but then positive temperature dependency, with its switching point (also the minimum point) at ∼400 K. Both product channel CH2OH + CO and HCCO + H2O are independent of pressure, whereas formation of CH3 + CO2 and collisional stabilization of CH2COOH are highly pressure dependent. Fitted modified Arrhenius expressions of the calculated rate constants are provided for the purpose of combustion modeling.

ß-Lactam Synthesis through Diodomethane Addition to Amide Dianions.

We present a novel route for the quick and easy synthesis of a broad range of ß-lactams. The synthesis involves a [3+1] cyclization of amide dianions with diiodomethane. In contrast to the seminal work of Hirai et al. from 1979, the reaction proved to be a general and efficient approach towards azetidinones. The ease of the process was confirmed by DFT calculations and its power demonstrated by a diversity-oriented synthesis of ß-lactams with four points of diversity determined by the choice of Ugi adducts as starting materials.

Are dinucleoside monophosphates relevant models for the study of DNA intrastrand cross-link lesions? The example of g[8-5m]T.

Oxidatively generated tandem lesions such as G[8-5m]T pose a potent threat to genome integrity. Direct experimental studies of the kinetics and thermodynamics of a specific lesion within DNA are very challenging, mostly due to the variety of products that can be formed in oxidative conditions. Dinucleoside monophosphates (DM) involving only the reactive nucleobases in water represent appealing alternative models on which most physical chemistry and structural techniques can be applied. However, it is not yet clear how relevant these models are. Here, we present QM/MM MD simulations of the cyclization step involved in the formation of G[8-5m]T from the guanine-thymine (GpT) DM in water, with the aim of comparing our results to our previous investigation of the same reaction in DNA ( Garrec , J. , Patel , C. , Rothlisberger , U. , and Dumont , E. ( 2012 ) J. Am. Chem. Soc. 134 , 2111 - 2119 ). We show that, despite the different levels of preorganization of the two systems, the corresponding reactions share many energetic and structural characteristics. The main difference lies in the angle between the G and T bases, which is slightly higher in the transition state (TS) and product of the reaction in water than in the reaction in DNA. This effect is due to the Watson-Crick H-bonds, which are absent in the {GpT+water} system and restrain the relative positioning of the reactive nucleobases in DNA. However, since the lesion is accommodated easily in the DNA macromolecule, the induced energetic penalty is relatively small. The high similarity between the two reactions strongly supports the use of GpT in water as a model of the corresponding reaction in DNA.

Two misfolding routes for the prion protein around pH 4.5.

Using molecular dynamics simulations, we show that the prion protein (PrP) exhibits a dual behavior, with two possible transition routes, upon protonation of H187 around pH 4.5, which mimics specific conditions encountered in endosomes. Our results suggest a picture in which the protonated imidazole ring of H187 experiences an electrostatic repulsion with the nearby guanidinium group of R136, to which the system responds by pushing either H187 or R136 sidechains away from their native cavities. The regions to which H187 and R136 are linked, namely the C-terminal part of H2 and the loop connecting S1 to H1, respectively, are affected in a different manner depending on which pathway is taken. Specific in vivo or in vitro conditions, such as the presence of molecular chaperones or a particular experimental setup, may favor one transition pathway over the other, which can result in very different [Formula: see text] monomers. This has some possible connections with the observation of various fibril morphologies and the outcome of prion strains. In addition, the finding that the interaction of H187 with R136 is a weak point in mammalian PrP is supported by the absence of the [Formula: see text] residue pair in non-mammalian species that are known to be resistant to prion diseases.

Prion versus doppel protein misfolding: new insights from replica-exchange molecular dynamics simulations.

The doppel (Dpl) and prion (PrP) proteins share a very similar fold (three helices and two short ß-strands), while they differ significantly in sequence (only 25% homologous) and in disease-related ß-rich conformations that occur for PrP only. In a previous study [Baillod, P., et al. (2012) Biochemistry 51, 9891-9899], we investigated the misfolding and rare, ß-rich folds of monomeric PrP with replica-exchange molecular dynamics (REMD) simulations. In the work presented here, we perform analogous simulations for Dpl with the aim of comparing the two systems and characterizing possible specificities of PrP for misfolding and amyloidogenesis. Our extensive simulations, which allow us to overcome high energy barriers via the REMD approach, sample several ß-rich folds, some of which are stable at room temperature, for both proteins. Per residue secondary structure propensities reveal that novel ß-sheets of Dpl and PrP are formed by amino acids belonging to the helices that are the least stable in the respective native structure, H1 for Dpl and H2 and H3 for PrP, in agreement with experimental data. Using a specific clustering method that allows discrimination against different ß-strand arrangements, seven ß-rich folds could be characterized for PrP and five for Dpl, which are clearly distinct and share only one single similar fold. A major difference between the two proteins is found in the free energy barriers leading to misfolded structures: they are approximately 3 times higher for Dpl than for PrP. This suggests that the difference in amyloidogenic behavior between PrP and Dpl might be due to kinetic reasons.

What singles out the G[8-5]C intrastrand DNA cross-link? Mechanistic and structural insights from quantum mechanics/molecular mechanics simulations.

Naturally occurring intrastrand oxidative cross-link lesions have proven to be a potent source of endogenous DNA damage. Among the variety of lesions that can be formed and have been identified, G[8-5]C damage (in which the C8 atom of a guanine is covalently bonded to the C5 atom of a nearby cytosine belonging to the same strand) occurs with a low incidence yet takes on special importance because of its high mutagenicity. Hybrid Car-Parrinello molecular dynamics simulations, rooted in density functional theory and coupled to molecular mechanics, have been performed to shed light on the cyclization process. The activation free energy of the reacting subsystem embedded in a solvated dodecamer is estimated to be ∼12.4 kcal/mol, which is ∼3 kcal/mol higher than the value for the prototypical G[8-5m]T lesion inferred employing the same theoretical framework [Garrec, J., Patel, C., Rothlisberger, U., and Dumont, E. (2012) J. Am. Chem. Soc.134, 2111-2119]. This study also situates the G[8-5m]mC lesion at an intermediate activation free energy (∼10.5 kcal/mol). The order of reactivity in DNA (T(•) > mC(•) > C(•)) is reversed compared to that in the reacting subsystems in the gas phase (C(•) > mC(•) > T(•)), stressing the crucial role of the solvated B-helix environment. The results of our simulations also characterize a more severe distortion for G[8-5]C than for methylene-bridged intrastrand cross-links.

Enhanced sampling molecular dynamics identifies PrP(Sc) structures harboring a C-terminal ß-core.

We perform a replica exchange molecular dynamics simulation corresponding to a 2.8 µs total time for the extensive enhanced sampling of the conformational space of the C-terminal part (residues 124-226) of the mouse prion protein (PrP); 1.3% of the conformations sampled display a high level of ß-structure (≥19 residues), allowing the assessment of ß-propensities along the sequence and highlighting the most structurally labile hot spots. A clustering algorithm is applied to sort the structures of this pool according to their fold. Ten ß-rich folds are thus defined and analyzed with regard to their topology, accumulation temperatures, and structural characteristics. In contrast to the so-called spiral and ß-helix models suggesting that the ß-rich core of the scrapie isoform (PrP(Sc)) comprises the N-terminal tail and part of the C-terminal domain up to helix 1 (H1), we present putative structural models for monomeric precursors of PrP(Sc) and PrP ß-oligomers that are characterized by a C-terminal ß-rich core, in agreement with the suggestions of a series of recent experiments.

Insights into intrastrand cross-link lesions of DNA from QM/MM molecular dynamics simulations.

DNA damages induced by oxidative intrastrand cross-links have been the subject of intense research during the past decade. Yet, the currently available experimental protocols used to isolate such lesions only allow to get structural information about linked dinucleotides. The detailed structure of the damaged DNA macromolecule has remained elusive. In this study we generated in silico the most frequent oxidative intrastrand cross-link adduct, G[8,5-Me]T, embedded in a solvated DNA dodecamer by means of quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations. The free energy of activation required to bring the reactant close together and to form the C-C covalent-bond is estimated to be ~10 kcal/mol. We observe that the G[8,5-Me]T tandem lesion is accommodated with almost no perturbation of the Watson-Crick hydrogen-bond network and induces bend and unwinding angles of ~20° and 8°, respectively. This rather small structural distortion of the DNA macromolecule compared to other well characterized intrastrand cross-links, such as cyclobutane pyrimidines dimers or cisplatin-DNA complex adduct, is a probable rationale for the known lack of efficient repair of oxidative damages.

Pushing the frontiers of first-principles based computer simulations of chemical and biological systems.

The Laboratory of Computational Chemistry and Biochemistry is active in the development and application of first-principles based simulations of complex chemical and biochemical phenomena. Here, we review some of our recent efforts in extending these methods to larger systems, longer time scales and increased accuracies. Their versatility is illustrated with a diverse range of applications, ranging from the determination of the gas phase structure of the cyclic decapeptide gramicidin S, to the study of G protein coupled receptors, the interaction of transition metal based anti-cancer agents with protein targets, the mechanism of action of DNA repair enzymes, the role of metal ions in neurodegenerative diseases and the computational design of dye-sensitized solar cells. Many of these projects are done in collaboration with experimental groups from the Institute of Chemical Sciences and Engineering (ISIC) at the EPFL.

Lipid Peroxidation in Membranes: The Peroxyl Radical Does Not "Float".

Lipid peroxidation is a fundamental phenomenon in biology and medicine involved in a wide range of diseases. Some key microscopic aspects of this reaction in cell membranes are still poorly studied. In particular, it is commonly accepted that the propagation of the radical reaction in lipid bilayers is hampered by the rapid diffusion of peroxyl intermediates toward the water interface, that is, out of the reaction region. We investigated the validity of this "floating peroxyl radical" hypothesis by means of molecular modeling. Combining quantum calculations of model systems and atomistic simulations of lipid bilayers containing lipid oxidation products, we show that the peroxyl radical does not "float" at the surface of the membrane. Instead, it remains located quite deep inside the bilayer. In light of our findings, several critical aspects of biological membranes' peroxidation, such as their protection mechanisms, need to be revisited. Our data moreover help in the design of more efficient antioxidants, localized within reach of the reaction propagating radical.