Oxo-Rhenium-Mediated Allylation of Furanoside Derivatives: A Computational Study on the Mechanism and the Stereoselectivity.

Properly substituted tetrahydrofuran (THF) rings are important building blocks in the synthesis of many natural metabolites. Having reliable procedures to control the stereoselectivity at the THF core while decorating it with different substituents is a fundamental requirement to achieve and fulfill the complexity of nature. We recently reported a new chemical approach to control the stereochemistry in the alkylation and arylation of furanoside derivatives by using a rhenium(V) complex to form an intermediate oxo-carbenium species able to react with proper soft nucleophiles. Here, we describe theoretical calculations, performed at the DFT B3LYP level, to disclose the important mechanistic features which regulate the entire catalytic cycle of the reaction of mono- and disubstituted furanosides with allyltrimethylsilane catalyzed by Re(O)Cl3(OPPh3)(Me2S). Moreover, the key factors governing the allylation step were investigated, confirming that the stereoselectivity, which is independent of the anomeric configuration of starting acetal, mainly arises from the orientation of the substituent at C-4, with only marginal contribution of the substituent at C-5. Finally, puckering Cremer-Pople parameters were used to take trace of the structural modifications throughout the catalytic cycle.

An In-Depth Computational Study of Alkene Cyclopropanation Catalyzed by Fe(porphyrin)(OCH3) Complexes. The Environmental Effects on the Energy Barriers.

Iron porphyrin methoxy complexes, of the general formula [Fe(porphyrin)(OCH3)], are able to catalyze the reaction of diazo compounds with alkenes to give cyclopropane products with very high efficiency and selectivity. The overall mechanism of these reactions was thoroughly investigated with the aid of a computational approach based on density functional theory calculations. The energy profile for the processes catalyzed by the oxidized [FeIII(Por)(OCH3)] (Por = porphine) as well as the reduced [FeII(Por)(OCH3)]- forms of the iron porphyrin was determined. The main reaction step is the same in both of the cases, that is, the one leading to the terminal-carbene intermediate [Fe(Por)(OCH3)(CHCO2Et)] with simultaneous dinitrogen loss; however, the reduced species performs much better than the oxidized one. Contrarily to the iron(III) profile in which the carbene intermediate is directly obtained from the starting reactant complex, the favored iron(II) process is more intricate. The initially formed reactant adduct between [FeII(Por)(OCH3)]- and ethyl diazoacetate (EDA) is converted into a closer reactant adduct, which is in turn converted into the terminal iron porphyrin carbene [Fe(Por)(OCH3)(CHCO2Et)]-. The two corresponding transition states are almost isoenergetic, thus raising the question of whether the rate-determining step corresponds to dinitrogen loss or to the previous structural and electronic rearrangement. The ethylene addition to the terminal carbene is a downhill process, which, on the open-shell singlet surface, presents a defined but probably short-living diradicaloid intermediate, though other spin-state surfaces do not show this intermediate allowing a direct access to the cyclopropane product. For the crucial stationary points, the more complex catalyst [Fe(2)(OCH3)], in which a sterically hindered chiral bulk is mounted onto the porphyrin, was investigated. The corresponding computational data disclose the very significant effect of the porphyrin skeleton on the reaction energy profile. Though the geometrical features around the reactive core of the system remain unchanged, the energy barriers become much lower, thus revealing the profound effects that can be exerted by the three-dimensional organic scaffold surrounding the reaction site.

Halide-Controlled Extending-Shrinking Motion of a Covalent Cage.

Herein, we present an example of covalent cages, whose flexible framework undergoes extending-shrinking motion under halide control. In the absence of halide anions, the free cage assumes a flattened conformation: the cavity is compressed along the C3 axis passing through the tertiary amines, and the two tribenzylamine platforms are eclipsed. Halide encapsulation promotes a large conformational rearrangement of the cage, involving an extension of the cavity along the C3 axis and shrinkage along the equatorial plane. Interestingly, the rearrangement is accompanied by the pyramidal inversion of the tertiary amines and by the rotation of the tribenzylamine-based platforms, which become staggered. The imidazolium-containing arms wrap around the spherical anion, leading to a racemic mixture of the M and P helical complexes. As expected from the flexible structure of the cage, the switch between the two limit conformations can be repeated for several cycles under alternating chemical stimuli (AgNO3/TBACl). This result is consistent with the low activation barriers determined by computational investigations. These also allowed us to quantify the energy difference between the shrunk and expanded cage conformations and to hypothesize an energetic pathway along which the conformational rearrangement can occur.

Development of Oxygen-Bridged Pyrazole-Based Structures as Cannabinoid Receptor 1 Ligands.

In this work, the synthesis of the cannabinoid receptor 1 neutral antagonists 8-chloro-1-(2,4-dichlorophenyl)-N-piperidin-1-yl-4,5-dihydrobenzo-1H-6-oxa-cyclohepta[1,2-c]pyrazole-3-carboxamide 1a and its deaza N-cyclohexyl analogue 1b has led to a deepening of the structure-activity studies of this class of compounds. A series of novel 4,5-dihydrobenzo-oxa-cycloheptapyrazoles analogues of 1a,b, derivatives 1c-j, was synthesized, and their affinity towards cannabinoid receptors was determined. Representative terms were evaluated using in vitro tests and isolated organ assays. Among the derivatives, 1d and 1e resulted in the most potent CB1 receptor ligands (KiCB1 = 35 nM and 21.70 nM, respectively). Interestingly, both in vitro tests and isolated organ assays evidenced CB1 antagonist activity for the majority of the new compounds, excluding compound 1e, which showed a CB1 partial agonist behaviour. CB1 antagonist activity of 1b was further confirmed by a mouse gastrointestinal transit assay. Significant activity of the new CB1 antagonists towards food intake was showed by preliminary acute assays, evidencing the potentiality of these new derivatives in the treatment of obesity.

Self-Assembly of Pseudorotaxane Structures from a Dicopper(II) Molecular Cage and Dicarboxylate Axles.

In this work, we employed for the first time a dinuclear bis[tris(2-aminoethyl)amine] cryptate to obtain the self-assembly of pseudorotaxane structures in an aqueous solution. The goal was achieved by exploiting the well-known affinity of the dicopper azacryptate with diphenyl spacers for the terephthalate anion. In particular, a series of molecular threads were synthesized by appending either alkyl or polyoxyethylene chains on both sides of the terephthalate benzene ring. The obtained dicarboxylic acids were precipitated as sodium salts, and their affinity toward the dicopper azacryptate was determined in a methanol/water mixture (pH 7). Experimental investigations showed that the chains' length and nature have a small impact on the 1:1 binding constants, whose values range between 4.98 and 5.18 log units. Computational studies indicated that the molecular axle is threaded through the azacryptate cavity, with the terephthalate group wedged between the two copper ions, coordinating both of them in the apical position (the one that, in the free azacryptate, is occupied by a water molecule). Compared to the inclusion complex with the plain terephthalate anion, a slight strain was found in the pseudorotaxane structure, induced by the inner chain of the thread inside the cavity. These results may be of great interest in all of the fields of science and technology in which host-guest recognition and molecular cages are applied.

Designing 'Totem' C2 -Symmetrical Iron Porphyrin Catalysts for Stereoselective Cyclopropanations.

The catalytic activity of the iron(III) C2 chiral porphyrin Fe(2)(OMe) in alkene cyclopropanation is herein reported. The catalyst promoted the reaction of differently substituted styrenes with diazo derivatives with trans-diastereoselectivities and enantioselectivities up to 99:1 and 87 %, respectively. In addition, high TON and TOF values (up to 10 000 and 120 000 h(-1) , respectively) were observed indicating good activity and stability of the catalyst in optimized experimental conditions. The study of the cyclopropanation reaction revealed that the porphyrin skeleton is composed of two 'totem' parts which were independently responsible for the observed enantio- and diastereoselectivities. To further our research we also investigated the catalytic role of the methoxy axial ligand coordinated to the iron atom. The molecular structure of Fe(2)(OMe) was optimized by DFT calculations which were also employed to achieve a better understanding of the mechanistic details of the carbene transfer reaction.

Molecular Architecture and Symmetry Properties of 1,3-Alternate Calix[4]arenes with Orientable Groups at the Para Position of the Phenolic Rings.

Two glycoclusters constituted by four fully acetylated ß-acetylmannosamine residues linked through trimethylenethioureido spacers to a calix[4]arene core and differing for the presence of methoxy or propoxy groups at the lower rim were synthesized. One of the two compounds is fixed in the 1,3-alternate geometry by the presence of the propoxy groups, while the other is potentially free to assume one of the different geometries allowed in calix[4]arene. Their similar NMR spectra in chloroform clearly suggest the same 1,3-alternate geometry. Both compounds were submitted to a conformational investigation with the DFT approach at the standard B3LYP/6-31G(d) level. The two glycocalixarenes showed a large conformational preference for the same geometry that put the mannosamine moiety of one substituent close to the thioureido group of the opposite substituent. This allows the formation of intramolecular hydrogen bonds and originates a series of through-space close contacts. A comparison with the NOESY maps evidence an excellent correspondence between experimental and theoretical data, thus giving an experimental validation of the highly symmetrical conformation that the two glycocalixarenes assume in apolar solvents.

Cone Calix[4]arenes with Orientable Glycosylthioureido Groups at the Upper Rim: An In-Depth Analysis of Their Symmetry Properties.

The two glycoclusters α- and ß-d-mannosylthioureidocalix[4]arenes 1 and 2 in the cone geometry have been submitted to a conformational investigation with the DFT approach at the standard B3LYP/6-31G(d) level and using a water continuum solvent model. After a reasoned choice of the level of calculation and the evaluation of the properties of the monomeric components of 1 and 2, the intrinsic conformational properties of cone calix[4]arenes with orientable groups at the upper rim were thoroughly analyzed. From the possible combinations of the directions that the groups may assume, 10 different geometries derive, all chiral. These geometries are interchangeable through two different processes, named breathing equilibrium and arrow rotation, that allow a dense network connection among them. When the modeling of whole macrocycles 1 and 2 was performed, a huge difference in their conformational behavior that heavily influences the presentation mode of their saccharidic moieties was found.

Computational mechanistic study of the Julia-Kocienski reaction.

This paper describes the first detailed computational mechanistic study of the Julia-Kocienski olefination between acetaldehyde (1) and ethyl 1-phenyl-1H-tetrazol-5-yl sulfone (2), considered a paradigmatic example of the reaction between unsubstituted alkyl PT sulfones and linear aliphatic aldehydes. The theoretical study was performed within the density functional approach through calculations at the B3LYP/6-311+G(d,p) level for all atoms except sulfur for which the 6-311+G(2df,p) basis set was used. All the different intermediates and transition states encountered along the reaction pathways leading to final E and Z olefins have been located and the relative energies calculated, both for the reactions with potassium- and lithium-metalated sulfones, in THF and toluene, respectively. We have essentially confirmed the complex multistep mechanistic manifold proposed by others; however, the formation of a spirocyclic intermediate in the Smiles rearrangement was excluded. Instead, we found that this step involves a concerted, though asynchronous, mechanism. Moreover, our calculations nicely fit with the diastereoselectivities observed experimentally for potassium- and lithium-metalated sulfones, in THF and toluene, respectively.

Multivalent presentation of a hydrolytically stable GM(3) lactone mimetic as modulator of melanoma cells motility and adhesion.

A hydrolytically stable mimetic of the tumour antigen GM(3) lactone is used to decorate multivalent scaffolds. Two of them positively interfere on melanoma cell adhesion, migration and resistance to apoptosis (anoikis). Notably, their ability to hamper melanoma-cells adhesion and reduce the metastatic potential is enhanced when the two scaffolds, presenting a different shape, are used in combination.

Crystallographic, spectroscopic, and theoretical investigation of the efficiently separated 21R and 21S-diastereoisomers of argatroban.

Argatroban (I), a potent noncovalent reversible thrombin inhibitor, is used as an anticoagulant for the parenteral treatment of heparin-induced thrombocytopenia (HIT) patients. By virtue of its pharmacological properties and the well-balanced risks and benefits, argatroban is now emerging as a clinically relevant antithrombotic agent. The availability of this drug as a mixture of 21R and 21S-diastereoisomers, in a ratio of roughly 64:36, prompted us to design an efficient separation setup of the two epimers. We pursued our efforts on their detailed structural analysis with the aim of understanding their different activity and aqueous solubility. These investigations were accompanied by a modeling study of the two diastereoisomers, with particular attention on the easy interconverting half-chair of the tetrahydroquinoline system and its preferred conformation, which is determined by the configuration at C21. These results, together with the analysis of their physicochemical profiles, provide new useful information for the development of the individual diastereoisomers.

Mechanism of falcipain-2 inhibition by α,ß-unsaturated benzo[1,4]diazepin-2-one methyl ester.

Falcipain-2 (FP-2) is a papain-family cysteine protease of Plasmodium falciparum whose primary function is to degrade the host red cell hemoglobin, within the food vacuole, in order to provide free amino acids for parasite protein synthesis. Additionally it promotes host cell rupture by cleaving the skeletal proteins of the erythrocyte membrane. Therefore, the inhibition of FP-2 represents a promising target in the search of novel anti-malarial drugs. A potent FP-2 inhibitor, characterized by the presence in its structure of the 1,4-benzodiazepine scaffold and an α,ß-unsaturated methyl ester moiety capable to react with the Cys42 thiol group located in the active site of FP-2, has been recently reported in literature. In order to study in depth the inhibition mechanism triggered by this interesting compound, we carried out, through ONIOM hybrid calculations, a computational investigation of the processes occurring when the inhibitor targets the enzyme and eventually leads to an irreversible covalent Michael adduct. Each step of the reaction mechanism has been accurately characterized and a detailed description of each possible intermediate and transition state along the pathway has been reported.

Chiroptical sensing of perrhenate in aqueous media by a chiral organic cage.

A chiral cage is proposed as an effective chiroptical sensor for perrhenate (surrogate for 99TcO4-) in water, fruit juice and artificial urine media. The key mechanism for the chiroptical sensing resides in the change of dihedral angle of the binaphthyl unit and H-bonds with the guest, resulting in ample changes of the CD signal as a consequence of the binding event.

Molecular dynamics simulations of the Salmonella typhi Vi antigenic polysaccharide and effects of the introduction of a zwitterionic motif.

A series of hexasaccharides corresponding to the Vi capsular polysaccharide, a polymer of α-(1→4)-galacturonic acid, and analogs containing a zwitterionic motif with various degrees of acetylation at positions 3 have been modeled. When submitted to molecular dynamics simulations in a water box, all the structures visited only two quite restricted regions of the φ/ψ conformational space both corresponding to extended geometries without any tendency towards supercoiling. The most stable conformation showed a clockwise helix arrangement of substituents on the molecular surface whereas the opposite arrangement was observed for the other conformation. The flexibility of the system and the hydrophobic character of the molecular surface are modulated by the 3-O-acetyl groups that confer rigidity to the system. In the zwitterionic analogs, the introduction of positive charges in the place of the acetamido groups alters the hydrophobicity that can be regained by methylation of the amino groups. The needed molecular flexibility can be obtained by the complete deacetylation at positions 3.

2,3-Carbamate mannosamine glycosyl donors in glycosylation reactions of diacetone-d-glucose. An experimental and theoretical study.

The role of the cyclic 2,3-N,O-carbamate protecting group in directing the selectivity of mannosylation reactions of diacetone-d-glucose, promoted by BSP/Tf2O via α-triflate intermediates, has been investigated through a combined computational and experimental approach. DFT calculations were used to locate the transition states leading to the α or ß anomers. These data indicate the preferential formation of the ß-adduct with mannosyl donors either equipped with the 4,6-O-benzylidene protection or without it. The synthetic results confirmed this preference, showing in both cases an α/ß selectivity of 4:6. This highlights a role for the 2,3-N,O-carbamate in sharp contrast with what described in the case of 2,3-O-carbonate mannosyl donors.

Stable GM3 lactone mimetic raises antibodies specific for the antigens expressed on melanoma cells.

Immunotherapy of tumors and of melanoma in particular has a long history, and recently this therapeutic approach found a reliable scientific rationale. This biological therapy aims to teach the patient's immune system to recognize the antigens expressed on tumor cells and destroy them, leaving normal cells intact. The success of this therapy highly depends on the selection of target antigens that are essential for tumors growth and progression. The overexpression of GM(3) ganglioside 1 and especially the expression of its metabolite GM(3) lactone 2 characterize murine and human melanomas, playing an important role in tumor progression and making such self-antigens potential targets for the immunotherapy of these neoplasms. Although more immunogenic than its precursor, GM(3) lactone 2 is unsuitable to be used in immunotherapy as a melanoma-associated antigen (MAA) because it is unstable under physiological conditions. We designed and synthesized the hydrolytically stable mimetic 3, which is remarkably simpler than the native lactone 2; after conjugation of 3 to the protein carrier keyhole-limpet hemocyanin (KLH), the obtained glycoprotein 5 was used as the immunogen in vivo to successfully elicit specific antimelanoma antibodies. In fact, no appreciable binding to GM(1) was observed. Capitalizing on the stability and on the reduced structural complexity of mimetic 3, the immunostimulant 5 we report represents a new promising synthetic glycoconjugate for the immunotherapy of melanoma.

Enantioselective synthesis and olfactory evaluation of bicyclic alpha- and gamma-ionone derivatives: the 3D arrangement of key molecular features relevant to the violet odor of ionones.

Violet smelling ionones 1-3, occurring in the headspace of different flowers, are well-known perfumery raw materials. With the goal to recognize the still ill-defined spatial arrangement of structural features relevant to the binding of ionones to olfactory G-protein coupled receptors, through B3LYP/6-31G(d) modeling studies we identified bicyclic compounds 7-9 as conformationally constrained 13-alkyl-substituted analogues of monocyclic alpha- and gamma-ionones. They were thus synthesized to evaluate the olfactory properties. The enantioselective syntheses of 7-9 entailed two common key steps: (i) a Diels-Alder reaction to construct the octalinic core and (ii) a Julia-Lythgoe olefination to install the alpha,beta-enone side chain. The odor thresholds of synthetic 7 and 9 were significantly lower than the corresponding parent ionones, and 9 showed the lowest threshold value among violet-smelling odorants examined so far. Modeling studies suggested a nearly identical spatial orientation of key hydrophobic and polar moieties of compounds 1, 3, and 4-9. Presumably, interaction of these moieties with ionone olfactory receptors (ORs) triggers a similar receptor code that is ultimately interpreted by the human brain as a pleasant woody-violet smell. These results open the way to studies aimed at identifying and modeling complementary binding sites on alpha-helical domains of ionone receptor proteins.

Cyclic glycopeptidomimetics through a versatile sugar-based scaffold.

Cyclic peptidomimetics are attracting structures to obtain a distinct, bioactive conformation. Even more attractive are sugar-containing cyclic peptidomimetics which present turn structures induced by the pyranose ring when incorporated in cyclic peptides. The use of a new and versatile saccharidic scaffold to achieve sugar-based peptidomimetics is here reported together with the successful synthesis of diastereomerically pure cyclic SAA peptidomimetics 15 and 16.

Modeling of synthetic phosphono and carba analogues of N-acetyl-alpha-D-mannosamine 1-phosphate, the repeating unit of the capsular polysaccharide from Neisseria meningitidis serovar A.

The conformational behavior of methyl (2-acetamido-2-deoxy-alpha-d-mannopyranosyl)phosphate 1, and its analogues, methyl C-(2-acetamido-2-deoxy-alpha-d-mannopyranosyl)methanephosphonate 2 and methyl O-(2-acetamido-2-deoxy-5a-carba-alpha-d-mannopyranosyl)phosphate , where a methylene group replaces, respectively, the anomeric and the pyranose oxygen atom, was investigated at the B3LYP/6-311+G(d,p) level [6-311+G(2df,p) for the phosphorus atom]. The energy of the optimized structures was recalculated using the continuum solvent model C-PCM choosing water as the solvent. The compounds exhibited several populated conformations, but they all showed a marked preference for the (4)C(1) geometry of the pyranose ring; this preference was almost complete for 1, very large for the phosphono analogue 2, and large for the carba analogue 3. To give experimental support to these results, compounds 2 and 3 were synthesized and characterized by NMR spectroscopy. The comparison of the theoretical and experimental vicinal coupling constants confirmed the marked preference for the (4)C(1) geometry in the case of 2 and suggested that the same holds true for compound 3.

Synthesis, molecular dynamics simulations, and biology of a carba-analogue of the trisaccharide repeating unit of Streptococcus pneumoniae 19F capsular polysaccharide.

The synthesis of a carba-analogue corresponding to the trisaccharide repeating unit of Streptococcus pneumoniae type 19F capsular polysaccharide, where a residue of carba-L-rhamnose has been inserted into the natural trisaccharide in place of L-rhamnose, is described. The conformational properties of the analogue were investigated with the aid of molecular dynamics simulations and were strictly analogous to those of the natural compound. The biological activity of the carba-analogue was comparable to that of the corresponding natural repeating unit, thus suggesting that this compound, more stable to hydrolysis, is a good mimic of the natural structure.