Molecular recognition at the active site of factor Xa: cation-π interactions, stacking on planar peptide surfaces, and replacement of structural water

Factor Xa, a serine protease from the blood coagulation cascade, is an ideal enzyme for molecular recognition studies, as its active site is highly shape-persistent and features distinct, concave sub-pockets. We developed a family of non-peptidic, small-molecule inhibitors with a central tricyclic core orienting a neutral heterocyclic substituent into the S1 pocket and a quaternary ammonium ion into the aromatic box in the S4 pocket. The substituents were systematically varied to investigate cation-π interactions in the S4 pocket, optimal heterocyclic stacking on the flat peptide walls lining the S1 pocket, and potential water replacements in both the S1 and the S4 pockets. Structure-activity relationships were established to reveal and quantify contributions to the binding free enthalpy, resulting from single-atom replacements or positional changes in the ligands. A series of high-affinity ligands with inhibitory constants down to K(i)=2 nM were obtained and their proposed binding geometries confirmed by X-ray co-crystal structures of protein-ligand complexes.     

Measuring the range of plasmonic interaction

When gold nanoparticles are covered with nanometric layers of transparent polyelectrolytes, the plasmon absorption spectrum A(λ) increases by a factor of approximately three and shifts to the red. These modifications of dissipative experimental observables stop when the cover layer thickness approaches the particle diameter. Spectral modifications of dispersive parameters like the reflection R, however, keep changing with increasing cover layer thickness. The shift of the plasmon resonance caused by two interacting particle layers is studied as a function of the separating distance between the two layers. We discuss these observations in the context of an effective medium theory and conclude that it can only be applied for a layer thickness on the order of the particle diameter.     

Stabilisation of water-soluble platinum nanoparticles by phosphonic acid derivatives

Sodium 2-(diphenylphosphino)ethyl phosphonate (1) was investigated as a stabilising agent for platinum nanoparticles (Pt-NPs) in aqueous solution. This phosphino phosphonate is known to stabilise rhodium nanoparticles (NPs) in water. Here we report that in the case of Pt-NPs this ligand is indirectly involved in the stabilisation mechanism and the actual stabilisation agent is the platinum complex Na(2)[Pt(1)(2)] (2). The reduction of platinum(II) salts in the presence of the phosphonates 1, 2, sodium 2-(diphenylphosphoryl)ethyl phosphonate (3) and 3,3,3-triphenylpropyl phosphonate (4) leads to stable platinum NPs with a remarkably narrow particle size distribution. These platinum NPs show high catalytic activity in the hydrogenation of 1-hexene and 1-chloro-3-nitrobenzene under biphasic as well as heterogeneous (supported on charcoal) conditions. The activity of the supported NPs was 30 times higher than the commercially available catalyst Pt(0) EnCat?. Furthermore, the single-crystal X-ray structures of (1)(MeOH)(2)(H(2)O)(2), (3)(H(2)O)(4), and (4)(2)(H(2)O)(17) have been determined.     

Synthesis of nitrobenzothiazolinethiones and related compounds via intramolecular displacement of nitro groups

A number of dinitroanilines on reaction with sodium hydride in dimethylformamide produced the sodium salt which, on further reaction with carbon disulfide, cyclized to nitrobenzothiazolinethiones. In several cases benzothiazolinethione sulfides and benzothiazolinethione disulfides were also isolated.     

Density functional theory computational study on the thermal cycloreversion of 2-acetoxy-2-methoxy-5,5-dimethyl-Delta3-1,3,4-oxadiazoline: evidence for a carbonyl ylide intermediate

Three [3 + 2] cycloreversions of 2-acetoxy-2-methoxy-5,5-dimethyl-Delta(3)-1,3,4-oxadiazolines were examined by computation at the density functional level of theory. The lowest activation energies are those for cycloreversion to 2-diazopropane and acetic methylcarbonic anhydride and for cycloreversion to N(2) and a carbonyl ylide. Those are the reactions that are observed experimentally. A third cycloreversion, to acetoxy(methoxy)diazomethane and acetone, has a much larger barrier. The carbonyl ylide is a real intermediate, but it fragments easily to acetone and acetoxy(methoxy)carbene. The lifetime of the ylide may be so short, in some cases, as to blur the distinction between a two-step cycloreversion of the oxadiazoline and a concerted process that generates three fragments in one step.     

Thermal decompositions of dinitropyridyl and dinitrothienyl dithiocarbamates and t-butyl trithiocarbonates

The title compounds on heating cyclized to yield 7-nitro-1,3-dithiolo[4,5-c]pyridin-2-one (III), 6-nitro-1,3-dithiolo[2,3-c]pyridin-2-one (VIIa), 6-nitrothieno[2,3-d]-1,3-dithiol-2-one (XIVa) and 6-nitrothteno[2,3-d]-1,3-dithiole-2-thione (XIVb).     

Gd12C6I17 – eine Verbindung mit kondensierten,C2-gefüllten Gd6I12-Clustern

Gd₁₂C₆I₁₇ — a Compound with Condensed, C₂-Containing Gd₆I₁₂ Clusters Gd₁₂C₆I₁₇ was isolated in black shining crystals from a reaction product of Gd, GdI₃ and graphite, heated in sealed tantalum capsules at 1170 K. The compound is monoclinic (C2/c; a = 1929.7(9), b = 1220.1(5), c = 1863.5(5) pm, = 90.37(3)°). The crystal structure is composed of linear units of 3 condensed Gd₆I₁₂ clusters (connection via trans-edges of the central Gd₆ octahedron), which are further linked via cis edges to form zig-zag chains. The centres of the Gd₆ octahedra are occupied by C₂ units. The distances d_{C? C} ≈ 145 pm correspond to a filling of the antibonding π* orbitals of the C₂ group, which, however, interact with empty d-orbitals of the metal atoms especially in the apices of the octahedra and thus loose their pure carbon character. The short Gd? C distances (d_{Gd? C} = 222 and 227 pm, respectively) are explained as due to multiple bonds. The occurrence of C₂ units and single C atoms, respectively, in lanthanide carbides and carbide halides is coupled to the electron concentration of the metal or cluster framework.     

Importance of Intermolecular Hydrogen Bonding for the Stereochemical Control of Allene–Enone (3+2) Annulations Catalyzed by a Bifunctional,Amino Acid Derived Phosphine Catalyst

The origin of stereoselectivity in the (3+2) annulation of allenes and enones catalyzed by an amino acid derived phosphine catalyst has been investigated by the use of dispersion‐corrected density functional theory. An intermolecular hydrogen bond between the intermediate zwitterion and the enone was found to be the key interaction in the two enantiomeric transition states. Additional stabilization is provided by intermolecular hydrogen‐bonding interactions between acidic positions on the catalyst backbone and the substrate. Enantioselectivity occurs because the intermolecular hydrogen bond in the transition state leading to the minor enantiomer is only possible at the expense of reactant distortion.     

Importance of Intermolecular Hydrogen Bonding for the Stereochemical Control of Allene–Enone (3+2) Annulations Catalyzed by a Bifunctional,Amino Acid Derived Phosphine Catalyst

The origin of stereoselectivity in the (3+2) annulation of allenes and enones catalyzed by an amino acid derived phosphine catalyst has been investigated by the use of dispersion‐corrected density functional theory. An intermolecular hydrogen bond between the intermediate zwitterion and the enone was found to be the key interaction in the two enantiomeric transition states. Additional stabilization is provided by intermolecular hydrogen‐bonding interactions between acidic positions on the catalyst backbone and the substrate. Enantioselectivity occurs because the intermolecular hydrogen bond in the transition state leading to the minor enantiomer is only possible at the expense of reactant distortion.