Molecular dynamics simulations and free energy calculations on the enzyme 4‐hydroxyphenylpyruvate dioxygenase

4‐Hydroxyphenylpyruvate dioxygenase is a relevant target in both pharmaceutical and agricultural research. We report on molecular dynamics simulations and free energy calculations on this enzyme, in complex with 12 inhibitors for which experimental affinities were determined. We applied the thermodynamic integration approach and the more efficient one‐step perturbation. Even though simulations seem well converged and both methods show excellent agreement between them, the correlation with the experimental values remains poor. We investigate the effect of slight modifications on the charge distribution of these highly conjugated systems and find that accurate models can be obtained when using improved force field parameters. This study gives insight into the applicability of free energy methods and current limitations in force field parameterization. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011     

Dipolar Rotors Orderly Aligned in Mesoporous Fluorinated Organosilica Architectures

New mesoporous covalent frameworks, based on hybrid fluorinated organosilicas, were prepared to realize a periodic architecture of fast molecular rotors containing dynamic dipoles in their structure. The mobile elements, designed on the basis of fluorinated p‐divinylbenzene moieties, were integrated into the robust covalent structure through siloxane bonds, and showed not only the rapid dynamics of the aromatic rings (ca. 10⁸ Hz at 325 K), as detected by solid‐state NMR spectroscopy, but also a dielectric response typical of a fast dipole reorientation under the stimuli of an applied electric field. Furthermore, the mesochannels are open and accessible to diffusing in gas molecules, and rotor mobility could be individually regulated by I₂ vapors. The iodine enters the channels of the periodic structure and reacts with the pivotal double bonds of the divinyl‐fluoro‐phenylene rotors, affecting their motion and the dielectric properties.     

Linking Deltahedral Zintl Clusters with Conjugated Organic Building Blocks: Synthesis and Characterization of the Zintl Triad [R‐Ge9‐CHCH?CHCH‐Ge9‐R]4−

The accessibility of triads with deltahedral Zintl clusters in analogy to fullerene–linker–fullerene triads is another example for the close relationship between fullerenes and Zintl clusters. The compound {[K(2.2.2‐crypt)]₄[RGe₉‐CHCH CHCH‐Ge₉R]}(toluene)₂ (R=(2Z,4E)‐7‐amino‐5‐aza‐hepta‐2,4‐dien‐2‐yl), containing two deltahedral [Ge₉] clusters linked by a conjugated (1Z,3Z)‐buta‐1,3‐dien‐1,4‐diyl bridge, was synthesized through the reaction of 1,4‐bis(trimethylsilyl)butadiyne with K₄Ge₉ in ethylenediamine and crystallized after the addition of 2.2.2‐cryptand and toluene. The compound was characterized by single‐crystal structure analysis as well asNMR and IR spectroscopy.     

The crank moments weighted by the parity of cranks

In this note, we introduce the 2kth crank moment \(\mu _{2k}(-1,n)\) weighted by the parity of cranks and show that \((-1)^n \mu _{2k}(-1,n)>0\) for \(n\ge k \ge 0\). When \(k=0\), the inequality \((-1)^n \mu _{2k}(-1,n)>0\) reduces to Andrews and Lewis’s inequality \((-1)^n(M_e(n)-M_o(n))>0\) for \(n\ge 0\), where \(M_e(n)\) (resp. \(M_o(n)\)) denotes the number of partitions of n with even (resp. odd) crank. Several generating functions of \(\mu _{2k}(-1,n)\) are also studied in order to show the positivity of \((-1)^n\mu _{2k}(-1,n)\).     

Solid supported chemical syntheses of both components of the lantibiotic lacticin 3147

Lantibiotics are antimicrobial peptides produced by bacteria. Some are employed for food preservation, whereas others have therapeutic potential due to their activity against organisms resistant to current antibiotics. They are ribosomally synthesized and posttranslationally modified by dehydration of serine and threonine residues followed by attack of thiols of cysteines to form monosulfide lanthionine and methyllanthionine rings, respectively. Chemical synthesis of peptide analogues is a powerful method to verify stereochemistry and access structure-activity relationships. However, solid supported synthesis of lantibiotics has been difficult due to problems in generating lanthionines and methyllanthionines with orthogonal protection and good stereochemical control. We report the solid-phase syntheses of both peptides of a two-component lantibiotic, lacticin 3147. Both successive and interlocking ring systems were synthesized on-resin, thereby providing a general methodology for this family of natural products.     

Mesoporous silicabis(ethylsulfanyl)propane palladium catalysts for hydrogenation and one-pot two-step Suzuki cross-coupling followed by hydrogenation

The solid phase catalytic activity of mesoporous silicabis(ethylsulfanyl)propane palladium catalysts for hydrogenation and novel one-pot two-step Suzuki cross-coupling followed by hydrogenation is described. The efficiency of catalytic hydrogenation was measured for substrate nitrobenzene with 5, 7 and 14 nm average pore diameter materials. The 5 nm pore material performed best and was also very effective in the catalytic hydrogenation of alkene, nitrile and imine substrates. Novel one-pot two-step Suzuki cross-coupling and hydrogenation was demonstrated using bromonitro- and bromodinitrobenzene and phenylboronic acid as substrates with conversion to the corresponding coupled amino compounds. As a consequence of the high affinity of the sulfur ligands for palladium, none was detected in leaching tests and the catalyst is easily separated and recycled.     

Antioxidant capacity and total phenolic contents of oregano (Origanum vulgare), lavender (Lavandula angustifolia) and lemon balm (Melissa officinalis) from Romania

The study reported here presents a comparative screening of three medicinal plants including oregano (Origanum vulgare L.), lavender (Lavandula angustifolia) and lemon balm (Melissa officinalis) having the same geographical origin, the Southeast region of Romania, and growing in the same natural conditions. The contents of total phenolics and total flavonoids for the extracts of these were determined. Furthermore, the total antioxidant capacity was also evaluated. It was found that Origanum vulgare and Melissa officinalis extracts present the most effective antioxidant capacity in scavenging DPPH radicals, while Lavandula angustifolia is less active. High performance liquid chromatography-mass spectrometry analysis was used to identify the components of extracts. Major phenolic acids identified in the analysed species were ferulic, rosmarinic, p-coumaric and caffeic, while predominant flavonoids were quercetin, apigenin kaempherol, which were present as glucosides.