Rhodopsin exhibits a preference for solvation by polyunsaturated docosohexaenoic acid

An all-atom molecular dynamics simulation of rhodopsin in a membrane environment has been carried out with lipid composition similar to that of the retinal membrane. The initial conformation of the protein was taken from the X-ray crystallographic structure (1F88), while those of the lipids came from a previous molecular dynamics simulation. During the course of the 12.5 ns simulation, the initially randomly placed lipids adopt an anisotropic solvation structure around the protein. The lipids, having one saturated stearic acid chain and one polyunsaturated docosohexaenoic acid chain with a zwitterionic phosphatidylcholine headgroup, arrange themselves to maximize contact between the polyunsaturated chain and the protein surface. This organization is driven by energetically favorable interactions between the transmembrance helices and the docosohexaenoyl chains that are largely of the van der Waals type. These observations are consistent with various experimental studies on rhodopsin and other G-protein coupled receptors and with the picture of extreme flexibility in polyunsaturated fatty acid chains that has arisen from recent NMR and computational work.     

Cyclohexylphosphonic acid

The title compound, C₆H₁₃O₃P, displays a crystallographic mirror plane. Bond lengths in the phosphonic acid moiety are P—O = 1.5557 (13) Å and P=O = 1.5089 (18) Å. The mol­ecules are linked via intermolecular hydrogen bonding to form a one‐dimensional chain of fused rings. There are no significant contacts between planes.     

Photon-induced dissociation with a four-sector tandem mass spectrometer

The feasibility of using photodissociation of protonated peptide molecules to sequence specific fragment ions with a 193-nm pulsed laser beam in a magnetic deflection tandem mass spectrometer of EBEB configuration was demonstrated. Although the short pulse (15 ns) and low repetition rate (100 Hz) of the excimer laser permitted the irradiation of only ～ 0.02% of the (M + H)⁺ ions exiting MS-1, a photon-induced decomposition spectrum of the heptapeptide angiotensio III (M _r 930.5) was produced that was practically the same (but with better signal-to-noise ratio) as that generated by collision-activated dissociation at the same low duty cycle. Because of the low and pulsed fragment ion currents, an array detector was used to record the spectra. A dependence between laser power and abundance of fragment ions was observed (increased power increases the relative abundance of ions of low mass). Laser power was varied from 6 to 80 mJ. Formation of fragment ions from a large peptide (melittin, M, 2844.75) was also observed. The results permit the design of modifications that may increase the fragment ion yield to 10% or higher, which would make photon-induced decomposition a useful method for magnetic deflection mass spectrometers.     

Übergangsmetallkomplexe mit Anionen von 1-substituierten 1,2,3,4-Tetrazolin-5-onen und -thionen und von 1,3-Thiazolin-2-thion

Transition Metal Complexes with Anions of 1-substituted Tetrazolinones and -thiones and of 1,3-Thiazolin-2-thione The preparation of a series of anionic and phosphine containing complexes with the ambivalent anions of 1-R-tetrazolin-5-ones and -5-thiones, and of 1,3-thiazolin-2-thione is reported. According to the i.r. and ¹H n.m.r. spectra the S-heterocycles are bonded through the exocyclic sulfur atom to the metal; in the oxotetrazolinate compounds coordination occurs via the N² or N⁴ ring atoms. The copper and silver complexes [(Ph₃P)MX]₂ (X = anionic heterocycle) have been found to be dimeric.     

Model Calculations on the Squalene Cyclization

As a model for the squalene cyclization the interaction between a methyl cation or a methyl radical and two double bonds has been studied using the CNDO/2 and INDO method. In both cases bond formation between the CH₃-group and one double bond is facilitated by a second one, but not in a concerted way.     

Synthesis of new thiazole analogues of pyochelin, a siderophore of Pseudomonas aeruginosa and Burkholderia cepacia. A new conversion of thiazolines into thiazoles

Three pyochelin analogues and their methyl esters all containing a thiazole ring have been synthesised from the same Weinreb amide key intermediate. One of these analogues called HPTT-COOH, a molecule released in the course of pyochelin and yersiniabactin biosynthesis, was efficiently synthesised using a new base induced conversion of the key compound 2′-(2-hydroxyphenyl)-2′-thiazoline-4′-(N-methoxy,N-methyl) carboxamide into 2′-(2-hydroxyphenyl)-2′-thiazole-4′-(N-methoxy,N-methyl) carboxamide.     

Energetic and stereochemical effects of the protein environment on substrate: a theoretical study of methylmalonyl-CoA mutase

QM/MM methods were used to study the isomerization step from (2R)-methylmalonyl-CoA to succinyl-CoA. A pathway via a "fragmentation-recombination" mechanism is ruled out on energetic grounds. For the other radicalic pathway, involving an addition recombination step, geometries and vibrational contributions have been determined, and a barrier height of 11.70 kcal/mol was found. The effect of adjacent hydrogen-donating groups was found to reduce the energy barrier by 1-2 kcal/mol each and thus to provide a significant catalytic effect for this reaction. By means of molecular dynamics studies, the stereochemistry of the methylmalonyl-CoA mutase catalyzed reaction was examined. It is shown that TYR89 is essential for maintaining stereoselectivity of the abstraction of a hydrogen in the backreaction. The subsequent selective formation of one isomer of methylmalonyl-CoA is probably due to the presence of a bulky side chain.     

Electron Impact Induced Fragmentation of Aromatic Alkoxyimines II [5]. Formation and Transformation of Heterocyclic Radical Cations in the Gas Phasea

 The molecular ion 1 of N-(n-propoxy)benzaldimine I rearranges by an 1,5-H-shift to the δ-distonic ion 2 which subsequently cyclizes to the α-distonic ion 3. Homolytic cleavage of the N–O bond in 3 results in the δ-distonic ion 4 which expels CH₂O leading to the β-distonic ion 5. Ion 5 is also formed from the molecular ions of tetrahydrooxazines II and III and from M^+• of phenylazetidine IVa. In a subsequent step, ion 5 cyclizes to the N-protonated 3,4-dihydroisoquinolinium ion 6. The syntheses of II–IV and their derivatives are described.     

Multicomponent coupling reactions for organic synthesis: chemoselective reactions with amide-aldehyde mixtures

The acid-catalyzed condensation chemistry of simple amides and aldehydes provides a highly prolific source of diverse reactants for irreversible follow-up reactions. Amide-aldehyde mixtures have been successfully employed in multicomponent syntheses of N-acyl alpha-amino acids (via palladium-catalyzed amidocarbonylation) and various cyclohexene, cyclohexadiene, and benzene derivatives (via the amide-aldehyde-dienophile (AAD) reaction).     

Radical para-benzoic acid derivatives: transmission of ferromagnetic interactions through hydrogen bonds at long distances

Investigation of the transmission of magnetic interactions through hydrogen bonds has been carried out for two different benzoic acid derivatives which bear either a tert-butyl nitroxide (NOA) or a poly(chloro)triphenylmethyl (PTMA) radical moiety. In the solid state, both radical acids formed dimer aggregates by the complementary association of two carboxylic groups though hydrogen bonding. This association ensured that atoms with most spin density are separated from one another by more than 15 A. Thus, no competing through-space magnetic exchange interactions are expected in these dimers and, hence, they provide good models to investigate whether noncovalent hydrogen bonds play a role in the long-range transmission of magnetic interactions. The nature of the magnetic exchange interaction and their strengths within similar dimer aggregates in solution was assessed by electron spin resonance (ESR) spectroscopy. In the case of radical NOA, low-temperature ESR experiments showed a weak ferromagnetic interaction between the two radicals in the dimer aggregates (which have the same geometry as in the solid state). In contrast, the corresponding solution ESR study performed with radical PTMA did not lead to any conclusive results, as aggregates were formed by noncovalent interactions other than hydrogen bonds. However, the bulkiness of the poly(chloro)triphenylmethyl radical prevented interdimer contacts in the solid state between regions of high spin density. Hence, solid-state measurements of the alpha phase of PTMA radical provided evidence of the intradimer interaction to confirm the transmission of a weak ferromagnetic interaction through the carboxylic acid bridges, as found for the NOA radical. Moreover, crystallization of the PTMA radical in presence of ethanol to form the beta phase of PTMA radical prevented the dimer formation; this resulted in the suppression of this interaction and provides further evidence of the magnetic exchange mechanism through noncovalent hydrogen bonds at long distances.