Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Gō-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T(opt). The optimal folding temperature T(opt) is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T(opt) and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T(opt) and start to diverge when the temperature is lower than T(opt). The distribution of FPT is close to a log-normal-like distribution at T > or = T(opt). At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.     

Reactions of dimethyl acetylenedicarboxylate—VI : Reaction with aldehyde and ketone phenylhydrazones

Benzaldehyde phenylhydrazone with dimethyl acetylenedicarboxylate gives dimethyl 1,3-diphenylpyrazoline-4,5-dicarboxylate, dimethyl 1,3-diphenylpyrazole-4,5-dicarboxylate and trimethyl 1-phenylpyrazole-3,4,5-tricarboxylate; p-chlorobenzaldehyde phenylhydrazone gives trimethyl 1-phenyl-3,4,5-tricarboxylate and 1,2-(bis-phenylazo)-1,2-di-p-chlorophenylethane. Under similar conditions, p-tolualdehyde phenylhydrazone gives only trimethyl 1-phenylpyrazole-3,4,5- tricarboxylate. Acetophenone phenylhydrazone with dimethyl acetylenedicarboxylate gives dimethyl 1,3-diphenylpyrazole-4,5-dicarboxylate. Benzophenone phenylhydrazone, on the other hand, gives a mixture of dimethyl 1,3-diphenylpyrazoline-4,5-dicarboxylate and dimethyl 1,3-diphenylpyrazole-4,5- dicarboxylate. Benzyl methyl ketone and dimethyl acetylenedicarboxylate gives an enamine maleate, which is the Michael addition product.     

Symmetry allowed π4s+π2s additions silacyclopentadienes

π⁴s+π²s cycloaddition of hexaphenylsilacyclopentadiene with ethyl acrylate gives rise to a bicyclosilaheptene derivative. High resolution NMR studies have shown that the ester group in this adduct is in the endo position and that the ester methylene protons are magnetically inequivalent. Similar cycloadditions of hexaphenylsilacyclopentadiene, 1,1-dimethyl-2,3,4,5-tetraphenylsilacyclopentadiene, 1-methyl-1,2,3,4,5-pentaphenylsilacyclopentadiene, and 1-methyl-1-vinyl-2,3,4,5-tetra-phenylsilacyclopentadiene with dienophiles like acrylonitrile, maleic anhydride and dibenzoylacetylene have been carried out. The stereochemistry of these adducts has been deduced on the basis of NMR studies. Mass spectral fragmentation studies of some of the silabicycloheptenes have been carried out.     

The indole side chain of tryptophan as a versatile pi-donor

Single-armed, 15- and 18-membered lariat ether receptor systems having indolylethyl side arms bind Na+ and K+ in the ring. The indole residue serves as a pi-donor to the ring-bound cation. Whether the five- or six-membered ring interacts most directly with Na+ or K+ depends on whether the sidearm is attached to indole's 3- or 5-position. This suggests that structural as well as electronic factors are important in pi-complexation of alkali metal cations.     

Comparative study of photodynamic properties of 13,15-N-cycloimide derivatives of chlorin p6

Comparative study of 13,15-[N-(2-hydroxyethyl)]cycloimide chlorin p6 (2), 13,15-(N-acetoxy)cycloimide chlorin p6 (3), 13,15-(N-hydroxy)cycloimide chlorin p6 methyl ester (4) and 13,15-(N-methoxy)cycloimide chlorin p6 methyl ester (5) together with the previously investigated 13,15-[N-(3-hydroxypropyl)]cycloimide chlorin p6 (1) was performed. The dependence of the key photodynamic properties of 1-5 on the introduced substituents was analyzed. The photoinduced cell-killing activity of 4 is 100- and 280-fold higher than that of chlorin p6 and Photogem, respectively, as estimated on A549 human lung adenocarcinoma cells. The activity is reduced eight times in the order 4 > 5 > 1 > 2 > 3. The intracellular accumulation of 1-5 occurs in cytoplasm in a monomeric form bound to the lipids of cellular membranes. This form of 1, 2, 3, 4 and 5 is characterized by the high quantum yield of singlet oxygen generation, which depends on the introduced substituents, 0.66, 0.59, 0.35, 0.51 and 0.73, respectively. The photostability is two-fold less for 1 and four-fold less for 2, 3 and 5 than for 4. The rates of cellular uptake and efflux of 1-5 vary widely, thus providing the way to optimize the pharmacological properties of the photosensitizer (PS) using the respective substituents. Modifying the substituents, 1-5 were targeted to different cellular organelles. The enhanced accumulation in the Golgi apparatus and mitochondria complemented with diffuse staining of intracellular membranous structures is a property of 1-4. Compound 5 accumulates selectively in the lipid droplets and stains weakly perinuclear structures. Temperature-sensitive mechanisms of transport are responsible for the 1-4 uptake. Diffusion can play a role in the internalization of 5 but not of 1-4. Endocytosis via caveolae, clathrin-dependent and adenosine triphosphate-dependent pathways are not noticeably involved in the 1-5 internalization. Independently from their intracellular localization 1, 4 and 5 are highly efficient near-IR PS, which induce predominantly an apoptotic type of cell death under conditions providing ca 50% level of phototoxicity and necrosis at the 100% level of phototoxicity.     

Novel synthesis of sterically hindered N-substituted lactams from imides

An efficient and practical synthesis of sterically hindered N-substituted lactams has been developed starting from simple starting materials. The stereochemistry of the synthetically useful N,N acetal intermediate has been established.     

The Synthesis of 4-Decarboxy-4-phosphono-O-2-isooxacephems, -isopenams and -isooxacephems Containing Phosphorus at the 3-Position

Two new types of iso-oxacephems have been synthesized in which a phosphonate group replaces either the carboxyl group or C(3). The latter compound exists as a stable trialkoxyphosphonium ylide. Potassium thioacetate and O₂ in DMF are transformed in an autocatalytic, probably sulfur-catalyzed process to CH₃COOK and sulfur; the latter two reagents are sufficient to transform the methanesulfonate 7 to the isopenam 15 .     

Analysis of the terphenyls by a compressed pellet infrared method involving micro-distillation

A quantitative compressed pellet infrared method used together with a micro-distillation to effect separation of the isomer has been developed and reported here for the analysis of ortho-, meta-, and para-terphonyl. The terphenyl content is determined on fractions isolated by distillation from radiation damaged samples. The compressed pellet infrared method is preferred instead of the more conventional solution technique since smaller quantities of isolated terphcnyl are required. The pellet method is applicable also to polyphenyls higher than the terphenyls. The solution technique is not due to the insolubility of the polyphenyls. It is expected that the compressed pellet spectral method developed here might well find application in the analysis of compounds other than polyphenyls. Results presented here appear to be the, first quantitative infrared data reported in the literaturu on polyphenyl compounds.     

A new synthesis of 1,3-dihydrobenzo[1,2]oxasiloles by a novel rearrangement of a pentavalent silicon intermediate

A new synthesis of benzo[1,2]oxasiloles is described, wherein an unprecedented intramolecular allylic transposition takes place probably involving a pentavalent silicon intermediate.     

A probe method for studying dibromocarbene by time resolved infrared spectroscopy

Dibromocarbene reacts with tertiary-butylisocyanide to form a ketenimine. The absolute rate constant of the reaction (k_TBI = 2.3 × 10⁹ M⁻¹ s⁻¹) was determined by laser flash photolysis techniques with UV-vis detection of the dibromocarbene-pyridine ylide. The ketenimine was detected by TRIR spectroscopy at 2040 cm⁻¹. Isocyanide trapping of carbenes to form ketenimines is proposed as a general method of studying IR silent carbenes by TRIR spectroscopy.