Camdas: An automated conformational analysis system using molecular dynamics

We present an automated conformational analysis program, CAMDAS (Conformational Analyzer with Molecular Dynamics And Sampling). CAMDAS performs molecular dynamics (MD) calculations for a target molecule and samples conformers from the trajectory of the MD. The program then evaluates the similarities between each of the sampled conformers in terms of the root- mean-square deviations of the atomic positions, clusters similar conformers, and finally prints out the clustered conformers. This MD-based conformational analysis is a broadly used method, and CAMDAS is intended to provide a convenient framework for the method. CAMDAS has the ability to find the representative conformers automatically from an arbitrarily given structure of the molecule. The accuracy of the program was examined using N- acetylalanine-N-methylamide, and the obtained result was consistent with that of the systematic search method. In the test calculation of cyclodecane, CAMDAS could identify most of the known conformers and their conformational enantiomers by examining only 5000 conformers. In addition, the potential-scaled method, which we have developed previously as an accelerating technique for MD, could find two additional conformers of cyclodecane that have not been reported. CAMDAS presents a convenient way to find the energetically possible conformers of a molecule, which is needed especially in the early stage of drug design.     

Synthesis of sodium-polystyrenesulfonate-grafted nanoparticles by core-cross-linking of block copolymer micelles

Sodium poly(styrenesulfonate)(polySSNa)-grafted polymer nanoparticles were synthesized by core-cross-linking of block copolymer micelles and subsequent chemical transformation. Block copolymers, poly(p-((1-methyl)silacyclobutyl)styrene-block-poly(neopentyl p-styrenesulfonate)s, polySBS-b-polySSPen, were synthesized by nitroxy-mediated living radical polymerization. The block copolymers formed micelles (R_h=15-23 nm, where R_h represents the hydrodynamic radius) with a polySBS core and polySSPen shell in acetone. The micelle core was cross-linked by ring-opening polymerization of silacyclobutyl groups in polySBS. Hydrolysis of the neopentyl groups provided polySSNa-grafted nanoparticles. The R_h of the particles before the hydrolysis ranged from 12 to 21 nm in acetone, while they varied to the range from 50 to 110 nm in water after the hydrolysis.     

Synthesis of poly (ethylene oxide)-b-polysilane by anionic polymerization of masked disilenes using a macroinitiator method

Poly(ethylene oxide-)-poly(1, 1-dimethyl-2, 2-dihexyldisilene) block copolymers (PEO-b-PMHS) were synthesized by the anionic polymerization of masked disilenes initiated with the potassium alkoxide of poly(ethylene glycol). The block copolymer self-assembled into polymer micelles in water accompanied by a transition in the polysilane conformation.     

Radical alkenylation of alpha-halo carbonyl compounds with alkenylindiums

Alkenylation reaction of alpha-halo carbonyl compounds with alkenylindiums proceeded via a radical process in the presence of triethylborane. Unactivated alkene moieties as well as a styryl group could be introduced by this method. The geometry of the carbon-carbon double bonds of the alkenylindiums was retained. Preparation of an alkenylindium via a hydroindation of 1-alkyne followed by radical alkenylation established an efficient one-pot strategy. [reaction: see text]     

Reaction of 2-methoxy-3H-azepine with NBS: efficient synthesis of 2-substituted 2H-azepines

[reaction: see text] The reaction of 2-methoxy-3H-azepines, in the presence or absence of a nucleophile, with N-bromosuccinimide (NBS) gave a regioselective 1,4-adduct from which the corresponding 2H-azepine derivatives were formed via base-promoted hydrogen bromide elimination, generally in moderate to quantitative yield. Competitive formation of 4-bromo-2-methoxy-3H-azepine by electrophilic substitutuion or 3H-azepin-2-yl 2H-azepin-2-yl ether by transetherification was minimized at lower reaction temperatures. Quantitative substitution of 2-(2',4',6'-trichlorophenoxy)-2H-azepine derivatives, formed in moderate yield from the respective 3H-azepine and NBS in the presence of 2,4,6-trichlorophenol (TCP), by various nucleophiles gave the corresponding 2-substituted 2H-azepine. Among these nucleophiles were alkanethiol and alkylamine that are not tolerated in the reaction of 3H-azepine and NBS.     

Microwave‐Assisted Palladium‐Catalyzed Direct Arylation of 1,4‐Disubstituted 1,2,3‐Triazoles with Aryl Chlorides

Treatment of 1,4‐disubstituted 1,2,3‐triazoles with aryl chlorides in the presence of potassium carbonate under palladium catalysis and microwave irradiation at 250 °C for 15 min leads to arylation of the triazole at the 5‐position. A variety of functional groups, including ester and hydroxy groups, are compatible. The procedure is suitable for the regioselective preparation of trisubstituted triazoles. Microwave irradiation accelerates the reaction, thus allowing the rapid synthesis of trisubstituted triazoles, which are difficult to synthesize selectively.     

Regiospecific allylation of acetals with allylsilanes catalyzed by iodotrimethylsilane. Synthesis of homoallylethers

Allylation of acetals with allylsilanes is catalyzed by iodotrimethylsilane to give the corresponding homoallyl ethers, with regiospecific transposition of the allyl group.     

Photophysical and (photo)electrochemical properties of a coumarin dye

A new coumarin dye, cyano-{5,5-dimethyl-3-[2-(1,1,6,6-tetramethyl-10-oxo-2,3,5,6-tetrahydro-1H,4H,10H-11-oxa-3a-aza-benzo[de]anthracen-9-yl)vinyl]cyclohex-2-enylidene}-acetic acid (NKX-2753), was prepared and characterized with respect to photophysical and electrochemical properties. It was employed as a dye sensitizer in dye-sensitized solar cells and showed efficient photon-to-electron conversion properties. The photocurrent action spectrum exhibited a broad feature with a maximum incident photon-to-electron conversion efficiency (IPCE) of 84% at 540 nm, which is comparable to that for the famous red dye RuL2(NCS)2 (known as N3), where L stands for 2,2'-bipyridyl-4,4'-dicarboxylic acid. The sandwich-type solar cell with NKX-2753, under illumination of full sun (AM1.5, 100 mW cm(-2)), produced 16.1 mA cm(-2) of short-circuit photocurrent, 0.60 V of open-circuit photovoltage, and 0.69 of fill factor, corresponding to 6.7% of overall energy conversion efficiency using 0.1 M LiI, 0.05 M I2, 0.1 M guanidinium thiocyanate, and 0.6 M 1,2-dimethyl-3-n-propyl-imidazolium iodide in dry acetonitrile as redox electrolyte. In comparison with its analogue NKX-2586 (Langmuir 2004, 20, 4205), NKX-2753 with an extra side ring on the alkene chain produced much higher IPCE values at the same conditions. The side ring acted as a spacer to efficiently prevent dye aggregation when adsorbed on the TiO2 surface, resulting in significant improvements of short-circuit photocurrent, open-circuit photovoltage, and fill factor compared with NKX-2586 that aggregated on the TiO2 surface.     

Photoelectron and penning ionization electron spectroscopic investigation of trimethylsilyl- and t-butyl-thiophenes

Penning ionization electron spectroscopy and CNDO/S calculations have been successfully applied to the analyses of the UV photoelectron spectra of 2- and 2,5-bistrimethylsilylthiophene and 2-t-butylthiophene. The relative intensities of the π type bands are greatly enhanced in the Penning spectra compared with those of the UV photoelectron spectra.