Pore morphologies in disordered nanoporous thin films

Materials with nanometer size heterogeneities are commonplace in the chemical and biological sciences (e.g, polymer blends, microemulsions, gels) and often exhibit complex morphologies. Although this morphology has a dramatic effect on the materials' properties, it is often difficult to accurately characterize. We describe a method, using small-angle X-ray scattering data, of generating representative three-dimensional morphologies of isotropic two-phase materials where the morphology is disordered, and we apply this to thin films containing nanometer sized pores with a range of porosities (4-44%). These representations provide a visualization of the pore morphology, give the pore size scale and extent of interconnection, and permit the determination of the transitions from closed pore to interconnected pores to bicontinuous morphology.     

ortho-metallation reactions involving some triphenyl phosphite complexes of osmium

Osmium triphenylphosphine complexes, OsH₄(PPh₃)₃, OsH₂ (CO)(PPh₃)₃ and OsHCl(CO)(PPh₃)₃ react with triphenyl phosphite in boiling organic solvents to yield triphenyl phosphite derivatives which subsequently undergo ortho-metallation reactions.     

A novel general route for the preparation of enantiopure imidazolines

A novel procedure for the preparation of enantiopure 1,4-disubstituted 2-imidazolines is reported. Enantiopure beta-amino alcohols are converted into N-hydroxyethylamides, which are reacted with excess thionyl chloride, or with thionyl chloride followed by phosphorus pentachloride to yield N-chloroethylimidoyl chlorides. These intermediates are treated with amines and anilines to produce N-chloroethylamidines, which are converted into imidazolines upon workup with aqueous hydroxide. The method is simple and efficient and has been used to prepare a wide variety of enantiopure imidazolines, in a modular fashion, from readily available amino alcohols.     

Syntheses and conformational analyses of some 3-amino-2,5-dioxo-2,3,4,5-tetrahydro-1H-1-benzazepine derivatives: X-ray crystal structure of 35–3-[[(1,1-dimethylethoxy)carbonyl]amino]-2,5-dioxo-2,3,4,5-tetrahydro-1H-1-benzazepine

The constrained dipeptide mimic 1 was synthesized from 2 in three steps with 65% overall yield. Analyses of the ¹H nmr data of a number of 3-amino-2,5-dioxo-2,3,4,5-tetrahydro-1H-1-benzazepine derivatives led to the conclusion that these compounds adopt a similar conformation and that this ring system is rigid. X-ray crystallography was used to define the structure of 3 , and computer-aided energy minimization of 6 gave a preferred conformation similar to that observed in the crystal of 3 .     

Synthesis of a diverse library of mechanism-based cysteine protease inhibitors

We report improvements of our method for the solid-phase synthesis of mechanism-based mercaptomethyl ketone inhibitors of cysteine proteases (Lee, A.; Huang, L.; Ellman, J. A. J. Am. Chem. Soc. 1999, 121, 9907-9914). Specifically, Fmoc-protected chloromethyl ketones were used, rather than the Alloc-protected counterparts. In addition, we further demonstrated that diverse polar functionality can be incorporated at the R1', R1, and R2 sites, in contrast to our previous efforts, where primarily hydrophobic groups were incorporated at these positions. On the basis of these results, a 2016-membered library of potential mercaptomethyl ketone inhibitors was prepared that incorporated diverse functionality. The library was screened against cathepsin B, which is implicated in cancer, resulting in the identification of single-digit nanomolar inhibitors. Because of the diverse functionality incorporated in this library, it should be a rich source of potent inhibitors against many other cysteine proteases.     

Macrocycle synthesis strategy based on step-wise “adding and reacting” three components enables screening of large combinatorial libraries

Macrocycles provide an attractive modality for drug development, but generating ligands for new targets is hampered by the limited availability of large macrocycle libraries. We have established a solution-phase macrocycle synthesis strategy in which three building blocks are coupled sequentially in efficient alkylation reactions that eliminate the need for product purification. We demonstrate the power of the approach by combinatorially reacting 15 bromoacetamide-activated tripeptides, 42 amines, and 6 bis-electrophile cyclization linkers to generate a 3780-compound library with minimal effort. Screening against thrombin yielded a potent and selective inhibitor (K_i = 4.2 ± 0.8 nM) that efficiently blocked blood coagulation in human plasma. Structure–activity relationship and X-ray crystallography analysis revealed that two of the three building blocks acted synergistically and underscored the importance of combinatorial screening in macrocycle development. The three-component library synthesis approach is general and offers a promising avenue to generate macrocycle ligands to other targets.

Combination of three efficient chemical reactions allows for solution-phase synthesis of 3780 macrocycles and identification of potent thrombin inhibitor.     

Hydrogen atom mediated Stone-Wales rearrangement of pyracyclene: a model for annealing in fullerene formation

We have investigated the Stone-Wales (SW) rearrangement of pyracyclene (C(14)H(12)) using quantum mechanical molecular modeling. Of particular interest in this study is the effect of an added hydrogen atom on the barriers to SW rearrangement. Hydrogen atoms are found in high abundance during combustion, and their effect upon isomerization of aromatic compounds to more stable species may play an important role in the combustion synthesis of fullerenes. We have calculated the barriers for the SW rearrangement in pyracyclene using density functional theory B3LYP/6-31G(d) and B3LYP/6-311G(d,p). Two mechanisms have been investigated: (i) a mechanism with two identical transition states of C(1) symmetry and a cyclobutyl intermediate and (ii) a mechanism with one transition state containing an sp(3) carbon (J. Am. Chem. Soc. 2003, 125, 5572-5580; Nature 1993, 366, 665-667). We find that the barriers for these mechanisms are 120.0 kcal mol(-1) for the cyclobutyl mechanism and 130.1 kcal mol(-1) for the sp(3) mechanism. Adding a hydrogen atom to the internal bridge carbon atoms of pyracyclene reduces the barrier of the cyclobutyl mechanisms to 67.0 kcal mol(-1) and the sp(3) mechanism to 73.1 kcal mol(-1). The bonding of carbon atoms in pyracyclene is similar to those found in isomers of C(60), and the barriers are low enough so that these reactions can become significant during fullerene synthesis in flames. Adding hydrogen atoms to the external bridge atoms on pyracyclene produces a smaller reduction in the SW barrier and adding hydrogen atoms to nonbridge external carbon atoms results in no reduction of the barrier.     

Application of NMR SHAPES screening to an RNA target

Several NMR screening techniques have been developed in recent years to aid in the identification of lead drug compounds. These NMR methods have traditionally been used for protein targets, and here we examine their applicability for an RNA target. We used the SHAPES compound library to test three different NMR screening methodologies: the saturation transfer difference (STD), the 2D trNOESY, and the WaterLOGSY experiments. We found that the WaterLOGSY experiment was the most sensitive method for our RNA target, the P4P6 domain of the Tetrahymena thermophila Group I intron. Using the WaterLOGSY experiment, we found that 23 of the 112 SHAPES compounds interact with P4P6. To identify which of these 23 hits bind through nonspecific interactions, we counterscreened with a linear duplex RNA control and identified one of the SHAPES compounds as interacting with P4P6 specifically. We thus demonstrated that the WaterLOGSY experiment in combination with the SHAPES compound library can be used to efficiently find RNA binding lead compounds.     

The boron-catalyzed polymerization of dimethylsulfoxonium methylide. A living polymethylene synthesis

Trialkyl and aryl organoboranes catalyze the polymerization of dimethylsulfoxonium methylide (1). The product of the polymerization is a tris-polymethylene organoborane. Oxidation affords linear telechelic alpha-hydroxy polymethylene. The polymer molecular weight was found to be directly proportional to the stoichiometric ratio of ylide/borane, and polydispersities as low as 1.01-1.03 have been realized. Although oligomeric polymethylene has been the most frequent synthetic target of this method, polymeric star organoboranes with molecular weights of 1.5 million have been produced. The average turnover frequency at 120 degrees C in 1,2,4,5-tetrachlorobenzene/toluene is estimated at >6 x 10(6) g of polymethylene (mol boron)(-1) h(-1). The mechanism of the polyhomologation reaction involves initial formation of a zwitterionic organoborane.ylide complex which breaks down in a rate-limiting 1,2-alkyl group migration with concomitant expulsion of a molecule of DMSO. The reaction was found to be first order in the borane catalyst and zero order in ylide. DMSO does not interfere with the reaction. The temperature dependence of the reaction rate yielded the following activation energy parameters (toluene, DeltaH(++) = 23.2 kcal/mol, DeltaS(++) = 12.6 cal deg/mol, DeltaG(++) = 19.5 kcal/mol; THF, DeltaH(++) = 26.5 kcal/mol, DeltaS(++) = 21.5 cal deg/mol, DeltaG(++) = 20.1 kcal/mol).     

The Crystal Structure of Ba3Cu2Al2F16: a Relative of Ba4Cu2Al3F21

Ba₃Cu₂Al₂F₁₆ is monoclinic: a = 7.334(1)Å, b = 5.320(2)Å, c = 16.022(1)Å, β = 96.34(1)°, Z = 2. Its crystal structure was solved in the space group P2₁ (No. 4) from synchrotron X‐ray single crystal data using 2685 unique reflections (2639 with F_o/σ(F_o) > 4). The final R factor is 0.044. The structure consists of a succession along the c‐axis of the cell of three layers of two different kinds of sheets developing in the (a, b) plane. The first one, formulated [(AlF₅)₂]_∞^4— and hereafter named A, is built up from infinite cis‐chains of aluminium‐fluorine octahedra [AlF₆], linked by two vertices and distanced by a. The second one, formulated [Cu₂AlF₁₁]_∞^4— and named B, is bidimensional. It is constituted of distorted copper‐fluorine octahedra [CuF₆], linked by edges, which form infinite chains interconnected by three vertices of isolated [AlF₆] octahedra. The stacking sequence of the sheets is (A, B, B)_∞. The barium ions, 12‐coordinated, are inserted between the sheets. The crystal structure of Ba₃Cu₂Al₂F₁₆ is closely related to that of Ba₄Cu₂Al₃F₂₁. Only the proportion and the stacking sequence of the two kinds of sheets in the c‐direction differ, according to two different compositions and two different symmetries.