Theory of the two step enantiomeric purification of 1,3 dimethylallene

An application of a recently proposed [P. Kral et al., Phys. Rev. Lett. 90, 033001 (2003)] two step optical control scenario to the purification of a racemic mixture of 1,3 dimethylallene is presented. Both steps combine adiabatic and diabatic passage phenomena. In the first step, three laser pulses of mutually perpendicular linear polarizations, applied in a "cyclic adiabatic passage" scheme, are shown to be able to distinguish between the L and D enantiomers due to their difference in matter-radiation phase. In the second step, which immediately follows the first, a sequence of pulses is used to convert one enantiomer to its mirror-imaged form. This scenario, which only negligibly populates the first excited electronic state, proves extremely useful for systems such as dimethylallene, which can suffer losses from dissociation and internal conversion upon electronic excitation. We computationally observe conversion of a racemic mixture of dimethylallene to a sample containing approximately 95% of the enantiomer of choice.     

A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains

PDZ domains are important scaffolding modules that typically bind to the C-termini of their interaction partners. Several structures of such complexes have been solved, revealing a conserved binding site in the PDZ domain and an extended conformation of the bound peptide. A compendium of information regarding PDZ complexes demonstrates that dissimilar C-terminal peptides bind to the same PDZ domain, and different PDZ domains can bind the same peptides. A detailed understanding of the PDZ-peptide recognition is needed to elucidate this complexity. To this end, we have designed a family of docking protocols for PDZ domains (termed PDZ-DocScheme) that is based on simulated annealing molecular dynamics and rotamer optimization, and is applicable to the docking of long peptides (20-40 rotatable bonds) to both known PDZ structures and to the more complicated problem of homology models of these domains. The resulting protocol reproduces the structures of PDZ complexes with peptides 4-8 amino acids long within 1-2 A from the experimental structure when the docking is performed to the original structure. If the structure of the target PDZ domain is an apo structure or a homology model, the docking protocol yields structures within 3 A in 9 out of 12 test cases. The automated docking procedure PDZ-DocScheme can serve in the generation of a structural context for validation of PDZ domain specificity from mutagenesis and ligand binding data.     

Stable Subnorms II

In this paper we continue our study of stability properties of subnorms on subsets of finite-dimensional, power-associative algebras over the real or the complex numbers.     

Living ring-opening metathesis polymerization of norbornenes bay-functionalized perylene diimides

Ring-opening metathesis polymerization (ROMP)-derived poly(oxanorbornene imide)s bearing bay-linked mono - alkoxy -M1 and 1,7-di-alkoxy M2 functionalized perylene diimides (PDIs) were synthesized using Grubb's third ( G3 ) and Hoveyda-Grubbs second generation ( HG2 ) ruthenium-alkylidene metathesis initiators. The mono-alkoxy-derived PDI-based non-ladderphane polymer poly M1 displayed 67% to 77% of the trans olefin content in the polymer chain depending on the initiator used for the polymerization. When using the symmetrical 1,7-di-alkoxy-derived PDI-based polymer poly M2 having the ladderphane type-structure, this displayed a significant amount of cis and trans olefin contents in the polymer chains, irrespective of the type of initiators used for the polymerization. ROMP of both monomers M1 and M2 proceeded in a well-controlled manner with a linear dependence of molecular weight on the monomer/initiator ratio using G3 as initiator. Optical properties of the ladderphane-based poly M2 and non-ladderphane-based poly M1 were characterized in both solution and the film state. X-ray diffraction (XRD) analysis for all the polymers showed significant π-stacking in the thin film state with ordered molecular packing and closer values of d-spacing for both poly M1 and poly M2 . Film morphology examined by AFM elucidated homogenous smooth polymer surface for both polymers in general, but with some irregularities observed for poly M1 . In addition, CV analysis revealed both polymers could be good candidates as electron-accepting materials, with excellent film-forming ability, and thermal stability.     

Three‐Component Self‐Assembly of a Series of Triply Interlocked Pd12 Coordination Prisms and Their Non‐Interlocked Pd6 Analogues

Template‐assisted formation of multicomponent Pd₆ coordination prisms and formation of their self‐templated triply interlocked Pd₁₂ analogues in the absence of an external template have been established in a single step through Pd? N/Pd? O coordination. Treatment of cis‐[Pd(en)(NO₃)₂] with K₃tma and linear pillar 4,4′‐bpy (en=ethylenediamine, H₃tma=benzene‐1,3,5‐tricarboxylic acid, 4,4′‐bpy=4,4′‐bipyridine) gave intercalated coordination cage [{Pd(en)}₆(bpy)₃(tma)₂]₂[NO₃]₁₂ ( 1 ) exclusively, whereas the same reaction in the presence of H₃tma as an aromatic guest gave a H₃tma‐encapsulating non‐interlocked discrete Pd₆ molecular prism [{Pd(en)}₆(bpy)₃(tma)₂(H₃tma)₂][NO₃]₆ ( 2 ). Though the same reaction using cis‐[Pd(NO₃)₂(pn)] (pn=propane‐1,2‐diamine) instead of cis‐[Pd(en)(NO₃)₂] gave triply interlocked coordination cage [{Pd(pn)}₆(bpy)₃(tma)₂]₂[NO₃]₁₂ ( 3 ) along with non‐interlocked Pd₆ analogue [{Pd(pn)}₆(bpy)₃(tma)₂](NO₃)₆ ( 3′ ), and the presence of H₃tma as a guest gave H₃tma‐encapsulating molecular prism [{Pd(pn)}₆(bpy)₃(tma)₂(H₃tma)₂][NO₃]₆ ( 4 ) exclusively. In solution, the amount of 3′ decreases as the temperature is decreased, and in the solid state 3 is the sole product. Notably, an analogous reaction using the relatively short pillar pz (pz=pyrazine) instead of 4,4′‐bpy gave triply interlocked coordination cage [{Pd(pn)}₆(pz)₃(tma)₂]₂[NO₃]₁₂ ( 5 ) as the single product. Interestingly, the same reaction using slightly more bulky cis‐[Pd(NO₃)₂(tmen)] (tmen=N,N,N′,N′‐tetramethylethylene diamine) instead of cis‐[Pd(NO₃)₂(pn)] gave non‐interlocked [{Pd(tmen)}₆(pz)₃(tma)₂][NO₃]₆ ( 6 ) exclusively. Complexes 1 , 3 , and 5 represent the first examples of template‐free triply interlocked molecular prisms obtained through multicomponent self‐assembly. Formation of the complexes was supported by IR and multinuclear NMR (¹H and ¹³C) spectroscopy. Formation of guest‐encapsulating complexes ( 2 and 4 ) was confirmed by 2D DOSY and ROESY NMR spectroscopic analyses, whereas for complexes 1 , 3 , 5 , and 6 single‐crystal X‐ray diffraction techniques unambiguously confirmed their formation. The gross geometries of H₃tma‐encapsulating complexes 2 and 4 were obtained by universal force field (UFF) simulations.     

Solvent-Free Condensation of Methyl Pyridinium and Quinolinium Salts with Aldehydes Catalyzed by DBU

Methylpyridinium and methylquinolinium salts were condensed under solvent-free conditions with aromatic aldehydes in the presence of 1,8-diazabicyclo[5.4.]undec-7-ene (DBU) as catalyst, by grinding at room temperature. The products are dyes or useful intermediates. The DBU can be easily recycled and reused.     

Lyotropic Liquid Crystal to Soft Mesocrystal Transformation in Hydrated Salt–Surfactant Mixtures

Hydrated CaCl₂, LiI, and MgCl₂ salts induce self‐assembly in nonionic surfactants (such as C₁₂H₂₅(OCH₂CH₂)₁₀OH) to form lyotropic liquid‐crystalline (LLC) mesophases that undergo a phase transition to a new type of soft mesocrystal (SMC) under ambient conditions. The SMC samples can be obtained by aging the LLC samples, which were prepared as thin films by spin‐coating, dip‐coating, or drop‐casting of a clear homogenized solution of water, salt, and surfactant over a substrate surface. The LLC mesophase exists up to a salt/surfactant mole ratio of 8, 10, and 4 (corresponding to 59, 68, and 40 wt % salt/surfactant) in the CaCl₂, LiI, and MgCl₂ mesophases, respectively. The SMC phase can transform back to a LLC mesophase at a higher relative humidity. The phase transformations have been monitored using powder X‐ray diffraction (PXRD), polarized optical microscopy (POM), and FTIR techniques. The LLC mesophases only diffract at small angles, but the SMCs diffract at both small and wide angles. The broad surfactant features in the FTIR spectra of the LLC mesophases become sharp and well resolved upon SMC formation. The unit cell of the mesophases expands upon SMC transformation, in which the expansion is largest in the MgCl₂ and smallest in the CaCl₂ systems. The POM images of the SMCs display birefringent textures with well‐defined edges, similar to crystals. However, the surface of the crystals is highly patterned, like buckling patterns, which indicates that these crystals are quite soft. This unusual phase behavior could be beneficial in designing new soft materials in the fields of phase‐changing materials and mesostructured materials, and it demonstrates the richness of the phase behavior in the salt–surfactant mesophases.