Identification of novel macrocyclic peptidase substrates via on-bead enzymatic cyclization

Peptidase-catalyzed formation of macrocyclic lactams on solid phase identifies ring systems that are favorably bound in the enzyme active site. We evaluated several cyclic peptide motifs linked by ester bonds between the P2 and P1' or the P1 and P2' side chains. The depsipeptide represented by structure 5 was readily generated by a variety of peptidases from precursor omega-amino acids or omega-amino esters. This strategy for identifying ring systems for potential macrocyclic transition state analogues was demonstrated with the serine peptidases trypsin and chymotrypsin, with the aspartic peptidase pepsin, and with the zinc peptidase thermolysin.     

An in situ atomic force microscopy study of uric acid crystal growth

Kidney stones are heterogeneous polycrystalline aggregates that can consist of several different building blocks. A significant number of human stones contain uric acid crystals as a crystalline component, though the molecular-level growth of this important biomaterial has not been previously well-characterized. In the present study, in situ atomic force microscopy (AFM) is used to investigate the real-time growth on the (100) surface of uric acid (UA) single crystals as a function of fundamental solution parameters. Layer-by-layer growth on UA (100) was found to be initiated at screw dislocation sites and to proceed via highly anisotropic rates which depend on the crystallographic direction. The smallest b-steps exhibited minimum heights corresponding to two molecular layers, while fast-moving c-steps more commonly showed monolayer heights. Growth kinetics measured under a range of flow rates, supersaturation levels, and pH values reveal linear trends in the growth kinetics, with faster growth attained in solutions with higher supersaturation and/or pH. The calculated kinetic parameters for UA growth derived from these experiments are in good agreement with the values reported for other crystal systems.     

A simple and efficient one step synthesis of benzoxazoles and benzimidazoles from carboxylic acids

Benzoxazoles or benzimidazoles can be rapidly and efficiently synthesized from a variety of carboxylic acids with 2-aminophenols or 1,2-phenylenediamines in one simple step, respectively. The use of commercially available PS-PPh₃ resin combined with microwave heating delivered a variety of benzoxazoles and benzimidazoles in high yields and purities.     

Microfabrication of three-dimensional bioelectronic architectures

The functionality and structural diversity of biological macromolecules has motivated efforts to exploit proteins and DNA as templates for synthesis of electronic architectures. Although such materials offer promise for numerous applications in the fabrication of cellular interfaces, biosensors, and nanoelectronics, identification of techniques for positioning and ordering bioelectronic components into useful patterns capable of sophisticated function has presented a major challenge. Here, we describe the fabrication of electronic materials using biomolecular scaffolds that can be constructed with precisely defined topographies. In this approach, a tightly focused pulsed laser beam capable of promoting protein photo-cross-linking in specified femtoliter volume elements is scanned within a protein solution, creating biomolecular matrices that either remain in integral contact with a support surface or extend as free-standing structures through solution, tethered at their ends. Once fabricated, specific protein scaffolds can be selectively metallized via targeted deposition and growth of metal nanoparticles, yielding high-conductivity bioelectronic materials. This aqueous fabrication strategy opens new opportunities for creating electronic materials in chemically sensitive environments and may offer a general approach for creating microscopically defined inorganic landscapes.     

Methyl abstraction kinetics of CpFe(CO)2Me using the benzyl radical clock

The rate constant for the methyl abstraction reaction of CpFe(CO)₂Me has been measured with the benzyl radical clock as (1.1 ± 0.2) × 10⁵ M⁻¹ s⁻¹ at room temperature. Time-resolved Fourier-transform Infrared (FTIR) absorption spectroscopy pointed towards the formation of the CpFe(CO)₂ radical upon benzyl abstraction. The main stable product has been established by a linear scan of the reaction mixture as Cp₂Fe₂(CO)₄ produced by the dimerization of the CpFe(CO)₂ radicals. The transition state structure for the abstraction process was also found at UB3LYP/6-311+G* level of theory to contain a planar CH₃ group.     

Comparison of the electrophilic and free-radical addition of halogens with hexafluoro-1,3-butadiene and 1,3-butadiene

Ionic and photochemical reaction of chlorine (Cl₂), bromine (Br₂) and iodine monochloride (ICl) to hexafluoro-1,3-butadiene (1) and 1,3-butadiene (2) were carried out under conditions that would provide product distributions under controlled ionic or free-radical conditions. Product distributions for ionic reaction of Cl₂ and Br₂ with 1 are similar and suggest a weakly-bridged halonium ion species. Theoretical calculations support weakly-bridged chloronium and bromonium ions for both dienes 1 and 2. There are more of the 1,4-dihalo-2-butene products from ionic halogenation of 1 than 2 which correlates with the greater charge density on carbon-4 of halonium ions from 1. Ionic and free-radical reactions of ICl with 1 give 8 and 2% of 3-chloro-4-iodohexafluoro-1-butene and 4-chloro-3-iodohexafluoro-1-butene, respectively. The minor cis-1,4-dihalo-2-butene products from 1 and 2 are reported when formed.     

Conjugate addition of (trimethylstannyl)copper reagents to α,β-acetylenic N,N-dimethylamides. Trapping of the intermediates with electrophiles

A study of the reaction of Me₃SnCu·.Me₂S (1) and [Me₃SnCuSPh]Li (2) with α,β - acetylenic N,N-dimethylamides 3 shows (a) that the overall process can be controlled experimentally so as to produce either N,N-dimethyl ($\text{E}$)-(4) or ($\text{Z}$)-3-trimethylstannyl-2-alkenamides (5), (b) that the initially formed intermediate derived from interaction of 2 and 3 is significantly more stable than that obtained by reaction of 2 and α,β-acetylenic esters, and (c) that the intermediate produced by treating 3 with 1 can be trapped with electrophiles other than proton.     

Transferable atom equivalent multicentered multipole expansion method

The transferability of atomic and functional group properties is an implicit concept in chemistry. The work presented here describes the use of Transferable Atom Equivalents (TAE) to represent molecular electrostatic potential fields through the use of integrated atomic multipole moments that are associated with each TAE atom type used in the reconstruction. TAE molecular surface distributions of electrostatic potentials are compared with analytical ab initio and empirical (Gasteiger) partial charge reference models for several conformations of test peptides. Surface electrostatic potential distributions computed using TAE multipole representations were found to converge at the octopole level, with incremental improvement observed when hexadecapoles were included. Molecular electrostatic potential fields that were produced using the TAE method were observed to be responsive to conformational changes and to compare well with ab initio reference distributions. Generation of TAE atom types and their associated multipoles does not involve fitting to sample electrostatic potential fields, but rather utilizes integrated AIM atomic electron density distributions within representative chemical environments. The RECON program was used for TAE reconstruction. RECON is capable of processing 5,000 drug-sized molecules or 25 proteins per minute per 1.7 GHz P4 Linux processor.     

Diaquabis(1,3‐propanediamine‐κ2N,N′)nickel(II) bis(sulfanilate)

The title compound, [Ni(C₃H₁₀N₂)₂(H₂O)₂](C₆H₆NO₃S)₂, contains alternating layers of sulfanilate anions and di­aqua­bis(1,3‐propane­di­amine)­nickel(II) cations. The Ni atom lies on an inversion centre and is hexacoordinated by the 1,3‐propane­di­amine ligands, which function as N,N′‐bidentate ligands, and the water mol­ecules, which are in a trans arrangement. The sulfanilate anions are arranged in layers, with the sulfonate and amine groups directed towards opposite sides of the layer. The structure is stabilized by a network of hydrogen bonding between the O and N atoms of the sulfanilate anions, the water mol­ecules, and the N atoms of the 1,3‐propane­di­amine ligands.     

Field gradient electrophoresis

The class of equilibrium gradient methods utilizes the opposition of two forces, at least one of which changes in magnitude with position, to separate and concentrate analytes. The drawback of many methods of this type is that the production of two opposing forces requires in comparison to standard methods, such as capillary electrophoresis, a relatively complex apparatus. In addition, for techniques such as electric field gradient focusing, hydrodynamic flow leads to Taylor dispersion, which limits the attainable concentration factor. We propose a new method, gradient field electrophoresis, which achieves analyte separation and focusing with only one spatially varying force, an electric field gradient. A model for the method is developed and used to analyze peak capacity. Experimental results for a protein (R-phycoerythrin) are given and compared to the model.