TBADH activity in water-miscible organic solvents: correlations between enzyme performance, enantioselectivity and protein structure through spectroscopic studies

The enantioselective reduction of 2-pentanone to (R)- and (S)-2-pentanol by Thermoanaerobacter (formerly Thermoanaerobium) brockii alcohol dehydrogenase (TBADH) in mixtures of water and water-miscible organic solvents was investigated. Significant enzymatic activity was retained in up to 87% methanol, ethanol and acetonitrile. The changes in enzyme activity as a function of organic solvent were correlated to structural alterations of TBADH with a series of spectroscopic studies (fluorescence, fluorescence quenching and circular dichroism (CD)). Interestingly, this study shows that the tetrameric form of TBADH is not critical for catalytic performance.     

Call for Papers: GRC, CADD, and statistics, and all that

Molecular modeling and the art of computer-aided drug discovery seldom make much use of statistics, despite being fields that can not calculate important properties with great reliability. The 2013 CADD Gordon conference intends to examine what prevents a more effective use of statistics in routine modeling and to raise consciousness as to what is possible. Practical methods will be discussed, deeper issues in applying standard approaches addressed and research on successes and failures in other disciplines presented by invited experts.     

Orientation and conformation of two [6]carbohelicenes in stretched polystyrene and a thermoresponsive polyaspartate

Two functionalized [6]carbohelicenes, one of which was also available in its two enantiomeric pure forms, were oriented in stretched polystyrene in CDCl₃, and in a recently introduced chiral thermoresponsive lyotropic polyaspartate (poly(benzyl)_0.5(phenethyl)_0.5-L-aspartate) in C₂D₂Cl₄. From the resulting ¹H,¹³C residual dipolar couplings, the helical pitch of a methylated [6]carbohelicene was determined and found to be in agreement with theoretical predictions and existing crystal structures (d(C2,C2′) ≈ 4.3 Å). For a second [6]carbohelicene with para-methoxyphenyl substituents, a clear conformational preference of the substituents was observed. The orientational properties of the two helicene enantiomers in the chiral polyaspartate are very similar, but both drastically change around 306 K. We suggest this behavior is due to an unusual phase transition in the liquid crystal.     

Synergistic Peptide and Gold Catalysis: Enantioselective Addition of Branched Aldehydes to Allenamides

The combination of a peptide catalyst and a gold catalyst is presented for enantioselective addition reactions between branched aldehydes and allenamides. The two catalysts act in concert to provide γ,δ-enamide aldehydes bearing a fully substituted, benzylic stereogenic center – a structural motif common in many natural products and therapeutically active compounds – with good yields and enantioselectivities. The reaction tolerates a variety of alkyl and alkoxy substituted aldehydes and the products can be elaborated into several chiral building blocks bearing either 1,4- or 1,5- functional group relationships. Mechanistic studies showed that the conformational features of the peptide are important for both the catalytic efficiency and stereochemistry, while a balance of acid/base additives is key for ensuring formation of the desired product over undesired side reactions.     

Efficient calculation of SAMPL4 hydration free energies using OMEGA,SZYBKI, QUACPAC,and Zap TK

Several submissions for the SAMPL4 hydration free energy set were calculated using OpenEye tools, including many that were among the top performing submissions. All of our best submissions used AM1BCC charges and Poisson–Boltzmann solvation. Three submissions used a single conformer for calculating the hydration free energy and all performed very well with mean unsigned errors ranging from 0.94 to 1.08 kcal/mol. These calculations were very fast, only requiring 0.5–2.0 s per molecule. We observed that our two single-conformer methodologies have different types of failure cases and that these differences could be exploited for determining when the methods are likely to have substantial errors.     

A rapid boundary perturbation algorithm for scattering by families of rough surfaces

In this paper we describe a novel algorithm for the computation of scattering returns by families of rough surfaces. This algorithm makes explicit use of the fact that some scattering profiles of engineering interest (e.g., traveling ocean waves) come in branches parameterized analytically by a bifurcation quantity. Our approach delivers recursions which not only can be implemented to yield a rapid, robust and high-order numerical scheme, but also give a new proof of analyticity of scattering quantities with respect to the bifurcation parameter of the surface family. The real advantage of this new approach is that it computes, in one step, the scattered field for all possible members of the family of surfaces. By contrast, other state-of-the-art schemes must restart when the returns from a new surface are desired, so that the cost of our new approach is greatly advantaged when the number of samples of the family reaches even modest values. Numerical results which verify the accuracy of our approach and demonstrate their utility in computing grating efficiencies scattered by traveling surface ocean waves are presented.     

Metabolic profiling of rodent biological fluids via 1H NMR spectroscopy using a 1 mm microlitre probe

The application of a 1 mm TXI (1H/13C/15N) microlitre NMR probe with z-gradient for metabolic profiling of biofluids is described. The probe was used to provide spectral profiles for rat blood plasma using only approximately 2 microl of fluid with a range of solvent suppression techniques. Using a similar amount of fluid, spectra were obtained from rat and mouse cerebrospinal fluid, demonstrating that the probe could be used to profile rodents metabolically via biofluids previously inaccessible to NMR analysis without the need for termination.     

Controlling the size and alignment of ZnO microrods using ZnO thin film templates deposited by pulsed laser ablation

The production of dense arrays of well aligned ZnO nano- and microrods with a controllable distribution of diameters is demonstrated. The rods were grown using a hydrothermal method, on pre-deposited ZnO thin films exhibiting a range of different grain sizes. These template ZnO thin films were deposited by pulsed laser ablation, at 193 nm, in a low background pressure of O₂; average grain sizes ranged from 10 nm (room temperature deposition) to 50 nm when deposited at a substrate temperature (T_sub) of 500 °C. The morphology of the ZnO microrod arrays grown onto these ZnO thin films was found to depend on the T_sub used during film deposition. Increasing T_sub resulted in a lower density of larger nanorods, with a more pronounced [0001] alignment. The diameters of the rods produced are typically an order of magnitude greater than the grain size of the template ZnO film. Thus the rods cannot be a direct continuation of the grain structure of the template films. Rather, we suggest that the rod diameter is controlled by the density of sites at which the initial nucleation occurs, which is expected to be higher on the smaller grain size films deposited at lower temperatures. The factor controlling the final size of the rods is thus the available free space into which they can grow, which is smaller at the higher nucleation densities. The increased extent of [0001] texturing of the thin film templates deposited at higher T_sub is proposed as the reason for the improved [0001] alignment of rods grown on these templates. PACS 81.07.De; 81.10.Dn; 52.38.Mf     

Enantioselective synthetic thalidomide receptors based upon DNA binding motifs

A series of molecularly imprinted polymer (MIP) synthetic receptors selective for the sedative thalidomide (5) have been designed and synthesized based upon the functional monomer 9-(2'-methacryloyloxyethyl)adenine (2). (1)H-NMR studies were used to establish the existence of DNA-like binding interactions between 2 and the template (5). A series of ethylene glycol dimethacrylate cross-linked copolymers was synthesized using either 2 or methacrylic acid, or a combination of these functional monomers. Zonal HPLC studies demonstrated enantioselectivity (alpha = 2.11) and ligand selectivity which could be attributed to the interaction of 2 with the imide moiety of 5. Compound 2 provided a more significant contribution to the binding of 5 than methacrylic acid, though a combination of these two functional monomers resulted in improved enantioselectivity. Frontal chromatographic and batch binding studies confirmed the observed differences in affinity of the imprinted and reference polymers for the template.