Kernel energy method: Basis functions and quantum methods

The kernel energy method (KEM) has been illustrated with peptides and has been shown to reduce the computational difficulty associated with obtaining ab initio quality quantum chemistry results for large biological compounds. In a recent paper, the method was illustrated by application to 15 different peptides, ranging in size from 4 to 19 amino acid residues, and was found to deliver accurate Hartree–Fock (HF) molecular energies within the model, using Slater‐type orbital (STO)‐3G basis functions. A question arises concerning whether the results obtained from the use of KEM are wholly dependent on the STO‐3G basis functions that were employed, because of their relative simplicity, in the first applications. In the present work, it is shown that the accuracy of KEM does not depend on a particular choice of basis functions. This is done by calculating the ground‐state energy of a representative peptide, ADPGV7B, containing seven amino acid residues, using seven different commonly employed basis function sets, ranging in size from small to medium to large. It is shown that the accuracy of the KEM does not vary in any systematic way with the size or mathematical completeness of the basis set used, and good accuracy is maintained over the entire variety of basis sets that have been tested. Both approximate HF and density functional theory (DFT) calculations are made. We conclude that the accuracy inherent in the KEM is not dependent on a particular choice of basis functions. The first application, to 15 different peptides mentioned above, employed only HF calculations. A second question that arises is whether the results obtained with the use of KEM will be accurate only within the HF approximation. Therefore, in the present work we also study whether KEM is applicable across a variety of quantum computational methods, characterized by differing levels of accuracy. The peptide, Zaib4, containing 74 atoms, was used to calculate its energy at seven different levels of accuracy. These include the semi‐empirical methods, AM1 and PM5, a DFT B3LYP model, and ab initio HF, MP2, CID, and CCSD calculations. KEM was found to be widely applicable across the spectrum of quantum methods tested. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Chemo- and Regioselective Additions of Nucleophiles to Cyclic Carbonates for the Preparation of Self-Blowing Non-Isocyanate Polyurethane Foams

Polyurethane (PU) foams are indisputably daily essential materials found in many applications, notably for comfort (for example, matrasses) or energy saving (for example, thermal insulation). Today, greener routes for their production are intensively searched for to avoid the use of toxic isocyanates. An easily scalable process for the simple construction of self-blown isocyanate-free PU foams by exploiting the organocatalyzed chemo- and regioselective additions of amines and thiols to easily accessible cyclic carbonates is described. These reactions are first validated on model compounds and rationalized by DFT calculations. Various foams are then prepared and characterized in terms of morphology and mechanical properties, and the scope of the process is illustrated by modulating the composition of the reactive formulation. With impressive diversity and accessibility of the main components of the formulations, this new robust and solvent-free process could open avenues for construction of more sustainable PU foams, and offers the first realistic alternative to the traditional isocyanate route.     

Room‐Temperature Decarboxylative Alkynylation of Carboxylic Acids Using Photoredox Catalysis and EBX Reagents

Alkynes are used as building blocks in synthetic and medicinal chemistry, chemical biology, and materials science. Therefore, efficient methods for their synthesis are the subject of intensive research. Herein, we report the direct synthesis of alkynes from readily available carboxylic acids at room temperature under visible‐light irradiation. The combination of an iridium photocatalyst with ethynylbenziodoxolone (EBX) reagents allowed the decarboxylative alkynylation of carboxylic acids in good yields under mild conditions. The method could be applied to silyl‐, aryl‐, and alkyl‐ substituted alkynes. It was particularly successful in the case of α‐amino and α‐oxo acids derived from biomass.     

Concerted Ring Opening and Cycloaddition of Chiral Epoxy Enolsilanes with Dienes

Silyl‐triflate‐catalyzed (4+3) cycloadditions of epoxy enolsilanes with dienes provide a mild and chemoselective synthetic route to seven‐membered carbocycles. Epoxy enolsilanes containing a terminal enolsilane and a single stereocenter undergo cycloaddition with almost complete conservation of enantiomeric purity, a finding that argues against the involvement of oxyallyl cation intermediates which have been previously proposed for these types of reactions. Reported are theoretical and experimental investigations of the cycloaddition mechanism. The major enantiomers of the cycloadducts are derived from S_N2‐like reactions of the silylated epoxide with the diene, in which stereospecific ring opening and formation of the two new C? C bonds occur in a single step. Calculations predict, and experiments confirm, that the observed small losses of enantiomeric purity are traced to a triflate‐mediated double S_N2 cycloaddition pathway.     

Solid phase extraction of DNA from biological samples in a post-based, high surface area poly(methyl methacrylate) (PMMA) microdevice

This work describes the performance of poly(methyl methacrylate) (PMMA) microfluidic DNA purification devices with embedded microfabricated posts, functionalized with chitosan. PMMA is attractive as a substrate for creating high surface area (SA) posts for DNA capture because X-ray lithography can be exploited for extremely reproducible fabrication of high SA structures. However, this advantage is offset by the delicate nature of the posts when attempting bonding to create a closed system, and by the challenge of functionalizing the PMMA surface with a group that invokes DNA binding. Methods are described for covalent functionalization of the post surfaces with chitosan that binds DNA in a pH-dependent manner, as well as for bonding methods that avoid damaging the underlying post structure. A number of geometric posts designs are explored, with the goal of identifying post structures that provide the requisite surface area without a concurrent rise in fluidic resistance that promotes device failure. Initial proof-of-principle is shown by recovery of prepurified human genomic DNA (hgDNA), with real-world utility illustrated by purifying hgDNA from whole blood and demonstrating it to be PCR-amplifiable.     

Electrospinning of a functional perfluorinated block copolymer as a powerful route for imparting superhydrophobicity and corrosion resistance to aluminum substrates

Superhydrophobic aluminum surfaces with excellent corrosion resistance were successfully prepared by electrospinning of a novel fluorinated diblock copolymer solution. Micro- and nanostructuration of the diblock copolymer coating was obtained by electrospinning which proved to be an easy and cheap electrospinning technology to fabricate superhydrophobic coating. The diblock copolymer is made of poly(heptadecafluorodecylacrylate-co-acrylic acid) (PFDA-co-AA) random copolymer as the first block and polyacrylonitrile (PAN) as the second one. The fluorinated block promotes hydrophobicity to the surface by reducing the surface tension, while its carboxylic acid functions anchor the polymer film onto the aluminum surface after annealing at 130 °C. The PAN block of this copolymer insures the stability of the structuration of the surface during annealing, thanks to the infusible character of PAN. It is also demonstrated that the so-formed superhydrophobic coating shows good adhesion to aluminum surfaces, resulting in excellent corrosion resistance.     

Single‐walled Carbon Nanotube Strings for Biosensor Development

Strings of single‐walled carbon nanotubes (SWCNT) were prepared using an aqueous dispersion of gellan gum wrapped nanotubes and crosslinked using Ca²⁺ ions. Various formulations were evaluated to determine the parameters for successful string formation; these included 8–12 % nanotube by weight, 60–70 % gellan gum, and 20–30 % KCl. Strings showed electrical conductivity when dried between ITO electrodes. Conductivity variations were observed and potential sources of the variation identified. Proteins were attached to the carbon nanotube strings with peroxidase enzymatic activity detected following horseradish peroxidase attachment. This work provides a basis for development of electronic biosensors based on these carbon nanotube strings.     

Single nucleotide polymorphism detection in the hMSH2 gene using conformation-sensitive CE

CE allows for highly reproducible analysis of DNA fragments which can be used to detect DNA mutations including SNPs. We have utilized a simple and direct CE analysis method for SNP analysis called conformation-sensitive CE (CSCE), based on the principle of single nucleotide different to produce conformational changes in the mildly denaturing solvent system. This method was applied to analysis of a mutation in the promoter region of the hMSH2 gene. This gene belongs to the human DNA mismatch repair system, which is responsible for recognizing and repairing mispaired nucleotides, and mutations in the hMSH2 gene are known to cause hereditary nonpolyposis colorectal cancer (HNPCC). PCR fragments generated from the promoter region of the hMSH2 gene, displaying either a C/C homozygote, C/T heterozygote, or T/T homozygote genotype, did not require further pretreatment before electrokinetic injection. The CE separation, using a 1xTris-borate-EDTA (TBE) buffer containing 3% w/v hydroxylethyl cellulose (HEC) and 6 M urea, was performed under reverse polarity with a separation temperature of 15 degrees C. The genotypes of 204 healthy volunteers and 13 colorectal cancer patients were determined using CSCE, and the results confirmed by DNA sequencing. While the CSCE separations were shown to be highly reproducible and sensitive for screening large populations, no correlation was observed between cancer patients and this hMSH2 gene polymorphism.     

The molecular basis of pharmacological chaperoning in human α-galactosidase

Fabry disease patients show a deficiency in the activity of the lysosomal enzyme α-galactosidase (α-GAL or α-Gal A). One proposed treatment for Fabry disease is pharmacological chaperone therapy, where a small molecule stabilizes the α-GAL protein, leading to increased enzymatic activity. Using enzyme kinetics, tryptophan fluorescence, circular dichroism, and proteolysis assays, we show that the pharmacological chaperones 1-deoxygalactonojirimycin (DGJ) and galactose stabilize the human α-GAL glycoprotein. Crystal structures of complexes of α-GAL and chaperones explain the molecular basis for the higher potency of DGJ over galactose. Using site-directed mutagenesis, we show the higher potency of DGJ results from an ionic interaction with D170. We propose that protonation of D170 in acidic conditions leads to weaker binding of DGJ. The results establish a biochemical basis for pharmacological chaperone therapy applicable to other protein misfolding diseases.     

Copolymer nanosphere encapsulated CdS quantum dots prepared by RAFT copolymerization: synthesis,characterization and mechanism of formation

Cadmium sulfide (CdS) quantum dots (QDs) encapsulated in block copolymer spheres were synthesized by an aqueous emulsion polymerization process. First, stable dispersions of CdS QDs in water were prepared using a polymer dispersant, either poly(acrylic acid) or a random copolymer having an average of ten acrylic acid and five butyl acrylate units. These polymer dispersants were prepared by reversible addition-fragmentation chain transfer polymerization. Then, the CdS QDs dispersed in water were encapsulated in a polystyrene shell using an emulsion polymerization process. Spectroscopic and microscopic techniques were used to characterize the resulting nanocomposites. Optical properties of QDs in polymer microspheres were investigated by UV-vis and fluorescence spectroscopic studies. Particle sizes of all CdS QD samples were calculated from absorption edges using Henglein's empirical curve. Transmission electron microscopy was used to determine the size and morphology of CdS QD samples. These observations were used to elucidate the mechanism of formation of the resulting well-defined polymer-encapsulated CdS nanoparticles.