Ab initio molecular orbital calculations at the HF/6-31G* level of theory and density functional theory calculations at the B3LYP/6-31G* level have been carried out on methyl R-D-arabinofuranoside (1). All 10 possible envelope forms were constructed and minimized, providing a partial energy surface which identified 3 E as the lowest energy north conformer and, depending on the level of theory used, either 2 E or E 1 as the southern hemisphere minimum. The southern conformation was the global minimum regardless of the level of theory. The energy profile identifies pseudorotation through the eastern pathway as the most favorable. Pseudorotation through the west is higher in energy and similar to inversion through the planar species. The dependence of structural parameters (i.e., bond distances, bond angles, dihedral angles, and interatomic distances) on the ring conformation have been determined. Energy profiles based on additional electron correlation and extended basis sets with the HF/6-31G* geometries are presented and provide qualitatively similar results to the B3LYP/6-31G* profile.
The potential energy surface of methyl beta-D-arabinofuranoside (3) has been studied by ab initio molecular orbital (HF/6-31G) and density functional theory (B3LYP/6-31G) calculations via minimization of the 10 possible envelope conformers. The partial potential energy surface identified that the global minimum and lowest energy northern conformer was E(2). In the HF calculations, (2)E was the most stable southern conformer, while the density functional theory methods identified (4)E as the local minimum in this hemisphere. Additional calculations at higher levels of theory showed that the B3LYP-derived energies of many of the envelope conformers of 3 are dependent upon the basis set used. It has also been demonstrated that B3LYP/6-31+G//B3LYP/6-31G single point energies are essentially the same as those obtained from full geometry optimizations at the B3LYP/6-31+G level. The northern and southern minima of the B3LYP/6-31+G surface are, respectively, the E(2) and (2)E conformers. The B3LYP/6-31G geometries were used to study the relationship between ring conformation and various structural parameters including bond angles, dihedral angles, bond lengths, and interatomic distances.
Two approaches for identifying the minimum energy conformers of methyl R-D-arabinofuranoside 1, in the gas phase have been explored and compared. In the first approach (the constrained envelope method), 30 previously reported envelope geometries of 1 were allowed to fully optimize at the B3LYP/6-31G* level. B3LYP/6-31+G** single-point energies of these optimized structures were also determined, which led to the identification of the 3 T 4 and 2 T 1 ring conformers as the Northern (N) and Southern (S) minima, respectively, with the latter being the global minimum. The importance of intramolecular hydrogen bonding was probed by optimizing another set of 30 envelope geometries with initial geometries biased against the formation of these stabilizing interactions. These calculations led to the same two families of low-energy ring conformers ( 3 T 4 and 2 T 1 ); however, the N, and not the S, conformer was the global minimum without hydrogen bonding. The second approach involved the identification of conformers for 1 through the use of a Monte Carlo search coupled with molecular mechanics and then further optimization of these structures at higher levels of theory (HF/6-31G* and B3LYP/6-31G*). Subsequent B3LYP/6-31+G** single-point energy calculations afforded results that are similar to the constrained envelope method, but the stochastic approach led to more lowenergy conformers, and to a new global minimum. A comparison of these computational results with the experimentally determined solution conformation of 1 is also presented.
Compared to conventional bench-top instruments, microfluidic devices possess advantageous characteristics including great portability potential, reduced analysis time (minutes), and relatively inexpensive production, putting them on the forefront of modern analytical chemistry. Fabrication of these devices, however, often involves polymeric materials with less-than-ideal surface properties, specific instrumentation, and cumbersome fabrication procedures. In order to overcome such drawbacks, a new hybrid platform is proposed. The platform is centered on the use of 5 interconnecting microfluidic components that serve as the injector or reservoirs. These plastic units are interconnected using standard capillary tubing, enabling in-channel detection by a wide variety of standard techniques, including capacitively-coupled contactless conductivity detection (C4D). Due to the minimum impact on the separation efficiency, the plastic microfluidic components used for the experiments discussed herein were fabricated using an inexpensive engraving tool and standard Plexiglas. The presented approach (named 52-platform) offers a previously unseen versatility: enabling the assembly of the platform within minutes using capillary tubing that differs in length, diameter, or material. The advantages of the proposed design are demonstrated by performing the analysis of inorganic cations by capillary electrophoresis on soil samples from the Atacama Desert.
Polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) hybrid systems typically use complex protein-protein interactions to facilitate direct transfer of intermediates between these multimodular megaenzymes. In the canal-associated neurons (CANs) of Caenorhabditis elegans, PKS-1 and NRPS-1 produce the nemamides, the only known hybrid polyketide-nonribosomal peptides biosynthesized by animals, through a poorly understood mechanism. Here, we use genome editing and mass spectrometry to map the roles of individual PKS-1 and NRPS-1 enzymatic domains in nemamide biosynthesis. Furthermore, we show that nemamide biosynthesis requires at least five additional enzymes expressed in the CANs that are encoded by genes distributed across the worm genome. We identify the roles of these enzymes and discover a mechanism for trafficking intermediates between a PKS and an NRPS. Specifically, the enzyme PKAL-1 activates an advanced polyketide intermediate as an adenylate and directly loads it onto a carrier protein in NRPS-1. This trafficking mechanism provides a means by which a PKS-NRPS system can expand its biosynthetic potential and is likely important for the regulation of nemamide biosynthesis.
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