Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs.

Both nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations are routinely used in understanding the conformational space sampled by peptides in the solution state. To investigate the role of single-residue change in the ensemble of conformations sampled by a set of heptapeptides, AEVXEVG with X = L, F, A, or G, comprehensive NMR, and MD simulations were performed. The rationale for selecting the particular model peptides is based on the high variability in the occurrence of tri-peptide E*L between the transmembrane ß-barrel (TMB) than in globular proteins. The ensemble of conformations sampled by E*L was compared between the three sets of ensembles derived from NMR spectroscopy, MD simulations with explicit solvent, and the random coil conformations. In addition to the estimation of global determinants such as the radius of gyration of a large sample of structures, the ensembles were analyzed using principal component analysis (PCA). In general, the results suggest that the -EVL- peptide indeed adopts a conformational preference that is distinctly different not only from a random distribution but also from other peptides studied here. The relatively straightforward approach presented herein could help understand the conformational preferences of small peptides in the solution state.

Draft genome sequence of Nitrobacter vulgaris DSM 10236T.

Here, we report the draft genome sequence of Nitrobacter vulgaris DSM 10236T, a nitrite-oxidizing bacterium isolated from a sewage system in Hamburg, Germany. The genome is 4.3 Mb in size with 4,585 predicted genes, including the full complement of genes necessary for growth on nitrite (narK, nxrA, nxrB, nxrC, and nxrD).

Modulations in restricted amide rotation by steric induced conformational trapping.

The rotation around the amide bond in N,N-diethyl-m-toluamide (m-DEET) has been studied extensively and often used in laboratory instructions to demonstrate the phenomenon of chemical exchange. Herein, we show that a simple modification to N,N-diethyl-o-toluamide (o-DEET) significantly alters the dynamics of the restricted rotation around the amide bond due to steric interactions between the ring methyl group and the two N-ethyl groups. This alters the classic two-site exchange due to restricted rotation around the amide bond, to a three-site exchange, with the third conformation trapped at a higher-energy state compared to the other two. This often overlooked phenomenon is elucidated using variable-temperature NMR, two-dimensional exchange spectroscopy and molecular modeling studies.

Chloride Substitution Reactions of Cycloruthenated (R)(C)-(+)-N,N-Dimethyl(1-phenylethyl)amine with Pseudohalides: Ruthenium Atom Stereochemistry.

The diastereoselectivity of chloride substitution by the pseudohalides azide, nitrite, thiocyanate, and cyanate in has been determined by a combination of (1)H and (13)C{(1)H} NMR spectroscopy, UV-visible spectroscopy, circular dichroism, infrared spectroscopy, and single-crystal X-ray crystallography. These chloride substitution reactions proceed with predominant retention of configuration at ruthenium. For the ambidentate ligands thiocyanate and nitrite, the major bonding mode is through their nitrogen donor atoms.

Single-Crystal (31)P NMR and X-ray Diffraction Study of a Molybdenum Phosphine Complex: (5-Methyldibenzophosphole)pentacarbonylmolybdenum(0).

The molecular structure of (5-methyldibenzophosphole)pentacarbonylmolybdenum(0), 1, has been determined by X-ray crystallography. The crystal is monoclinic C2/c, Z = 8, with unit cell dimensions of: a = 31.113(2) Å, b =7.7917(5) Å, c = 17.9522(12) Å, and beta = 122.135(4) degrees. Least-squares refinement converged to R(F) = 0.0245 for 2407 independent reflections. The molecular structure is typical of phosphine-substituted metal carbonyls. It contains an approximate mirror plane which bisects the dibenzophosphole framework. Phosphorus-31 NMR spectra of powder and single-crystal samples of 1 have been obtained with cross-polarization and (1)H high-power decoupling. The (31)P CP/MAS NMR spectra exhibit exceptionally well-resolved satellites due to spin-spin coupling interactions with (95,97)Mo (I = (5)/(2)). Using first-order perturbation theory, the multiplets have been analyzed to yield (1)J((95,97)Mo,(31)P) = 123(2) Hz and estimates of the molybdenum nuclear quadrupolar coupling constants, chi((95)Mo) = -0.87 MHz and chi((97)Mo) = 10.1 MHz. Phosphorus-31 NMR spectra of a large single crystal of 1 have been investigated as a function of orientation about three orthogonal axes in the applied magnetic field. Analysis of the data yields the three principal components of the phosphorus chemical shift tensor, delta(11) = 112 ppm, delta(22) = -23 ppm, and delta(33) = -40 ppm; delta(22) lies close to the Mo-P bond (8 degrees ), while delta(11) lies in the approximate mirror plane. The phosphorus chemical shift tensor determined for 1 is compared with the limited anisotropic phosphorus shift data available in the literature.