Localized molecular orbital studies of transition metal complexes. II: Simple π-accepting ligands

Localized molecular orbitals (LMOs) for several octahedral complexes are presented. Wavefunctions are calculated within the PRDDO approximations and localized by the Boys criterion. Complexes of general formula (NH₃)_x(CO)_6-xM, M = Cr⁰ or Mn⁺ and x = 1, 2, or 3 illustrate the general trends for carbonyl complexes. Weak to moderate π-bonding results in three equivalent inner shell LMOs dominantly of metal 3s, 3p and 3d character but highly delocalized to the carbonyls. These three LMOs flank the M-CO bond axis. Other π back-bonding situations result in metal-ligand double bonds which are nonequivalent and have σ-π separability [(NH₃)₅(py)Mn⁺] and also equivalent double bonds [(NH₃)₅(NO)Cr⁺].     

An ab initio study of the geometries and rotational barriers of 1-, 2-, and 5-phenylimidazole

The torsional barrier was calculated in the 3-21G basis set for 1-, 2-, and 5-phenylimidazole. Full geometry optimization was carried out at inter-ring torsional angles of 0°, 30°, 60°, 90°, 120°, 150°, 180°, and additional intermediate angles. All torsional potential energies were found to be symmetric with respect to the 90° conformation. The 2-phenylimidazole torsional energy exhibits a minimum at 0° (and 180°) and a maximum at 90° with a barrier height of 5.83 kcal/mol relative to the 0° conformation. The minima in the 1- and 5-phenylimidazole torsional potential energies correspond to non-planar conformations, resulting in a double-well potential with maxima at 0° (180°) and 90°. The 1-phenylimidazole minima are located at 46.5 and 133.5°; the 5-phenylimidazole minima, at 35.3 and 144.7°. In the 0° (180°) and 90° conformations, 1-phenylimidazole exhibits torsional barriers of 1.84 and 0.75 kcal/mol, respectively, relative to the energy of the 46.5° conformation. For 5-phenylimidazole, these barriers are 0.94 and 1.89 kcal/mol, relative to the energy of the 35.3° conformation. The energy of 5-phenylimidazole in the 35.3° conformation corresponds to a relative tautomeric energy difference of 1.80 kcal/mol compared to the 0° conformer of the 4-phenylimidazole tautomer.     

Extension of AOAC official method 999.14 (choline in infant formula and milk) to the determination of choline in dietary supplements

AOAC Official Method 999.14 is applicable for the determination of choline in milk and infant formulas. To date, its use has not been extended beyond these matrixes. We modified Official Method 999.14 and applied it to the determination of choline in a range of choline-containing dietary supplements. Dietary supplement tablets, capsules, wafers, softgels, liquid products, and drink powders were included. We found that the standard curve could be extended to cover a wider range of choline concentrations and defined a procedure for the use of Norit for samples in which the vitamin C content was high enough to interfere with the analysis. Recoveries of choline added to infant formula powders and to representative dietary supplement tablets, capsules, powdered drink mix, and wafer products were 85-114%. The use of Norit during the procedure did not affect the recovery of choline added to infant formula powders or to dietary supplements. An alkaline digestion was included for use with a product containing lecithin as the sole source of choline. Ten of 11 dietary supplement products analyzed by the modified method contained amounts of choline at or above declarations found on the product labels. The remaining product contained about 40% of the label-declared amount of choline.     

Phase behavior in model homopolymer/CO2 and surfactant/CO2 systems: discontinuous molecular dynamics simulations

Discontinuous molecular dynamics simulations are performed on surfactant (HmTn)/solvent systems modeled as a mixture of single-sphere solvent molecules and freely jointed surfactant chains composed of m slightly solvent-philic head spheres (H) and n solvent-philic tail spheres (T), all of the same size. We use a square-well potential to account for the head-head, head-solvent, tail-tail, and tail-solvent interactions and a hard-sphere potential for the head-tail and solvent-solvent interactions. We first simulate homopolymer/supercritical CO2 (scCO2) systems to establish the appropriate interaction parameters for a surfactant/scCO2 system. Next, we simulate surfactant/scCO2 systems and explore the effect of the surfactant volume fraction, packing fraction, and temperature on the phase behavior. The transition from the two-phase region to the one-phase region is located by monitoring the contrast structure factor of the equilibrated surfactant/scCO2 system, and the micelle to unimer transition is located by monitoring the aggregate size distribution of the equilibrated surfactant/scCO2 system. We find a two-phase region, a micelle phase, and a unimer phase with increasing packing fraction at fixed temperature or with increasing temperature at fixed packing fraction. The phase diagram for the surfactant/scCO2 system in the surfactant volume fraction-packing fraction plane and the density dependence of the critical micelle concentration are in qualitative agreement with experimental observations. The phase behavior of a surfactant/scCO2 system can be directly related to the solubilities of the corresponding homopolymers that serve as the head and tail blocks for the surfactant. The influence of surfactant structure (head and tail lengths) on the phase transitions is explored.     

Toward a general strategy for the synthesis of 3,4-dihydroxyprolines from pentose sugars

A general strategy is proposed, wherein a pentose sugar gamma-lactone can be converted, via a series of nine reactions, to a 3,4-dihydroxyproline, suitably protected for use in peptide synthesis. Thus, D-ribonolactone (6) has been converted to N-fluorenylmethoxycarbonyl-3,4-di-O-tert-butyldimethylsilyloxy-D-2,3-cis-3,4-cis-proline (7) in 18.9% overall yield. Likewise, L-arabinonolactone (11) has been converted to N-fluorenylmethoxycarbonyl-3,4-di-O-tert-butyldimethylsilyloxy-L-2,3-cis-3,4-trans-proline (36) in 13.7% overall yield and L-lyxonolactone (12) to N-fluorenylmethoxycarbonyl-3,4-di-O-tert-butyldimethylsilyloxy-L-2,3-trans-3,4-cis-proline (37) in 11.2% overall yield. These building blocks have also been fully deprotected to give the free amino acids. We believe that this series of reactions ought to be applicable to the synthesis of any of the eight stereoisomers of 3,4-dihydroxyproline, by judicious selection of the pentose starting material.     

New natural product families from an environmental DNA (eDNA) gene cluster

Uncultured bacteria represent a potentially rich source of new and useful natural products. Studying these natural products requires the development of effective yet straightforward methods to access the small-molecule chemical diversity produced by uncultured bacteria. In this study, DNA extracted directly from soil samples (environmental DNA, eDNA) was used to construct cosmid libraries in Escherichia coli, and these clones were then assayed for the production of antibiosis. A 13 open reading frame (ORF) biosynthetic gene cluster (feeA-M) found in one of the antibacterial active clones, CSLC-2, confers to E. coli the production of two new families of natural products that are derived from long chain N-acyltyrosines. The fee gene cluster and three families of the long chain acyl phenols derived from tyrosine (families 1, 2, and 3) are described.     

The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase

This paper describes the application of PRO_–LEADS to the flexible docking of ligands into crystallographically derived enzyme structures that are assumed to be rigid. PRO_–LEADS uses a Tabu search methodology to perform the flexible search and an empirically derived estimate of the binding affinity to drive the docking process. The paper tests the extent to which the assumption of a rigid enzyme compromises the accuracy of the results. All-pairs docking experiments are performed for three enzymes (thrombin, thermolysin and influenza virus neuraminidase) based on six or more ligand-enzyme crystal structures for each enzyme. In 76% of the cases, PRO_–LEADS can successfully identify the correct ligand conformation as the lowest energy configuration when the enzyme structure is derived from that ligand's crystal structure, but the methodology only docks 49% of the cases successfully when the ligand is docked against enzyme crystal structures derived from other ligands. Small movements in the enzyme structure lead to an under-prediction in the energy of the correct binding mode by up to 14 kJ/mol and in some cases this under-prediction can lead to the native mode not being recognised as the lowest energy solution. The type of movements responsible for mis-docking are: the movement of sidechains as a result of changes in C position; the movement of sidechains without changes in C position; the movement of flexible portions of main chains to facilitate the formation of hydrogen bonds; and the movement of metal atoms bound to the enzyme active site. The work illustrates that the assumption of a rigid active site can lead to errors in identification of the correct binding mode and the assessment of binding affinity, even for enzymes which show relatively small shift in atomic positions from one ligand to the next. A good docking code, such as PRO_–LEADS, can usually dock successfully if there is induced fit in relatively rigid enzymes but there remains the need to develop improved strategies for dealing with enzyme flexibility. The work implies that treatments of enzyme flexibility which focus only on sidechain rotations will not deal with the critical shifts responsible for mis-docking of ligands in thrombin, thermolysin and neuraminidase. The paper demonstrates the utility of all pairs docking experiments as a method of assessing the effectiveness of docking methodologies in dealing with enzyme flexibility.     

Comparison of the extended kalman filter and marquardt algorithms for processing kinetic data

The extended Kalman filter and Marquardt's gradient expansion algorithm for nonlinear least squares are compared with respect to accuracy and precision of parameter extimates, computational burden, sensitivity to initial parameter estimates and ability to indicate model errors. Fits of synthetic first-order data and combined first- and zero-order data produce estimates of equivalent precision and accuracy in most cases. Similar results were obtained for both simulated and experimental data for combined zero-order/first-order processes. However, for the simulated zero-order/first-order data with small zero-order components processed over two half-lives of the first-order process, the Kalman filter overestimated the zero-order rate constant by a substantially larger amount than the Marquardt algorithm. Significant differences in computational burden and sensitivity to initial parameter estimates are demonstrated; however, neither algorithm has a significant advantage over the other for the detection of model error.     

A comparison of electrometric and gasometric methods for following autoxidations

Gasometric and electrometric methods for determining oxygen in the study of photosensitized reactions are compared. The oxygen electrode must be calibrated against known solutions similar in composition to the solutions used in the reactions that are studied. The electrode can be used to study initial reaction rates whereas this is impossible for fast reactions with the Warburg apparatus.     

Controlled release of 4-hydroperoxycyclophosphamide from the fatty acid dimer-sebacic acid copolymer

Controlled polymeric release of chemotherapeutic agents has shown promise in the management of malignant gliomas. 4-Hydroperoxycyclophosphamide (4HC), loaded on the fatty acid dimer–sebacic acid copolymer (FAD:SA, 1:1), significantly prolonged survival in rats implanted with F98 and 9L gliomas. Here, we studied the in vitro and in vivo release kinetics in phosphate-buffered saline and rat brain of 20% 4HC/FAD:SA (wt:wt), the optimal dose for treatment of rat gliomas. In vitro release under infinite sink conditions was steady over the initial 12 hr to a peak of 20–35% of impregnated drug, consistent with early phase control via surface erosion. Release over the next 3 weeks was minimal, consistent with barrier formation around the polymer by an oily fatty acid dimer degradation product and consequent slowing of release. However, the polymer started to disintegrate by day 4, and there were minimal visible remnants by 3 weeks. Thus, a considerable amount of polymer-carried drug was probably lost in the disintegrating fragments. Also, drug loss is expected from its inherent hydrolytic instability. In vivo release into brain revealed two peak levels of drug at 0–1 hr and 5–20 days. With loaded polymer implanted intraperitoneally or cyclophosphamide injected systemically, peak brain drug levels were measured in 2–8 hr, with substantial decrease by 48 hr without a second peak. Brain levels were substantially higher than blood levels at all time periods. We conclude that FAD:SA (1:1) adequately protects the otherwise labile 4HC, allowing effective and substained drug release in vivo. Furthermore, it should be possible to modify the polymer to adjust the time of peak release for more beneficial therapeutic effects.