One site fits both: A model for the ternary complex of folate + NADPH in R67 dihydrofolate reductase, a D2 symmetric enzyme

R67 dihydrofolate reductase (DHFR) is a novel enzyme that confers resistance to the antibiotic trimethoprim. The crystal structure of R67 DHFR displays a toroidal structure with a central active-site pore. This homotetrameric protein exhibits 222 symmetry, with only a few residues from each chain contributing to the active site, so related sites must be used to bind both substrate (dihydrofolate) and cofactor (NADPH) in the productive R67 DHFR?NADPH?dihydrofolate complex. Whereas the site of folate binding has been partially resolved crystallographically, an interesting question remains: how can the highly symmetrical active site also bind and orient NADPH for catalysis? To model this ternary complex, we employed DOCK and SLIDE, two methods for docking flexible ligands into proteins using quite different algorithms. The bound pteridine ring of folate (Fol I) from the crystal structure of R67 DHFR was used as the basis for docking the nicotinamide-ribose-P_i (NMN) moiety of NADPH. NMN was positioned by both DOCK and SLIDE on the opposite side of the pore from Fol I, where it interacts with Fol I at the pore's center. Numerous residues serve dual roles in binding. For example, Gln 67 from both the B and D subunits has several contacts with the pteridine ring, while the same residue from the A and C subunits has several contacts with the nicotinamide ring. The residues involved in dual roles are generally amphipathic, allowing them to make both hydrophobic and hydrophilic contacts with the ligands. The result is a `hot spot' binding surface allowing the same residues to co-optimize the binding of two ligands, and orient them for catalysis.     

In-lens cryo-high resolution scanning electron microscopy: methodologies for molecular imaging of self-assembled organic hydrogels.

The micro- and nanoarchitectures of water-swollen hydrogels were routinely analyzed in three dimensions at very high resolution by two cryopreparation methods that provide stable low-temperature specimens for in-lens high magnification recordings. Gemini surfactants (gS), poly-N-isopropylacrylamides (p-NIP Am), and elastin-mimetic di- (db-E) and triblock (tb-E) copolymer proteins that form hydrogels have been routinely analyzed to the sub-10-nm level in a single day. After they were quench or high pressure frozen, samples in bulk planchets were subsequently chromium coated and observed at low temperature in an in-lens field emission SEM. Pre-equilibrated planchets (4-40 degrees C) that hold 5-10 microl of hydrogel facilitate dynamic morphological studies above and below their transition temperatures. Rapidly frozen samples were fractured under liquid nitrogen, low-temperature metal coated, and observed in-lens to assess the dispersion characteristics of micelles and fragile colloidal assemblies within bulk frozen water. Utilizing the same planchet freezing system, the cryoetch-HRSEM technique removed bulk frozen water from the hydrogel matrix by low-temperature, high-vacuum sublimation. The remaining frozen solid-state sample faithfully represented the hydrogel matrix. Cryo- and cryoetch-HRSEM provided vast vistas of hydrogels at low and intermediate magnifications whereas high magnification recordings and anaglyphs (stereo images) provided a three-dimensional prospective and measurements on a molecular level.     

Reactions of CF3-enones with ethyl nitroacetate and nitromethane: synthesis of CF3-γ-nitroketones

Reactions of α,β-unsaturated CF₃-ketones with nitromethane and ethyl nitroacetate have been investigated. We found that α,β-unsaturated trifluoromethylketones react with ethyl nitroacetate in the presence of calcinated potassium fluoride to form two classes of 1,4-conjugated addition products: CF₃-γ-nitroketones and 6,6,6-trifluoro-2-nitro-5-oxohexanoates in nearly quantitative yields. The products obtained are precursors for CF₃-pyrrolidine synthesis.     

TiCl(OPr)3 and NaBH(OAc)3: an efficient reagent combination for the reductive amination of aldehydes by electron-deficient amines

Sodium triacetoxyborohydride, NaBH(OAc)₃ with tri-isopropoxytitanium chloride, TiCl(OⁱPr)₃ is a useful reagent combination for reductive amination. Electron-deficient amines and heteroaromatic amines such as 2-aminopyrimidine and 2-aminothiazole can be reductively alkylated at room temperature to afford the corresponding secondary amines in good yields.     

A mixed‐valence chloride‐bridged (pincer)IrIII–(diene)IrI complex

The title compound, [2,6‐bis(di‐tert‐butylphosphino)phenyl‐1κ³P,C¹,P′]di‐μ‐chlorido‐1:2κ⁴Cl:Cl‐(2η⁴‐cycloocta‐2,5‐diene)hydrido‐1κH‐diiridium(I,III) hexane hemisolvate, [Ir₂(C₈H₁₂)(C₂₄H₄₃P₂)Cl₂H]·0.5C₆H₁₄ or [(^tBuPCP)IrH(μ₂‐Cl)₂Ir(COD)][^tBuPCP is κ³‐2,6‐(^tBu₂PCH₂)₂C₆H₃ and COD is η⁴‐2,5‐cyclooctadiene], is an Ir^III/Ir^I dimer bridged by two chloride ions. The Ir₂Cl₂ framework is nearly planar, with a dihedral angle of 13.04 (4)° between the two Ir centers. The compound was isolated as a hexane hemisolvate. A list of distances found in Ir(PCP) compounds is given.     

Experimental and theoretical studies of charge transfer and deuterium ion transfer between D2O+ and C2H4

The charge transfer and deuterium ion transfer reactions between D(2)O(+) and C(2)H(4) have been studied using the crossed beam technique at relative collision energies below one electron volt and by density functional theory (DFT) calculations. Both direct and rearrangement charge transfer processes are observed, forming C(2)H(4) (+) and C(2)H(3)D(+), respectively. Independent of collision energy, deuterium ion transfer accounts for approximately 20% of the reactive collisions. Between 22 and 36 % of charge transfer collisions occur with rearrangement. In both charge transfer processes, comparison of the internal energy distributions of products with the photoelectron spectrum of C(2)H(4) shows that Franck-Condon factors determine energy disposal in these channels. DFT calculations provide evidence for transient intermediates that undergo H/D migration with rearrangement, but with minimal modification of the product energy distributions determined by long range electron transfer. The cross section for charge transfer with rearrangement is approximately 10(3) larger than predicted from the Rice-Ramsperger-Kassel-Marcus isomerization rate in transient complexes, suggesting a nonstatistical mechanism for H/D exchange. DFT calculations suggest that reactive trajectories for deuterium ion transfer follow a pathway in which a deuterium atom from D(2)O(+) approaches the pi-cloud of ethylene along the perpendicular bisector of the C-C bond. The product kinetic energy distributions exhibit structure consistent with vibrational motion of the D-atom in the bridged C(2)H(4)D(+) product perpendicular to the C-C bond. The reaction quantitatively transforms the reaction exothermicity into internal excitation of the products, consistent with mixed energy release in which the deuterium ion is transferred in a configuration in which both the breaking and the forming bonds are extended.     

Parallel separations of oligonucleotides with optically gated sample introduction on multichannel microchips

With the release of the human genome sequence, there has been increasing attention given to other genetic analyses, including the detection of genetic variations and fast sequencing of multiple samples for pharmacogenomics studies. Rapid injections of samples in multiplexed separation channels by optically gated sample introduction are shown here for DNA separation. Serial separations of four amino acids are shown in less than four seconds on a microchip with four multiplexed channels. Five short oligonucleotides have also been rapidly separated in 2% LPA with four channels using this technique. In addition, multiple unique samples have been simultaneously separated and five-base resolution has been demonstrated.     

A novel effective electrophile: β-trifluoroacetylketene diphenyldithioacetal S,S-tetroxide

A synthesis of a novel electrophilic reagent--β-trifluoroacetylketene diphenyldithioacetal S,S-tetroxide 3 is described. The reaction of 3 with various electron-rich aromatics such as 1,3-dimethoxybenzene, 2-methylthiophene, N-methylpyrrole, and 2-methylindole was investigated. In the course of these reactions an unusual migration of a phenylsulfonyl group takes place. An easy and ready for scale-up procedure for the synthesis of previously unknown β-aryl, α-phenylsulphonyl substituted α,β-unsaturated trifluoromethyl ketones is reported.     

One-pot synthesis of cyclic enecarbamates from lactam carbamates

A general, practical and efficient one-pot synthesis of cyclic enecarbamates is described. The protocol proceeds via reduction of lactam carbamate with Super-Hydride^®, followed by in situ dehydration with trifluoroacetic anhydride (TFAA) and diisopropylethylamine (DIPEA).     

Nucleation and growtn of polythiophene films on gold electrodes

The nucleation and growth of polythiophene films on gold electrodes has been studied using potentiostatic steps. The mechanism has been deduced and estimates made of the kinetic parameters. Dissolution of the gold substrate at potentials where thiophene polymerisation occurs is suppressed by the initial rapid formation of a monolayer of polymer. The data indicate that formation of bulk film occurs by the instantaneous nucleation and three-dimensional growth of polymer on top of this monolayer. Rate constants for growth parallel to the surface on the bare gold substrate and the covering polymer layer are surprisingly very similar. Growth perpendicular to the surface is slightly more rapid, typically by a factor of 1.5–3, although it is less dependent on potential. The high density of nuclei results in their overlap at an early stage, after which growth is only possible perpendicular to the surface. Within a narrow potential range, the observation of maxima and minima in current-time transients is interpreted in terms of the “death” and “rebirth” of growing centres.