Rate constants from the reaction path Hamiltonian. I. Reactive flux simulations for dynamically correct rates

As ab initio electronic structure calculations become more accurate, inherent sources of error in classical transition state theory such as barrier recrossing and tunneling may become major sources of error in calculating rate constants. This paper introduces a general method for diabatically constructing the transverse eigensystem of a reaction path Hamiltonian in systems with many degenerate transverse frequencies. The diabatically constructed reaction path Hamiltonian yields smoothly varying coupling constants that, in turn, facilitate reactive flux calculations. As an example we compute the dynamically corrected rate constant for the chair to boat interconversion of cyclohexane, a system with 48 degrees of freedom and a number of degenerate frequencies. The transmission coefficients obtained from the reactive flux simulations agree with previous results that have been calculated using an empirical potential. Furthermore, the calculated rate constants agree with experimental values. Comparison to variational transition state theory shows that, despite finding the true bottleneck along the reaction pathway, variational transition state theory only accounts for half of the rate constant reduction due to recrossing trajectories.     

pH dependent self-assembly of dimetallic lanthanide complexes

pH dependent self-association has been observed in a series of DO3A-derived lanthanide complexes bearing a carboxylate group that can act as a bridging ligand at high pH, switching on the luminescence from the lanthanide.     

Hamaker constants in integrated circuit metalization

A new method for determining Hamaker constants was examined for materials of interest in integrated circuit manufacture. An ultra-high vacuum atomic force microscope and an atomic force microscope operated in a nitrogen environment were used to measure the interaction forces between metals, dielectrics, and barriers used during the metalization portion of integrated circuit manufacturing. The materials studied included copper, silver, titanium nitride, silicon dioxide, poly(tetrafluoroethylene), and parylene-N. Spheres coated with a material of interest were mounted on AFM cantilevers and brought into contact with substrates of interest. The interaction force was measured as the cantilever approached the substrate but before the two surfaces came into contact, and also when the particle was pulled out of contact with the substrate. The Hamaker constant calculation from the contact measurement is based on an adhesion model that quantifies the contribution of geometrical, morphological and mechanical properties of materials to the measured adhesion force. Hamaker constants determined with this new approach were compared with values found by using the Derjaguin approximation for a sphere to describe the interaction force as the cantilever approaches the surface. Both approaches produced similar values for most of the systems studied, with variations of less than 10%.     

On-line on-chip post-column derivatisation reactions for pre-ionisation of analytes and cluster analysis in gradient micro-liquid chromatography/electrospray mass spectrometry

A system is presented that demonstrates the principle of on-line and on-chip post-column derivatisation reactions in micro-high-performance liquid chromatography (micro-HPLC) hyphenated to electrospray time-of-flight mass spectrometry (ESI-TOFMS). In this micro-HPLC-chip-MS set-up, the analytes are separated using gradient micro-HPLC and subsequently derivatised on-chip and detected. One of the major limitations of MS detection is its dependency on the degree of ionisation, which is widely variable and compound-specific. Optimising and controlling the degree of ionisation in a simple manner would allow MS detection to be truly generic. One way of achieving this is by pre-ionisation of analytes using simple derivatisation procedures that are both rapid and quantitative. Performing this in situ on the system described here overcomes issues of sample handling and efficiency losses when time-consuming "bench chemistry" is necessary prior to analysis. The power of the system is demonstrated by the separation of primary and secondary amines, which are subsequently derivatised with a positively charged phosphonium complex and detected in an enhanced manner. Typically, molecular cations (M(+)) are detected showing that the ionisation process is dominated by the phosphonium species, leading to more constant ionisation for a variety of compounds. In addition, stable isotopically labelled ((12)C/(13)C)-phosphonium reagent is used for the reactions, allowing for inherent signal/noise (S/N) improvement and automated data processing using cluster analysis. A similar reaction scheme is used for the derivatisation of ketones and aldehydes, also demonstrating dramatic increases in sensitivity, especially with increasing temperature. Minimal loss in chromatographic fidelity in terms of retention times is observed by the introduction of the micromixer chip into the system. Optimal flow rates in micro-HPLC and ESI-MS are compatible with flow rates for the chip as well as a multitude of in-line optical detectors including UV and fluorescence. In addition, the micromixer chip can be positioned pre-column if preferred. The system is robust, easily fully automated and applicable to a wide variety of reactions. The system has a major advantage in its simple robust connection to the "normal scale" outside world.     

RECOVERY FROM DAMAGE INDUCED BY ACRIDINE PLUS NEAR-ULTRAVIOLET LIGHT IN ESCHERICHIA COLI

Abstract— Escherichia coli cells treated with sublethal doses of acridine plus near-UV light exhibit an effective split-dose recovery response that requires an incubation period of about 30–45 min. Studies of the metabolic requirements for split-dose recovery revealed the following: (a) DNA synthesis is not required for split-dose recovery; (b) inhibition of electron transport or protein synthesis reduces the efficiency of split-dose recovery by about one-half; (c) inhibition of phospholipid synthesis or cell wall synthesis completely eliminates the split-dose recovery response. These results suggest an involvement of membrane repair mechanisms in response to damage by acridine plus near-UV light. Additional evidence for such a process was provided by more direct assays for membrane recovery. It was found that cells treated with sublethal doses of acridine plus near-UV light are sensitive to low concentrations of detergents, and lose that sensitivity upon incubation. Likewise, treated cells are susceptible to lethal osmotic shock, but can recover from this susceptibility if incubated after treatment but prior to exposure to low osmotic conditions. Based on accumulating evidence, we propose that E. coli cells are capable of repairing membrane damage resulting from exposure to acridine plus near-UV light.     

Structure and conformational isomerism of the major dimer of 2,3-naphthoquinodimethane

The major product from 2,3-naphthoquinodimethane formed by cyclisation of $\text{o}$-dipropadienylbenzene was found to be the dimer 5 containing an eight-membered ring, for which the inversion barrier was determined by dynamic ¹H NMR spectrometry, ΔG3 = 18 kcal/mole.     

The crystal structure of 4,4′-dipyridinium tetracyanooxothiocyanatorhenate(V)

Summary The light purple crystals of (4,4-dipyridinium) [ReO(NCS)(CN)₄] crystallize in the monoclinic space group P2₁/m witha=6.615(1),b=16.043(1),c=8.405(1) Å,=93.20(1)°,z=2. The anisotropic refinement of the 1770 observed reflections converged to R=0.041.The [ReO(NCS)(CN)₄]^2– ion has a distorted octahedral geometry. The rhenium atom is displaced by 0.30 Å out of the plane formed by the four carbon atoms towards the terminal oxo ligand. Bond distances: Re=0 =1.67(1), Re–N=2.12(1) and Re–C_av=2.11(1)Å. The thiocyanate ion is nitrogen bonded to the rhenium atom.     

Enantioselective Synthesis: Steric and electronic effects of the substrates upon stereoselectivity in the gold(I)-catalyzed aldol reaction with chiral ferrocenylamine ligands,preliminary communication

Enantioselectivity in the gold(I)-catalyzed aldol reaction with chiral ferrocenylamine ligands is strongly dependent upon both the steric and electronic effects of the substrates. In the reaction of pyridine-2-, 3-, and 4-carbaldehydes with ethyl 2-isocyanoacetate, surprisingly and significantly different enantioselectivities were observed in the formation of the cis- and trans-dihydro-oxazoles that must be due to electronic rather than steric effects. The first example of double stereodifferentiation in the gold(l)-catalyzed aldol reaction is reported.     

The crystal structure of tetraethylammonium aquatetracyanooxorhenate(V)

Summary The crystal structure of the tetraethylammonium salt of [ReO(H₂O)(CN)₄]^– has been determined from threedimensional x-ray diffraction data. The light blue crystals are monoclinic, space group P2₁/m witha=8.760(1),b=9.518(5),c=11.718(1) Å, =102.63(1)^o with two molecules per unit cell. The final R value using 2009 observed reflections and anisotropic thermal parameters for all the non-hydrogen atoms was 0.038. The [ReO(H₂O)(CN)₄]^– ion has a distorted octahedral geometry with the rhenium atom displaced by 0.30 Å out of the plane formed by the four carbon atoms of the cyano ligands towards the oxo ligand. Bond distances: Re=O=1.667(8), Re–OH₂=2.142(7) and Re–C (average)=2.11(1) Å.     

Synthesis of pyrimido[4,5-e][1,4]oxazepin-5-ones

Eighteen novel pyrimido[4,5-e][1,4]oxazepin-5-ones were prepared directly via the reaction of either ethyl 4-chloro-2-phenyl-5-pyrimidinecarboxylate (Ia) or ethyl 4-chloro-2-m-chlorophenyl-5-pyrimidinecarboxylate (Ib) with a variety of substituted 2-(alkylamino)ethanols. A typical example was the preparation of 8,9-dihydro-9-methyl-2-phenylpyrimido[4,5-e][1,4]-oxazepin-5(7H)-one (IIa) from the reaction of Ia with 2-(methylamino)ethanol. Hydrolytic cleavage of the lactone ring in IIa with sodium hydroxide solution, followed by acidification with hydrochloric acid afforded 4-[(2-hydroxyethyl)methylamino]-2-phenyl-5-pyrimidinecarboxylic acid (IV). Reactions of IIa with concentrated ammonium hydroxide or hydrazine also caused cleavage of the lactone ring, giving the corresponding amide (V) or hydrazide (VI), respectively. Structural assignments were supported by infrared and nuclear magnetic resonance spectra.