Engineering and Characterization of Cytochrome P450 Enzymes for Nitrogen-Atom Transfer Reactions

The creation of novel enzyme activity is a great challenge to protein engineers, but nature has done so repeatedly throughout the process of natural selection. I begin by outlining the multitude of distinct reactions catalyzed by a single enzyme class, cytochrome P450 monooxygenases. I discuss the ability of cytochrome P450 to generate reactive intermediates capable of diverse reactivity, suggesting this enzyme can also be used to generate novel reactive intermediates in the form of metal-carbenoid and nitrenoid species. I then show that cytochrome P450 from Bacillus megaterium (P450_BM3) and its isolated cofactor can catalyze metal-nitrenoid transfer in the form of intramolecular C–H bond amination. Mutations to the protein sequence can enhance the reactivity and selectivity of this transformation significantly beyond that of the free cofactor. Next, I demonstrate an intermolecular nitrene transfer reaction catalyzed by P450_BM3 in the form of sulfide imidation. Understanding that sulfur heteroatoms are strong nucleophiles, I show that increasing the sulfide nucleophilicity through substituents on the aryl sulfide ring can dramatically increase reaction productivity. To explore engineering nitrenoid transfer in P450BM3, active site mutagenesis is employed to tune the regioselectivity intramolecular C–H amination catalysts. The solution of the crystal structure of a highly selective variant demonstrates that hydrophobic residues in the active site strongly modulate reactivity and regioselectivity. Finally, I use a similar strategy to develop P450-based catalysts for intermolecular olefin aziridination, demonstrating that active site mutagenesis can greatly enhance this nitrene transfer reaction. The resulting variant can catalyze intermolecular aziridination with more than 1000 total turnovers and enantioselectivity of up to 99% ee.

Nonclassical excitation and quantum interference in a three level atom

Non-classical properties and quantum interference (QI) in two-photon excitation of a three level atom (|1〉), |2〉, |3〉) in a ladder configuration, illuminated by multiple fields in non-classical (squeezed) and/or classical (coherent) states, is studied. Fundamentally new effects associated with quantum correlations in the squeezed fields and QI due to multiple excitation pathways have been observed. Theoretical studies and extrapolations of these findings have revealed possible applications which are far beyond any current capabilities, including ultrafast nonlinear mixing, ultrafast homodyne detection and frequency metrology. The atom used throughout the experiments was Cesium, which was magneto-optically trapped in a vapor cell to produce a Doppler-free sample. For the first part of the work the |1〉 → |2〉 → |3〉 transition (corresponding to the 6S_1/2F = 4 → 6P_3/2F' = 5 → 6D_5/2F" = 6 transition) was excited by using the quantum-correlated signal (Ɛ_s) and idler (Ɛ_i) output fields of a subthreshold non-degenerate optical parametric oscillator, which was tuned so that the signal and idler fields were resonant with the |1〉 → |2〉 and |2〉 → |3〉 transitions, respectively. In contrast to excitation with classical fields for which the excitation rate as a function of intensity has always an exponent greater than or equal to two, excitation with squeezed-fields has been theoretically predicted to have an exponent that approaches unity for small enough intensities. This was verified experimentally by probing the exponent down to a slope of 1.3, demonstrating for the first time a purely non-classical effect associated with the interaction of squeezed fields and atoms. In the second part excitation of the two-photon transition by three phase coherent fields Ɛ₁ , Ɛ₂ and Ɛ₀, resonant with the dipole |1〉 → |2〉 and |2〉 → |3〉 and quadrupole |1〉 → |3〉 transitions, respectively, is studied. QI in the excited state population is observed due to two alternative excitation pathways. This is equivalent to nonlinear mixing of the three excitation fields by the atom. Realizing that in the experiment the three fields are spaced in frequency over a range of 25 THz, and extending this scheme to other energy triplets and atoms, leads to the discovery that ranges up to 100's of THz can be bridged in a single mixing step. Motivated by these results, a master equation model has been developed for the system and its properties have been extensively studied.

Strong atom-light interactions along nanostructures: Transition from free-space to nanophotonic interfaces

An exciting frontier in quantum information science is the integration of otherwise "simple'' quantum elements into complex quantum networks. The laboratory realization of even small quantum networks enables the exploration of physical systems that have not heretofore existed in the natural world. Within this context, there is active research to achieve nanoscale quantum optical circuits, for which atoms are trapped near nano-scopic dielectric structures and "wired'' together by photons propagating through the circuit elements. Single atoms and atomic ensembles endow quantum functionality for otherwise linear optical circuits and thereby enable the capability of building quantum networks component by component. Toward these goals, we have experimentally investigated three different systems, from conventional to rather exotic systems : free-space atomic ensembles, optical nano fibers, and photonics crystal waveguides. First, we demonstrate measurement-induced quadripartite entanglement among four quantum memories. Next, following the landmark realization of a nanofiber trap, we demonstrate the implementation of a state-insensitive, compensated nanofiber trap. Finally, we reach more exotic systems based on photonics crystal devices. Beyond conventional topologies of resonators and waveguides, new opportunities emerge from the powerful capabilities of dispersion and modal engineering in photonic crystal waveguides. We have implemented an integrated optical circuit with a photonics crystal waveguide capable of both trapping and interfacing atoms with guided photons, and have observed the collective effect, superradiance, mediated by the guided photons. These advances provide an important capability for engineered light-matter interactions, enabling explorations of novel quantum transport and quantum many-body phenomena.

Applications of nuclear magnetic resonance spectroscopy to the study of medium-sized rings. I. Conformational properties of cycloheptane. II. Conformational properties of cycloöctane

Conformational equilibrium in medium-sized rings has been investigated by the temperature variation of the fluorine-19 n.m.r. spectra of 1, 1-difluorocycloalkanes and various substituted derivatives of them. Inversion has been found to be fast on the n.m.r. time scale at -180˚ for 1, 1-difluorocycloheptane, but slow for 1, 1-difluoro-4, 4-dimethylcycloheptane at -150˚. At low temperature, the latter compound affords a single AB pattern with a chemical-shift difference of 841 cps. which has been interpreted in terms of the twist-chair conformation with the methyl groups on the axis position and the fluorine atoms in the 4-position. At room temperature, the n.m.r. spectrum of 1, 1-difluoro-4-t-butylcycloheptane affords an AB pattern with a chemical-shift difference of 185 cps. The presence of distinct trans and gauche couplings from the adjacent hydrogens has been interpreted to suggest the existence of a single predominant form, the twist chair with the fluorine atoms on the axis position.

Investigation of 1, 1-difluorocycloöctane and 1, 1, 4, 4-tetrafluorocycloöctane has led to the detection of two kinetic processes both having activation energies of 8-10 kcal./mole but quite different A values. In light of these results eleven different conformations of cycloöctane along with a detailed description of the ways in which they may be interconverted are discussed. An interpretation involving the twist-boat conformation rapidly equilibrating through the saddle and the parallel-boat forms at room temperature is compatible with the results.

Proton magnetic resonance studies of ribonucleic acid complexes. I. Complexes of biological bases and oligonucleotides with RNA. II. Template recognition and the degeneracy of the genetic code

Part I. Complexes of Biological Bases and Oligonucleotides with RNA

The physical nature of complexes of several biological bases and oligonucleotides with single-stranded ribonucleic acids have been studied by high resolution proton magnetic resonance spectroscopy. The importance of various forces in the stabilization of these complexes is also discussed.

Previous work has shown that purine forms an intercalated complex with single-stranded nucleic acids. This complex formation led to severe and stereospecific broadening of the purine resonances. From the field dependence of the linewidths, T₁ measurements of the purine protons and nuclear Overhauser enhancement experiments, the mechanism for the line broadening was ascertained to be dipole-dipole interactions between the purine protons and the ribose protons of the nucleic acid.

The interactions of ethidium bromide (EB) with several RNA residues have been studied. EB forms vertically stacked aggregates with itself as well as with uridine, 3'-uridine monophosphate and 5'-uridine monophosphate and forms an intercalated complex with uridylyl (3' → 5') uridine and polyuridylic acid (poly U). The geometry of EB in the intercalated complex has also been determined.

The effect of chain length of oligo-A-nucleotides on their mode of interaction with poly U in D₂0 at neutral pD have also been studied. Below room temperatures, ApA and ApApA form a rigid triple-stranded complex involving a stoichiometry of one adenine to two uracil bases, presumably via specific adenine-uracil base pairing and cooperative base stacking of the adenine bases. While no evidence was obtained for the interaction of ApA with poly U above room temperature, ApApA exhibited complex formation of a 1:1 nature with poly U by forming Watson-Crick base pairs. The thermodynamics of these systems are discussed.

Part II. Template Recognition and the Degeneracy of the Genetic Code

The interaction of ApApG and poly U was studied as a model system for the codon-anticodon interaction of tRNA and mRNA in vivo. ApApG was shown to interact with poly U below ~20°C. The interaction was of a 1:1 nature which exhibited the Hoogsteen bonding scheme. The three bases of ApApG are in an anti conformation and the guanosine base appears to be in the lactim tautomeric form in the complex.

Due to the inadequacies of previous models for the degeneracy of the genetic code in explaining the observed interactions of ApApG with poly U, the "tautomeric doublet" model is proposed as a possible explanation of the degenerate interactions of tRNA with mRNA during protein synthesis in vivo.

Optimizing the Curie temperature of pseudo-binary RxR2-x ' Fe-17 (R, R ' = rare earth) for magnetic refrigeration

Several pseudo-binary RxR2-x'Fe-17 alloys (with R = Y, Ce, Pr, Gd and Dy) were synthesized with rhombohedral Th2Zn17-type crystal structure determined from x-ray and neutron powder diffraction. The choice of compositions was done with the aim of tuning the Curie temperature (T-C) in the 270 +/- 20 K temperature range, in order to obtain the maximum magneto-caloric effect around room temperature. The investigated compounds exhibit broad isothermal magnetic entropy changes, Delta S-M(T), with moderate values of the refrigerant capacity, even though the values of Delta S-M(Peak) are relatively low compared with those of the R2Fe17 compounds with R = Pr or Nd. The reduction on the Delta S-M(Peak) is explained in terms of the diminution in the saturation magnetization value. Furthermore, the Delta S-M(T) curves exhibit a similar caret-like behavior, suggesting that the magneto-caloric effect is mainly governed by the Fe-sublattice. A single master curve for Delta S-M/Delta S-M(Peak)(T) under different values of the magnetic field change are obtained for each compound by rescaling of the temperature axis.

Efficient Synthesis of Single-Chain Polymer Nanoparticles via Amide Formation

Single-chain technology (SCT) allows the transformation of individual polymer chains to folded/collapsed unimolecular soft nanoparticles. In this work we contribute to the enlargement of the SCT toolbox by demonstrating the efficient synthesis of single-chain polymer nanoparticles (SCNPs) via intrachain amide formation. In particular, we exploit cross-linking between active methylene groups and isocyanate moieties as powerful "click" chemistry driving force for SCNP construction. By employing poly(methyl methacrylate)- (PMMA-) based copolymers bearing beta-ketoester units distributed randomly along the copolymer chains and bifunctional isocyanate cross-linkers, SCNPs were successfully synthesized at r.t. under appropriate reaction conditions. Characterization of the resulting SCNPs was carried out by means of a combination of techniques including size exclusion chromatography (SEC), infrared (IR) spectroscopy, proton nuclear magnetic resonance (H-1 NMR) spectroscopy, dynamic light scattering (DLS), and elemental analysis (EA).

Multiple single unit recording in the cortex of monkeys using independently moveable microelectrodes.

Simultaneous recording from multiple single neurones presents many technical difficulties. However, obtaining such data has many advantages, which make it highly worthwhile to overcome the technical problems. This report describes methods which we have developed to permit recordings in awake behaving monkeys using the 'Eckhorn' 16 electrode microdrive. Structural magnetic resonance images are collected to guide electrode placement. Head fixation is achieved using a specially designed headpiece, modified for the multiple electrode approach, and access to the cortex is provided via a novel recording chamber. Growth of scar tissue over the exposed dura mater is reduced using an anti-mitotic compound. Control of the microdrive is achieved by a computerised system which permits several experimenters to move different electrodes simultaneously, considerably reducing the load on an individual operator. Neurones are identified as pyramidal tract neurones by antidromic stimulation through chronically implanted electrodes; stimulus control is integrated into the computerised system. Finally, analysis of multiple single unit recordings requires accurate methods to correct for non-stationarity in unit firing. A novel technique for such correction is discussed.

Dynamic properties of superconducting magnetic bearings

The potential use of YBa2j as an active component in a magnetic bearing is being investigated. Although the load bearing capacity is high and increases with the square of the magnetic field trapped, the stiffness is low. Both the stiffness and the lévitation height are a function of the loading history of the bearing. At Cambridge we have been investigating the effects of dynamic loading such as single large excursions from steady state loads and cyclically applied loads such as vibrations. Since a superconducting bearing has little inherent damping cyclic loads applied at or near its natural frequency can have catastrophic effects. The information being gathered at Cambridge will be used to enable these effects to be mitigated in the bearing design process. © 1997 IEEE.

Microstructure and superconducting properties of single grains of Y-Ba-Cu-O containing Y-2411(M) and Y2O3

Y-Ba-Cu-O (YBCO) single grains have the potential to generate large trapped magnetic fields for engineering applications, and research on the processing and properties of this material has attracted interest world-wide over the past 20 years. In particular, the introduction of flux pinning centers to the large grain microstructure to improve its current density Jc, and hence trapped field, has been investigated extensively. Y2Ba 4CuMO2 [Y-2411(M)], where M = Nb, Ta, Mo, W, Ru, Zr, Bi and Ag, has been discovered recently to form very effective flux pinning centers due primarily to its ability to form nano-size inclusions in the superconducting phase matrix. However, the addition of the Y-2411(M) phase to the precursor composition complicates the melt-processing of single grains. The addition of Y2O3 to the precursor composition, however, broadens the growth window of single YBCO grains containing Y-2411 (M). We report an investigation of the microstructures and superconducting properties of single grains of this composition grown by top seeded melt growth (TSMG). © 2010 IEEE.

Magnetization process of a single chain of nanomagnets

We have investigated the magnetization reversal process of a single chain of identical nanomagnetic dots fabricated from 30 nm thick Ni 80Fe20. The structures consist of two 5 μm wide support wires bridged with a single chain of identical dots of diameter δ in the range 100-250 nm. For fields applied perpendicular to the single chain, we observed an unusual size dependent hysteretic behavior in the magnetoresistance curve at high field. This is due to the magnetostatic interaction arising from the proximity of the magnetic charges. We are able to deduce from a simple micromagnetic simulation that the reversal process in the chain of dots with δ=100nm is mediated by a collective process of nearly coherent spin rotation. The magnetotransport measurements along the chain reveal a complex magnetization reversal process in the chain of nanomagnets. © 2002 American Institute of Physics.

Magnetic anisotropy of BaM ferrites

Using the point charge model with weak field scheme, a calculation of the single ion anisotropy of Fe3+ ionsn at all crystal sites in BaFe12O19 was made by perturbation theory. The results show that in addition to the 2b site, all other sites have non-negligible contributions. © 1983.

Calculating transport AC losses in stacks of high temperature superconductor coated conductors with magnetic substrates using FEM

In this paper, the authors investigate the electromagnetic properties of stacks of high temperature superconductor (HTS) coated conductors with a particular focus on calculating the total transport AC loss. The cross-section of superconducting cables and coils is often modeled as a two-dimensional stack of coated conductors, and these stacks can be used to estimate the AC loss of a practical device. This paper uses a symmetric two dimensional (2D) finite element model based on the H formulation, and a detailed investigation into the effects of a magnetic substrate on the transport AC loss of a stack is presented. The number of coated conductors in each stack is varied from 1 to 150, and three types of substrate are compared: non-magnetic weakly magnetic and strongly magnetic. The non-magnetic substrate model is comparable with results from existing models for the limiting cases of a single tape (Norris) and an infinite stack (Clem). The presence of a magnetic substrate increases the total AC loss of the stack, due to an increased localized magnetic flux density, and the stronger the magnetic material, the further the flux penetrates into the stack overall. The AC loss is calculated for certain tapes within the stack, and the differences and similarities between the losses throughout the stack are explained using the magnetic flux penetration and current density distributions in those tapes. The ferromagnetic loss of the substrate itself is found to be negligible in most cases, except for small magnitudes of current. Applying these findings to practical applications, where AC transport current is involved, superconducting coils should be wound where possible using coated conductors with a non-magnetic substrate to reduce the total AC loss in the coil. © 2011 Elsevier B.V. All rights reserved.

Magnetic sensor with compensation for lead and coil resistance

A measurement system for magnetic fields or electric currents uses a single-core fluxgate, magneto-inductive or magneto-impedance device driven from a radio frequency excitation source. Flux nulling feedback circuitry is provided to maintain the core of the sensor at substantially zero net flux and improve the linearity and dynamic response of the sensor system. A high pass filter is provided for reducing the dc effects of the ohmic resistance of the coil and lead wires on the effectiveness of the flux nulling feedback.

Fluxgate magnetic sensor with overload detection

A measurement system for magnetic fields and electric currents uses a single-core fluxgate device driven with a radio frequency excitation source and is provided with a means to indicate saturation of the core of the sensor. A means is provided for detecting overload of the sensor as the core approaches continuous saturation using a pair of demodulators and a comparator.