Quantum Logic Spectroscopy with Ions in Thermal Motion.

A mixed-species geometric phase gate has been proposed for implementing quantum logic spectroscopy on trapped ions, which combines probe and information transfer from the spectroscopy to the logic ion in a single pulse. We experimentally realize this method, show how it can be applied as a technique for identifying transitions in currently intractable atoms or molecules, demonstrate its reduced temperature sensitivity, and observe quantum-enhanced frequency sensitivity when it is applied to multi-ion chains. Potential applications include improved readout of trapped-ion clocks and simplified error syndrome measurements for quantum error correction.

Non-native Co-, Mn-, and Ti-oxyhydroxide nanocrystals in ferritin for high efficiency solar energy conversion.

Quantum dot solar cells seek to surpass the solar energy conversion efficiencies achieved by bulk semiconductors. This new field requires a broad selection of materials to achieve its full potential. The 12 nm spherical protein ferritin can be used as a template for uniform and controlled nanocrystal growth, and to then house the nanocrystals for use in solar energy conversion. In this study, precise band gaps of titanium, cobalt, and manganese oxyhydroxide nanocrystals within ferritin were measured, and a change in band gap due to quantum confinement effects was observed. The range of band gaps obtainable from these three types of nanocrystals is 2.19-2.29 eV, 1.93-2.15 eV, and 1.60-1.65 eV respectively. From these measured band gaps, theoretical efficiency limits for a multi-junction solar cell using these ferritin-enclosed nanocrystals are calculated and found to be 38.0% for unconcentrated sunlight and 44.9% for maximally concentrated sunlight. If a ferritin-based nanocrystal with a band gap similar to silicon can be found (i.e. 1.12 eV), the theoretical efficiency limits are raised to 51.3% and 63.1%, respectively. For a current matched cell, these latter efficiencies become 41.6% (with an operating voltage of 5.49 V), and 50.0% (with an operating voltage of 6.59 V), for unconcentrated and maximally concentrated sunlight respectively.

Sensitive detection of surface- and size-dependent direct and indirect band gap transitions in ferritin.

Ferritin is a protein nano-cage that encapsulates minerals inside an 8 nm cavity. Previous band gap measurements on the native mineral, ferrihydrite, have reported gaps as low as 1.0 eV and as high as 2.5-3.5 eV. To resolve this discrepancy we have used optical absorption spectroscopy, a well-established technique for measuring both direct and indirect band gaps. Our studies included controls on the protein nano-cage, ferritin with the native ferrihydrite mineral, and ferritin with reconstituted ferrihydrite cores of different sizes. We report measurements of an indirect band gap for native ferritin of 2.140 ± 0.015 eV (579.7 nm), with a direct transition appearing at 3.053 ± 0.005 eV (406.1 nm). We also see evidence of a defect-related state having a binding energy of 0.220 ± 0.010 eV . Reconstituted ferrihydrite minerals of different sizes were also studied and showed band gap energies which increased with decreasing size due to quantum confinement effects. Molecules that interact with the surface of the mineral core also demonstrated a small influence following trends in ligand field theory, altering the native mineral's band gap up to 0.035 eV.

Effects of the E177K mutation in D-amino acid transaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity.

D-Amino acid transaminase is a bacterial enzyme that uses pyridoxal phosphate (PLP) as a cofactor to catalyze the conversion of D-amino acids into their corresponding alpha-keto acids. This enzyme has already been established as a target for novel antibacterial agents through suicide inactivation by a number of compounds. To improve their potency and specificity, the detailed enzyme mechanism, especially the role of its PLP cofactor, is under investigation. Many PLP-dependent transaminases have a negatively charged amino acid residue forming a salt-bridge with the pyridine nitrogen of its cofactor that promotes its protonation to stabilize the formation of a ketimine intermediate, which is subsequently hydrolyzed in the normal transaminase reaction pathway. However, alanine racemase has a positively charged arginine held rigidly in place by an extensive hydrogen bond network that may destabilize the ketimine intermediate, and make it too short-lived for a transaminase type of hydrolysis to occur. To test this hypothesis, we changed Glu-177 into a titratable, positively charged lysine (E177K). The crystal structure of this mutant shows that the positive charge of the newly introduced lysine side chain points away from the nitrogen of the cofactor, which may be due to electrostatic repulsions not being overcome by a hydrogen bond network such as found in alanine racemase. This mutation makes the active site more accessible, as exemplified by both biochemical and crystallographic data: CD measurements indicated a change in the microenvironment of the protein, some SH groups become more easily titratable, and at pH 9.0 the PMP peak appeared around 315 nm rather than at 330 nm. The ability of this mutant to convert L-alanine into D-alanine increased about 10-fold compared to wild-type and to about the same extent as found with other active site mutants. On the other hand, the specific activity of the E177K mutant decreased more than 1000-fold compared to wild-type. Furthermore, titration with L-alanine resulted in the appearance of an enzyme-substrate quinonoid intermediate absorbing around 500 nm, which is not observed with usual substrates or with the wild-type enzyme in the presence of L-alanine. The results overall indicate the importance of charged amino acid side chains relative to the coenzyme to maintain high catalytic efficiency.

Substrate inhibition of D-amino acid transaminase and protection by salts and by reduced nicotinamide adenine dinucleotide: isolation and initial characterization of a pyridoxo intermediate related to inactivation.

D-Amino acid transaminase, a pyridoxal phosphate (PLP) enzyme, is inactivated by its natural substrate, D-alanine, concomitant with its alpha-decarboxylation [Martinez del Pozo, A., Yoshimura, T., Bhatia, M. B., Futaki, S., Manning, J. M., Ringe, D., and Soda, K. (1992) Biochemistry 31, 6018-6023; Bhatia, M. B., Martinez del Pozo, A., Ringe, D., Yoshimura, T., Soda, K., and Manning, J. M. (1993) J. Biol. Chem. 268, 17687-17694]. beta-Decarboxylation of d-aspartate to d-alanine leads also to this inactivation [Jones, W. M., van Ophem, P. W., Pospischil, M. A., Ringe, D., Petsko, G., Soda, K., and Manning, J. M. (1996) Protein Sci. 5, 2545-2551]. Using a high-performance liquid chromatography-based method for the determination of pyridoxo cofactors, we detected a new intermediate closely related to the inactivation by d-alanine; its formation occurred at the same rate as the inactivation and upon reactivation it reverted to PLP. Conditions were found under which it was characterized by ultraviolet-visible spectral analysis and mass spectroscopy; it is a pyridoxamine phosphate-like compound with a C2 fragment derived from the substrate attached to the C'-4 of the pyridinium ring and it has a molecular mass of 306 consistent with this structure. In the presence of d-serine, slow accumulation of a quinonoid intermediate is also related to inactivation. The inactivation can be prevented by salts, which possibly stabilize the protonated aldimine coenzyme complex. The reduced cofactor, nicotinamide adenine dinucleotide, prevents D-aspartate-induced inactivation. Both of these events also are related to formation of the novel intermediate.