A QM/MM Study of Nitrite Binding Modes in a Three-Domain Heme-Cu Nitrite Reductase

Copper-containing nitrite reductases (CuNiRs) play a key role in the global nitrogen cycle by reducing nitrite (NO2−) to nitric oxide, a reaction that involves one electron and two protons. In typical two-domain CuNiRs, the electron is acquired from an external electron-donating partner. The recently characterised Rastonia picketti (RpNiR) system is a three-domain CuNiR, where the cupredoxin domain is tethered to a heme c domain that can function as the electron donor. The nitrite reduction starts with the binding of NO2− to the T2Cu centre, but very little is known about how NO2− binds to native RpNiR. A recent crystallographic study of an RpNiR mutant suggests that NO2− may bind via nitrogen rather than through the bidentate oxygen mode typically observed in two-domain CuNiRs. In this work we have used combined quantum mechanical/molecular mechanical (QM/MM) methods to model the binding mode of NO2− with native RpNiR in order to determine whether the N-bound or O-bound orientation is preferred. Our results indicate that binding via nitrogen or oxygen is possible for the oxidised Cu(II) state of the T2Cu centre, but in the reduced Cu(I) state the N-binding mode is energetically preferred.

Low Frequency Raman Modes of Bi2 −x PbxSr1.6Ln0.4CuO6 −δ

Raman measurements were made on polycrystalline Bi2xPbxSr1:6Ln0:4CuO6 for Ln=fLa,Nd, Sm, Eug with various x and doping states. Our measurements suggest a signi cant Bicontribution to the 118cm1 mode but not to the 70cm1 mode which instead shifts to lowerfrequencies with increasing number of CuO2 layers in the Bi-based family. Shifts in the O(2)Srapical oxygen mode can be attributed to unit cell contraction within experimental error.

Optical phonons polarized along the c axis of YBa2Cu3O6+x, for x = 0.5 → 0.95

The c-axis polarized phonon spectra of single crystals of YBa2Cu3O6+x, were measured for the doping range x = 0.5 → 0.95, between 10 and 300 K. The low background electronic conductivity, determined by Kramers–Kronig analysis of the reflectance, leads to a rich phonon structure. With decreased doping the five normally-active B1u modes broaden and the high-frequency apical-oxygen mode splits into two components. We associate the higher of these with the two-fold coordinated copper "sticks". The 155 cm−1 low-frequency mode, which involves the apical and the chain oxygens, splits into at least three components with decreasing doping. Some phonon anomalies that occur near Tc in the highly doped material occur well above Tc in the oxygen-reduced systems. An unusual broad phonon band develops in the normal state at ≈ 400 cm−1, which becomes more intense at low doping and low temperatures, borrowing oscillator strength from apical- and plane-oxygen modes resulting in a major transformation of the phonon spectrum below ≈150 K.