Hydroxylamine oxidoreductase (HAO) from the autotrophic nitrifying bacterium Nitrosomonas europaea catalyzes the oxidation of NH 2 OH to NO 2 -. The enzyme contains eight hemes per subunit which participate in catalysis and electron transport. NO is found to bind to the enzyme and inhibit electron flow to the acceptor protein, cytochrome c 554 . NO is found to oxidize either partially or fully reduced HAO, but NO will not reduce ferric HAO. Since NO can be reduced but not oxidized to product by HAO, NO is not considered to be a long-lived intermediate in the catalytic mechanism. Substrate oxidation occurs in the presence of bound NO or cyanide, suggesting a second interaction site for substrate with HAO and providing a means for recovery of the NO-inhibited form of the enzyme. Upon addition of NO to oxidized HAO, the integer-spin EPR signal from the active site vanishes, an IR band from NO appears at 1920 cm -1 , and a diamagnetic quadrupole iron doublet appears in Mössbauer spectroscopy with δ ) 0.06 mm/s and ∆Eq ) 2.1 mm/s. The NO stretching frequency and Mössbauer parameters are characteristic of an {FeNO} 6 heme complex. New Mössbauer data on ferric myoglobin-NO are also presented for comparison. The results indicate that NO binds to heme P460 and that the loss of the integer-spin EPR signal is due to the conversion of heme P460 to a diamagnetic S ) 0 state and concomitant loss of magnetic interaction with neighboring heme 6. In previous studies where the heme P460-heme 6 interaction was affected by substrate or cyanide binding, a signal attributable to heme 6 was not observable. In contrast, in this work, the NO-induced loss of the signal is accompanied by the appearance of a previously unobserved large g max (or HALS) low-spin EPR signal from heme 6.

In this paper, we present simulations of the decay of quantum coherence between vibrational states of I(2) in its ground (X) electronic state embedded in a cryogenic Kr matrix. We employ a numerical method based on the semiclassical limit of the quantum Liouville equation, which allows the simulation of the evolution and decay of quantum vibrational coherence using classical trajectories and ensemble averaging. The vibrational level-dependent interaction of the I(2)(X) oscillator with the rare-gas environment is modeled using a recently developed method for constructing state-dependent many-body potentials for quantum vibrations in a many-body classical environment [J. M. Riga, E. Fredj, and C. C. Martens, J. Chem. Phys. 122, 174107 (2005)]. The vibrational dephasing rates gamma(0n) for coherences prepared between the ground vibrational state mid R:0 and excited vibrational state mid R:n are calculated as a function of n and lattice temperature T. Excellent agreement with recent experiments performed by Karavitis et al. [Phys. Chem. Chem. Phys. 7, 791 (2005)] is obtained.

In this paper we describe an application of the trajectory-based semiclassical Liouville method for modeling coherent molecular dynamics on multiple electronic surfaces to the treatment of the evolution and decay of quantum electronic coherence in many-body systems. We consider a model representing the coherent evolution of quantum wave packets on two excited electronic surfaces of a diatomic molecule in the gas phase and in rare gas solvent environments, ranging from small clusters to a cryogenic solid. For the gas phase system, the semiclassical trajectory method is shown to reproduce the evolution of the electronic-nuclear coherence nearly quantitatively. The dynamics of decoherence are then investigated for the solvated systems using the semiclassical approach. It is found that, although solvation in general leads to more rapid and extensive loss of quantum coherence, the details of the coupled system-bath dynamics are important, and in some cases the environment can preserve or even enhance quantum coherence beyond that seen in the isolated system.

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In this paper, we present a method for constructing simple state-dependent many-body potentials for quantum vibrations in a classical bath. The approach is based on an adiabatic separation between high-frequency quantum vibrational modes of the solute and the lower frequency classical motion of the solvent, and on a first-order perturbation theory description of the dependence of the quantum energies on bath configuration. In the simplest realization of the method, the delocalized quantum probability density of the vibrational mode is approximated by a sum of two delta functions, with positions and weights chosen to represent the lowest three moments of the exact distribution. Thus, in the many-body description of the system, each atom describing the quantum vibration is represented by a pair of particles. These quantum particles are held in rigid relative position and interact with the bath via potentials the magnitudes of which are modified by the delta-function weights. The resulting approach allows the classical molecular dynamics of molecules in arbitrary quantum vibrational states to be simulated with a little more effort than a purely classical description. The applicability of the method is illustrated in many-body simulations of the dephasing of vibrational superposition states of I(2) in a cryogenic krypton matrix, yielding results in good agreement with experiment.

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Electron emission into a nanogap is not instantaneous, which presents a difficulty in simulating ultra-fast behavior using particle models. A method of approximating the transmission and reflection delay (TARD) times of a wave packet interacting with barriers described by a delta function, a metal–insulator–metal (MIM, rectangular) barrier, and a Fowler Nordheim (FN, triangular) barrier is given and has application to simulation. It is based on the superposition of a finite number of exact basis states obtained from Schrödinger’s equation, analogous to how quantum carpets are simulated. As a result, it can exactly and uniquely follow exponentially small tunneling currents. A Bohm-like trajectory is obtained from the time evolution of the density: it shows delay in both the transmitted and reflected packets that can be simply evaluated. The relations to prior studies of the analytic [Formula: see text]-function barrier and the Wigner distribution function (WDF) methods are described. A comparison of the TARD times is contrasted to alternate times in the Büttiker–Landauer (BL) and McColl–Hartman (MH) times; the MH approach is further reformulated explicitly in terms of Gamow factors to consider how the McColl–Hartman effect is to be related, particularly in the case of the FN barrier of field emission.