Ethylene biosynthesis by 1-aminocyclopropane-1-carboxylic acid oxidase: a DFT study

The reaction catalyzed by the plant enzyme 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO) was investigated by using hybrid density functional theory. ACCO belongs to the non-heme iron(II) enzyme superfamily and carries out the bicarbonate-dependent two-electron oxidation of its substrate ACC (1-aminocyclopropane-1-carboxylic acid) concomitant with the reduction of dioxygen and oxidation of a reducing agent probably ascorbate. The reaction gives ethylene, CO(2), cyanide and two water molecules. A model including the mononuclear iron complex with ACC in the first coordination sphere was used to study the details of O-O bond cleavage and cyclopropane ring opening. Calculations imply that this unusual and complex reaction is triggered by a hydrogen atom abstraction step generating a radical on the amino nitrogen of ACC. Subsequently, cyclopropane ring opening followed by O-O bond heterolysis leads to a very reactive iron(IV)-oxo intermediate, which decomposes to ethylene and cyanoformate with very low energy barriers. The reaction is assisted by bicarbonate located in the second coordination sphere of the metal.     

The lowest 2A' excited state of the water-hydroxyl complex

Vertical and adiabatic excitation energies of the lowest (2)A(') excited state in the water-hydroxyl complex have been determined using coupled cluster, multireference configuration interaction, multireference perturbation theory, and density-functional methods. A significant redshift of about 0.4 eV in the vertical excitation energy of the complex compared to that of the hydroxyl radical monomer is found with the coupled cluster calculations validating previous results. Electronic excitation leads to a structure with near-equal sharing of the hydroxyl hydrogen by both oxygen atoms and a concomitantly large redshift of the adiabatic excitation energy of approximately 1 eV relative to the vertical excitation energy. The combination of redshifts ensures that the electronic transition in the complex lies well outside the equivalent excitation in the hydroxyl radical monomer. The complex is approximately five times more strongly bound in the excited state than in the ground state.     

An overlooked series of gas phase diatomic metal oxide ions that are long-lived

Although the "Golden" years of spectroscopy and the major studies on ionization processes now are behind us, as with many branches of science, much yet remains to be gleaned from such topics that is both full of interest and of significance to present day research. Presented here is one such overlooked example, an observation that relates to both these fields. An analysis is presented for the periodic table concerning the gas-phase thermochemical nature of MO+ and MO2+ ions. Unexpectedly, a pattern of 18 elements has been identified that exhibit the potential for having long-lived MO+ ions. Normally such molecular ions are expected to decay extremely rapidly by dissociative recombination with electrons, but in particular, 12 of this group behave not like molecules but rather as atomic ions. These are the diatomic oxide ions of Sc, Y, La, Zr, Hf, Ce, Pr, Nd, Pm, Gd, Tb, and Th. In the gas phase, they decay by much slower three-body recombination channels. As may be noted, these elements are located in the first two columns of the transition elements, among the earlier rare earths and an actinide. From all the elements, UO2+ is the only dioxide ion that behaves similarly. These findings now elevate the potential importance of these ions and should facilitate their spectral characterization. Moreover, subsequent comparisons with spectra of well-known isoelectronic and isovalent neutral monoxides and other diatomics will help in the stimulation of further theoretical advances. In addition, once characterized, an ease of spectrally monitoring such ionic states will provide a useful analytical tool.     

Understanding the low-frequency quasilocalized modes in disordered colloidal systems

In disordered colloidal systems, we experimentally measure the normal modes with the covariance matrix method and clarify the origin of low-frequency quasilocalization at the single-particle level. We observe important features from both jamming and glass simulations: There is a plateau in the density of states [D(ω)] which is suppressed upon compression, as predicted by jamming; within the same systems, we also find that the low-frequency quasilocalization originates from the large vibrations of defective structures coupled with transverse excitations, consistent with a recent glass simulation. The coexistence of these features demonstrates an experimental link between jamming and glass. Extensive simulations further show that such a structural origin of quasilocalization is universally valid for various temperatures and volume fractions.     

Modeling of solvent flow effects in enzyme catalysis under physiological conditions

A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with absorbing boundaries are combined with densities obtained from explicit simulation to obtain the overall probability density for the total reaction cycle time of the enzymatic system. The method is used to investigate the catalytic transfer of a phosphoryl group in a phosphoglycerate kinase-ADP-bis phosphoglycerate system, one of the steps of glycolysis. The direct simulation of the enzyme-substrate binding and reaction is carried out using an elastic network model for the protein, and the solvent motions are described by multiparticle collision dynamics which incorporates hydrodynamic flow effects. Systems where solvent-enzyme coupling occurs through explicit intermolecular interactions, as well as systems where this coupling is taken into account by including the protein and substrate in the multiparticle collision step, are investigated and compared with simulations where hydrodynamic coupling is absent. It is demonstrated that the flow of solvent particles around the enzyme facilitates the large-scale hinge motion of the enzyme with bound substrates, and has a significant impact on the shape of the probability densities and average time scales of substrate binding for substrates near the enzyme, the closure of the enzyme after binding, and the overall time of completion of the cycle.     

Shock-induced collapse of a cylindrical air cavity in water: a Free-Lagrange simulation

A Free-Lagrange CFD code is used to simulate the collapse of a cylindrical air cavity in water by a 1.9 GPa incident shock. The Lagrangian treatment allows the air/water interface to be tracked throughout the interaction. The incident shock is partially transmitted into the cavity, within which it experiences multiple reflections. The upstream cavity wall involutes to form a high-speed jet which, on impact with the far cavity wall, produces an intense blast wave. Heating of the gas within the cavity is highly non-isentropic, and is dominated by shock heating. The predicted final gas temperature is of order 12000 K, although the modelling assumptions used here lead to over-prediction of temperature during the later stages of collapse. Received 14 September 1999 / Accepted 28 June 2000     

A New Mechanism for β‐Lactamases: Class D Enzymes Degrade 1β‐Methyl Carbapenems through Lactone Formation

β‐Lactamases threaten the clinical use of carbapenems, which are considered antibiotics of last resort. The classical mechanism of serine carbapenemase catalysis proceeds through hydrolysis of an acyl‐enzyme intermediate. We show that class D β‐lactamases also degrade clinically used 1β‐methyl‐substituted carbapenems through the unprecedented formation of a carbapenem‐derived β‐lactone. β‐Lactone formation results from nucleophilic attack of the carbapenem hydroxyethyl side chain on the ester carbonyl of the acyl‐enzyme intermediate. The carbapenem‐derived lactone products inhibit both serine β‐lactamases (particularly class D) and metallo‐β‐lactamases. These results define a new mechanism for the class D carbapenemases, in which a hydrolytic water molecule is not required.