On the mechanism of the N-glycosydic bond hydrolysis of 2��-deoxyguanosine: insights from first principles calculations

The effect of the activation of the nucleobase (leaving group) or the activation of the water molecule (nucleophile) by a general acid or a general base on the hydrolysis of the N-glycosydic bond of 2??-deoxyguanosine has been analyzed by means of density functional methods. First, we have considered two limiting cases: (1) the activation of the guanine by protonation at N7 and (2) the nucleophile attack by a hydroxyl ion, to separately evaluate the two kinds of activation. Next, we have studied the simultaneous activation of the leaving group and the nucleophile by introducing models of amino acid residues such as a formic acid (HCOOH) and imidazolium (C₃N₂H₅ ⁺), methylammonium (CH₃NH₃ ⁺) and formate (HCOO^?) ions in the system. It is shown that protonation of the nucleobase greatly catalyzes the hydrolysis of the N-glycosydic bond, the reaction occurring through a stepwise (D_N*A_N) mechanism with a discrete oxocarbenium ion intermediate. However, when a H₂O nucleophile molecule is activated by a formate anion, the reaction mechanism is a concerted A_ND_N but with different degrees of dissociative character of the transition structure depending on the acid that is activating the nucleobase.     

Black-body emission from nanostructured materials

Photoluminescence (PL) experiments on materials of low thermal conductance can cause black-body emission from the sample even at low intensities of laser excitation. This thermal emission may be misinterpreted in terms of quantum emission. Although the quantum origin of most radiative emissions in nanostructured materials such as porous silicon is well established, we show in this paper that SiC nanoparticles and mechanically milled Si do exhibit thermal emission at typical excitation intensities for PL measurements provided the samples are under vacuum. An Si membrane was also investigated and the fact that it did not emit black-body radiation is explained with a simple analysis of the heating in materials of reduced dimensionality.     

The influence of solvation on the mechanism of ethylene and benzene methylation

By means of the MINDO/3 method, elcctrophilic attack of CH⁺₃ and CH⁺₃OH⁺₂ on ethylene and benzene has been studied in order to discuss the timing or desolvalion. Partial desolvation at the transition stale is found. The implications of this fact are analyzed.     

Experimental correlation between photoemission matrix elements and LEED intensities in superperiodic structures

A direct comparison between photoemission measurements and band structure calculations is sometimes tricky. Matrix element effects may affect considerably the spectral weight of the electronic states and prevent the expected translational symmetry of the band structure from being observed. We show how matrix element effects can be qualitatively described to a certain extent by making an analogy between photoemission and low energy electron diffraction. We have tested this approach in two superperiodic systems. We have first explained the intensity distribution in different Brillouin zones of a surface state in Si(1 1 1)-(7 × 7), where the surface state spectral intensity does not exhibit the (7 × 7) symmetry. We have also compared the LEED intensity of superperiodic LEED spots with the energy dependence of bulk bands on a facetted Si surface as measured by photoemission.     

Spin-polarized electron tunneling in bcc FeCo/MgO/FeCo(001) magnetic tunnel junctions

In combining spin- and symmetry-resolved photoemission, magnetotransport measurements and ab initio calculations we detangled the electronic states involved in the electronic transport in Fe(1-x)Co(x)(001)/MgO/Fe(1-x)Co(x)(001) magnetic tunnel junctions. Contrary to previous theoretical predictions, we observe a large reduction in TMR (from 530 to 200% at 20 K) for Co content above 25 atomic% as well as anomalies in the conductance curves. We demonstrate that these unexpected behaviors originate from a minority spin state with Δ(1) symmetry that exists below the Fermi level for high Co concentration. Using angle-resolved photoemission, this state is shown to be a two-dimensional state that occurs at both Fe(1-x)Co(x)(001) free surface, and more importantly at the interface with MgO. The combination of this interface state with the peculiar density of empty states due to chemical disorder allows us to describe in details the complex conduction behavior in this system.     

Kemp Elimination Reaction Catalyzed by Electric Fields

The Kemp elimination reaction is the most widely used in the de novo design of new enzymes. The effect of two different kinds of electric fields in the reactions of acetate as a base with benzisoxazole and 5-nitrobenzisoxazole as substrates have been theoretically studied. The effect of the solvent reaction field has been calculated using the SMD continuum model for several solvents; we have shown that solvents inhibit both reactions, the decrease of the reaction rate being larger as far as the dielectric constant is increased. The diminution of the reaction rate is especially remarkable between aprotic organic solvents and protic solvents as water, the electrostatic term of the hydrogen bonds being the main factor for the large inhibitory effect of water. The presence of an external electric field oriented in the direction of the charge transfer (z axis) increases it and, so, the reaction rate. In the reaction of the nitro compound, if the electric field is oriented in an orthogonal direction (x axis) the charge transfer to the NO₂ group is favored and there is a subsequent increase of the reaction rate. However, this increase is smaller than the one produced by the field in the z axis. It is worthwhile mentioning that one of the main effects of external electric fields of intermediate intensity is the reorientation of the reactants. Finally, the implications of our results in the de novo design of enzymes are discussed.     

Enumeration of labelled chain graphs and labelled essential directed acyclic graphs

A chain graph is a digraph whose strong components are undirected graphs and a directed acyclic graph (ADG or DAG) G is essential if the Markov equivalence class of G consists of only one element. We provide recurrence relations for counting labelled chain graphs by the number of chain components and vertices; labelled essential DAGs by the number of vertices. The second one is a lower bound for the number of labelled essential graphs. The formula for labelled chain graphs can be extended in such a way, that allows us to count digraphs with two additional properties, which essential graphs have.