On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations

The way in which enzymes influence the rate of chemical processes is still a question of debate. The protein promotes the catalysis of biochemical processes by lowering the free energy barrier in comparison with the reference uncatalyzed reaction in solution. In this article we are reporting static and dynamic aspects of the enzyme catalysis in a bimolecular reaction, namely a methyl transfer from S-adenosylmethionine to the hydroxylate oxygen of a substituted catechol catalyzed by catechol O-methyltransferase. From QM/MM optimizations, we will first analyze the participation of the environment on the transition vector. The study of molecular dynamics trajectories will allow us to estimate the transmission coefficient from a previously localized transition state as the maximum in the potential of mean force profile. The analysis of the reactive and nonreactive trajectories in the enzyme environment and in solution will also allow studying the geometrical and electronic changes, with special attention to the chemical system movements and the coupling with the environment. The main result, coming from both analyses, is the approximation of the magnesium cation to the nucleophilic and the hydroxyl group of the catecholate as a result of a general movement of the protein, stabilizing in this way the transition state. Consequently, the free energy barrier of the enzyme reaction is dramatically decreased with respect to the reaction in solution.     

Multichannel digital transmission in an optical network of communicating molecules

In present telecommunication networks, information transfer relies on the interplay of optical and electrical signals. Data are communicated optically but processed electronically. Methods to maintain the propagating signals solely at the optical level must be developed to overcome the transmission capacities and speed limits imposed by the electronic components. We have demonstrated that molecular switches can be used to gate optical signals in response to optical signals. We have realized a simple optical network consisting of three light sources, one cell containing a solution of three fluorescent molecules, one cell containing a solution of a three-state molecular switch and a detector. The light emitted by the three fluorophores is absorbed by the three states of the molecular switch. Using this simple operating principle, we have shown that multichannel digital transmission can be implemented on an ensemble of communicating molecules relying exclusively on the interplay of optical inputs and optical outputs.     

Electron impact mass spectrometric investigation of pyrrole mono-, di- and tri-carboxylic acids

The electron impact-induced fragmentation processes of pyrrole-2-, -3-, -2,3-, -3,4-, -2,5- and -2,3,4-carboxylic acids were investigated with the aid of metastable ion, collisional and deuterium labelling experiments. The general behaviour of these compounds is discussed in detail, together with the reasonable structures of the more relevant fragment ions.     

Controlling the self-assembly of a deoxiguaninosine on mica

We report a tapping mode scanning force microscopy investigation on the growth from solutions of a lipophilic deoxiguanosine derivative on the basal plane of a muscovite mica surface. By varying the chemical composition of the substrate surface it is possible to drive the self-assembly towards either layered thin films, which are very likely to consist of guanosine quartets, or nanoribbons, comprising hydrogen bonded networks. Both these two architectures, which are peculiar to the guanine base itself, are of notable importance for the fabrication of molecular nanowires. Moreover, the first arrangement provides evidence that the guanosine is able to behave as ionophore, thus, suggesting its utilization in the development of solid-state ion selective sensors.     

Conformational and photophysical studies on porphyrin-containing donor-bridge-acceptor compounds. Charge separation in micellar nanoreactors

Photophysical studies with semi-rigid, 1, and flexible, 2, donor-bridge-acceptor (D-b-A2+) molecules with D a porphyrin and A2+ a methyl viologen moiety, were performed in neat polar solvents as well as included in surfactant (DTAB) aqueous and in reverse AOT/n-alkane micelles. The micelles acted as nanoreactors for the photoinduced electron transfer reaction upon laser excitation. In spite of the longer lifetime of the charge separated (CS) state in the semi-rigid tetrad 1(ca. 200 ns vs. ca. 100 ns for the flexible dyad 2), the CS formation quantum yield, for example in acetonitrile, was lower for the former (phi(CS) = 0.13) than for the latter (0.58). Comparison of the time-resolved fluorescence data in neat solvent and in the micelles yielded the phi(CS) values in the dilute micellar solutions. Application of laser-induced optoacoustic spectroscopy at various temperatures to 1 dissolved in a polar organic solvent (benzonitrile, BZN) included in aqueous DTAB nanoreactors afforded structural volume changes for the production in hundreds of ps of the CS state upon excitation of a polar molecule. The contraction during CS formation upon excitation of the collapsed conformer in BZN is attributed to the entering of solvent into the open molecular cavity. The opening upon formation of the CS state due to photoinduced electron transfer in the 1 collapsed conformation arises from the repulsion of the two positively charged ends in this state, as previously calculated. Inclusion of 1 in reverse AOT micelles in various n-alkanes also led to a contraction upon excitation, but the data had much more error due to the limited range of variability of the ratio of thermoelastic parameters. The data obtained with the more flexible "supermolecule" 2 showed the predicted large conformation flexibility of these molecules.     

Lewis acid promoted aldol additions of α-thiosilylketeneacetals to α-alkoxy aldehydes: diastereoselective synthesis of syn-α-methylene-β-hydroxy-∂-alkoxy esters.

MgBr₂ mediated addition of Methyl α-methylthio propionate silylketene acetal to α and α,β-alkoxy aldehydes is highly 3,4 $\text{syn}$-selective (18:1). $\text{syn}$-α- methylene-β- hydroxy-?-alkoxy esters (6) and (8) are synthesized.     

Interaction between zigzag single-wall carbon nanotubes and polymers: a density-functional study

Density-functional all-electrons calculations within local-density approximation show that the two isoelectronic polymers poly(para-phenylene) and poly(para-borazylene) weakly interact with zigzag single-walled carbon nanotubes. The analysis of the electronic properties of the joint systems, both with the polymer inside and outside the nanotubes, reveals a physisorption process with small changes in band structures and densities of states with respect to the constituents. We evaluate the potential barrier arising between polymers and nanotubes. Finally, we remark a generic selectivity of poly(para-phenylene) with respect to the electronic behavior of nanotubes, leading to a change in the density of states of metallic tubules.