Unravelling Enzymatic Features in a Supramolecular Iridium Catalyst by Computational Calculations

Non-biological catalysts following the governing principles of enzymes are attractive systems to disclose unprecedented reactivities. Most of those existing catalysts feature an adaptable molecular recognition site for substrate binding that are prone to undergo conformational selection pathways. Herein, we present a non-biological catalyst that is able to bind substrates via the induced fit model according to in-depth computational calculations. The system, which is constituted by an inflexible substrate-recognition site derived from a zinc-porphyrin in the second coordination sphere, features destabilization of ground states as well as stabilization of transition states for the relevant iridium-catalyzed C−H bond borylation of pyridine. In addition, this catalyst appears to be most suited to tightly bind the transition state rather than the substrate. Besides these features, which are reminiscent of the action modes of enzymes, new elementary catalytic steps (i. e. C−B bond formation and catalyst regeneration) have been disclosed owing to the unique distortions encountered in the different intermediates and transition states.     

Variational transition state theory without the minimum-energy path

In this paper we propose a method for carrying out variational transition state theory calculations without first obtaining a converged minimum-energy path (MEP). We illustrate the method in two ways, first of all by employing an unconverged MEP and secondly by using a dynamically optimized distinguished reaction path. Preliminary tests of the algorithm for the reactions OH+H₂→H₂O+H and C₂H₅→C₂H₄+H are very encouraging. Received: 22 January 1997 / Accepted: 11 March 1997     

Controlling Antibacterial Activity Exclusively with Visible Light: Introducing a Tetra-ortho-Chloro-Azobenzene Amino Acid

The introduction of a novel tetra-ortho-chloroazobenzene amino acid (CEBA) has enabled photoswitching of the antimicrobial activity of tyrocidine A analogues by using exclusively visible light, granting spatiotemporal control under benign conditions. Compounds bearing this photoswitchable amino acid become active upon irradiation with red light, but quickly turn-off upon exposure to other visible light wavelengths. Critically, sunlight quickly triggers isomerisation of the red light-activated compounds into their original trans form, offering an ideal platform for self-deactivation upon release into the environment. Linear analogues of tyrocidine A were found to provide the best photocontrol of their antimicrobial activity, leading to compounds active against Acinetobacter baumannii upon isomerisation. Exploration of their N- and C-termini has provided insights into key elements of their structure and has allowed obtaining new antimicrobials displaying excellent strain selectivity and photocontrol.     

Analysis of NH3-TPD Profiles for CuSSZ-13 SCR Catalyst of Controlled Al Distribution – Complexity Resolved by First Principles Thermodynamics of NH3 Desorption,IR and EPR Insight into Cu Speciation**

NH₃ temperature-programmed desorption (NH₃-TPD) is frequently used for probing the nature of the active sites in CuSSZ-13 zeolite for selective catalytic reduction (SCR) of NO_x. Herein, we propose an interpretation of NH₃-TPD results, which takes into account the temperature-induced dynamics of NH₃ interaction with the active centers. It is based on a comprehensive DFT/GGA+D and first-principles thermodynamic (FPT) modeling of NH₃ adsorption on single Cu²⁺, Cu⁺, [CuOH]⁺ centers, dimeric [Cu-O-Cu]²⁺, [Cu-O₂²⁻-Cu]² species, segregated CuO nanocrystals and Brønsted acid sites (BAS). Theoretical TPD profiles are compared with the experimental data measured for samples of various Si/Al ratios and distribution of Al within the zeolite framework. Copper reduction, its relocation, followed by the intrazeolite olation/oxolation processes, which are concomitant with NH₃ desorption, were revealed by electron paramagnetic resonance (EPR) and IR. DFT/FPT results show that the peaks in the desorption profiles cannot be assigned univocally to the particular Cu and BAS centers, since the observed low-, medium- and high-temperature desorption bands have contributions coming from several species, which dynamically change their speciation and redox states during NH₃-TPD experiment. Thus, a rigorous interpretation of the NH₃-TPD profiles of CuSSZ-13 in terms of the strength and concentration of the active centers of a particular type is problematic. Nonetheless, useful connections for molecular interpretation of TPD profiles can be established between the individual component peaks and the corresponding ensembles of the adsorption centers.     

Acid-Catalyzed RNA-Oligomerization from 3’,5’-cGMP

The assembly of ancient informational polymers from nucleotide precursors is the central challenge of life's origin on our planet. Among the possible solutions, dry polymerization of 3’,5’-cyclic guanosine monophosphate (3’,5’-cGMP) has been proposed as a candidate to create oligonucleotides of 15–20 units in length. However, the reported sensitivity of the reaction to the presence of cations raised questions of whether this chemistry could be relevant in a geological context. The experiments in this study show that the presence of cations is not restrictive as long as the reaction is conducted in an acidic environment, in contrast to previous reports that suggested optimal conditions at pH 9.     

Comprehensive Characterization of the Self-Folding Cavitand Dynamics

The conformational equilibria and guest exchange process of a resorcin[4]arene derived self-folding cavitand receptor have been characterized in detail by molecular dynamics simulations (MD) and ¹H EXSY NMR experiments. A multi-timescale strategy for exploring the fluxional behaviour of this system has been constructed, exploiting conventional MD and accelerated MD (aMD) techniques. The use of aMD allows the reconstruction of the folding/unfolding process of the receptor by sampling high-energy barrier processes unattainable by conventional MD simulations. We obtained MD trajectories sampling events occurring at different timescales from ns to s: 1) rearrangement of the directional hydrogen bond seam stabilizing the receptor, 2) folding/unfolding of the structure transiting partially open intermediates, and 3) guest departure from different folding stages. Most remarkably, reweighing of the biased aMD simulations provided kinetic barriers that are in very good agreement with those determined experimentally by ¹H NMR. These results constitute the first comprehensive characterization of the complex dynamic features of cavitand receptors. Our approach emerges as a valuable rational design tool for synthetic host-guest systems