Free-Energy Landscape of the SN2 Reaction CH3Br + Cl- → CH3Cl + Br- in Different Liquid Environments

Excited state relaxation mechanisms and tautomerism effects in 2,6-Diamino-8-Azapurine

The photochemistry of 9H-2,6-diamino-8-azapurine (9H-8AZADAP), a promising fluorescent probe, was investigated using the Multi-State Complete-Active-Space Second-Order Perturbation Theory (MS-CASPT2) quantum chemical method, along with the Average Solvent Electrostatic Configuration and Free Energy Gradient (ASEC-FEG) and Polarizable Continuum Model (PCM) to take into account water solvation effects. For both isolated and solvated species, the main photochemical event is initiated by the absorption of light from ground-state to the bright 1(ππ* La) state, which undergoes barrierless evolution to its minimum energy region (1(ππ* La)min) without crossing any other potential energy surface (PES). Subsequently, the excess of energy is released through fluorescence. From the 1(ππ* La)min region, two radiationless decay pathways back to the initial ground state, mediated by two distinct conical intersections between the ground and 1(ππ* La) states, are found to be unlikely due to the presence of high energy barriers in both environments. Our results also indicate that the solvation effects are more pronounced when using the ASEC-FEG method, which predicts larger structural and energy changes, especially concerning energetic barriers. Based on the free energy perturbation theory (FEP), a hypothetical thermodynamic cycle was devised, from which we infer that in an aqueous environment the N3 site is the most favorable for protonation. We also conclude that the 8H-8AZADAP tautomer is responsible for the fluorescent band observed experimentally at 410 nm and elucidates the mechanism of phototautomerism.

ArcaNN: automated enhanced sampling generation of training sets for chemically reactive machine learning interatomic potentials

The emergence of artificial intelligence is profoundly impacting computational chemistry, particularly through machine-learning interatomic potentials (MLIPs). Unlike traditional potential energy surface representations, MLIPs overcome the conventional computational scaling limitations by offering an effective combination of accuracy and efficiency for calculating atomic energies and forces to be used in molecular simulations. These MLIPs have significantly enhanced molecular simulations across various applications, including large-scale simulations of materials, interfaces, chemical reactions, and beyond. Despite these advances, the construction of training datasets-a critical component for the accuracy of MLIPs-has not received proportional attention, especially in the context of chemical reactivity, which depends on rare barrier-crossing events that are not easily included in the datasets. Here we address this gap by introducing ArcaNN, a comprehensive framework designed for generating training datasets for reactive MLIPs. ArcaNN employs a concurrent learning approach combined with advanced sampling techniques to ensure an accurate representation of high-energy geometries. The framework integrates automated processes for iterative training, exploration, new configuration selection, and energy and force labeling, all while ensuring reproducibility and documentation. We demonstrate ArcaNN's capabilities through two paradigm reactions: a nucleophilic substitution and a Diels-Alder reaction. These examples showcase its effectiveness, the uniformly low error of the resulting MLIP everywhere along the chemical reaction coordinate, and its potential for broad applications in reactive molecular dynamics. Finally, we provide guidelines for assessing the quality of MLIPs in reactive systems.

Synthesis and characterization of new quaternized galactomannan derivatives with antibacterial activity

The continuous increase in bacterial resistance requires the study and development of new biocompatible antibacterial materials. Galactomannan gum was extracted from endosperms of Dimorphandra gardneriana seeds, modified through quaternization reactions (with NaOH/CHPTAC), and evaluated for antimicrobial activity. Four quaternized derivatives were obtained (QG1-QG4). The derivatives were characterized by FTIR, NMR, and rheology, which confirmed the cationization. The galactomannan structure was theoretically studied, and Zeta potential exhibited positive increase in the charge of quaternized derivatives, changing from -3.2 mV (unmodified galactomannan) to +59.35 mV (QG4). Elemental analysis revealed an increase in degree of substitution (DS) between the derivatives, of which QG4 exhibited the highest DS (0.51). QG4 exhibited a bactericidal effect in the antimicrobial test for determination of minimal inhibitory and bactericidal concentrations, against Gram-positive bacteria. Atomic force microscopy showed an increase in bacterial cell surface roughness and decrease in cell height after treatment with QG4. QG3 and QG4 demonstrated antibiofilm potential, showing 50 % and 40 % of inhibition, respectively. After MTT assay, cell viability was maintained approximately 100 % for all derivatives at concentrations of 20 mg/mL on RAW 264.7 macrophages and 86 % with 250 μg/mL on L929 cells. Galactomannan was successfully modified, demonstrating strong antibacterial activity, concomitant to the increase in DS, Zeta potential and reduction of molar mass, with good biocompatibility. Therefore, this study presents a new material with potential for development of formulations for biomedical applications, from industrial waste, strengthening of the D. gardneriana production chain.

Blueshift in Trifurcated Hydrogen Bonds: A Tradeoff between Tetrel Bonding and Steric Repulsion

We have quantum chemically investigated the origin of the atypical blueshift of the H-C bond stretching frequency in the hydrogen-bonded complex X- •••H3 C-Y (X, Y=F, Cl, Br, I), as compared to the corresponding redshift occurring in Cl- •••H3 N and Cl- •••H3 C-H, using relativistic density functional theory (DFT) at ZORA-BLYP-D3(BJ)/QZ4P. Previously, this blueshift was attributed, among others, to the contraction of the H-C bonds as the H3 C moiety becomes less pyramidal. Herein, we provide quantitative evidence that, instead, the blueshift arises from a direct and strong X- •••C interaction of the HOMO of A- with the backside lobe on carbon of the low-lying C-Y antibonding σ* LUMO of the H3 C-Y fragment. This X- •••C bond, in essence a tetrel bond, pushes the H atoms towards a shorter H-C distance and makes the H3 C moiety more planar. The blueshift may, therefore, serve as a diagnostic for tetrel bonding.

Origin of the Microsolvation Effect on the Central Barriers of SN2 Reactions

We have quantitatively analyzed the microsolvation effect on the central barriers of microsolvated bimolecular nucleophilic substitution (S_N2) reactions by means of a two-step energy decomposition procedure. According to the first energy decompositions, an obvious increase in the central barrier for a microsolvated S_N2 reaction against its unsolvated counterpart can be mainly ascribed to the fact that the interaction between the solute and the conjunct solvent becomes less attractive from the reactant complex to the transition state. On the basis of the second energy decompositions with symmetry-adapted perturbation theory, this less attractive interaction in the transition state is primarily due to the interplay of the changes in the electrostatic, exchange, and induction components. However, the contribution of the change for the dispersion component is relatively small. A distinct linear correlation has also been observed between the changes of the total interaction energies and those of the corresponding electrostatic components for the microsolvated S_N2 reactions studied in this work. Moreover, the two-step energy decomposition procedure employed in this work is expected to be extensively applied to the gas phase reactions mediated by molecules or clusters.