Kudi: A free open-source python library for the analysis of properties along reaction paths

Non-covalent interactions and charge transfer in the CO 2 activation by low-valent group 14 complexes

CONTEXT

The CO2 activation by low-valent group 14 catalysts encompasses the rupture of varied covalent bonds in a single transition state through a concerted pathway. The bond between the central main group atom and the hydride in the complex is elongated to trigger the formation of the C-H bond with CO2 accompanied by the concomitant formation of the E-O bond between the complex and CO2 to lead the corresponding formate product. Prior studies have established that besides the apolar nature of CO2 , its initial interaction with the complex is primarily governed by electrostatic interactions. Notably, other stabilizing interactions and the transfer of charge between catalysts and CO2 during the initial phases of the reaction have been ignored. In this study, we have quantified the non-covalent interactions and charge transfer that facilitate the activation of CO2 by group 14 main group complex. Our findings indicate that electrostatic interactions predominantly stabilize the complex and CO2 in the reactant region. However, induction energy becomes the main stabilizing force as the reaction progresses towards the transition state, surpassing electrostatics. Induction contributes about 50% to the stabilization at the transition state, followed by electrostatics (40%) and dispersion interactions (10%). Atomic charges calculated with the minimal basis iterative stockholder (MBIS) method reveal larger charge transfer for the back-side reaction path in which CO2 approaches the catalysts in contrast to the front-side approach. Notably, it was discovered that a minor initial bending of CO2 to approximately 176 ∘ initiates the charge transfer process for all systems. Furthermore, our investigation of group 14 elements demonstrates a systematic reduction in both activation energies and charge transfer to CO2 while descending in group 14.

METHODS

All studied reactions were characterized along the reaction coordinate obtained with the intrinsic reaction coordinate (IRC) methodology at the M06-2X/6-31 g(d,p) level of theory. Gibbs free energy in toluene was computed using electronic energies at the DLPNO-CCSD(T)/cc-pVTZ-SSD(E) level of theory. Vibrational and translational entropy corrections were applied to provide a more accurate description of the obtained Gibbs free energies. To better characterize the changes in the reaction coordinate for all reactions, the reaction force analysis (RFA) has been employed. It enables the partition of the reaction coordinate into the reactant, transition state, and product regions where different stages of the mechanism occur. A detailed characterization of the main non-covalent driving forces in the initial stages of the activation of CO2 by low-valent group 14 complexes was performed using symmetry-adapted perturbation theory (SAPT). The SAPT0-CT/def2-SVP method was employed for these computations. Charge transfer descriptors based on atomic population using the MBIS scheme were also obtained to complement the SAPT analyses.

Insights into the variations of kinetic and potential energies in a multi-bond reaction: the reaction electronic flux perspective

CONTEXT

The debate over whether kinetic energy (KE) or potential energy (PE) are the fundamental energy components that contribute to forming covalent bonds has been enduring and stimulating over time. However, the supremacy of these energy components in reactions where multiple bonds are simultaneously formed or broken has yet to be explored. In this study, we use the reaction electronic flux (REF), an effective tool for investigating changes in driving electronic activity when bond formation or dissociation occurs in a chemical reaction, to examine the fluctuations in the KE and PE in a multi-bond reaction. To that end, the activation of CO2 by low-valent group 14 catalysts through a concerted σ -bond metathesis mechanism is analyzed. The findings of this preliminary study suggest that the REF can be utilized as a tool to rationalize alterations in the KE and PE in a multi-bond reaction. Specifically, analyses across the reaction coordinate reveal that changes in the KE and PE precede activation in the REF, stimulating the electronic activity where bond formation or dissociation processes dominate.

METHODS

The activation of CO2 by the low-valent LEH catalysts (L = N,N'-bis(2,6-diisopropyl phenyl)- β -diketiminate; E = Si, Ge, Sn, and Pb) was studied along the reaction coordinate at the M06-2X/6-31 G(d,p)-LANL2DZ(E) level of theory. The respective minimum energy path calculations were obtained using the intrinsic reaction coordinate (IRC) procedure. The reaction electronic flux (REF) was calculated through the computation of the electronic chemical potential using the frontier molecular orbital approximation. Mayer bond orders along the reaction coordinate have been determined using the NBO 3.1 program in Gaussian16. Most of the reaction coordinate quantities reported in this study (REF, KE, PE, among others) have been determined using the Kudi program and custom Python scripts.

In-depth exploration of catalytic sites on amorphous solid water: I. The astrosynthesis of aminomethanol

Chemical processes taking place on ice-grain mantles are pivotal to the complex chemistry of interstellar environments. In this study, we conducted a comprehensive analysis of the catalytic effects of an amorphous solid water (ASW) surface on the reaction between ammonia (NH3) and formaldehyde (H2CO) to form aminomethanol (NH2CH2OH) using density functional theory. We identified potential catalytic sites based on the binding energy distribution of NH3 and H2CO reactants, on a set-of-clusters surface model composed of 22 water molecules and found a total of 14 reaction paths. Our results indicate that the catalytic sites can be categorized into four groups, depending on the interactions of the carbonyl oxygen and the amino group with the ice surface in the reactant complex. A detailed analysis of the reaction mechanism using Intrinsic Reaction Coordinate and reaction force analysis, revealed three distinct chemical events for this reaction: formation of the C-N bond, breaking of the N-H bond, and formation of the O-H hydroxyl bond. Depending on the type of catalytic site, these events can occur within a single, concerted, albeit asynchronous, step, or can be isolated in a step-wise mechanism, with the lowest overall transition state energy observed at 1.3 kcal mol-1. A key requirement for the low-energy mechanism is the presence of a pair of dangling OH bonds on the surface, found at 5% of the potential catalytic sites on an ASW porous surface.

Python tools for structural tasks in chemistry

In recent decades, the use of computational approaches and artificial intelligence in the scientific environment has become more widespread. In this regard, the popular and versatile programming language Python has attracted considerable attention from scientists in the field of chemistry. It is used to solve a variety of chemical and structural problems, including calculating descriptors, molecular fingerprints, graph construction, and computing chemical reaction networks. Python offers high-quality visualization tools for analyzing chemical spaces and compound libraries. This review is a list of tools for the above tasks, including scripts, libraries, ready-made programs, and web interfaces. Inevitably this manuscript does not claim to be an all-encompassing handbook including all the existing Python-based structural chemistry codes. The review serves as a starting point for scientists wishing to apply automatization or optimization to routine chemistry problems.

Interacting Quantum Atoms Analysis of the Reaction Force: A Tool to Analyze Driving and Retarding Forces in Chemical Reactions

The analysis of the reaction force and its topology has provided a wide range of fruitful concepts in the theory of chemical reactivity over the years, allowing to identify chemically relevant regions along a reaction profile. The reaction force (RF), a projection of the Hellmann-Feynman forces acting on the nuclei of a molecular system onto a suitable reaction coordinate, is partitioned using the interacting quantum atoms approach (IQA). The exact IQA molecular energy decomposition is now shown to open a unique window to identify and quantify the chemical entities that drive or retard a chemical reaction. The RF/IQA coupling offers an extraordinarily detailed view of the type and number of elementary processes that take reactants into products, as tested on two sets of simple reactions.

High level potential energy surface and mechanism of Al(CH3)2OCH3-promoted lactone polymerization: initiation and propagation

A hitherto unreported, second transition state (TS2) is the stationary state with the highest relative energy of the Al(CH₃)₂OCH₃ + glycolide initiation reaction.