Can molecular and atomic descriptors predict the electrophilicity of Michael acceptors?

The Amsterdam Modeling Suite

In this paper, we present the Amsterdam Modeling Suite (AMS), a comprehensive software platform designed to support advanced molecular and materials simulations across a wide range of chemical and physical systems. AMS integrates cutting-edge quantum chemical methods, including Density Functional Theory (DFT) and time-dependent DFT, with molecular mechanics, fluid thermodynamics, machine learning techniques, and more, to enable multi-scale modeling of complex chemical systems. Its design philosophy allows for seamless coupling between components, facilitating simulations that range from small molecules to complex biomolecular and solid-state systems, making it a versatile tool for tackling interdisciplinary challenges, both in industry and in academia. The suite also emphasizes user accessibility, with an intuitive graphical interface, extensive scripting capabilities, and compatibility with high-performance computing environments.

Towards a complete description of the reaction mechanisms between nitrenium ions and water

CONTEXT

Nitrenium ions are intermediates in the metabolic routes producing the highly carcinogenic nitrosamines and binding to DNA molecules. The reaction mechanism of nitrenium molecules with explicit water molecules is sensibly dependent on the number of waters: when a second molecule is involved, it acts as a catalyst for the reaction, lowering intrinsic activation barriers regardless of the substituent. For all cases, the reaction force constants and reaction electron flux indicate highly synchronous reactions for n = 1 . Conversely, for n = 2 highly non-synchronous reactions are obtained, involving two separate proton transfers happening early and late in the reaction path. As a test case, for the simplest[ NH 2 ] + + 2 H 2 O reactions, orbital interactions within the NBO paradigm, bond orders, and their derivatives indicate that each individual proton transfer is highly synchronous.

METHODS

Molecular geometries were optimized and characterized at the B3LYP/6-311++G(d, p) level. Intrinsic reaction coordinates were calculated. CCSD(T) single point energies with the same basis were computed on all stationary points. The reaction force, reaction force constant, and reaction electron flux are used to study the evolution of the reacting systems. Natural bond orbitals are used to understand the primitive changes driving the reaction.

Synergy of experimental and computational chemistry: structure and biological activity of Zn(II) hydrazone complexes

In this paper, three different Zn(II) complexes with (E)-2-(2-(1-(6-bromopyridin-2-yl)ethylidene)hydrazinyl)-N,N,N-trimethyl-2-oxoethan-1-aminium chloride (HLCl) have been synthesized and characterized by single crystal X-ray diffraction, elemental analysis, IR and NMR spectroscopy. All complexes are mononuclear, with the ligand (L) coordinated in a deprotonated formally neutral zwitterionic form via NNO donor set atoms. Complex 1 forms an octahedral geometry with the composition [ZnL2](BF4)2, while complexes 2 [ZnL(NCO)2] and 3 [ZnL(N3)2] form penta-coordinated geometry. Density functional theory (DFT) calculations were performed to enhance our understanding of the structures of the synthesized complexes and the cytotoxic activity of the complexes was tested against five human cancer cell lines (HeLa, A549, MDA-MB-231, K562, LS 174T) and normal human fibroblasts MRC-5. Additionally, antibacterial and antifungal activity of these complexes was tested against a panel of Gram-negative and Gram-positive bacteria, two fungal strains, and a yeast strain. It is noteworthy that all three complexes show selective antifungal activity comparable to that of amphotericin B. Molecular docking analysis predicted that geranylgeranyl pyrophosphate synthase, an enzyme essential for sterol biosynthesis, is the most likely target for inhibition by the tested complexes.

Expanding horizons in conceptual density functional theory: Novel ensembles and descriptors to decipher reactivity patterns

Conceptual density functional theory (CDFT) and the quantum reactivity descriptors stemming from it have proven to be valuable tools for understanding the chemical behavior of molecules. This article is presented as being intrinsically of dual character. In a first part, it briefly reviews, in a deliberately didactical way, the main ensembles in CDFT, while the second half presents two additional ensembles, where the chemical hardness acts as a natural variable, and their respective reactivity descriptors. The evaluation of these reactivity descriptors on common organic chemical reagents are presented and discussed.

Revisiting nucleophilicity: an index for chemical reactivity from a CDFT approach

CONTEXT

Understanding and predicting the nucleophilic reactivity are paramount in elucidating organic chemical reactions and designing new synthetic pathways. In this study, we propose a nucleophilicity index within the framework of Conceptual Density Functional Theory (CDFT). Through rigorous theoretical formulations, we introduce an original quantum reactivity descriptor that captures the nucleophilic propensity of molecules based on their electronic structure and chemical environment. Subsequently, this proposed index is applied to a series of nucleophiles (pyrrolidines derivatives), spanning a diverse range of chemical functionalities. Our computational assessments reveal insightful correlations between the predicted nucleophilicity index and experimental observations of nucleophilic behavior. Thereby, they offer a promising avenue for advancing the understanding of organic reactivity and guiding synthetic efforts.

METHODS

Experimentally, Mayr's experimental parameters accounting for nucleophilicity were selected for the pyrrolidines. This study used DFT calculations at the B3LYP/Aug-cc-pVTZ level of theory using the Gaussian 16 program. Geometry optimization was thus performed, and the methodology employed for the computation of quantum reactivity descriptor is presented. Solvent effect was also taken into account using IEFPCM, and empirical dispersion correction (GD3) was employed.

Interactions and reactivity in crystalline intermediates of mechanochemical cyclorhodation reactions

There is experimental evidence that solid mixtures of the rhodium dimer [Cp*RhCl2]2 and benzo[h] quinoline (BHQ) produce two different polymorphic molecular cocrystals called 4α and 4β under ball milling conditions. The addition of NaOAc to the mixture leads to the formation of the rhodacycle [Cp*Rh-(BHQ)Cl], where the central Rh atom retains its tetracoordinate character. Isolate 4β reacts with NaOAc leading to the same rhodacycle while isolate 4α does not under the same conditions. We show that the puzzling difference in reactivity between the two cocrystals can be traced back to fundamental aspects of the intermolecular interactions between the BHQ and [Cp*RhCl2]2 fragments in the crystalline environment. To support this view, we report a number of descriptors of the nature and strength of chemical bonds and intermolecular interactions in the extended solids and in a cluster model. We calculate formal quantum mechanical descriptors based on electronic structure, electron density, and binding and interaction energies including an energy decomposition analysis. Without exception, all descriptors point to 4β being a transient structure higher in energy than 4α with larger local and global electrophilic and nucleophilic powers, a more favorable spatial and energetic distribution of the frontier orbitals, and a more fragile crystal structure.

Aza-Michael Addition in Explicit Solvent: A Relative Energy Gradient-Interacting Quantum Atoms Study

Aza-Michael additions are key reactions in organic synthesis. We investigate, from a theoretical and computational point of view, several examples ranging from weak to strong electrophiles in dimethylsulfoxide treated as explicit solvent. We use the REG-IQA method, which is a quantum topological energy decomposition (Interacting Quantum Atoms, IQA) coupled to a chemical-interpretation calculator (Relative Energy Gradient, REG). We focus on the rate-limiting addition step in order to unravel the different events taking place in this step, and understand the influence of solvent on the reaction, with an eye on predicting the Mayr electrophilicity. For the first time, a link is established between an REG-IQA analysis and experimental values.

The Role of Crystalline Intermediates in Mechanochemical Cyclorhodation Reactions Elucidated by in-Situ X-ray Powder Diffraction and Computation

The occurrence of crystalline intermediates in mechanochemical reactions might be more widespread than previously assumed. For example, a recent study involving the acetate-assisted C-H activation of N-Heterocycles with [Cp*RhCl2 ]2 by ball milling revealed the formation of transient cocrystals between the reagents prior to the C-H activation step. However, such crystalline intermediates were only observed through stepwise intervallic ex-situ analysis, and their exact role in the C-H activation process remained unclear. In this study, we monitored the formation of discrete, stoichiometric cocrystals between benzo[h]quinoline and [Cp*RhCl2 ]2 by ball milling using in-situ synchrotron X-ray powder diffraction. This continuous analysis revealed an initial cocrystal that transformed into a second crystalline form. Computational studies showed that differences in noncovalent interactions made the [Cp*RhCl2 ]2 unit in the later-appearing cocrystal more reactive towards NaOAc. This demonstrated the advantage of cocrystal formation before the acetate-assisted metalation-deprotonation step, and how the net cooperative action of weak interactions between the reagents in mechanochemical experiments can lead to stable supramolecular assemblies, which can enhance substrate activation under ball-milling conditions. This could explain the superiority of some mechanochemical reactions, such as acetate-assisted C-H activation, compared to their solution-based counterparts.

ElectroPredictor: An Application to Predict Mayr's Electrophilicity E through Implementation of an Ensemble Model Based on Machine Learning Algorithms

Electrophilicity (E) is one of the most important parameters to understand the reactivity of an organic molecule. Although the theoretical electrophilicity index (ω) has been associated with E in a small homologous series, the use of w to predict E in a structurally heterogeneous set of compounds is not a trivial task. In this study, a robust ensemble model is created using Mayr's database of reactivity parameters. A combination of topological and quantum mechanical descriptors and different machine learning algorithms are employed for the model's development. The predictability of the model is assessed using different statistical parameters, and its validation is examined, including a training/test partition, an applicability domain, and a y-scrambling test. The global ensemble model presents a Q5-fold2 of 0.909 and a Qext2 of 0.912, demonstrating an excellent predictability performance of E values and showing that w is not a good descriptor for the prediction of E, especially for the case of neutral compounds. ElectroPredictor, a noncommercial Python application (https://github.com/mmoreno1/ElectroPredictor), is developed to predict E. QM9, a well-known large dataset containing 133885 neutral molecules, is used to perform a virtual screening (94.0% coverage). Finally, the 10 most electrophilic molecules are analyzed as possible new Mayr's electrophiles, which have not yet been experimentally tested. This study confirms the necessity to build an ensemble model using nonlinear machine learning algorithms, topographic descriptors, and separating molecules into charged and neutral compounds to predict E with precision.

[Fe4S4] cubane in sulfite reductases: new insights into bonding properties and reactivity

The dissimilatory sulfite reductase enzyme has very characteristic active site where the substrate binds to an iron site, ligated by a siroheme macrocycle and a thiol directly connected to a [Fe₄S₄] cluster. This arrangement gives the enzyme remarkable efficiency in reducing sulfite and nitrite all the way to hydrogen sulfide and ammonia. For the first time we present a theoretical study where substrate binding modalities and activation are elucidated using active site models containing proton supply side chains and the [Fe₄S₄] cluster. Density functional theory (DFT) was deployed in conjunction with the energy decomposition scheme (as implemented in AMS), the quantum theory of atoms in molecules (QTAIM), and conceptual DFT (cDFT) descriptors. We quantified the role of the electrostatic interactions inside the active site created by the side chains as well as the influence of the [Fe₄S₄] cluster on the substrate binding. Furthermore, using conceptual DFT results we shed light of the activation process, thus, laying foundation for further mechanistic studies. We found that the bonding of the ligands to the iron complex is dominated by electrostatic interactions, but the presence of the [Fe₄S₄] cubane leads to substantial changes in electronic interaction. The spin state of the cubane, however, affects the binding energy only marginally. The conceptual DFT results show that the presence of the [Fe₄S₄] cubane affects the reactivity of the active site as it is involved in electron transfer. This is corroborated by an increase in the electrophilicity index, thus making the active site more prone to react with the ligands. The interaction energies between the ligand and the siroheme group are also increased upon the presence of the cubane group, thus, suggesting that the siroheme group is not an innocent spectator but plays an active role in the reactivity of the dSIR active site.

The explicit role of electron exchange in the hydrogen bonded molecular complexes

We applied a set of advanced bonding descriptors to establish the hidden electron density features and binding energy characteristics of intermolecular DH∙∙∙A hydrogen bonds (OH∙∙∙O, NH∙∙∙O and SH∙∙∙O) in 150 isolated and solvated molecular complexes. The exchange-correlation and Pauli potentials as well as corresponding local one-electron forces allowed us to explicitly ascertain how electron exchange defines the bonding picture in the proximity of the H-bond critical point. The electron density features of DH∙∙∙A interaction are governed by alterations in the electron localization in the H-bond region displaying itself in the exchange hole. At that, they do not depend on the variations in the exchange hole mobility. The electrostatic interaction mainly defines the energy of H-bonds of different types, whereas the strengthening/weakening of H-bonds in complexes with varying substituents depends on the barrier height of the exchange potential near the bond critical point. Energy variations between H-bonds in isolated and solvated systems are also caused the electron exchange peculiarities as follows from the corresponding potential and the interacting quantum atom analyses complemented by electron delocalization index calculations. Our approach is based on the bonding descriptors associated with the characteristics of the observable electron density and can be recommended for in-depth studies of non-covalent bonding.

Atom-Condensed Fukui Function in Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide

Local reactivity descriptors such as atom-condensed Fukui functions are promising computational tools to study chemical reactivity at specific sites within a molecule. Their applications have been mainly focused on isolated molecules in their most stable conformation without considering the effects of the surroundings. Here we propose to combine quantum mechanics/molecular mechanics Born-Oppenheimer molecular dynamics simulations to obtain the microstates (configurations) of a molecular system using different representations of the molecular environment and calculate Boltzmann-weighted atom-condensed local reactivity descriptors based on conceptual density functional theory. Our approach takes the conformational fluctuations of the molecular system and the polarization of its electron density by the environment into account, allowing us to analyze the effect of the molecular environment on reactivity. In this contribution, we apply the method mentioned above to the catalytic fixation of carbon dioxide by crotonyl-CoA carboxylase/reductase and study if the enzyme alters the reactivity of its substrate compared with an aqueous solution. Our main result is that the protein environment activates the substrate by the elimination of solute-solvent hydrogen bonds from aqueous solution in the two elementary steps of the reaction mechanism: the nucleophilic attack of a hydride anion from NADPH on the α,β-unsaturated thioester and the electrophilic attack of carbon dioxide on the formed enolate species.