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.

Determining the Factors accounting for Reaction Selectivity A Relative Energy Gradient - Interacting Quantum Atoms and Natural Bonding Orbitals Study.

Identifying the main physicochemical properties accounting for the course of a reaction is of utmost importance to rationalize chemical syntheses. To this aim, the relative energy gradient (REG) method is an appealing approach because it is an unbiased and automatic process to extract the most relevant pieces of energy information. Initially formulated within the interacting quantum atoms (IQA) framework for a single reaction, here we extend the REG method to natural bond orbitals (NBO) analysis and to the case of two competitive processes. This development enables the determination of the driving forces of any chemical selectivity. We illustrate the extended REG method on the case study of ring opening in cyclobutenes, which is an important instance of the so-called torquoselectivity.

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.

Predicting the activity of methoxyphenol derivatives antioxidants: II-Importance of the nature of the solvent on the mechanism, a DFT study.

The various mechanisms of primary antioxidant action of a series of 2-Methoxyphenols are investigated in the present work. The electronic properties have just been studied in a joint article, so that we focus here on Hydrogen Atom Transfer (HAT), Single Electron Transfer-Proton Transfer (SET-PT) and Sequential Proton-Loss Electron-Transfer (SPLET) mechanisms. The two computational approaches used in the previous study of the structure and reactivity of these compounds [Computational and Theoretical Chemistry 1229 (2023) 114287] provide identical mechanisms trends in gas phase. In gas media, hydrogen atom transfer (HAT) is more favored. On the contrary, the solvent polarity has a significant effect on the mechanism of the antioxidant activity, since the polarity of the solvent increases the contribution of the SPLET mechanism.

Insight into the Varying Reactivity of Different Catalysts for CO2 Cycloaddition into Styrene Oxide: An Experimental and DFT Study.

The cycloaddition of CO2 into epoxides to form cyclic carbonates is a highly sought-after reaction for its potential to both reduce and use CO2, which is a greenhouse gas. In this paper, we present experimental and theoretical studies and a mechanistic approach for three catalytic systems. First, as Lewis base catalysts, imidazole and its derivatives, then as a Lewis acid catalyst, ZnI2 alone, and after that, the combined system of ZnI2 and imidazole. In the former, we aimed to discover the reasons for the varied reactivities of five Lewis base catalysts. Furthermore, we succeeded in reproducing the experimental results and trends using DFT. To add, we emphasized the importance of non-covalent interactions and their role in reactivity. In our case, the presence of a hydrogen bond was a key factor in decreasing the reactivity of some catalysts, thus leading to lower conversion rates. Finally, mechanistically understanding this 100% atom economy reaction can aid experimental chemists in designing better and more efficient catalytic systems.

Understanding the mechanism and regio- and stereo selectivity of [3 + 2] cycloaddition reactions between substituted azomethine ylide and 3,3,3-trifluoro-1-nitroprop-1-ene, within the molecular electron density theory.

The selectivity and the nature of the molecular mechanism of the [3 + 2] cycloaddition (32CA) reaction between 2-(dimethylamino)-1H-indene-1,3(2H)-dione (AY11) and trans(E)-3,3,3-trifluoro-1-nitroprop-1-ene(FNP10) has been studied, in which the molecular electron density theory using density functional theory methods at the MPWB1K/6-31G(d) computational level was used. Analysis of the global reactivity indices permits us to characterize FNP10 as a strong electrophile and AY11 as a strong nucleophile. Four reactive pathways associated with the ortho/meta regioselective channels and endo/exo stereoselective approaches modes have been explored and characterized in the gas phase and in the benzene solvent. The analysis of the relative energies associated with the different reaction pathways indicates that the 32CA reactions of the azomethine ylide (AY) with the nitroalkene (FNP) is meta regioselective with high endo stereoselectivity. This result is in good agreement with the experimental observations. electron localization function topological analysis of the most favored reactive pathways allows for characterizing the mechanism of this 32CA reactions as a non-concerted two-stage one-step mechanism. Finally, non-covalent interactions and quantum theory of atoms in molecule analyses at the meta/endo transition state structure indicate that the presence of different several weak interactions, namely, CF and NH contributed in favoring the formation of a meta-endo cycloadduct.

Formation Mechanism of Inter-Crosslink in DNA by Nitrogen Oxides Pollutants through A Diazonium Intermediate.

Outdoor air pollution is a mixture of multiple atmospheric pollutants, among which nitrogen oxide (NOx) stands out due to its association with several diseases. NOx reactivity can conduct to DNA damage as severe as interstrand crosslinks (ICL) formation, that in turn is able to block DNA replication and transcription. Experimental studies have suggested that the ICL formation due to NOx is realized through a diazonium intermediate (DI). In this work, we have modeled the DI structure, including a DNA double-strand composed of two base pairs GC/CG, being diazotized as one of the guanine nucleotides. The structural stability of DNA with DI lesion was essayed through 500 ns molecular dynamics simulations. It was found that the DNA structure of the oligonucleotide is stable when the DI is present since the loss of a Guanine-Cytosine hydrogen bond is replaced by the presence of two cation-π interactions. Additionally, we have studied the mechanism of formation of a crosslink between the two guanine nucleobases from the modeled DI by carrying out DFT calculations at the M06-L/DNP+ level of theory. Our results show that the mechanism is thermodynamically favored by a strong stabilization of the ICL product, and the process is kinetically viable since its limiting stage is accessible.

Molecular interactions from the density functional theory for chemical reactivity: Interaction chemical potential, hardness, and reactivity principles.

In the first paper of this series, the authors derived an expression for the interaction energy between two reagents in terms of the chemical reactivity indicators that can be derived from density functional perturbation theory. While negative interaction energies can explain reactivity, reactivity is often more simply explained using the "|dµ| big is good" rule or the maximum hardness principle. Expressions for the change in chemical potential (µ) and hardness when two reagents interact are derived. A partial justification for the maximum hardness principle is that the terms that appear in the interaction energy expression often reappear in the expression for the interaction hardness, but with opposite sign.

Molecular Interactions From the Density Functional Theory for Chemical Reactivity: The Interaction Energy Between Two-Reagents.

Reactivity descriptors indicate where a reagent is most reactive and how it is most likely to react. However, a reaction will only occur when the reagent encounters a suitable reaction partner. Determining whether a pair of reagents is well-matched requires developing reactivity rules that depend on both reagents. This can be achieved using the expression for the minimum-interaction-energy obtained from the density functional reactivity theory. Different terms in this expression will be dominant in different circumstances; depending on which terms control the reactivity, different reactivity indicators will be preferred.

Reactivity and a Charge-Transfer Model Analysis in Aminopolycarboxylic-Metal Complexes.

In the present work, we have calculated several density functional theory (DFT) reactivity descriptors for the aminopolycarboxylate (APC) acids at the B3LYP/6311++G (d,p) levels of theory, aiming to analyze their reactivity. Reactivity descriptors such as ionization energy, molecular hardness, electrophilicity, and condensed Fukui function local indices have been determined to predict the reactivity of APCs. The influence of the solvent was taken into account by employing the CPCM model. The results indicate that the solvation slightly modifies the tendency of the reactivity of the APCs studied. On the other hand, we applied a global and local charge-transfer partitioning model, which introduces two charge-transfer channels [one for accepting electrons (electrophilic) and another for donating one (nucleophilic)] to the complexation reaction of a set of APC acids with transition metals (Mn, Co, and Ni targets enlarged by Fe, Cu, and Zn). The correlation between the charges obtained for the interaction between APC acids and transition metal stability constants provides support for their interpretation as measures of the electrophilicity and nucleophilicity of a chemical species and, at the same time, allows one to describe the donation and back-donation processes in terms of the DFT of chemical reactivity. Also, the application of dual descriptors for these acids provides valuable information concerning the atoms in the reactants playing the most important roles in the reaction, thus helping to improve our understanding of the reaction under study.

Polarisation of Electron Density and Electronic Effects: Revisiting the Carbon-Halogen Bonds.

Electronic effects (inductive and mesomeric) are of fundamental importance to understand the reactivity and selectivity of a molecule. In this article, polarisation temperature is used as a principal index to describe how electronic effects propagate in halogeno-alkanes and halogeno-alkenes. It is found that as chain length increases, polarisation temperature decreases. As expected, polarisation is much larger for alkenes than for alkanes. Finally, the polarisation mode of the carbon-fluorine bond is found to be quite different and might explain the unusual reactivity of fluoride compounds.

A Dynamic View of the Interaction of Histone Tails with Clustered Abasic Sites in a Nucleosome Core Particle.

Apurinic/apyrimidinic sites are the most common forms of DNA damage under physiological conditions, yet their structural and dynamical behavior within nucleosome core particles has just begun to be investigated and is dramatically different from that of abasic sites in B-DNA. Clusters of two or more abasic sites are repaired even less efficiently and hence constitute hot spots of high mutagenicity notably due to enhanced double-strand break formation. On the basis of an X-ray structure of a 146 bp DNA wrapped onto a histone core, we investigate the structural behavior of two bistranded abasic sites positioned at mutational hot spots during microsecond-range molecular dynamics simulations. Our simulations allow us to probe interactions of histone tails at clustered abasic site locations, with a definitive assignment of the key residues involved in the NCP-catalyzed formation of DNA-protein cross-linking in line with recent experimental findings, and pave the way for a systematic assessment of the response of histone tails to DNA lesions.

Understanding the intermolecular Diels-Alder cycloaddition promotion: Activation strain model/energy decomposition analysis model and conceptual density functional theory viewpoints.

The present work reports the computational study of the major Diels-Alder reaction between 2-bromocycloalkenone and a variety of mono- and di-substituted dienes. Through density functional theory (DFT) calculations and subsequent activation strain model/energy decomposition analysis/conceptual DFT (C-DFT) analyses, the key factors governing the activation barriers heights, and thus reactivity, are characterized. In contrast with a previous study, steric effects do not appear to control reactivity. Conversely, in all presented cases, a subtle interplay between deformation and interaction energies is evidenced at transition states. In the end, neither term alone is enough to explain or predict reactivity. Yet a simple C-DFT descriptor allows to predict with a reasonable efficiency the activation barriers: the excitation energy needed to observe a charge transfer from the diene to the dienophile. Theoretical elements are provided to support the use of this descriptor.

A computational investigation of the selectivity and mechanism of the Lewis acid catalyzed oxa-Diels-Alder cycloaddition of substituted diene with benzaldehyde.

The selectivity and the mechanism of the uncatalyzed and AlCl3 catalyzed hetero-Diels-Alder reaction (HDR) between ([E]-4-methylpenta-2,4-dienyloxy)(tert-butyl)dimethylsilane 1 and benzaldehyde 2 have been studied using density functional theory at the MPWB1K/6-31G(d) level of theory. The uncatalyzed HDR between diene 1 and alkene 2 is characterized by a polar character and proceeds via an asynchronous one-step mechanism for the meta paths and synchronous for the ortho ones. In the presence of AlCl3 catalyst, the mechanism changes to be stepwise, while the first step is the rate-determining step. The activation energies widely decrease, and the polar character increases dramatically. A large analysis of the mechanism is performed using the activation strain model/energy decomposition analysis (ASM/EDA) model, the natural bond orbital (NBO) and state specific dual descriptors (SSDDs). The obtained results indicate that the combined interaction energy associated with the distortion of the reactants in these HDR are at the origin of the observed kinetics. NBO analyses were applied to estimate the Lewis-acid catalyst donor-acceptor interaction with the molecular system. The SSDD analysis shed light into the orientation effects on the reaction kinetics by providing important information about charge transfer interactions during the chemical reaction. It indicates that the more favorable HDR pathway have the lowest excitation energies, facilitating the interaction between diene 1 and benzaldehyde 2 moieties. Non-covalent interaction (NCI) and QTAIM analyses of the meta-endo structure indicate that the presence of several weak NCIs formed at this approach is at the origin of the meta-endo selectivity.

The density polarization reveals directions of electron displacements due to the substituent effect: Analysis performed on a metal-organic Mo-Oxo catalyst.

Some Mo-oxo complexes bearing pyridine rings have the capability for dihydrogen production from water. However, energy barrier and overall energy vary depending on the effect exerted by several substituent groups located at different positions around one or more pyridine rings which are ligands of these compounds. Based on the Karunadasa and coworkers investigation where the para-position was experimentally tested in compounds derivatised from the 2,6-bis[1,1-bis(2-pyridil)ethyl]-pyridine oxo-molybdenum complex synthesized (Karunadasa et al., Nature, 2010, 464, 1329), we tested the combined effect of electron-withdrawing and electron-donating groups simulated as perturbations represented by point-charges. Then, we used the density polarization concept, δρ(r), a local reactivity descriptor corresponding to the partially integrated linear response function, χ(r, r') (a non-local reactivity descriptor), which is able to reveal different displacements of π-electrons on molecular structures. We perturbed the para-positions in the pentadentate ligand 2,6-bis[1,1-bis(2-pyridil)ethyl]-pyridine in the Mo-based complex by means of point-charges. They were located in three different configurations of the organic ligand (trans, geminal, and cis) which could help to explain energy barriers and overall energy of reactions catalyzed by this type of Mo-complexes. Our results indicate that the trans configuration of point-charges induces the most amount of fraction of electron shifted on the complex. A Mo-based complex bearing the same trans configuration for electron-withdrawing and electron-donating substituent groups (cyano and amino, respectively), leads to a kinetically more favorable H2 release than the cis or geminal configuration of the substituent groups aforementioned.

A statistical thermodynamics view of electron density polarisation: application to chemical selectivity.

A fundamental link between conceptual density functional theory and statistical thermodynamics is herein drawn, showing that intermolecular electrostatic interactions can be understood in terms of effective work and heat exchange. From a more detailed analysis of the heat exchange in a perturbation theory framework, an associated entropy can be subsequently derived, which appears to be a suitable descriptor for the local polarisability of the electron density. A general rule of thumb is evidenced: the more the perturbation can be spread, both through space and among the excited states, the larger the heat exchange and entropy.

Nucleosomal embedding reshapes the dynamics of abasic sites.

Apurinic/apyrimidinic (AP) sites are the most common DNA lesions, which benefit from a most efficient repair by the base excision pathway. The impact of losing a nucleobase on the conformation and dynamics of B-DNA is well characterized. Yet AP sites seem to present an entirely different chemistry in nucleosomal DNA, with lifetimes reduced up to 100-fold, and the much increased formation of covalent DNA-protein cross-links leading to strand breaks, refractory to repair. We report microsecond range, all-atom molecular dynamics simulations that capture the conformational dynamics of AP sites and their tetrahydrofuran analogs at two symmetrical positions within a nucleosome core particle, starting from a recent crystal structure. Different behaviours between the deoxyribo-based and tetrahydrofuran-type abasic sites are evidenced. The two solvent-exposed lesion sites present contrasted extrahelicities, revealing the crucial role of the position of a defect around the histone core. Our all-atom simulations also identify and quantify the frequency of several spontaneous, non-covalent interactions between AP and positively-charged residues from the histones H2A and H2B tails that prefigure DNA-protein cross-links. Such an in silico mapping of DNA-protein cross-links gives important insights for further experimental studies involving mutagenesis and truncation of histone tails to unravel mechanisms of DPCs formation.

Substituent Effect on the Himbert Intramolecular Arene/Allene Diels-Alder Reaction: NBO Analysis and State Specific Dual Descriptors.

Conceptual density functional theory has been applied to study the Himbert intramolecular arene/allene Diels-Alder reaction. The effect of substitutions at different positions on the kinetics of these reactions has been analyzed. Therefore, from the calculation of the activation energies of more than 27 reactions involving concerted mechanisms, the selectivity of these reactions can be predicted and rationalized with the aid of conceptual DFT descriptors. An application of the two concepts, natural population analysis (NBO) and the state-specific dual descriptor (SSDD) for evaluating substituent effects, allows the investigation of the different interactions that promote a reaction compared to another. The SSDDs computed for the transition state structures provide important information about charge transfer interactions during the chemical reaction. In our case, the SSDD results show that the substituents promoting Himbert reaction have the lowest excitation energies, a fact which facilitates the allene/arene interaction. The NBO results show that according to the nature of the substituent, the Himbert reaction stands as a normal-electron demand or reverse. Thus, the interactions favoring each reaction are mentioned. The geometric deformation observed in the case of OCH3 is at the origin to the emergence of other low interactions between diene and dienophile as well as a strong electronic delocalization stabilizing the arene moiety. The calculated synchronicity indexes show that the Himbert intramolecular Diels-Alder reactions are very synchronous.

Wetting the lock and key enthalpically favours polyelectrolyte binding.

By using a combination of readily accessible experimental and computational experiments in water, we explored the factors governing the association between polyanionic dyn[4]arene and a series of α,ω-alkyldiammonium ions of increasing chain length. We found that the lock-and-key concept based on the best match between the apolar and polar regions of the molecular partners failed to explain the observed selectivities. Instead, the dissection of the energetic and structural contributions demonstrated that the binding events were actually guided by two crucial solvent-related phenomena as the chain length of the guest increases: the expected decrease of the enthalpic cost of guest desolvation and the unexpected increase of the favourable enthalpy of complex solvation. By bringing to light the decisive enthalpic impact of complex solvation during the binding of polyelectrolytes by inclusion, this study may provide a missing piece to a puzzle that one day could display the global picture of molecular recognition in water.

Raman spectroscopy combined with advanced chemometric methods: A new approach for detergent deformulation.

Deformulation of a commercial surfactant mixture using Raman spectroscopy and advanced chemometric tools have been investigated. Since the use of surfactants is drastically expanding, their fine identification and quantification are required for quality control and regulation. Dilution of the detergent mixtures combined with Raman spectroscopy for signal extraction tools allowed the extraction of the first information concerning the composition of the mixture. The raw materials identified were thus used in an experimental design to obtain a robust model for the determination of detergent composition. The combination of chemometric tools (independent component analysis and Partial Least Square) and spectroscopic methods provided pertinent information for detergent composition. This methodology can easily be transposed to the industrial world.