Electrostatics for probing lone pairs and their interactions

Topology of electrostatic potential and electron density reveals a covalent to non-covalent carbon-carbon bond continuum

The covalent and non-covalent nature of carbon-carbon (CC) interactions in a wide range of molecular systems can be characterized using various methods, including the analysis of molecular electrostatic potential (MESP), represented as V(r), and the molecular electron density (MED), represented as ρ(r). These techniques provide valuable insights into the bonding between carbon atoms in different molecular environments. By uncovering a fundamental exponential relationship between the distance of the CC bond and the highest eigenvalue (λv1) of V(r) at the bond critical point (BCP), this study establishes the continuum model for all types of CC interactions, including transition states. The continuum model is further delineated into three distinct regions, namely covalent, borderline cases, and non-covalent, based on the gradient, , with the bond distance of the CC interaction. For covalent interactions, this parameter exhibits a more negative value than -5.0 a.u. Å-1, while for non-covalent interactions, it is less negative than -1.0 a.u. Å-1. Borderline cases, which encompass transition state structures, fall within the range of -1.0 to -5.0 a.u. Å-1. Furthermore, this study expands upon Popelier's analysis of the Laplacian of the MED, denoted as ∇2ρ, to encompass the entire spectrum of covalent, non-covalent, and borderline cases of CC interactions. Therefore, the present study presents compelling evidence supporting the concept of a continuum model for CC bonds in chemistry. Additionally, this continuum model is further explored within the context of C-N, C-O, C-S, N-N, O-O, and S-S interactions, albeit with a limited dataset.

Quantum chemical studies on the binding domain of SARS-CoV-2 S-protein: human ACE2 interface complex

A two-layer ONIOM(B3LYP/6-31G*:PM7) method is used to model the binding of several drug/drug-like molecules (L) at the SARS-CoV-2 S-protein: human ACE2 protein interface cavity. The selected molecules include a set of thirty-five ligands from the study of Smith and Smith which showed a high docking score in the range of -7.0 to -7.7 kcal/mol and another set of seven repurposing drugs, viz. favipiravir, remdesivir, EIDD, galidesivir, triazavirin, ruxolitinib, and baricitinib. The ONIOM model of the cavity (M) showed a highly polarized electron distribution along its top-to-bottom direction while Ls with lengths in the range 1.0 - 1.5 nm fitted well inside the cavity in a head-to-tail fashion to yield ML complexes. The ligands showed a large variation in the ONIOM-level binding energy (Eb), in the range -2.7 to -85.4 kcal/mol. The Eb of ML complexes better than -40.0 kcal/mol is observed for myricetin, fidarestat, protirelin, m-digallic acid, glucogallin, benserazide hydrochlorideseradie, remdesivir, tazobactum, sapropterin, nitrofurantoin, quinonoid, pyruvic acid calcium isoniazid, and aspartame, and among them the highest Eb -85.4 kcal/mol is observed for myricetin. A hydroxy substitution is suggested for the phenyl ring of aspartame to improve its binding behavior at the cavity, and the resulting ligand 43 showed the best Eb -84.5 kcal/mol. The ONIOM-level study is found to be effective for the interpretation of the noncovalent interactions resulting from residues such as arginine, histidine, tyrosine, lysine, carboxylate, and amide moieties in the active site and suggests rational design strategies for COVID-19 drug development.Communicated by Ramaswamy H. Sarma.

Enhancement of Atmospheric Nucleation Precursors on Iodic Acid-Induced Nucleation: Predictive Model and Mechanism

Iodic acid (IA) has recently been recognized as a key driver for new particle formation (NPF) in marine atmospheres. However, the knowledge of which atmospheric vapors can enhance IA-induced NPF remains limited. The unique halogen bond (XB)-forming capacity of IA makes it difficult to evaluate the enhancing potential (EP) of target compounds on IA-induced NPF based on widely studied sulfuric acid systems. Herein, we employed a three-step procedure to evaluate the EP of potential atmospheric nucleation precursors on IA-induced NPF. First, we evaluated the EP of 63 precursors by simulating the formation free energies (ΔG) of the IA-containing dimer clusters. Among all dimer clusters, 44 contained XBs, demonstrating that XBs are frequently formed. Based on the calculated ΔG values, a quantitative structure-activity relationship model was developed for evaluating the EP of other precursors. Second, amines and O/S-atom-containing acids were found to have high EP, with diethylamine (DEA) yielding the highest potential to enhance IA-induced nucleation by combining both the calculated ΔG and atmospheric concentration of considered 63 precursors. Finally, by studying larger (IA)_1-3(DEA)_1-3 clusters, we found that the IA-DEA system with merely 0.1 ppt (2.5×10⁶ cm^-3) DEA yields comparable nucleation rates to that of the IA-iodous acid system.

Electrostatic Potential for Exploring Electron Delocalization in Infinitenes, Circulenes, and Nanobelts

The π-conjugation, aromaticity, and stability of the newly synthesized 12-infinitene and of other infinitenes comprising 8-, 10-, 14-, and 16-arene rings are investigated using density functional theory. The π-electron delocalization and aromatic character rooted in infinitenes are quantified in terms of molecular electrostatic potential (MESP) topology. Structurally, the infinitene bears a close resemblance of its helically twisted structure to the infinity symbol. The MESP topology shows that infinitene possesses an infinity-shaped delocalization of the electron density that streams over the fused benzenoid rings. The parameter ∑i=13Δλi, derived from the eigenvalues (λ_i) corresponding to the MESP minima, is used for quantifying the aromatic character of arene rings of infinitene. The structure, stability, and MESP topology features of 8-, 10-, 12-, 14-, and 16-infinitenes are also compared with the corresponding isomeric circulenes and carbon nanobelts. Further, the strain in all such systems is evaluated by considering the respective isomeric planar benzenoid hydrocarbons as reference systems. The 12-infinitene turns out to be the most aromatic and the least strained among all the systems examined.

A density fitting scheme for the fast evaluation of molecular electrostatic potential

Molecular electrostatic potential (MEP) is a significant and crucial physical quantity that can be applied to a large number of scenarios, such as the prediction of nucleophilic or electrophilic attacks, fitting atomic charges, σ-hole, and so forth. The computational cost for the MEP has an O(N² ) scaling with the increase of atoms, which is intractable and laborious for macromolecules. Herein, a density fitting molecular electrostatic potential (DF-MEP) is used to reduce the computational costs for the macromolecular MEP. It is found that the accuracy of DF-MEP is almost identical to the conventional molecular electrostatic potential (Conv-MEP), while the computational costs can be reduced to an O(N) scaling, for example, the computational time of 699,200 grids for the Trp-cage molecule (304 atoms) only takes 16.6 s at the B3LYP-D3(BJ)/def2-SVP level of theory with 16 CPU cores compared with 3060.2 s for the Conv-MEP method.

A combined crystallography and DFT study on ring-shaped Cucurbit[n]urils: structures, surface character, and host-guest recognition

A combined crystallography and DFT study of cucurbit[n]urils (n = 5-8, 10) was carried out, and PBE0 was certified to be the most rational density functional method for optimization task. Steric hindrance and electronic effect of the hindered lone pair electrons in cucurbit[n]urils were qualitatively measured by bond order analysis, lone pair electron (LP) visualization and electrostatic potential (ESP) study. Together with energy decomposition analysis of some selected host-guest systems, we quantitatively verified the effect of size/cavity and noncovalent interaction in host-guest recognition. This solid study revealed that lone pairs electrons affect not only on host-guest identification mode but also on geometry stability, which pave the avenue for further sophisticated applications.

Pivotal role of water molecules in the photodegradation of pymetrozine: New insights for developing green pesticides

Photodegradation of the insecticide pymetrozine (PYM) was studied on surface of wax films, and in aqueous and nonaqueous phase. The half-life of PYM on the wax surface was approximately 250 times longer than in water. Scavenging experiments, laser flash photolysis, and spectra analysis indicated the first singlet excited state of PYM (S1 *_PYM) to be the most important photoinduced species initiating the photodegradation. Quantum chemistry calculations identified significant molecular torsion and changes in the structure C-CN-N of S1 *_PYM, and the absolute charges of the CN atoms increased and the bond strength weakened. Free energy surface analysis, and O¹⁸ labeling experiments further confirmed that the mechanism was two-step photoinduced hydrolysis. The first step is the hydrolysis of S1 *_PYM at CN upon reaction with 2-3 water molecules (one H₂O molecule as the catalyst). The second step is an intramolecular hydrogen transfer coupled with the cleavage of C-N bond and formation of two cyclic products. During the interactions, water molecules experience catalytic activation by transferring protons, while there is a negligible solvent effect. Clarifying the detailed photodegradation mechanisms of PYM is beneficial for the development of green pesticides that are photostable and effective on leaf surfaces, and photolabile and detoxified in the aquatic environment.

Hydration patterns of rings in drugs and relationship to lipophilicity: A DFT study

Rings are one of the major scaffold components of drugs in medicinal chemistry, due to their unique electronic distribution, scaffold rigidity, and three-dimensionality while lipophilicity is considered as a vital parameter of rings that can influence the reactivity, metabolic stability, and toxicity. We have analyzed the electronic features, hydration patterns, solvation effect and lipophilicity data for 51 most widely used ring systems in drugs. Molecular electrostatic potential (MESP) topology analysis has been used to assess the electronic distribution in rings which provided an easy interpretation of the most suitable hydration patterns of the ring with H₂ O molecule. Further, the global minimum of ring…H₂ O complex has been utilized to predict lipophilicity (logP) with the incorporation of implicit solvation effect. Classification of ring systems based on their molecular weight into four categories, viz. small ring 'sr', medium ring 'mr', large ring 'lr' and extra large ring 'xlr' systems has led to the finding of strong correlations between logP and hydration energy with R = 0.942, 0.933, 0.968 and 0.933, respectively. The micro solvation model is found to be useful for locating the hydrophobic-hydrophilic border for each category of rings in terms of hydration energy whereas the implicit solvation model used for two solvents, n-octanol and water on the most stable hydrated structure led to a global correlation between logP and solvation energy ratio. This correlation predicts a limiting logP value -7.03 for the most hydrophilic ring system and also suggests a clear partitioning of the ring molecules into hydrophobic and hydrophilic classes. The MESP topology-guided approach to understand the electronic features and hydration patterns of rings in drugs lead to powerful predictions on their lipophilicity behavior.

Theoretical exploration of diverse electron-deficient core and terminal groups in A–DA′D–A type non-fullerene acceptors for organic solar cells

The influences triggered by the structurally diverse electron-withdrawing terminal group and fuse-ring electron-deficient core on the performance of NFAs OSCs are comprehensively investigated by using DFT, TD-DFT and Marcus charge transfer theory.

The use of electrostatic potential at nuclei in the analysis of halogen bonding

Molecular electrostatic potential data at interacting nuclei provide strong evidence of bond formation in many intermolecular halogen bonded complexes.

Localized orbital locator as a descriptor for quantification and digital presentation of lone pairs: benchmark calculations of 4-substituted pyridines

The parameters of the (3,-3) critical point in the localized orbital locator topology near a heteroatom have been found to reflect the changes in the size, density and electron energy of the lone pair and correlate with the donor ability of the lone pair carrying heteroatom.

Electrostatic Potential Topology for Probing Molecular Structure, Bonding and Reactivity

Following the pioneering investigations of Bader on the topology of molecular electron density, the topology analysis of its sister field viz. molecular electrostatic potential (MESP) was taken up by the authors’ groups. Through these studies, MESP topology emerged as a powerful tool for exploring molecular bonding and reactivity patterns. The MESP topology features are mapped in terms of its critical points (CPs), such as bond critical points (BCPs), while the minima identify electron-rich locations, such as lone pairs and π-bonds. The gradient paths of MESP vividly bring out the atoms-in-molecule picture of neutral molecules and anions. The MESP-based characterization of a molecule in terms of electron-rich and -deficient regions provides a robust prediction about its interaction with other molecules. This leads to a clear picture of molecular aggregation, hydrogen bonding, lone pair–π interactions, π-conjugation, aromaticity and reaction mechanisms. This review summarizes the contributions of the authors’ groups over the last three decades and those of the other active groups towards understanding chemical bonding, molecular recognition, and reactivity through topology analysis of MESP.

New insights in chemical reactivity from quantum chemical topology

Based on the quantum chemical topology of the modified electron localization function ELF_x , an efficient and robust mechanistic methodology designed to identify the favorable reaction pathway between two reactants is proposed. We first recall and reshape how the supermolecular interaction energy can be evaluated from only three distinct terms, namely the intermolecular coulomb energy, the intermolecular exchange-correlation energy and the intramolecular energies of reactants. Thereafter, we show that the reactivity between the reactants is driven by the first-order variation in the coulomb intermolecular energy defined in terms of the response to changes in the number of electrons. Illustrative examples with the formation of the dative bond B-N involved in the BH₃ NH₃ molecule and the typical formation of the hydrogen bond in the canonical water dimer are presented. For these selected systems, our approach unveils a noticeable mimicking of E_dual onto the DFT intermolecular interaction energy surface calculated between the both reactants. An automated reaction-path algorithm aimed to determine the most favorable relative orientations when the two molecules approach each other is also outlined.

A density functional theory study on the electronic and adsorption characteristics of cyclo M9N9 (M = B and Al)

On the basis of experimental and theoretical calculations conducted for cyclo C₁₈, we predicted two novel inorganic cyclo M₉N₉ (M = B and Al) molecules. Because of the significant difference in electronegativity between M and N atoms, M-N bonds were ionic. Furthermore, the interaction of cyclo M₉N₉ with cyclopropylpiperazine (CPPP) was investigated. In cyclo M₉N₉, each M atom could adsorb one CPPP molecule. The CPPP molecules exhibited a preference to remain outside cyclo M₉N₉ molecules. Depending on the structural characteristics of CPPP molecules, the exciting part is that up to four CPPP molecules could be adsorbed on the exterior surface of cyclo M₉N₉. We calculated adsorption energies and analyzed the main structural parameters in the process. The research results indicated that adsorption on cyclo Al₉N₉ was energetically more favorable than that on cyclo B₉N₉. The cyclo M₉N₉ have considerable potential in the future. Graphical abstract.

Mechanism and Stereoselectivity of the Elementometalation Process of Activated Alkyne RCCR(RCO2 Me) by Cp2 TaH3

The elementometalation process is a fundamental chemical step in several catalytic cycles. In this work, density functional theory computations have elucidated the detailed elementometalation mechanism of activated alkyne RCCR(RCO₂ Me) by Cp₂ TaH₃ and rationalized the selectivity in experimental findings. The calculated results show that in the formation process of (E)-olefin monohydride((E)-Pro), the Gibbs free energy barrier is low and the entire reaction is spontaneous and exothermic; thus, (E)-Pro can be formed easily. The formation of (Z)-η² -olefin monohydride complex ((Z)-Pro) is difficult due to its high Gibbs free energy barrier. The formation process (E)-Pro consists of the following five steps: hydride H1-shift, conformational isomerism 1, hydride H2-shift, conformational isomerism 2, and olefin coordination process. Topological analysis shows that there is a five-membered ring plane structure in the reaction pathway and that the final product (E)-Pro belongs to a typical η² -olefin monohydride complex. Our calculated results provide an explanation for experimental observations and useful insights for further development of olefin functionalization. © 2019 Wiley Periodicals, Inc.

Electrostatic Topographical Viewpoint of π-Conjugation and Aromaticity of Hydrocarbons

A molecular electrostatic potential (MESP) topographical study has been conducted for a variety of conjugated hydrocarbons at B3LYP/6-311+G(d,p) level of theory to understand their π-conjugation features and aromaticity. The value of MESP minimum (V_m) is related to the localized and delocalized distribution of π-electron density. The V_m values are located interior to the rings in polycyclic benzenoid hydrocarbons (PBHs), whereas they lie outside the boundary of the rings in antiaromatic and in fused systems consisting of aromatic and antiaromatic moieties. The V_m points lie on top and bottom of the π-regions in linear polyenes and annulenes, while a degenerate distribution of CPs around the midpoint region of triple bonds is observed in alkynes. The eigenvalues λ₁, λ₂, and λ₃ of the Hessian matrix at V_m(MESP minima) are used to define the aromatic character of the cyclic structures. The eigenvalues follow the trend λ₁ ≫ λ₂ > λ₃ ≅ 0 in PBHs, λ₁ > λ₂ > λ₃ ≅ 0 in linear polyenes, and λ₁ > λ₂ > λ₃ ≠ 0 in antiaromatic systems. The difference in the aromatic character of PBHs from that of benzene is related to the deviations Δλ₁, Δλ₂, and Δλ₃. The total deviation ∑_i=1³Δλ_i is found to be ≤ 0.011 au for all aromatic systems and lies between 0.011 and 0.035 au for all nonaromatic systems. For antiaromatic systems, its value is found to be above 0.035 au. Further, ∑_i=1³Δλ_i gives a direct interpretation of Clar's aromatic sextet structures for PBHs. In summary, MESP topography mapping is a powerful technique to quantify the localized and delocalized π-electron distribution in a variety of unsaturated hydrocarbon systems.

Tuning Stacking Interactions between Asp-Arg Salt Bridges and Heterocyclic Drug Fragments

Stacking interactions can play an integral role in the strength and selectivity of protein-drug binding and are of particular interest given the ubiquity and variety of heterocyclic fragments in drugs. In addition to traditional stacking interactions between aromatic rings, stacking interactions involving heterocyclic drug fragments and protein salt bridges have also been observed. These "salt-bridge stacking interactions" can be quite strong but are not well understood. We studied stacked dimers of the acetate···guanidinium ion pair with a diverse set of 63 heterocycles using robust ab initio methods. The computed interaction energies span more than 10 kcal mol^-1, indicating the sensitivity of these salt-bridge stacking interactions to heterocycle features. Trends in both the strength and preferred geometry of these interactions can be understood through analyses of the electrostatic potentials and electric fields above the heterocycles. We have developed new heterocycle descriptors that quantify these effects and used them to create robust predictors of the strength of salt-bridge stacking interactions both in the gas phase and a protein-like dielectric environment. These predictive tools, combined with a set of qualitative guidelines, should facilitate the choice of heterocycles that maximize salt-bridge stacking interactions in drug binding sites.

Hidden Dicarbene Nature of Acetylenes and Captodative Bonding on Carbon

DFT derived molecular electrostatic potential (MESP), ¹³C NMR chemical shift (δ), bond order and coordination reactions show that alkynes (RCCR) attain 1,2-dicarbene nature during CCR angle bending. Alkyne carbon atoms of bent structures exhibit MESP features unique to lone-pair bearing atoms, δ around 200 ppm typical for carbene centers and large reduction in CC triple bond character. Lone pair bearing atoms of R substituents enhance the carbene character. The bent alkynes can be trapped with Lewis acids (BH₃, BF₃, AlF₃ and AlCl₃) as the lone pairs developed on carbon centers provide strong donor type dative bonding. The dative bond gives a formal valence electron count six on carbon and suggests the for-mation of acceptor type dative bonding to carbon from Lewis base (NH₃). Reaction of alkynes with (Lewis acid-Lewis base) systems yield (Lewis acid)₂-Alkyne-Lewis base)₂ complexes which are exothermic and exergonic for many cases. These complexes are examples of captodative carbon(II) compounds.