Molecular Electrostatic Potential Reorganization Theory to Describe Positive Cooperativity in Noncovalent Trimer Complexes

Can we quantitatively evaluate the mutual impacts of intramolecular metal-ligand bonds the same as intermolecular noncovalent bonds?

In this paper, we have reviewed several equations for calculating the cooperative energy of two chemical bonds between three fragments/species, regardless of whether they are atoms, ions or molecules, and whether the bonds between them are intra- or intermolecular. It is emphasized that two chemical bonds upon cooperation in a new compound change the bond dissociation energy of each other exactly by the same quantitative value, their cooperative energy, regardless of the nature of the bonds or whether one bond is very weak and another one is very strong. However, the final benefit/drawback of weak bonds from this cooperation can be considerably larger than that of strong bonds. The above statements are supported by a computational study on the various types of inter- and intramolecular chemical bonds.

Unraveling pnicogen bonding cooperativity: Insights from molecular electrostatic potential analysis

A theoretical investigation on the cooperativity of a series of binary, ternary, and quaternary complexes interconnected by pnicogen bonds has been conducted using calculations at the M06-2X/aug-cc-pVTZ level of density functional theory. By measuring changes in the molecular electrostatic potential (MESP) at the nucleus of interacting atoms in all of the complexes, it is possible to quantify the substantial reorganization of the electron density triggered by the formation of pnicogen bonds. The positive change in MESP, indicating a loss of electron density from the donor molecule in a dimer, facilitates the acceptance of electron density from a third molecule, resulting in the formation of a ternary complex with a stronger pnicogen bond compared to the one present in the binary complex. Similarly, the acceptor molecule in a dimer with a negative change in MESP showed an enhanced tendency to donate electron density to an electron-deficient third molecule. The MESP analysis provided valuable insights into the donor/acceptor characteristics of pnicogen bonds within the quaternary complexes. The proposed MESP hypotheses are consistent with the positive cooperativity observed in the pnicogen-bonded clusters. To quantify the changes in MESP, both at the donor atom (ΔVdonor ) and the acceptor atom (ΔVacceptor ), for all pnicogen bonds in the cluster, the total change in MESP (ΔΔVn ) was measured as ΔΔVn  = ∑(ΔVdonor )-∑(ΔVacceptor ). Remarkably, ΔΔVn exhibited a strong linear relationship with the sum of the bond energies of the pnicogen bonds in the cluster. This establishes the MESP analysis as a robust approach for understanding the strength and cooperative behavior of pnicogen-bonded clusters. Additionally, the MESP features provided clear evidence of pnicogen bond formation, further supporting the reliability of this approach.

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.

Polycyclic Aromatic Hydrocarbons as Anode Materials in Lithium-Ion Batteries: A DFT Study

The structure and energetics of the interactive behavior of Li⁺ and Li with polycyclic aromatic hydrocarbons (PAHs) have been studied at the wB97XD/6-311G(d,p) level of DFT. The electron distribution in the PAHs, analyzed using the topology of the molecular electrostatic potential (MESP), led to the categorization of their aromatic rings into five types, viz R_s, R_n, R_d, R_b, and R_e. Among the different rings, sextet-type R_s and naphthalene-type R_n rings showed the highest interaction with Li⁺. The change in MESP at the nucleus of Li⁺ (ΔV_Li⁺) due to the formation of the complex Li⁺...PAH is found to be proportional to the adsorption energy (E₁). In Li...PAH, the spin density on Li is close to zero, suggesting the formation of Li⁺...PAH^•- due to the electron transfer from Li to PAH. The adsorption energy (E₂) for Li...PAH does not correlate with the change in MESP at the nucleus of Li, whereas the dissociation energy (E₃) of Li⁺...PAH^•- to yield Li⁺ and PAH^•- correlates well with the MESP data, ΔV_Li. The study confirms that the change in MESP at the nucleus of Li⁺ due to complex formation gives a quantitative measure of the electronic effect of the cation-π binding. The cell potential (V_cell) is predicted for the lithium ion battery (LIB) using the Li⁺...PAH and Li...PAH adsorption energies. On the basis of the V_cell data, "carbon nanoflake"-type systems, viz coronene, circumbiphenyl, C₄₂H₁₆, and C₅₀H₁₈ are suggested as good anode materials for LIBs.

Xenon Derivatives as Aerogen Bond-Donating Catalysts for Organic Transformations: A Theoretical Study on the Metaphorical "Spherical Cow in a Vacuum" Provides Insights into Noncovalent Organocatalysis

Computations indicate that cationic and noncharged xenon derivatives should exhibit higher catalytic activity than their iodine-based noncovalent organocatalytic congeners. Perfluorophenyl xenonium(II) is expected to demonstrate the best balance between catalytic activity and chemical stability for use in organocatalysis. Comparing its catalytic activity with that of isoelectronic perfluoroiodobenzene indicates that the high catalytic activity of cationic noncovalent organocatalysts is predominantly attributed to the electrostatic interactions with the reaction substrates, which cause the polarization of ligated species during the reaction progress. In contrast, the electron transfer and covalent contributions to the bonding between the catalyst and substrate have negligible effects. The dominant effect of electrostatic interactions results in a strong negative correlation between the calculated Gibbs free energies of activation for the modeled reactions and the highest potentials of the σ-holes on the central atoms of the catalysts. No such correlation is observed for noncharged catalysts.

Noncovalent Interaction- and Steric Effect-Controlled Regiodivergent Selectivity in Dimeric Manganese-Catalyzed Hydroarylation of Internal Alkynes: A Computational Study

Selective hydroarylation of internal alkynes catalyzed by a dimeric manganese complex provides a powerful strategy for the construction of multisubstituted alkenes. In this work, density functional theory (DFT) calculations and experimental studies were carried out to explore the mechanism and origin of regiodivergent hydroarylation of internal alkynes reported by our group. The results demonstrate that this reaction first proceeds via a bimetallic mechanism to generate the active catalyst that subsequently undergoes a monometallic mechanism to run the three-stage catalytic cycle: alkyne migratory insertion, protonation, and active catalyst regeneration. Alkyne migratory insertion is considered as the regioselectivity-determining step. Energy decomposition analyses on insertion transition states suggest that the interaction between the substrate and catalyst is mainly responsible for the observed exclusive γ-selectivity of 1a, while the deformation of these two sections induced by the sterically hindered phenyl group and aryl group accounts for the complete β-position arylation of 1e. The decrease of γ-selectivity with the regulation of a tertiary alcohol motif in 1a originates from the reduced noncovalent interaction. The computational results provide important insights into the origin of regiodivergent selectivities and useful information for further designing and adjusting the strategy in Mn-catalyzed alkyne hydroarylation.

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.

Guanidine as a strong CO2 adsorbent: a DFT study on cooperative CO2 adsorption

Among the various carbon capture and storage (CCS) technologies, the direct air capture (DAC) of CO2 by engineered chemical reactions on suitable adsorbents has attained more attention in recent times. Guanidine (G) is one of such promising adsorbent molecules for CO2 capture. Recently Lee et al. (Phys. Chem. Chem. Phys., 2015, 17, 10925-10933) reported an interaction energy (ΔE) of -5.5 kcal mol-1 for the GCO2 complex at the CCSD(T)/CBS level, which was one of the best non-covalent interactions observed for CO2 among several functional molecules. Here we show that the non-covalent GCO2 complex can transform to a strongly interacting G-CO2 covalent complex under the influence of multiple molecules of G and CO2. The study, conducted at M06-2X/6-311++G** level density functional theory, shows ΔE = -5.7 kcal mol-1 for GCO2 with an NC distance of 2.688 Å while almost a five-fold increase in ΔE (-27.5 kcal mol-1) is observed for the (G-CO2)8 cluster wherein the N-C distance is 1.444 Å. All the (G-CO2)n clusters (n = 2-10) show a strong N-CO2 covalent interaction with the N-C distance gradually decreasing from 1.479 Å for n = 2 to 1.444 Å for n = 8 ≅ 9, 10. The N-CO2 bonding gives (G+)-(CO2-) zwitterion character for G-CO2 and the charge-separated units preferred a cyclic arrangement in (G-CO2)n clusters due to the support of three strong intermolecular OHN hydrogen bonds from every CO2. The OHN interaction is also enhanced with an increase in the size of the cluster up to n = 8. The high ΔE is attributed to the large cooperativity associated with the N-CO2 and OHN interactions. The quantum theory of atoms in molecules (QTAIM) analysis confirms the nature and strength of such interactions, and finds that the total interaction energy is directly related to the sum of the electron density at the bond critical points of N-CO2 and OHN interactions. Further, molecular electrostatic potential analysis shows that the cyclic cluster is stabilized due to the delocalization of charges accumulated on the (G+)-(CO2-) zwitterion via multiple OHN interactions. The cyclic (G-CO2)n cluster formation is a highly exergonic process, which reveals the high CO2 adsorption capability of guanidine.

Competition between Inter and Intramolecular Tetrel Bonds: Theoretical Studies Complemented by CSD Survey

Crystal structures document the ability of a TF₃ group (T=Si, Ge, Sn, Pb) situated on a naphthalene system to engage in an intramolecular tetrel bond (TB) with an amino group on the adjoining ring. Ab initio calculations evaluate the strength of this bond and evaluate whether it can influence the ability of the T atom to engage in a second, intermolecular TB with another nucleophile. A very strong CN^- anionic base can approach the T either along the extension of a T-C or T-F bond and form a strong TB with an interaction energy approaching 100 kcal/mol, although this bond is weakened a bit by the presence of the internal T⋅⋅⋅N bond. The much less potent NCH base engages in a correspondingly longer and weaker TB, less than 10 kcal/mol. Such an intermolecular TB is weakened by the presence of the internal TB, to the point that it only occurs for the two heavier tetrel atoms Sn and Pb.