A unified molecular‐wide and electron density based concept of chemical bonding

All-body concept and quantified limits of cooperativity and related effects in homodromic cyclic water clusters from a molecular-wide and electron density-based approach

We strongly advocate distinguishing cooperativity from cooperativity-induced effects. From the MOWeD-based approach, the origin of all-body cooperativity is synonymous with physics- and quantum-based processes of electron (e) delocalization throughout water clusters. To this effect, over 10 atom-pairs contribute to the total e-density at a BCP(H,O) between water molecules in a tetramer. Intermolecular all-body e-delocalization, that is, cooperativity, is an energy-minimizing process that fully explains non-additive increase in stability of a water molecule in clusters with an increase in their size. A non-linear change in cooperativity and cooperativity-induced effects, such as (i) structural (e.g., a change in d(O,O)) or topological intra- and intermolecular properties in water clusters (e.g., electron density or potential energy density at bond critical points) is theoretically reproduced by the proposed expression. It predicted the limiting value of delocalized electrons by a H2O molecule in homodromic cyclic clusters to be 1.58e. O-atoms provide the vast majority of electrons that "travel throughout a cluster predominantly on a privileged exchange quantum density highway" (⋅⋅⋅O-H⋅⋅⋅O-H⋅⋅⋅O-H⋅⋅⋅) using Bader's classical bond paths as density bridges linking water molecules. There are, however, additional electron exchange channels that are not seen on molecular graphs as bond paths. A 3D visual representation of the "privileged" and "additional" exchange channels as well as detailed intra- and inter-molecular patterns of e-sharing and (de)localizing is presented. The energy stabilizing contribution made by three O-atoms of neighboring water molecules was found to be large (-597 kcal/mol in cyclic hexamer) and 5 times more significant than that of a classical O-H⋅⋅⋅O intermolecular H-bond.

Anticancer Activities of Re(I) Tricarbonyl and Its Imidazole-Based Ligands: Insight from a Theoretical Approach

Rhenium complexes have been observed experimentally to exhibit good inhibitory activity against malignant cells. Hence, our motivation is to explore this activity from a theoretical perspective. In the present study, density functional theory (DFT) and in silico molecular docking approaches were utilized to unravel the unique properties of metal-based rhenium tricarbonyl complexes as effective anticancer drugs. All DFT calculations and geometric optimizations were conducted using the well-established hybrid functional B3LYP-GD(BJ)/Gen/6-311++G(d,p)/LanL2DZ computational method. The FT-IR spectroscopic characterization of the complexes: fac-[Re(Pico)(CO)₃(Pz)] (R1), fac-[Re(Pico)(CO)₃(Py)] (R2), fac-[Re(Dfpc)(CO)₃(H₂O)] (R3), fac-[Re(Dfpc)(CO)₃(Pz)] (R4), fac-[Re(Dfpc)(CO)₃(Py)] (R5), fac-[Re(Tfpc)(CO)₃(H₂O)] (R6), fac-[Re(Tfpc)(CO)₃(Py)] (R7), and fac-[Re(Tfpc)(CO)₃(Im)] (R8) was explored. To gain insights into the electronic structural properties, bioactivity, and stability of these complexes, the highest occupied molecular orbital-lowest unoccupied molecular orbital analysis, binding energy, and topological analysis based on quantum theory of atoms-in-molecules were considered. The anticancer activities of the complexes were measured via in silico molecular docking against human BCL-2 protein (IG5M) and proapoptotic (agonist) BAX 1 protein (450O). The results showed that the studied complexes exhibited good binding affinity (-3.25 to -10.16 kcal/mol) and could cause significant disruption of the normal physiological functions of the studied proteins. The results of DFT calculations also showed that the studied complexes exhibited good stability and are suitable candidates for the development of anticancer agents.

Coordination Sites for Sodium and Potassium Ions in Nucleophilic Adeninate Contact ion-Pairs: A Molecular-Wide and Electron Density-Based (MOWED) Perspective

The adeninate anion (Ade-) is a useful nucleophile used in the synthesis of many prodrugs (including those for HIV AIDS treatment). It exists as a contact ion-pair (CIP) with Na+ and K+ (M+) but the site of coordination is not obvious from spectroscopic data. Herein, a molecular-wide and electron density-based (MOWED) computational approach implemented in the implicit solvation model showed a strong preference for bidentate ion coordination at the N3 and N9 atoms. The N3N9-CIP has (i) the strongest inter-ionic interaction, by -30 kcal mol-1, with a significant (10-15%) covalent contribution, (ii) the most stabilized bonding framework for Ade-, and (iii) displays the largest ion-induced polarization of Ade-, rendering the N3 and N9 the most negative and, hence, most nucleophilic atoms. Alkylation of the adeninate anion at these two positions can therefore be readily explained when the metal coordinated complex is considered as the nucleophile. The addition of explicit DMSO solvent molecules did not change the trend in most nucleophilic N-atoms of Ade- for the in-plane M-Ade complexes in M-Ade-(DMSO)4 molecular systems. MOWED-based studies of the strength and nature of interactions between DMSO solvent molecules and counter ions and Ade- revealed an interesting and unexpected chemistry of intermolecular chemical bonding.

The Nature of the Polar Covalent Bond

Quantum chemical calculations using density functional theory are reported for the diatomic molecules LiF, BeO, and BN. The nature of the interatomic interactions is analyzed with the EDA-NOCV method, and the results are critically discussed and compared with data from QTAIM, NBO and Mayer approaches. Polar bonds, like nonpolar bonds, are caused by the interference of wave functions, which lead to an accumulation of electronic charge in the bonding region. Polar bonds generally have a larger percentage of electrostatic bonding to the total attraction, but nonpolar bonds may also possess large contributions from Coulombic interaction. The term "ionic contribution" refers to VB structures and is misleading because it refers to separate fragments with negligible overlap that occur only in the solid state and in solution, not in a molecule. The EDA-NOCV method gives detailed information about the individual orbital contributions, which can nicely be identified by visual inspection of the associated deformation densities. It is very important, particularly for polar bonds to distinguish between the interatomic interactions of the final dissociation products after bond rupture and the interactions between the fragments in the eventually formed bond.

Disrupting bonding in azoles through beryllium bonds: Unexpected coordination patterns and acidity enhancement

Although triazoles and tetrazole are amphoteric and may behave as weak acids, the latter property can be hugely enhanced by beryllium bonds. To explain this phenomenon, the structure and bonding characteristics of the complexes between triazoles and tetrazoles with one and two molecules of BeF₂ have been investigated through the use of high-level G4 ab initio calculations. The formation of the complexes between the N basic sites of the azoles and the Be center of the BeF₂ molecule and the (BeF₂)₂ dimer leads to a significant bonding perturbation of both interacting subunits. The main consequence of these electron density rearrangements is the above-mentioned increase in the intrinsic acidity of the azole subunit, evolving from a typical nitrogen base to a very strong nitrogenous acid. This effect is particularly dramatic when the interaction involves the (BeF₂)₂ dimer, that is, a Lewis acid much stronger than the monomer. Although the azoles investigated have neighboring N-basic sites, their interaction with the (BeF₂)₂ dimer yields a monodentate complex. However, the deprotonated species becomes extra-stabilized because a second N-Be bond is formed, leading to a new five-membered ring, with the result that the azole-(BeF₂)₂ complexes investigated become stronger nitrogenous acids than oxyacids such as perchloric acid.

A Molecular-Wide and Electron Density-Based Approach in Exploring Chemical Reactivity and Explicit Dimethyl Sulfoxide (DMSO) Solvent Molecule Effects in the Proline Catalyzed Aldol Reaction

Modelling of the proline (1) catalyzed aldol reaction (with acetone 2) in the presence of an explicit molecule of dimethyl sulfoxide (DMSO) (3) has showed that 3 is a major player in the aldol reaction as it plays a double role. Through strong interactions with 1 and acetone 2, it leads to a significant increase of energy barriers at transition states (TS) for the lowest energy conformer 1a of proline. Just the opposite holds for the higher energy conformer 1b. Both the ‘inhibitor’ and ‘catalyst’ mode of activity of DMSO eliminates 1a as a catalyst at the very beginning of the process and promotes the chemical reactivity, hence catalytic ability of 1b. Modelling using a Molecular-Wide and Electron Density-based concept of Chemical Bonding (MOWED-CB) and the Reaction Energy Profile–Fragment Attributed Molecular System Energy Change (REP-FAMSEC) protocol has shown that, due to strong intermolecular interactions, the HN-C-COOH (of 1), CO (of 2), and SO (of 3) fragments drive a chemical change throughout the catalytic reaction. We strongly advocate exploring the pre-organization of molecules from initially formed complexes, through local minima to the best structures suited for a catalytic process. In this regard, a unique combination of MOWED-CB with REP-FAMSEC provides an invaluable insight on the potential success of a catalytic process, or reaction mechanism in general. The protocol reported herein is suitable for explaining classical reaction energy profiles computed for many synthetic processes.

Intrinsic Dynamic and Static Nature of π···π Interactions in Fused Benzene-Type Helicenes and Dimers, Elucidated with QTAIM Dual Functional Analysis

The intrinsic dynamic and static nature of the π···π interactions between the phenyl groups in proximity of helicenes 3-12 are elucidated with the quantum theory of atoms-in-molecules dual functional analysis (QTAIM-DFA). The π···π interactions appear in C-∗-C, H-∗-H, and C-∗-H, with the asterisks indicating the existence of bond critical points (BCPs) on the interactions. The interactions of 3-12 are all predicted to have a p-CS/vdW nature (vdW nature of the pure closed-shell interaction), except for 2Cbay-∗-7Cbay of 10, which has a p-CS/t-HBnc nature (typical-HBs with no covalency). (See the text for definition of the numbers of C and the bay and cape areas). The natures of the interactions are similarly elucidated between the components of helicene dimers 6:6 and 7:7 with QTAIM-DFA, which have a p-CS/vdW nature. The characteristic electronic structures of helicenes are clarified through the natures predicted with QTAIM-DFA. Some bond paths (BPs) in helicenes appeared or disappeared, depending on the calculation methods. The static nature of Ccape-∗-Ccape is very similar to that of Cbay-∗-Cbay in 9-12, whereas the dynamic nature of Ccape-∗-Ccape appears to be very different from that of Cbay-∗-Cbay. The results will be a guide to design the helicene-containing materials of high functionality.