Molecular Orbital Energy Decomposition Analysis Research Articles

Preferred Electric Field Mechanism for Frustrated Lewis Pair Reactivity.

This study employs computational methods to investigate the mechanism of H2 activation by frustrated Lewis pair (FLP) species, including both intermolecular and intramolecular nitrothane/borane FLP systems. Previous studies have proposed two qualitative reactivity mechanism models to explain the facile cleavage of H2 by FLPs. The findings of this study support the electric field mechanism as the favorable pathway for H2 cleavage. Utilizing frontier molecular orbital theory and energy decomposition analysis, the study explores the electronic structure and nature of the reactions under an external electric field (EEF). Analysis using the activation strain model highlights the significant influence of geometrical deformation energies of FLPs on the activation barriers of H2 activation reactions. Computational results suggest that H2 activation by FLP molecules follows the electric field mechanism, indicating the potential of the FLP/EEF combination as an effective activator for inert molecules.

Electron Dynamics in Alkane C-H Activation Mediated by Transition Metal Complexes.

Alkanes, ideal raw materials for industrial chemical production, typically exhibit limited reactivity due to their robust and weakly polarized C-H bonds. The challenge lies in selectively activating these C-H bonds under mild conditions. To address this challenge, various C-H activation mechanisms have been developed. Yet, classifying these mechanisms depends on the overall stoichiometry, which can be ambiguous and sometimes problematic. In this study, we utilized density functional theory calculations combined with intrinsic bond orbital (IBO) analysis to examine electron flow in the four primary alkane C-H activation mechanisms: oxidative addition, σ-bond metathesis, 1,2-addition, and electrophilic activation. Methane was selected as the representative alkane molecule to undergo C-H heterolytic cleavage in these reactions. Across all mechanisms studied, we find that the CH3 moiety in methane consistently uses an electron pair from the cleaved C-H bond to form a σ-bond with the metal. Yet, the electron pair that accepts the proton differs with each mechanism: in oxidative addition, it is derived from the d-orbitals; in σ-bond metathesis, it resulted from the metal-ligand σ-bonds; in 1,2-addition, it arose from the π-orbital of the metal-ligand multiple bonds; and in electrophilic activation, it came from the lone pairs on ligands. This detailed analysis not only provides a clear visual understanding of these reactions but also showcases the ability of the IBO method to differentiate between mechanisms. The electron flow discerned from IBO analysis is further corroborated by results from absolutely localized molecular orbital energy decomposition analysis, which also helps to quantify the two predominant interactions in each process. Our findings offer profound insights into the electron dynamics at play in alkane C-H activation, enhancing our understanding of these critical reactions.

Boiling, critical, and freezing temperatures in light of molecular descriptors: correlation and causation.

In the pursuit of tracking some physicochemical properties of fluids down to the molecular level, ab initio molecular surface analyses were performed on 169 molecules. This included electrostatic potential (EP), average local ionization energy (ALIE), and electron localization function (ELF) mapped onto an electron density isosurface value of 0.001 au. Using stepwise linear regression (SLR) analysis, it was found that besides the well-studied EP, ALIE and ELF played important roles in determining the normal boiling and freezing points and critical temperatures of fluids. Apparently, the ALIE and ELF were relevant to the attractive polarization forces and repulsive Pauli forces, respectively, between molecules. To further demonstrate and rationalize this assumption, a localized molecular orbital energy decomposition analysis (LMO-EDA) was carried out. In the LMO-EDA analysis, the complexes of the helium atom, He, and ClCl, ClBr, ClI, OCO, OCS, OCSe, and CO/OC molecules were investigated, where the helium atom faced different molecular sites in each molecule. Fortunately, the results showed that lower the ALIE value on a molecular site, the stronger (i.e., more attractive) the polarization interaction energy. The results also indicated that higher the ELF value on a molecular site, the stronger (i.e., more repulsive) the Pauli interaction. The work is aimed to present novel molecular-based rationales to physical chemists, chemical engineers, and materials scientists.

Dispersion, Rehybridization, and Pentacoordination: Keys to Understand Clustering of Boron and Aluminum Hydrides and Halides.

The structure, stability, and bonding characteristics of dimers and trimers involving BX3 and AlX3 (X = H, F, Cl) in the gas phase, many of them explored for the first time, were investigated using different DFT (B3LYP, B3LYP/D3BJ, and M06-2X) and ab initio (MP2 and G4) methods together with different energy decomposition formalisms, namely, many-body interaction-energy and localized molecular orbital energy decomposition analysis. The electron density of the clusters investigated was analyzed with QTAIM, electron localization function, NCIPLOT, and adaptive natural density partitioning approaches. Our results for triel hydride dimers and Al2X6 (X = F, Cl) clusters are in good agreement with previous studies in the literature, but in contrast with the general accepted idea that B2F6 and B2Cl6 do not exist, we have found that they are predicted to be weakly bound systems if dispersion interactions are conveniently accounted for in the theoretical schemes used. Dispersion interactions are also dominant in both homo- and heterotrimers involving boron halide monomers. Surprisingly, B3F9 and B3Cl9 C3v cyclic trimers, in spite of exhibiting rather strong B-X (X = F, Cl) interactions, were found to be unstable with respect to the isolated monomers due to the high energetic cost of the rehybridization of the B atom, which is larger than the two- and three-body stabilization contributions when the cyclic is formed. Another important feature is the enhanced stability of both homo- and heterotrimers in which Al is the central atom because Al is systematically pentacoordinated, whereas this is not the case when the central atom is B, which is only tri- or tetra-coordinated.

Influence of the metal - support and metal - metal interactions on Pd nucleation and NO adsorption in a Pd4/γ-Al2O3 (110D) model.

The role played by the metal - support (MSI) and metal - metal (MMI) interactions on two important processes in controlling the catalyst performance - nucleation and molecular adsorption - has been investigated using density functional theory (DFT), by means of B3LYP functional, combined with localized molecular orbital energy decomposition analysis (LMOEDA), and natural bond orbital (NBO) calculations, with aid of a Pd4/γ-alumina (110D) model (Pd4/Al13O23H7). Our results indicate the occurrence of an electronic metal - support interaction (EMSI) which induces a most intense charge transfer in the Pd4 → γ-alumina backdonation direction, most expressive in Pd → Al, promoting an electronic redistribution within the units and attenuating the MMI. Nevertheless, the MSI/MMI synergistic effect seems to favor slightly the nucleation of a fifth palladium atom, leading to a distorted square pyramidal arrangement for Pd5. The LMOEDA analysis points to a mostly covalent character in the Pd - Al bonds, whereas the Pd - O bonds are mainly electrostatic in nature. The palladium atoms deposited on oxygen anions are the acid centers, where both NO molecule and an additional palladium atom anchor more strongly. In addition, the MSI/MMI effect, through the electronic and geometric contributions, drives the adsorption of the NO molecule to the mode which most favors the Pd → NO (4dz2 → 2π*) backdonation (bridge mode). MSI and MMI effects on the nature of the Pd - O (electrostatic) and Pd - Al (covalent) bonds, charge transfer into Pd4/γ-Al2O3 (110D) interface (back donation) and preferential site for adsorption of a single NO molecule and an additional Pd atom (Pd - O).

Assessing the Interplay between Functional-Driven and Density-Driven Errors in DFT Models of Water.

We investigate the interplay between functional-driven and density-driven errors in different density functional approximations within density functional theory (DFT) and the implications of these errors for simulations of water with DFT-based data-driven potentials. Specifically, we quantify density-driven errors in two widely used dispersion-corrected functionals derived within the generalized gradient approximation (GGA), namely BLYP-D3 and revPBE-D3, and two modern meta-GGA functionals, namely strongly constrained and appropriately normed (SCAN) and B97M-rV. The effects of functional-driven and density-driven errors on the interaction energies are first assessed for the water clusters of the BEGDB dataset. Further insights into the nature of functional-driven errors are gained from applying the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) to the interaction energies, which demonstrates that functional-driven errors are strongly correlated with the nature of the interactions. We discuss cases where density-corrected DFT (DC-DFT) models display higher accuracy than the original DFT models and cases where reducing the density-driven errors leads to larger deviations from the reference energies due to the presence of large functional-driven errors. Finally, molecular dynamics simulations are performed with data-driven many-body potentials derived from DFT and DC-DFT data to determine the effect that minimizing density-driven errors has on the description of liquid water. Besides rationalizing the performance of widely used DFT models of water, we believe that our findings unveil fundamental relations between the shortcomings of some common DFT approximations and the requirements for accurate descriptions of molecular interactions, which will aid the development of a consistent, DFT-based framework for the development of data-driven and machine-learned potentials for simulations of condensed-phase systems.

Theoretical study on Xe⋯N non-covalent interactions: Three hybridization N with XeO3 and XeOF2

The interactions of complexes of XeOF2 and XeO3 with a series of different hybridization N-containing donors are studied by means of DFT and MP2 calculations. The aerogen bonding interaction energies range from 6.5 kcal/mol to 19.9 kcal/mol between XeO3 or XeOF2 and typical N-containing donors. The sequence of interaction for N-containing hybridization is sp3>sp2>sp, and XeO3 is higher than XeOF2. For some donors of sp2 and sp3 hybridization, the steric effect plays a minor role in the interaction with the evidence of reduced density gradient plots. The dominant stable part is the electrostatic interaction. In complex of XeO3, the weight of polarization is larger than dispersion, while the situation is opposite for XeOF2 complexes. Except for the sum of the maximum value of molecular electrostatic potential on Xe atom and minimum value of molecular electrostatic potential on N atom, the otherfive interaction parameters including the potential energy density at bond critical point, the equilibrium distances, interaction energies with the basis set superposition error correction, localized molecular orbital energy decomposition analysis interaction energies, and the electron charge density, show great linear correlation coefficients with each other.

Development of a Many-Body Force Field for Aqueous Alkali Metal and Halogen Ions: An Energy Decomposition Analysis Guided Approach.

Aqueous solutions of alkyl/alkaline metal and halide ions play a crucial functional role in biological systems such as proteins, membranes, and nucleic acids and for interfacial chemistry in geomedia and in the atmosphere. We present the MB-UCB many-body force field for monovalent and divalent ions that includes polarization, charge penetration to describe the short-range permanent electrostatics accurately, as well as a model for charge transfer to better describe the quantum mechanical potential energy surface and its components obtained from the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA). We find that the MB-UCB force field is in very good agreement with a validation suite of ion-ion and ion-water cluster data, exhibiting overall better cancellation of errors among energy components, unlike the case for other many-body potentials that do not utilize an EDA scheme. However, limitations in the functional form for the classical many-body energy components do limit the best achievable accuracy through complete cancellation of error and warrant further study.

Halogen Bonding Propensity in Solution: Direct Observation and Computational Prediction.

Halogen-bonded complexes are often designed by consideration of electrostatic potential (ESP) predictions. ESP predictions do not capture the myriad variables associated with halogen bond (XB) donors and acceptors; thus, binding interaction cannot be quantitatively predicted. Here, a discrepancy between predictions based on ESP energy difference (ΔVs ) and computed gas phase binding energy (ΔEbind ) motivated the experimental determination of the relative strength of halogen bonding interactions in solution by Raman spectroscopic observation of complexes formed from interacting five iodobenzene-derived XB donors and four pyridine XB acceptors. Evaluation of ΔEbind coupled with absolutely-localized molecular orbital energy decomposition analysis (ALMO-EDA) deconvolutes halogen bonding energy contributions and reveals a prominent role for charge transfer (CT) interactions. Raman spectra reveal ΔEbind accurately predicts stronger interactions within iodopentafluorobenzene (IPFB) complexes than with 1-iodo-3,5-dinitrobenzene (IDNB) complexes even though IPFB has similar electrostatics to IDNB and contains a smaller σ-hole.

The nature of halogen bond in model OC∙∙∙XY systems from the energy decomposition analysis perspective

This work represents the theoretical study results of the halogen bond's nature, based upon six model complexes of OC∙∙∙XY type, in which X and Y are halogen atoms. Local Molecular Orbital Energy Decomposition Analysis (LMOEDA), Quantum Theory Atom in Molecules (QTAIM), including geometrical parameters, the values and energy of intermolecular interaction and Molecular Electrostatic Potential (MESP) have been referred to in this investigation. A critical assessment of the LMOEDA studies is also presented. This shows a strong dependency of the results on calculation methods. Some DFT methods have as expected given very consistent results; however, Grimme’s dispersion corrections and some long-range separated functions in DFT do not work with the used decomposition energy procedure. Electron density and Laplacian values confirm linear dependencies in connection to halogen bond energy than in the case of ΔEint = f(RC∙∙∙X). MESP calculations also confirm the usefulness of σ-hole theory.

Estimation of resonance assisted hydrogen bond (RAHB) energies using properties of ring critical points in some dihydrogen-bonded complexes

Intramolecular hydrogen bond (IHB) interactions have investigated in aza-boron-hydrogen rings after formation of dihydrogen bond (DHB) interactions with some substituted aza-boron-hydrogen molecules. These molecules include electron-donating and electron-withdrawing groups. The IHB energies in the dihydrogen-bonded complexes have estimated using a method based on properties of ring critical points (RCPs). There is linear relationship between results of this method and molecular tailoring approach (MTA). Geometrical parameters, spectroscopic information, electronic properties based on atoms in molecules (AIM) method, and natural bond orbital (NBO) analysis have used to find effects of DHB on strength of the IHB interaction. Moreover, aromaticity of resonance-assisted hydrogen bond (RAHB) rings have evaluated using the para delocalization index (PDI), the aromatic fluctuation index (FLU), the average two center index (ATI), and the nucleus-independent chemical shift (NICS) to find relation between π-electron delocalization (π-ED) and properties of these rings. Results show that DHB leads to increase of strength of the IHB interaction. In addition, the PDI benchmark has the best correlation with the IHB descriptors. Additionally, localized molecular orbital energy decomposition analysis (LMO-EDA) reveals that the key components of interaction energies are exchange and electrostatic energy, respectively. Finally, new relations obtained for estimation of the IHB energies based on RCP characteristics and quantum mechanical descriptors.

Au-decorated semiconducting AlN nanosheet as an electronic sensor for theophylline drug

ABSTRACT Density functional theory calculations based on the TPSS functional were performed to investigate the potential application of the pristine AlN nanosheet (AlNNS) as well as the Au-decorated AlNNS (Au@AlNNS) in the detection of the theophylline (TP) drug. We found that the pristine sheet weakly adsorbed the drug, and its sensing response was about 6.0. After the Au-decoration on the AlNNS, the TP drug was powerfully adsorbed onto the Au@AlNNS with the adsorption energy of −1.33 eV, and the sensing response increased to 689.2. The localised molecular orbital energy decomposition analysis illustrated that the electrostatic attraction is stronger than the covalent interaction after the TP adsorption onto the Au@AlNNS. Based on the partial density of state analysis, the TP drug created a new state through the HOMO–LUMO gap of Au@AlNNS, which significantly increased the electrical conductivity. A short recovery time of 2.51 s was attained for the TP desorption from the Au@AlNNS surface. The water solvent weakened the adsorption process and decreased the sensing response to 524.6. Based on the results, we suggested the Au@AlNNS as a biosensor for the TP drug recognition.

Halogen Bonds Stabilised by an Electronic Exchange Channel

AbstractThe σ‐hole is an important concept which has been widely used lately to describe the halogen bond (XB) essentially as electrostatic in nature. However, this idea is not free of controversy. For the sake of this work, localised molecular orbital energy decomposition analysis (LMOEDA), interacting quantum atom (IQA) method and analysis of the electrostatic potential have been applied to O−Cl⋅⋅⋅B (B=CO, PH3, SH2, CS, NH3, OH−) complexes. The results show that in their equilibrium geometry the stabilizing effect that arises from the Pauli exclusion principle is larger in magnitude than the electrostatic interactions. Besides, it appears that an electronic exchange channel is established at a certain approach distance between the monomers.

The Importance of Strain (Preorganization) in Beryllium Bonds.

In order to explore the angular strain role on the ability of Be to form strong beryllium bonds, a theoretical study of the complexes of four beryllium derivatives of ortho closo-carboranes with eight molecules (CO, N2, NCH, CNH, OH2, SH2, NH3, and PH3) acting as Lewis bases has been carried out at the G4 computational level. The results for these complexes, which contain besides Be other electron-deficient elements, such as B, have been compared with the analogous ones formed by three beryllium salts (BeCl2, CO3Be and SO4Be) with the same set of Lewis bases. The results show the presence of large and positive values of the electrostatic potential associated to the beryllium atoms in the isolated four beryllium derivatives of ortho-carboranes, evidencing an intrinsically strong acidic nature. In addition, the LUMO orbital in these systems is also associated to the beryllium atom. These features led to short intermolecular distances and large dissociation energies in the complexes of the beryllium derivatives of ortho-carboranes with the Lewis bases. Notably, as a consequence of the special framework provided by the ortho-carboranes, some of these dissociation energies are larger than the corresponding beryllium bonds in the already strongly bound SO4Be complexes, in particular for N2 and CO bases. The localized molecular orbital energy decomposition analysis (LMOEDA) shows that among the attractive terms associated with the dissociation energy, the electrostatic term is the most important one, except for the complexes with the two previously mentioned weakest bases (N2 and CO), where the polarization term dominates. Hence, these results contribute to further confirm the importance of bending on the beryllium environment leading to strong interactions through the formation of beryllium bonds.

An energy decomposition analysis approach to the rotational barriers of amides and thioamides

The most popular interpretation for the origin of rotational barrier in amides is the electron delocalization of the nitrogen lone pair over the NCO π system. Many attempts have been made to quantify the extent of delocalization in amide and amide like systems. An alternative approach to understand rotational barriers is the energy decomposition analysis (EDA) class of methods. In this work, the rotational barrier of a series of amides is investigated using the Canonical Molecular Orbital Energy Decomposition Analysis (CMOEDA) method. Based on CMOEDA, it was possible to explain i) the origin of the rotational barriers, ii) the energy difference between the two transition states (TS1/TS2) and iii) the variation in the rotational barrier as structural modifications are introduced. Regarding the origin of the rotational barrier, for instance, it was verified that electrostatic and polarization interactions are responsible for building the barrier, while exchange-repulsion contributes to decrease its value.

Structural Basis of Activin Receptor-Like Kinase 2 (R206H) Inhibition by Bis-heteroaryl Pyrazole-Based Inhibitors for the Treatment of Fibrodysplasia Ossificans Progressiva Identified by the Integration of Ligand-Based and Structure-Based Drug Design Approaches

Fibrodysplasia ossificans progressiva (FOP) is a rare but severe genetic disorder in which acute inflammation elicits progressive heterotopic ossification in the muscles, tendons, and ligaments. Classic FOP is caused by the R206H mutation in ALK2/ACVR1. While several activin receptor-like kinase 2 (ALK2) inhibitors were found to be efficacious in animal models of FOP, most of the ALK2 (R206H) inhibitors lacked sufficient oral bioavailability for efficacy. Previously, the synthesis of a series of novel bis-heteroaryl pyrazole-based ALK2 (R206H) inhibitors that achieved both substantial potency and an improved ADMET profile was reported. In the present study, the detailed procedure of the in silico approach employed to identify the initial bis-heteroaryl pyrazole-based ALK2 (R206H) inhibitor RK-59638 and the analysis of the ALK2 (R206H) RK-59638 complex structure to guide the synthetic optimization of the chemical series, obtaining RK-71807 showing improved potency and metabolic stability, were described. According to the initial in silico screening, the screening efficiencies and chemical diversity of the hit compounds of both ligand-based and structure-based methods were evaluated. Then, X-ray structures of ALK2 (R206H) and the inhibitors were analyzed to assess the structure–activity relationships of the synthesized compounds. The 3D-RISM analysis indicated the existence of the additional hydrogen bond via water molecules restricting the attachment point in the pyrazole scaffold. The quantum mechanics calculation of the newly determined ALK2 (R206H) RK-71807 complex structure using a fragment molecular orbital method and pair interaction energy decomposition analysis was employed to evaluate the interaction energies between the inhibitor and each of the amino acid residues and decompose them to electrostatic, exchange-repulsion, and charge transfer energies. The pattern of decomposed interaction energies was then compared to that formed by RK-59638 and LDN-193189 to investigate the structural basis of ALK2 (R206H) inhibition.

Nickel-catalysed anti-Markovnikov hydroarylation of unactivated alkenes with unactivated arenes facilitated by non-covalent interactions.

Anti-Markovnikov additions to alkenes have been a longstanding goal of catalysis, and anti-Markovnikov addition of arenes to alkenes would produce alkylarenes that are distinct from those formed by acid-catalysed processes. Existing hydroarylations are either directed or occur with low reactivity and low regioselectivity for the n-alkylarene. Herein, we report the first undirected hydroarylation of unactivated alkenes with unactivated arenes that occurs with high regioselectivity for the anti-Markovnikov product. The reaction occurs with a nickel catalyst ligated by a highly sterically hindered N-heterocyclic carbene. Catalytically relevant arene- and alkene-bound nickel complexes have been characterized, and the rate-limiting step was shown to be reductive elimination to form the C-C bond. Density functional theory calculations, combined with second-generation absolutely localized molecular orbital energy decomposition analysis, suggest that the difference in activity between catalysts containing large and small carbenes results more from stabilizing intramolecular non-covalent interactions in the secondary coordination sphere than from steric hindrance.

Investigation of resonance assisted hydrogen bond (RAHB) in some pyridine-based complexes: Intramolecular and intermolecular interactions

Intra- and intermolecular hydrogen bonding interactions in some pyridine-based complexes that have R groups without (H, –C2H5, and –C4H9) and with (−C2H3, –C4H5, –C6H7, and –C8H9) π-conjugated system were investigated using quantum mechanical calculations to know role of resonance on strength of interactions. Geometrical parameters and electronic properties based on atoms in molecules (AIM) analysis were studied to interpret the interactions. Also, aromaticity of the rings of the complexes was evaluated using aromatic fluctuation index (FLU) and para-delocalization index (PDI) to connect the mentioned benchmark to energy of the hydrogen bond interactions. Indeed, localized molecular orbital energy decomposition analysis (LMO-EDA) was employed to realize contribution of components of energy in stability of the complexes.

A DFT/EDA study of ethanol decomposition over Pt, Cu and Rh metal clusters

Ethanol reforming has emerged in the last decades as a powerful solution for the energy problem, providing a way for hydrogen production from a renewable and environmentally friendly source. In the search for the best catalyst for this process, it is crucial to understand the reaction mechanism in all its details. In this work, we compare the reaction mechanism for the ethanol decomposition over Pt, Cu and Rh. The approach presented here involves the use of metal clusters treated by effective core potential basis set and the remaining species treated with all electrons. DFT calculations (B3LYP-D3) were used to construct the potential energy surface for all the steps in the path from ethanol to CH4, CH3CH3 and CH2CH2. Canonical molecular orbital energy decomposition analysis (CMOEDA) was used to understand the distinct behavior of the three metals. After the formation of acetaldehyde, the reaction over Pt and Rh easily continues towards the C–C bond breaking, which is much more difficult for Cu. The better capability of Pt and Rh to stabilize transition states is, in most cases, explained by a more malleable electron density in these clusters. This malleability allows the clusters to adjust the electron density to better deal with charge transfers taking place throughout every reaction step.

Basicity of N-heterocyclic carbene and its main-group analogues

In this study, the N-heterocyclic carbene (NHC) imidazole-2-ylidene and its analogues species of group13-15 are considered to study their basicity. Proton affinity (PA) and gas phase basicity (GPB) of each species are calculated at the B3LYP/def2-TZVP level of theory. It is found that PA and GPB decrease down a group and along a period. The acidity of the conjugate acid (pKa) of the NHC analogues are computed in solution giving comparable result to the gas phase ones. The binding energies (ΔEbind) of the adduct formation of the carbene analogues with BH3, BF3 and BCl3 are computed at the same level of theory and follows the same trend. Further interaction energies (ΔEint) of the borane adduct are calculated using localized molecular orbital energy decomposition analysis (LMO-EDA) showing electrostatic (ΔEel) as the dominant factor. Donor-acceptor interaction has been justified from Charge decomposition and Natural bond orbital (NBO) analysis.