A new way of studying chemical reactions: a hand-in-hand URVA and QTAIM approach

Reaction mechanism - explored with the unified reaction valley approach

One of the ultimate goals of chemistry is to understand and manipulate chemical reactions, which implies the ability to monitor the reaction and its underlying mechanism at an atomic scale. In this article, we introduce the Unified Reaction Valley Approach (URVA) as a tool for elucidating reaction mechanisms, complementing existing computational procedures. URVA combines the concept of the potential energy surface with vibrational spectroscopy and describes a chemical reaction via the reaction path and the surrounding reaction valley traced out by the reacting species on the potential energy surface on their way from the entrance to the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting species is registered by a change in the normal vibrational modes spanning the reaction valley and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction, with curvature minima reflecting minimal change and curvature maxima indicating the location of important chemical events such as bond breaking/formation, charge polarization and transfer, rehybridization, etc. A decomposition of the path curvature into internal coordinate components or other coordinates of relevance for the reaction under consideration, provides comprehensive insight into the origin of the chemical changes taking place. After giving an overview of current experimental and computational efforts to gain insight into the mechanism of a chemical reaction and presenting the theoretical background of URVA, we illustrate how URVA works for three diverse processes, (i) [1,3] hydrogen transfer reactions; (ii) α-keto-amino inhibitor for SARS-CoV-2 Mpro; (iii) Rh-catalyzed cyanation. We hope that this article will inspire our computational colleagues to add URVA to their repertoire and will serve as an incubator for new reaction mechanisms to be studied in collaboration with our experimental experts in the field.

Studies on charge transfer of enalapril maleate: from solid-state to molecular dynamics

INTRODUCTION

Enalapril maleate is an antihypertensive ethyl ester pro-drug with two crystalline forms. A network of hydrogen bonds in both polymorphs plays an important role on solid-state stability, charge transfer process and degradation reactions (when exposed to high humidity, temperature and/or pH changes).

COMPUTATIONAL PROCEDURES

Supramolecular arrangement was proposed by Hirshfeld surface using the CrystalExplorer17 software and quantum theory of atoms in molecules. The electronic structure properties were calculated using the functional hybrid M06-2X with 6-311++G** base function employing diffuse and polarization functions to improve the description of hydrogen atoms on intermolecular interactions. Also, the H+ charge transfer between enalapril and maleate molecules was performed using Car-Parrinello molecular dynamics with the Verlet algorithm. In both simulations, the temperature of the ionic system was maintained around 300 K using the Nosé-Hoover thermostat and the electronic system evolved without the use of the thermostat.

RESULTS

This work evaluates the effect of maleate on the structural stability of enalapril maleate solid state. The electronic structural analysis points out a partially covalent character for N1-H∙∙∙O7 interaction; and the molecular dynamic showed a decentralized hydrogen on maleate driving a decomposition by charge transfer process while a centered hydrogen driving the stabilization. The charge transfer process and the mobility of the proton (H+) between enalapril and maleate molecules was demonstrated using supramolecular modeling analyses and molecular dynamics calculations.

Chalcogen Bond as a Factor Stabilizing Ligand Conformation in the Binding Pocket of Carbonic Anhydrase IX Receptor Mimic

It is postulated that the overexpression of Carbonic Anhydrase isozyme IX in some cancers contributes to the acidification of the extracellular matrix. It was proved that this promotes the growth and metastasis of the tumor. These observations have made Carbonic Anhydrase IX an attractive drug target. In the light of the findings and importance of the glycoprotein in the cancer treatment, we have employed quantum-chemical approaches to study non-covalent interactions in the binding pocket. As a ligand, the acetazolamide (AZM) molecule was chosen, being known as a potential inhibitor exhibiting anticancer properties. First-Principles Molecular Dynamics was performed to study the chalcogen and other non-covalent interactions in the AZM ligand and its complexes with amino acids forming the binding site. Based on Density Functional Theory (DFT) and post-Hartree-Fock methods, the metric and electronic structure parameters were described. The Non-Covalent Interaction (NCI) index and Atoms in Molecules (AIM) methods were applied for qualitative/quantitative analyses of the non-covalent interactions. Finally, the AZM-binding pocket interaction energy decomposition was carried out. Chalcogen bonding in the AZM molecule is an important factor stabilizing the preferred conformation. Free energy mapping via metadynamics and Path Integral molecular dynamics confirmed the significance of the chalcogen bond in structuring the conformational flexibility of the systems. The developed models are useful in the design of new inhibitors with desired pharmacological properties.

Mechanistic Details of the Sharpless Epoxidation of Allylic Alcohols—A Combined URVA and Local Mode Study

In this work, we investigated the catalytic effects of a Sharpless dimeric titanium (IV)–tartrate–diester catalyst on the epoxidation of allylalcohol with methyl–hydroperoxide considering four different orientations of the reacting species coordinated at the titanium atom (reactions R1–R4) as well as a model for the non-catalyzed reaction (reaction R0). As major analysis tools, we applied the URVA (Unified Reaction Valley Approach) and LMA (Local Mode Analysis), both being based on vibrational spectroscopy and complemented by a QTAIM analysis of the electron density calculated at the DFT level of theory. The energetics of each reaction were recalculated at the DLPNO-CCSD(T) level of theory. The URVA curvature profiles identified the important chemical events of all five reactions as peroxide OO bond cleavage taking place before the TS (i.e., accounting for the energy barrier) and epoxide CO bond formation together with rehybridization of the carbon atoms of the targeted CC double bond after the TS. The energy decomposition into reaction phase contribution phases showed that the major effect of the catalyst is the weakening of the OO bond to be broken and replacement of OH bond breakage in the non-catalyzed reaction by an energetically more favorable TiO bond breakage. LMA performed at all stationary points rounded up the investigation (i) quantifying OO bond weakening of the oxidizing peroxide upon coordination at the metal atom, (ii) showing that a more synchronous formation of the new CO epoxide bonds correlates with smaller bond strength differences between these bonds, and (iii) elucidating the different roles of the three TiO bonds formed between catalyst and reactants and their interplay as orchestrated by the Sharpless catalyst. We hope that this article will inspire the computational community to use URVA complemented with LMA in the future as an efficient mechanistic tool for the optimization and fine-tuning of current Sharpless catalysts and for the design new of catalysts for epoxidation reactions.

Impact of covalent modifications on the hydrogen bond strengths in diaminotriazine supramolecules

Melamine (M) is a popular triamine triazine compound in the field of supramolecular materials. In this work, we have computationally investigated how substituents can be exploited to improve the binding strength of M supramolecules. Two types of covalent modifications were studied: the substitution of an H atom within an amine group -NHR, and the replacement of the whole -NH 2 group (R = H, F, CH 3 and COCH 3 ). Through our dispersion-corrected density functional theory computations, we explain which covalent modification will show the best self-assembling capabilities, and why the binding energy is enhanced. Our charge density and molecular orbital analyses indicate that the best substituents are those that generate a charge accumulation on the endocyclic N atom, providing an improvement of the electrostatic attraction. At the same time the substituent assists the main N-H⋅⋅⋅N hydrogen bonds by interacting with the amino group of the other monomer. We also show how the selected group notably boosts the strength of hexameric rosettes. This research, therefore, provides molecular tools for the rational design of emerging materials based on uneven hydrogen-bonded arrangements.

BF3–Catalyzed Diels–Alder Reaction between Butadiene and Methyl Acrylate in Aqueous Solution—An URVA and Local Vibrational Mode Study

In this study we investigate the Diels–Alder reaction between methyl acrylate and butadiene, which is catalyzed by BF3 Lewis acid in explicit water solution, using URVA and Local Mode Analysis as major tools complemented with NBO, electron density and ring puckering analyses. We considered four different starting orientations of methyl acrylate and butadiene, which led to 16 DA reactions in total. In order to isolate the catalytic effects of the BF3 catalyst and those of the water environment and exploring how these effects are synchronized, we systematically compared the non-catalyzed reaction in gas phase and aqueous solution with the catalyzed reaction in gas phase and aqueous solution. Gas phase studies were performed at the B3LYP/6-311+G(2d,p) level of theory and studies in aqueous solution were performed utilizing a QM/MM approach at the B3LYP/6-311+G(2d,p)/AMBER level of theory. The URVA results revealed reaction path curvature profiles with an overall similar pattern for all 16 reactions showing the same sequence of CC single bond formation for all of them. In contrast to the parent DA reaction with symmetric substrates causing a synchronous bond formation process, here, first the new CC single bond on the CH2 side of methyl acrylate is formed followed by the CC bond at the ester side. As for the parent DA reaction, both bond formation events occur after the TS, i.e., they do not contribute to the energy barrier. What determines the barrier is the preparation process for CC bond formation, including the approach diene and dienophile, CC bond length changes and, in particular, rehybridization of the carbon atoms involved in the formation of the cyclohexene ring. This process is modified by both the BF3 catalyst and the water environment, where both work in a hand-in-hand fashion leading to the lowest energy barrier of 9.06 kcal/mol found for the catalyzed reaction R1 in aqueous solution compared to the highest energy barrier of 20.68 kcal/mol found for the non-catalyzed reaction R1 in the gas phase. The major effect of the BF3 catalyst is the increased mutual polarization and the increased charge transfer between methyl acrylate and butadiene, facilitating the approach of diene and dienophile and the pyramidalization of the CC atoms involved in the ring formation, which leads to a lowering of the activation energy. The catalytic effect of water solution is threefold. The polar environment leads also to increased polarization and charge transfer between the reacting species, similar as in the case of the BF3 catalyst, although to a smaller extend. More important is the formation of hydrogen bonds with the reaction complex, which are stronger for the TS than for the reactant, thus stabilizing the TS which leads to a further reduction of the activation energy. As shown by the ring puckering analysis, the third effect of water is space confinement of the reacting partners, conserving the boat form of the six-member ring from the entrance to the exit reaction channel. In summary, URVA combined with LMA has led to a clearer picture on how both BF3 catalyst and aqueous environment in a synchronized effort lower the reaction barrier. These new insights will serve to further fine-tune the DA reaction of methyl acrylate and butadiene and DA reactions in general.

Electronic Distribution of SN2 IRC and TS Structures: Infrared Intensities of Imaginary Frequencies

A novel IRC-TS-CCTDP method to investigate transition states (TS) is proposed in which changes in the molecular geometry follow atomic displacements corresponding to the imaginary frequency normal coordinate. Electronic charge structure changes can be analyzed using the charge-charge-transfer-dipolar polarization (CCTDP) model. An application is presented for the gas-phase S_N2 reaction transition state structures for nine NuCX₃LG^- systems, with Nu and LG = H, F, Cl and X = H, F. Using quantum theory of atoms in molecules (QTAIM) at the QCISD/aug-cc-pVTZ level, atomic charges and atomic dipoles were obtained and applied to calculate the CCTDP contributions to their imaginary normal mode intensities. The results show that the imaginary bands are exceptionally strong, ranging from 1217 to 16 086 km·mol^-1, much higher than the stretching intensities found in the methyl halides (that are all less than 100 km·mol^-1). For all systems, the CT contributions are responsible for 63% of the total dipole moment derivatives. The charge contributions are slightly higher for transition states where X = F. Dipolar polarization contributions are always small and only reflect the molecular orientation change when the nucleophile displaces the leaving group and, therefore, can be neglected. The same occurs for contributions from the X atoms. Only atoms aligned with the reaction axis Nu^--C-LG contribute to the total intensity. Almost all of the infrared intensities are determined by electron transfers from the nucleophile to carbon and subsequently from carbon to the leaving group. The mechanism of charge transfer revealed by the CCTDP model is consistent with the well-accepted reaction mechanism. Open-access codes for performing the IRC-TS-CCTDP analysis are described and provided for potential users in the Supporting Information.

From the Electron Density Gradient to the Quantitative Reactivity Indicators: Local Softness and the Fukui Function

Important reactivity measures such as the local softness, the Fukui function, and the global hardness have been calculated directly from first principles with the use of the electron density function, beyond the finite difference approximation. Our recently derived density gradient theorem and the principle of nearsightedness of the electronic matter have been instrumental in obtaining the original, albeit approximate, result on the local softness of an atom. By integration of the local softness s(r), we obtain the global softness S and the Fukui function f(r) = s(r)/S. Local and global softness values have also been calculated analytically for the basic hydrogenic orbitals; the general relation to the atomic number S = σZ ^-2 has been demonstrated, with constants σ characteristic for each orbital type. Global hardness η = 1/S calculated for atoms and ions has been favorably tested against its conventional measure given by the finite difference approximation: (I - A). Calculated test results for atoms and ions in rows 1-4 of the periodic table have been presented.

One-to-One Correspondence between Reaction Pathways and Reactive Orbitals

The one-to-one correspondence between reaction pathways in the potential energy theory and reactive orbitals in the electronic theory for reactions is presented. In this study, the reactive orbital energy method is applied to the intrinsic reaction coordinates of the global reaction route map generated by an automated reaction path search method. The reactive orbital energy method specifies the pairs of occupied and unoccupied reactive orbitals driving chemical reactions and determines whether the reactions are electron transfer-driven or dynamics-driven. Surprisingly, it is found that the reactive orbital pairs are determined one by one for the electron transfer-driven reaction pathways from an identical molecule. The reactive orbital energy method is also found to provide the sophisticated interpretations of reactions for the electronic motions. This one-to-one correspondence is expected to trigger the unification of the potential energy theory and the electronic theory for reactions that have been independently developed.

Theoretical Insights into [NHC]Au(I) Catalyzed Hydroalkoxylation of Allenes: A Unified Reaction Valley Approach Study

Hydroxylation is an effective approach for the synthesis of carbon-oxygen bonds and allylic ethers. The [NHC]Au(I) catalyzed intermolecular hydroalkoxylation of allene was studied at the DFT and Coupled Cluster level of theory. Using the Unified Reaction Valley Approach (URVA), we carry out a comprehensive mechanistic analysis of [NHC]Au(I)-catalyzed and noncatalyzed reactions. The URVA study of several possible reaction pathways reveal that the [NHC]Au(I) catalyst enables the hydroalkoxylation reaction to occur via a two step mechanism based upon the Au ability to switch between π- and σ-complexation. The first step of the mechanism involves the formation of a CO bond after the transition state with no energy penalty. Following the CO bond breakage, the OH bond breaks and CH bond forms during the second step of the mechanism, as the catalyst transforms into the more stable π-Au complex. The URVA results were complemented with local vibrational mode analysis to provide measures of intrinsic bond strength for Au(I)-allene interactions of all stationary points, and NBO analysis was applied in order to observe charge transfer events along the reaction pathway. Overall, the π-Au C═C interactions of the products are stronger than those of the reactants adding to their exothermicity. Our work on the hydroxylation of allene provides new insights for the design of effective reaction pathways to produce allylic ethers and also unravels new strategies to form C-O bonds by activation of C═C bonds.

Understanding the Chloride Affinity of Barbiturates for Anion Receptor Design

Due to their potential binding sites, barbituric acid (BA) and its derivatives have been used in metal coordination chemistry. Yet their abilities to recognize anions remain unexplored. In this work, we were able to identify four structural features of barbiturates that are responsible for a certain anion affinity. The set of coordination interactions can be finely tuned with covalent decorations at the methylene group. DFT-D computations at the BLYP-D3(BJ)/aug-cc-pVDZ level of theory show that the C-H bond is as effective as the N-H bond to coordinate chloride. An analysis of the electron charge density at the C-H⋅⋅⋅Cl^- and N-H⋅⋅⋅Cl^- bond critical points elucidates their similarities in covalent character. Our results reveal that the special acidity of the C-H bond shows up when the methylene group moves out of the ring plane and it is mainly governed by the orbital interaction energy. The amide and carboxyl groups are the best choices to coordinate the ion when they act together with the C-H bond. We finally show how can we use this information to rationally improve the recognition capability of a small cage-like complex that is able to coordinate NaCl.

Quantifying bond strengths via a Coulombic force model: application to the impact sensitivity of nitrobenzene, nitrogen-rich nitroazole, and non-aromatic nitramine molecules

The quantification of bond strengths is a useful and general concept in chemistry. In this work, a Coulombic force model based on atomic electric charges computed using the accurate distributed multipole analysis (DMA) partition of the molecular charge density was employed to quantify the weakest N-NO₂ and C-NO₂ bond strengths of 19 nitrobenzene, 11 nitroazole, and 10 nitramine molecules. These bonds are known as trigger linkages because they are usually related to the initiation of an explosive. The three families of explosives combine different types of molecular properties and structures ranging from essentially aromatic molecules (nitrobenzenes) to others with moderate aromaticity (nitroazoles) and non-aromatic molecules with cyclic and acyclic skeletons (nitramines). We used the results to investigate the impact sensitivity of the corresponding explosives employing the trigger linkage concept. For this purpose, the computed Coulombic bond strength of the trigger linkages was used to build four sensitivity models that lead to an overall good agreement between the predicted values and available experimental sensitivity values even when the model included the three chemical families simultaneously. We discussed the role of the trigger linkages for determining the sensitivity of the explosives and rationalized eventual discrepancies in the models by examining alternative decomposition mechanisms and features of the molecular structures.

Local Vibrational Mode Analysis of π–Hole Interactions between Aryl Donors and Small Molecule Acceptors

11 aryl–lone pair and three aryl–anion π –hole interactions are investigated, along with the argon–benzene dimer and water dimer as reference compounds, utilizing the local vibrational mode theory, originally introduced by Konkoli and Cremer, to quantify the strength of the π –hole interaction in terms of a new local vibrational mode stretching force constant between the two engaged monomers, which can be conveniently used to compare different π –hole systems. Several factors have emerged which influence strength of the π –hole interactions, including aryl substituent effects, the chemical nature of atoms composing the aryl rings/ π –hole acceptors, and secondary bonding interactions between donors/acceptors. Substituent effects indirectly affect the π –hole interaction strength, where electronegative aryl-substituents moderately increase π –hole interaction strength. N-aryl members significantly increase π –hole interaction strength, and anion acceptors bind more strongly with the π –hole compared to charge neutral acceptors (lone–pair donors). Secondary bonding interactions between the acceptor and the atoms in the aryl ring can increase π –hole interaction strength, while hydrogen bonding between the π –hole acceptor/donor can significantly increase or decrease strength of the π –hole interaction depending on the directionality of hydrogen bond donation. Work is in progress expanding this research on aryl π –hole interactions to a large number of systems, including halides, CO, and OCH3− as acceptors, in order to derive a general design protocol for new members of this interesting class of compounds.

Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review

The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far out into the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting molecules is registered by a change in their normal vibrational modes and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction with curvature minima reflecting minimal change and curvature maxima, the location of important chemical events such as bond breaking/forming, charge polarization and transfer, rehybridization, etc. A unique decomposition of the path curvature into internal coordinate components provides comprehensive insights into the origins of the chemical changes taking place. After presenting the theoretical background of URVA, we discuss its application to four diverse catalytic processes: (i) the Rh catalyzed methanol carbonylation—the Monsanto process; (ii) the Sharpless epoxidation of allylic alcohols—transition to heterogenous catalysis; (iii) Au(I) assisted [3,3]-sigmatropic rearrangement of allyl acetate; and (iv) the Bacillus subtilis chorismate mutase catalyzed Claisen rearrangement—and show how URVA leads to a new protocol for fine-tuning of existing catalysts and the design of new efficient and eco-friendly catalysts. At the end of this article the pURVA software is introduced. The overall goal of this article is to introduce to the chemical community a new protocol for fine-tuning existing catalytic reactions while aiding in the design of modern and environmentally friendly catalysts.

The Connectivity Matrix: A Toolbox for Monitoring Bonded Atoms and Bonds

The concept of a connectivity matrix, essential for the reaction fragility (RF) spectra technique for monitoring electron density evolution in a chemical reaction, has been supported with a novel formulation for the diagonal matrix elements; their direct link to the electron density function ρ(r) has been demonstrated. By combining the concept with the atomization energy of a system, the separation of the potential energy into atomic and/or bond contributions has been achieved. The energy derivative diagrams for atoms and bonds that are variable along a reaction path provide new insight into the reaction mechanism. Diagonalization of the connectivity matrix resulted in the eigenvectors that provide information on a role of individual atoms in the development of structural changes along a reaction path.

Bond Softening Indices Studied by the Fragility Spectra for Proton Migration in Formamide and Related Structures

Computational scheme to obtain bond softening index λ, defined within the conceptual DFT, has been obtained with the use of the reaction fragility (RF) concept. Numerical results were obtained with the RF spectra for the proton transfer reaction in formamide molecule (H₂NCHO) and the water assisted proton migration in H₂NCHO·H₂O complex. Double proton transfer reaction in the formamide dimer, (H₂NCHO)₂, and its analogues, (H₂NCHS)₂ and (H₂NCHO)·(H₂NCHS), have also been studied. The atomic and bond RF spectra clearly describe the density reorganization in the backbone of each molecule, resulting from proton displacement in the systems. The obtained softening indices have been calculated for hydrogen atoms in the reactant state (RS) and product state (PS) configuration. These indices provide fine characteristics for the local sensitivity of the reacting system to a disturbance of the position of a chosen atom.