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  1. 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 ofmore »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 M pro ; (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.« less
    Free, publicly-accessible full text available June 8, 2024
  2. The catalytic effects of iridium pincer complexes for the hydrogenation of carbon dioxide were investigated with the Unified Reaction Valley Approach (URVA), exploring the reaction mechanism along the reaction path traced out by the reacting species on the potential energy surface. Further details were obtained with the Local Mode Analysis performed at all stationary points, complemented by the Natural Bond Orbital and Bader’s Quantum Atoms in Molecules analyses. Each of the five reaction paths forming the catalytic cycle were calculated at the DFT level complemented with DLPNO-CCSD(T) single point calculations at the stationary points. For comparison, the non-catalytic reaction was also investigated. URVA curvature profiles identified all important chemical events taking place in the non-catalyzed reaction and in the five reactions forming the catalytic cycle, and their contribution to the activation energy was disclosed. The non-catalytic reaction has a large unfavorable activation energy of 76.3 kcal/mol, predominately caused by HH bond cleave in the H2 reactant. As shown by our study, the main function of the iridium pincer catalyst is to split up the one–step non-catalytic reaction into an energy efficient multistep cycle, where HH bond cleavage is replaced by the cleavage of a weaker IrH bond with a smallmore »contribution to the activation energy. The dissociation of the final product from the catalyst requires the cleavage of an IrO bond, which is also weak, and contributes only to a minor extent to the activation energy. This, in summary, leads to the substantial lowering of the overall activation barrier by about 50 kcal/mol for the catalyzed reaction. We hope that this study inspires the community to add URVA to their repertoire for the investigation of catalysis reactions.« less
    Free, publicly-accessible full text available December 1, 2023
  3. In this work, we analyzed five groups of different dihydrogen bonding interactions and hydrogen clusters with an H3+ kernel utilizing the local vibrational mode theory, developed by our group, complemented with the Quantum Theory of Atoms–in–Molecules analysis to assess the strength and nature of the dihydrogen bonds in these systems. We could show that the intrinsic strength of the dihydrogen bonds investigated is primarily related to the protonic bond as opposed to the hydridic bond; thus, this should be the region of focus when designing dihydrogen bonded complexes with a particular strength. We could also show that the popular discussion of the blue/red shifts of dihydrogen bonding based on the normal mode frequencies is hampered from mode–mode coupling and that a blue/red shift discussion based on local mode frequencies is more meaningful. Based on the bond analysis of the H3+(H2)n systems, we conclude that the bond strength in these crystal–like structures makes them interesting for potential hydrogen storage applications.
    Free, publicly-accessible full text available January 1, 2024
  4. We introduce in this work a unique parameter for the quantitative assessment of the intrinsic strength of the π interaction between two monomers forming a complex. The new parameter is a local intermonomer stretching force constant, based on the local mode theory, originally developed by Konkoli and Cremer, and derived from the set of nine possible intermonomer normal vibrational modes. The new local force constant was applied to a diverse set of more than 70 molecular complexes, which was divided into four groups. Group 1 includes atoms, ions, and small molecules interacting with benzene and substituted benzenes. Group 2 includes transition metal hydrides and oxides interacting with benzene while Group 3 involves ferrocenes, chromocenes, and titanium sandwich compounds. Group 4 presents an extension to oxygen π–hole interactions in comparison with in-plane hydrogen bonding. We found that the strength of the π interactions in these diverse molecular complexes can vary from weak interactions with predominantly electrostatic character, found, e.g., for argon–benzene complexes, to strong interactions with a substantial covalent nature, found, e.g., for ferrocenes; all being seamlessly described and compared with the new intermonomer local mode force constant, which also outperforms other descriptors such as an averaged force constant or amore »force constant guided by the electron density bond paths. We hope that our findings will inspire the community to apply the new parameter also to other intermonomer π interactions, enriching in this way the broad field of organometallic chemistry with a new efficient assessment tool.« less
    Free, publicly-accessible full text available January 1, 2024
  5. Free, publicly-accessible full text available January 1, 2024
  6. Free, publicly-accessible full text available December 15, 2023
  7. Free, publicly-accessible full text available December 1, 2023
  8. Abstract Two-dimensional infrared spectroscopy has reported highly delocalized in-plane base vibrations in the fingerprint region of nucleotide monophosphates, suggesting the involvement of base pair C=O and C=C ring bonds and considerable interaction between C=O bond stretches. The high delocalization results in congested vibrational spectra, which complicates the assignment of the peaks. This congestion also extends to Watson–Crick base pairs. We applied in this work the characterization of normal mode procedure, a special feature of our local mode analysis, and could for the first time identify the C=O and C=C bonds being engaged in base pair coupling and quantify their contribution to each of the delocalized fingerprint vibration. In addition, a detailed and quantitative description of the hydrogen bonds involved in the Watson–Crick base pairs was provided. Based on the results of this study, we developed a new protocol to elucidate on the assignment of bands in the vibrational spectra of nucleic acids by probing the vibrational space for specific interactions between functional groups prior to and upon base pairing. This protocol will aid to fill the gap between deoxyribonucleic acid structural information and vibrational spectroscopy experiments by facilitating the interpretation of spectra on a quantitative basis.
    Free, publicly-accessible full text available December 1, 2023
  9. 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 stationarymore »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.« less
  10. In this work, we investigated bonding features of 15 ruthenium(II) nitrile complexes of the type [Ru(tpy)(L)-(CH 3 CN)] n+ , containing the tridentate tpy ligand (tpy = 2,2′:6′,2″-terpyridine) and various bidentate ancillary ligands L; 12 compounds originally synthesized by Loftus et al. [J. Phys. Chem. C 123, 10291–10299 (2019)] and three new complexes. We utilized local vibrational force constants derived from the local mode theory as a quantitative measure of bond strength complemented with the topological analysis of the electron density and the natural bond orbital analysis. Loftus et al. suggested that nitrile dissociation occurs after light induced singlet–triplet transition of the original complexes and they used as a measure of nitrile release efficiency quantum yields for ligand exchange in water. They observed larger quantum yields for complexes with smaller singlet–triplet energy gaps. The major goal of this work was to assess how the Ru–NC and Ru–L bond strengths in these 15 compounds relate to and explain the experimental data of Loftus et al., particularly focusing on the question whether there is a direct correlation between Ru–NC bond strength and measured quantum yield. Our study provides the interesting result that the compounds with the highest quantum yields also have themore »strongest Ru–NC bonds suggesting that breaking the Ru–NC bond is not the driving force for the delivery process rather than the change of the metal framework as revealed by first results of a unified reaction valley approach investigation of the mechanism. Compounds with the highest quantum yield show larger electronic structure changes upon singlet–triplet excitation, i.e., larger changes in bond strength, covalency, and difference between the singlet and triplet HOMOs, with exception of the compound 12. In summary, this work provides new insights into the interplay of local properties and experimental quantum yields forming in synergy a useful tool for fine tuning of existing and future design of new nitrile releasing ruthenium compounds. We hope that this work will bring theoretical and experimental studies closer together and serves as an incubator for future collaboration between computational chemists and their experimental colleagues.« less