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

Ordon, Piotr; Zaklika, Jarosław; Jędrzejewski, Mateusz; Komorowski, Ludwik

doi:10.1021/acs.jpca.9b09426

Cited by 6 publications

(7 citation statements)

References 74 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The formamide molecule has been chosen for a working example for three types of reactions: an internal rotation (ROT) around the C–N bond ( R1 ), an internal proton transfer (PT) between NH 2 and CO groups ( R2 ), and the double proton transfer (DPT) mediated by a water molecule ( R3 ). The set of three types of well understood processes involving the same molecule (NH 2 CHO) allows for testing the results of the proposed method of energy separation between atoms; the fragility spectra for these three processes have been reported separately. , Evolution of eigenvalues and the corresponding eigenvectors of the connectivity matrix at three key stages of the reaction (RS → TS → PS) has been presented for the internal proton transfer reaction in formamide ( R2 ).…”

Section: Results and Discussionmentioning

confidence: 99%

“…The set of three types of well understood processes involving the same molecule (NH 2 CHO) allows for testing the results of the proposed method of energy separation between atoms; the fragility spectra for these three processes have been reported separately. 42,43 Evolution of eigenvalues and the corresponding eigenvectors of the connectivity matrix at three key stages of the reaction (RS → TS → PS) has been presented for the internal proton transfer reaction in formamide (R2).…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2020

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Results and Discussionmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…in previous work. 95 The relatively high contributions to overall anharmonicity parameter A from the two non-bonding contacts in the system (H4-C2 and H4-H5) is an interesting novel discovery in this reaction.…”

Section: Anharmonic Parameter A and Major Contributions From Bonds/c...mentioning

confidence: 99%

“…H2N-CHO molecule has been considered in the planar configuration, as established in the former works. 95 The TS structure has been identified by means of the QST2 algorithm and verified with the frequency calculation for the normal vibrational modes. The reaction progress parameter () has been calculated in the mass-weighted coordinates at 105 points over reaction path covering the range (-2.90 <  < +2.50).…”

Section: Computational Detailsmentioning

confidence: 99%

“…for the proton exchanging atoms. 95 It is now helpful to recall the fragilities for all atoms in the system (6) as well as for all their possible contacts (15), as they play crucial role in calculation of the anharmonicity parameters for the reaction A and its contributions. Since the atomic fragilities represent a sum of fragilities calculated for all bonds/contacts of each atom…”

Section: Reaction Fragilities For Atoms and Bondsmentioning

confidence: 99%

See 1 more Smart Citation

Monitoring Evolution of Atoms and Bonds on a Reaction Path by the Reaction Fragility Method

Ordon

Komorowski

2022

Preprint

Self Cite

View full text Add to dashboard Cite

. The theoretic foundations of the novel method for the comprehensive studies on the mechanism of the evolution of the electronic structure in a chemical reaction have been presented. Our method provides quantification for both the sequence of bond forming and breaking and the degree of bond (order) modifications along the chemical reaction path. The new Density Functional Connectivity Matrix has been introduced: its elements are the divergences of the Hellmann–Feynman forces for atoms in a molecule over the atomic displacements. They have been proved to describe to what extend atoms in a molecule are actually connected with chemical bonds or bonding interactions. The matrix provided foundation for the Reaction Fragility Method. (i) With the use of the Conceptual Density Functional Theory we have completed the road map to characterization of the properties of atoms and bonds in a molecule. We have derived the new gradient theorem, essential for demonstrating the direct link between divergences of the Hellman-Feynman forces on the nuclei and the linear response function of electron density. (ii) The vibrational energy of a system has been decomposed into the atomic fragility modes through diagonalization of the DF Connectivity Matrix, by analogy with the formalism of the normal modes. We present numerical results for the evolution of the atomic fragility modes on the reaction path in the test reaction of the internal proton transfer in H2N-CHO molecule. The visualization of the involvement of bonds and/or contacts between individual atoms on consecutive steps of the reaction has been demonstrated. (iii) The bond fragilities introduced in previous works clearly deliver description of the anharmonic effects for all bonds/contacts in the reacting system. Here we demonstrate how the bond fragilities provide a unique measure of the anharmonic effects in the system, reflecting the response of the vibrational electronic energy to changes in the distances between atoms. The additive contributions from all bonds are combined to the unique global anharmonicity parameter, the third electron energy derivative over the reaction progress. This quantity can be used as a measure of the global changes in a molecule, when they are triggered step by step along a specific reaction path.

show abstract