Structure-Property Relationship in Selected Naphtho- and Anthra-Quinone Derivatives on the Basis of Density Functional Theory and Car–Parrinello Molecular Dynamics

Kizior, Beata; Panek, Jarosław J.; Szyja, Bartłomiej M.; Jezierska, Aneta

doi:10.3390/sym13040564

Cited by 5 publications

(7 citation statements)

References 49 publications

(88 reference statements)

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“…This fact of similar electron density distribution in both phases is in agreement with our earlier remarks on the energetic parameters. The PCM results confirmed our expectations, based on previous experience [ 88 , 89 ], that the introduction of solvent did not change the molecular covalent skeleton topology.…”

Section: Resultssupporting

confidence: 90%

“…This is most likely another instance where the strong correlation between bridges is affecting the energy profiles of the hydrogen bridge scans. Such a small influence of the PCM solvent on the potential energy surface was observed in earlier studies on intramolecular hydrogen bonds in naphtho- and anthraquinone derivatives [ 88 , 89 ]. Comparing the energy profiles of the studied compounds in the gas phase and in the solvent, we can see that the presence of solvent does not affect significantly the shape of the energy profile, which is coupled with small impact on the electron density distribution.…”

Section: Resultssupporting

confidence: 58%

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Comprehensive Empirical Model of Substitution—Influence on Hydrogen Bonding in Aromatic Schiff Bases

Krupka

Pocheć

Panek

et al. 2022

IJMS

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In this work, over 500 structures of tri-ring aromatic Schiff bases with different substitution patterns were investigated to develop a unified description of the substituent effect on the intramolecular hydrogen bridge. Both proximal and distal effects were examined using Density Functional Theory (DFT) in the gas phase and with solvent reaction field (Polarizable Continuum Model (PCM) and water as the solvent). In order to investigate and characterize the non-covalent interactions, a topological analysis was performed using the Quantum Theory of Atoms In Molecules (QTAIM) theory and Non-Covalent Interactions (NCI) index. The obtained results were summarized as the generalized, empirical model of the composite substituent effect, assessed using an additional group of simple ring-based Schiff bases. The composite substituent effect has been divided into separate increments describing the different interactions of the hydrogen bridge and the substituent: the classical substituent effect, involving resonance and induction mediated through the ring, steric increment based on substituent proximity to the bridge elements, and distal increment, derived from substitution on the distal ring.

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Section: Resultssupporting

confidence: 90%

Section: Resultssupporting

confidence: 58%

Comprehensive Empirical Model of Substitution—Influence on Hydrogen Bonding in Aromatic Schiff Bases

Krupka

Pocheć

Panek

et al. 2022

IJMS

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“…The values of electron density and its Laplacian at Bond Critical Points (BCPs) of intramolecular hydrogen bonds for both compounds are shown in Table 2. The electron density values at the hydrogen bridge BCPs are consistent with our previous calculations performed for 2,3-dichloronaphthazarin [71]. The covalent O8-H BP1 /O5-H BP2 bonds are stronger than those formed after proton transfer (O1-H BP1 /O4-H BP2 ).…”

Section: Geometric and Electronic Structure Description Of Naphthazarin Derivatives Monomers With Special Emphasis On Intramolecular Hydrsupporting

confidence: 90%

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

et al. 2021

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Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller–Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers’ stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm−1–1700 cm−1 and 2300 cm−1–3400 cm−1 in the gas phase and 600 cm−1–1800 cm−1 and 2200 cm−1–3400 cm−1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm−1–1700 cm−1 and 2300 cm−1–3300 cm−1 for the gas phase and one broad absorption region in the solid state between 700 cm−1 and 3100 cm−1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.

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“…Thus, it is one of the methods applied very often to obtain a detailed characteristic of intra- and intermolecular interactions; see, e.g., Refs. [ 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 ]. These interactions play a fundamental role in chemistry, biochemistry, and biology in determining the structure and physico-chemical properties of systems [ 32 , 33 , 34 ].…”

Section: Introductionmentioning

confidence: 99%

Unraveling the Nature of Hydrogen Bonds of “Proton Sponges” Based on Car-Parrinello and Metadynamics Approaches

Kizior

Michalczyk

Panek

et al. 2023

IJMS

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The nature of intra- and intermolecular non-covalent interactions was studied in four naphthalene derivatives commonly referred to as “proton sponges”. Special attention was paid to an intramolecular hydrogen bond present in the protonated form of the compounds. The unsubstituted “proton sponge” served as a reference structure to study the substituent influence on the hydrogen bond (HB) properties. We selected three compounds substituted by methoxy, amino, and nitro groups. The presence of the substituents either retained the parent symmetry or rendered the compounds asymmetric. In order to reveal the non-covalent interaction properties, the Hirshfeld surface (HS) was computed for the crystal structures of the studied compounds. Next, quantum-chemical simulations were performed in vacuo and in the crystalline phase. Car–Parrinello molecular dynamics (CPMD), Path Integral Molecular Dynamics (PIMD), and metadynamics were employed to investigate the time-evolution changes of metric parameters and free energy profile in both phases. Additionally, for selected snapshots obtained from the CPMD trajectories, non-covalent interactions and electronic structure were studied. Quantum theory of atoms in molecules (QTAIM) and the Density Overlap Regions Indicator (DORI) were applied for this purpose. It was found based on Hirshfeld surfaces that, besides intramolecular hydrogen bonds, other non-covalent interactions are present and have a strong impact on the crystal structure organization. The CPMD results obtained in both phases showed frequent proton transfer phenomena. The proton was strongly delocalized in the applied time-scale and temperature, especially in the PIMD framework. The use of metadynamics allowed for tracing the free energy profiles and confirming that the hydrogen bonds present in “proton sponges” are Low-Barrier Hydrogen Bonds (LBHBs). The electronic and topological analysis quantitatively described the temperature dependence and time-evolution changes of the electronic structure. The covalency of the hydrogen bonds was estimated based on QTAIM analysis. It was found that strong hydrogen bonds show greater covalency, which is additionally determined by the proton position in the hydrogen bridge.

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Structure-Property Relationship in Selected Naphtho- and Anthra-Quinone Derivatives on the Basis of Density Functional Theory and Car–Parrinello Molecular Dynamics

Cited by 5 publications

References 49 publications

Comprehensive Empirical Model of Substitution—Influence on Hydrogen Bonding in Aromatic Schiff Bases

Comprehensive Empirical Model of Substitution—Influence on Hydrogen Bonding in Aromatic Schiff Bases

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

Unraveling the Nature of Hydrogen Bonds of “Proton Sponges” Based on Car-Parrinello and Metadynamics Approaches

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