Non-Covalent Forces in Naphthazarin—Cooperativity or Competition in the Light of Theoretical Approaches

Jezierska, Aneta; Błaziak, Kacper; Klahm, Sebastian; Lüchow, Arne; Panek, Jarosław J.

doi:10.3390/ijms22158033

Cited by 8 publications

(13 citation statements)

References 96 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This is also true for the gas phase trajectory of 2 . These results are in agreement with the data for naphthazarin [ 61 ]: it was shown that when an asynchronous proton jump occurs, it is very probable that a second proton transfer will follow within a few O-H oscillation periods. From this point of view, it is interesting to note that the solid state simulation of 2 , where the protons are more delocalized, also exhibits important motion correlations.…”

Section: Resultssupporting

confidence: 92%

“…This shows that from a thermodynamic point of view the molecular forms are preferred, but not strongly, over the PT forms. The trans forms through which the double-proton transfer proceeds [ 61 ] are even higher in energy, e.g., for 1 the differences with respect to the molecular forms are: 5.30/4.65 kcal/mol (B3LYP), 2.82/1.26 kcal/mol (PBE) and 6.81/6.23 kcal/mol (

B97XD). However, these values are all well within the range thermally accessible to the extended molecules at room temperature, especially when the effects of donor–acceptor distance modulation are accounted for (see the Car–Parrinello study below).…”

Section: Resultsmentioning

confidence: 99%

“…Before discussing the details of the proton potential functions, it is necessary to consider whether single- or double-proton transfer should be pursued. Our DFT and CPMD results for naphthazarin [ 61 ] indicate that the simultaneous double-proton transfer is less probable and leads to higher barriers, which is assumed to be the effect of deeper modification of aromaticity than in the case of the single-proton transfer event. However, the single-proton transfer enables the second proton transfer (PT) event to happen very fast but not simultaneously, in the order of several O-H stretching periods.…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

et al. 2021

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Resultssupporting

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…Any PT event is recorded in both bridges at the same time. Our earlier study on naphthazarin [ 39 ] has shown that this process is not ideally synchronous, but the delay between the PT events in the two bridges is only a few OH stretching periods, less than 0.1 ps. The current study shows the same behavior of correlated, but not ideally synchronous, proton motions in the two bridges of a given molecule.…”

Section: Resultsmentioning

confidence: 99%

“…The nature of hydrogen bonds was investigated experimentally and theoretically, see, e.g., Refs. [ 37 , 38 , 39 ]. The presence of this kind of bonding introduces non-covalent interactions into the molecule.…”

Section: Introductionmentioning

confidence: 99%

How Substitution Combines with Non-Covalent Interactions to Modulate 1,4-Naphthoquinone and Its Derivatives Molecular Features—Multifactor Studies

Pocheć

Kułacz

Panek

et al. 2021

IJMS

Self Cite

View full text Add to dashboard Cite

Substitution is well-known to modulate the physico-chemical properties of molecules. In this study, a combined, multifactor approach was employed to determine a plethora of substitution patterns using –Br and –O-H in 1,4-naphthoquinone and its derivatives. On the basis of classical Density Functional Theory (DFT), 25 models divided into three groups were developed. The first group contains 1,4-naphthoquinone and its derivatives substituted only by –Br. The second group consists of compounds substituted by –Br and one –O-H group. As a result of the substitution, an intramolecular hydrogen bond was formed. The third group also contains –Br as a substituent, but two –O-H groups were introduced and two intramolecular hydrogen bonds were established. The simulations were performed at the ωB97XD/6-311++G(2d,2p) level of theory. The presence of substituents influenced the electronic structure of the parent compound and its derivatives by inductive effects, but it also affected the geometry of the 2 and 3 groups, due to the intramolecular hydrogen bonding and the formation of a quasi-ring/rings. The static DFT models were applied to investigate the aromaticity changes in the fused rings based on the Harmonic Oscillator Model of Aromaticity (HOMA). The OH stretching was detected for the compounds from groups 2 and 3 and further used to find correlations with energetic parameters. The evolution of the electronic structure was analyzed using Hirshfeld atomic charges and the Substituent Active Region (cSAR) parameter. The proton reaction path was investigated to provide information on the modulation of hydrogen bridge properties by diverse substitution positions on the donor and acceptor sides. Subsequently, Car–Parrinello Molecular Dynamics (CPMD) was carried out in the double-bridged systems (group 3) to assess the cooperative effects in double –O-H-substituted systems. It was determined that the –O-H influence on the core of the molecule is more significant than that of –Br, but the latter has a major impact on the bridge dynamics. The competitive or synergic effect of two –Br substituents was found to depend on the coupling between the intramolecular hydrogen bridges. Thus, the novel mechanism of a secondary (cooperative) substituent effect was established in the double-bridged systems via DFT and CPMD results comparison, consisting of a mediation of the bromine substitutions’ influence by the cooperative proton transfer events in the hydrogen bridges.

show abstract

Investigation of intramolecular hydrogen bonding in naphthoquinone derivatives by quantum chemical calculations

Sharma

Verma

Singh

et al. 2022

J of Physical Organic Chem

View full text Add to dashboard Cite

Intramolecular hydrogen‐bonded naphthoquinone derivatives are investigated using both DFT (density functional theory) and MP2 (Møller–Plesset perturbation theory) method. Three different sets of naphthoquinone derivatives, each set consisting of syn and anti conformers with respect to the substitution by (–OH/–NH2) at peri and para position of the ring, are considered for investigation. In all cases, the syn conformer is found to be energetically more stable compared with the anti conformer. However, the hydrogen bond strength of the anti conformer is found to be more as obtained from NBO (natural bond orbital) analysis and QTAIM (quantum theory of atoms in molecules) theory. The O···H–O interactions are associated with covalent character while O···H–N interactions are noncovalent in nature. The NCI (noncovalent interaction) isosurface clearly indicates the formation of O···H–O and O···H–N intramolecular hydrogen bond. The energy partition analysis indicates electrostatic interaction as the dominant force in stabilizing these systems. The aromaticity calculation by HOMA (harmonic oscillator model of aromaticity) index and Bird index indicate the syn conformer with higher aromaticity compared to the anti conformer. The overall stability of the syn conformers is thus dominated by the aromatic stabilization energy instead of hydrogen bonding energy. The global reactivity descriptors further support the higher stability of the syn conformers according to maximum hardness principle (MHP) and minimum electrophilicity principle (MEP).

show abstract

Non-Covalent Forces in Naphthazarin—Cooperativity or Competition in the Light of Theoretical Approaches

Cited by 8 publications

References 96 publications

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

How Substitution Combines with Non-Covalent Interactions to Modulate 1,4-Naphthoquinone and Its Derivatives Molecular Features—Multifactor Studies

Investigation of intramolecular hydrogen bonding in naphthoquinone derivatives by quantum chemical calculations

Contact Info

Product

Resources

About