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

2021 ◽  
Vol 22 (19) ◽  
pp. 10357
Author(s):  
Michał Pocheć ◽  
Karol Kułacz ◽  
Jarosław J. Panek ◽  
Aneta Jezierska
Keyword(s):  
Electronic Structure ◽  
Density Functional ◽  
Parent Compound ◽  
Chemical Properties ◽  
Intramolecular Hydrogen Bonding ◽  
Cooperative Effects ◽  
Molecular Features ◽  
Physico Chemical ◽  
Donor And Acceptor ◽  
Intramolecular Hydrogen

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.

scholarly journals Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car–Parrinello Molecular Dynamics and Electronic Structure Inspection

2021 ◽  
Vol 22 (10) ◽  
pp. 5220
Author(s):  
Jarosław J. Panek ◽  
Joanna Zasada ◽  
Bartłomiej M. Szyja ◽  
Beata Kizior ◽  
Aneta Jezierska
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Quantum Effects ◽  
Potential Of Mean Force ◽  
Probability Density Distribution ◽  
Donor And Acceptor ◽  
Nuclear Quantum Effects ◽  
Vibrational Features

The O-H...N and O-H...O hydrogen bonds were investigated in 10-hydroxybenzo[h]quinoline (HBQ) and benzo[h]quinoline-2-methylresorcinol complex in vacuo, solvent and crystalline phases. The chosen systems contain analogous donor and acceptor moieties but differently coupled (intra- versus intermolecularly). Car–Parrinello molecular dynamics (CPMD) was employed to shed light onto principle components of interactions responsible for the self-assembly. It was applied to study the dynamics of the hydrogen bonds and vibrational features as well as to provide initial geometries for incorporation of quantum effects and electronic structure studies. The vibrational features were revealed using Fourier transformation of the autocorrelation function of atomic velocity and by inclusion of nuclear quantum effects on the O-H stretching solving vibrational Schrödinger equation a posteriori. The potential of mean force (Pmf) was computed for the whole trajectory to derive the probability density distribution and for the O-H stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The electronic structure changes of the benzo[h]quinoline-2-methylresorcinol dimer and trimers were studied based on Constrained Density Functional Theory (CDFT) whereas the Electron Localization Function (ELF) method was applied for all systems. It was found that the bridged proton is localized on the donor side in both investigated systems in vacuo. The crystalline phase simulations indicated bridged proton-sharing and transfer events in HBQ. These effects are even more pronounced when nuclear quantization is taken into account, and the quantized Pmf allows the proton to sample the acceptor area more efficiently. The CDFT indicated the charge depletion at the bridged proton for the analyzed dimer and trimers in solvent. The ELF analysis showed the presence of the isolated proton (a signature of the strongest hydrogen bonds) only in some parts of the HBQ crystal simulation. The collected data underline the importance of the intramolecular coupling between the donor and acceptor moieties.

scholarly journals NMR of Natural Products as Potential Drugs

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3763
Author(s):  
Poul Erik Hansen
Keyword(s):  
Natural Products ◽  
Hydrogen Bonding ◽  
Density Functional ◽  
Chemical Shifts ◽  
Isotope Effects ◽  
Density Functional Theory Calculations ◽  
Intramolecular Hydrogen Bonding ◽  
Chemical Equilibria ◽  
Nmr Techniques ◽  
Intramolecular Hydrogen

This review outlines methods to investigate the structure of natural products with emphasis on intramolecular hydrogen bonding, tautomerism and ionic structures using NMR techniques. The focus is on 1H chemical shifts, isotope effects on chemical shifts and diffusion ordered spectroscopy. In addition, density functional theory calculations are performed to support NMR results. The review demonstrates how hydrogen bonding may lead to specific structures and how chemical equilibria, as well as tautomeric equilibria and ionic structures, can be detected. All these features are important for biological activity and a prerequisite for correct docking experiments and future use as drugs.

scholarly journals New theoretical insights on tautomerism of hyperforin—a prenylated phloroglucinol derivative which may be responsible for St. John’s wort ( Hypericum perforatum ) antidepressant activity

2019 ◽  
Vol 31 (2) ◽  
pp. 657-666
Author(s):  
Wojciech P. Oziminski ◽  
Agata Wójtowicz
Keyword(s):  
Density Functional ◽  
Parent Compound ◽  
Antidepressant Activity ◽  
Functional Theory ◽  
Tautomeric Forms ◽  
Stability Order ◽  
Enol Tautomer ◽  
Intramolecular Hydrogen ◽  
Gradual Transformation ◽  
Tautomeric Mixture

AbstractThe thermodynamic aspects of keto-enol tautomerism of hyperforin were investigated theoretically using density functional theory methods. At the B3LYP/aug-cc-pVTZ//B3LYP/aug-cc-pVDZ level of theory the enol tautomer dominates the tautomeric mixture and the second enol tautomer 1OH-HB has Gibbs free energy higher by 1.2 kcal/mol, despite possessing an intramolecular hydrogen bond. The purely keto tautomer is less stable by 3.3 kcal/mol compared with the 1OH tautomer, which means that the percentage of the keto tautomer in the tautomeric mixture is only about 0.4%. This is a different picture than in the parent compound of hyperforin—the phloroglucinol, where the keto tautomer is more stable than corresponding enol 1OH tautomer by 0.6 kcal/mol. To explain this difference, several in-between model molecules reflecting gradual transformation from phloroglucinol to hyperforin were build, and all the tautomeric forms were optimized for each molecule. It turned out that the addition of an aliphatic three-carbon bridge to phloroglucinol ring is crucial for the reversal of the tautomer stability order to that for hyperforin. The probable reason is the unfavorable strain in the keto tautomer introduced by the carbon bridge, which forces a specific geometric configuration which destabilizes in consequence the keto tautomer. This picture of hyperforin tautomerism underlines the dominance of enol tautomers, which can be important when studying the antidepressant activity of hyperforin—its interactions with neurotransmitters receptors.

Effects of particle size and edge structure on the electronic structure, spectroscopic features, and chemical properties of Au(111)-supported MoS2 nanoparticles

2016 ◽  
Vol 188 ◽  
pp. 323-343 ◽  
Author(s):  
Albert Bruix ◽  
Jeppe V. Lauritsen ◽  
Bjørk Hammer
Keyword(s):  
Electronic Structure ◽  
Active Sites ◽  
Density Functional ◽  
Computational Models ◽  
Chemical Properties ◽  
Structural Motif ◽  
Edge Structure ◽  
Catalytically Active ◽  
Level Shifts ◽  
And Chemical Properties

Materials based on MoS2 are widely used as catalysts and their structure usually consists of single-layered MoS2 nanoparticles whose edges are known to constitute the catalytically active sites. Methods based on density functional theory are used in this work to calculate the electronic structure of representative computational models of MoS2 nanoparticles supported on Au(111). By considering nanoparticles with different edge-terminations, compositions, and sizes, we describe how the electronic structure, Mo3d core-level shifts, and chemical properties (i.e. H adsorption and S vacancy formation) depend on the MoS2 nanoparticle size and structure. In addition, site-specific properties, largely inaccessible when using only slab models of MoS2 edges, are reported, which reveal that the edge sites are not uniform along the nanoparticle and largely depend on the proximity to the corners of the triangular NPs, especially when interacting with a metallic support. Furthermore, a structural motif where H atoms adsorb favourably in a bridging position between two Mo atoms is proposed as an active site for the hydrogen evolution reaction.

Properties of the Magnetic Hydride YFe2H4 from First Principles Calculations

2003 ◽  
Vol 801 ◽  
Author(s):  
D.J. Singh ◽  
M. Gupta
Keyword(s):  
Magnetic Properties ◽  
Electronic Structure ◽  
First Principles ◽  
Density Functional Calculations ◽  
Density Functional ◽  
Parent Compound ◽  
Laves Phase ◽  
Lattice Expansion ◽  
First Principles Calculations ◽  
Electronic And Magnetic Properties

ABSTRACTYFe2H4 is a ferromagnetic metal with magnetization higher than the Laves phase parent compound, YFe2. Here, the electronic and magnetic properties of YFe2H4 are studied using density functional calculations, in order to elucidate the reasons for this. The electronic structure of YFe2H4 differs from that of YFe2 both because of the lattice expansion upon hydriding and because of chemical interactions involving H. However, the main reason for the increased magnetization is found to be the lattice expansion.

Switching On/Off the Intramolecular Hydrogen Bonding of 2-Methoxyphenol Conformers: An NMR Study

2020 ◽  
Vol 73 (3) ◽  
pp. 222
Author(s):  
Frederick Backler ◽  
Feng Wang
Keyword(s):  
Hydrogen Bonding ◽  
Chemical Shift ◽  
1H Nmr ◽  
Density Functional ◽  
Point Group ◽  
Decomposition Analysis ◽  
Intramolecular Hydrogen Bonding ◽  
Group Symmetry ◽  
Energy Decomposition Analysis ◽  
Intramolecular Hydrogen

Intramolecular hydrogen bonding of 2-methoxyphenol (2-MP, guaiacol) is studied using NMR spectroscopy combined with quantum mechanical density functional theory (DFT) calculations. The hydrogen bonding of OH⋯O and HO⋯H is switched on in the conformers of anti–syn (AS, 99.64% dominance) and anti–gauche (AG), respectively, with respect to the anti–anti (AA) conformer (without either such hydrogen bonding interactions). It confirms that the 13C and 1H NMR chemical shift of AS dominates the measured NMR spectra, as the AS conformer reproduces the measurements in CDCl3 solvent (RMSD of 1.86ppm for 13C NMR and of 0.27ppm for 1H NMR). The chemical shift of hydroxyl H(1) at 5.66 pm is identified as the fingerprint of the OH(1)⋯OCH3 hydrogen bonding in AS, as it exhibits a significant deshielding from H(1) of AA (4.24ppm) and H(1) of AG (4.38ppm) without such OH(1)⋯OCH3 hydrogen bonding. The AG conformer (C1 point group symmetry) possesses a less strong hydrogen bonding of HO⋯HCH2O, with the methoxyl group out of the aromatic phenol plane. The substituent effect of AG due to the resonance interaction of methoxyl being out of plane in a concentrated solution shifts the ortho- and para-aromatic carbons, C(3)/C(5), of the AG to ~125.05/125.44ppm from the corresponding carbons in AS at 108.81/121.60ppm. The hydrogen bonding exhibits inwards reduction of IR frequency regions of AS and AG from AA. Finally, energy decomposition analysis (EDA) indicates that there is a steric energy of 45.01kcal mol−1 between the AS and AG when different intramolecular hydrogen bonding is switched on.

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