scholarly journals Resonance-assisted stabilisation of hydrogen bonds probed by NMR spectroscopy and path integral molecular dynamics

2015 ◽  
Vol 51 (73) ◽  
pp. 13986-13989 ◽  
Author(s):  
M. Dračínský ◽  
L. Čechová ◽  
P. Hodgkinson ◽  
E. Procházková ◽  
Z. Janeba
Keyword(s):  
Molecular Dynamics ◽  
Nmr Spectroscopy ◽  
Hydrogen Bonds ◽  
Path Integral ◽  
Quantum Effects ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen ◽  
Nuclear Quantum Effects

Nuclear quantum effects are shown to be important for resonance stabilisation of intramolecular hydrogen bonds.

scholarly journals Molecular dynamics of (Z)-1-(2-hydroxy-5-methyl-3-nitrophenyl)ethanone oxime and (E)-2-hydroxy-5-methylacetophenone thiosemicarbazone in solution studied by NMR spectroscopy

2012 ◽  
Vol 10 (1) ◽  
pp. 241-247 ◽  
Author(s):  
Ibrahim Mamedov ◽  
Uwe Eichhoff ◽  
Abel Maharramov ◽  
Musa Bayramov ◽  
Yegana Mamedova
Keyword(s):  
Molecular Dynamics ◽  
Nmr Spectroscopy ◽  
Hydrogen Bonds ◽  
Rotational Barrier ◽  
Intramolecular Hydrogen Bonds ◽  
Barrier Energy ◽  
Intramolecular Hydrogen

AbstractThe formation of hydrogen bonds and the molecular dynamics for molecules (Z)-1-(2-hydroxy-5-methyl-3-nitrophenyl)ethanone oxime and (E)-2-hydroxy-5-methylacetophenone thiosemicarbazone, (E)-4-bromoacetophenone thiosemicarbazone have been investigated in solution using NMR. The results confirm the formation of different O-H…O type intramolecular hydrogen bonds in the oxime molecule. The rotational barrier energy and energy of intramolecular hydrogen bonds have been determined.

Influence of Intramolecular Charge Transfer and Nuclear Quantum Effects on Intramolecular Hydrogen Bonds in Azopyrimidines

2017 ◽  
Vol 82 (19) ◽  
pp. 10350-10359 ◽  
Author(s):  
Kateřina Bártová ◽  
Lucie Čechová ◽  
Eliška Procházková ◽  
Ondřej Socha ◽  
Zlatko Janeba ◽  
...  
Keyword(s):  
Charge Transfer ◽  
Hydrogen Bonds ◽  
Intramolecular Charge Transfer ◽  
Quantum Effects ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen ◽  
Nuclear Quantum Effects

scholarly journals Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5642
Author(s):  
Karol Kułacz ◽  
Michał Pocheć ◽  
Aneta Jezierska ◽  
Jarosław J. Panek
Keyword(s):  
Perturbation Theory ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Gas Phase ◽  
Quantum Effects ◽  
Broad Absorption ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen ◽  
Nuclear Quantum Effects

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.

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 Car–Parrinello and path integral molecular dynamics study of the intramolecular hydrogen bonds in the crystals of benzoylacetone and dideuterobenzoylacetone

2014 ◽  
Vol 16 (42) ◽  
pp. 23026-23037 ◽  
Author(s):  
Piotr Durlak ◽  
Zdzisław Latajka
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Path Integral ◽  
Molecular Crystal ◽  
Short Hydrogen Bond ◽  
Deuterated Analogue ◽  
Dynamics Simulations ◽  
Intramolecular Hydrogen

The dynamics of the intramolecular short hydrogen bond in the molecular crystal of benzoylacetone and its deuterated analogue are investigated using ab initio molecular dynamics simulations.

Synthesis of 4-Aryl-3(5)-(2-hydroxyphenyl)pyrazoles by Reaction of Isoflavones and their 4-Thio Analogues with Hydrazine Derivatives

2007 ◽  
Vol 60 (12) ◽  
pp. 905 ◽  
Author(s):  
Albert Lévai ◽  
Artur M. S. Silva ◽  
José A. S. Cavaleiro ◽  
José Elguero ◽  
Ibon Alkorta ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Nmr Spectroscopy ◽  
Hydrogen Bonds ◽  
Hydrazine Hydrate ◽  
1H Nmr ◽  
Theoretical Calculations ◽  
Intramolecular Hydrogen Bonds ◽  
Nmr Study ◽  
Intramolecular Hydrogen ◽  
New Compounds

4-Aryl-3(5)-2-(hydroxyphenyl)pyrazoles have been prepared by the reaction of isoflavones and their 4-thio analogues with hydrazine hydrate and phenylhydrazine in hot pyridine. The reaction mechanism for the formation of these pyrazoles is discussed. All the new compounds have been fully characterized by NMR spectroscopy. In [D6]DMSO, a 1H NMR study allows observation of the presence of both pyrazole annular tautomers, due to the presence of intramolecular hydrogen bonds in each tautomer (OH···N and NH···O). Theoretical calculations have been carried out on tautomers and conformers of compounds 20 (3(5)-(2-hydroxy-4-methoxyphenyl)-5(3)-methyl-4-phenylpyrazole) and 21 (3(5)-(2-hydroxy-4-methoxyphenyl)-4-(2-methoxyphenyl)-5(3)-methylpyrazole), including the absolute shieldings (GIAO/B3 LYP/6–311++G**) of 21.

Determination of intramolecular hydrogen bonds in amikacin in water solution by NMR spectroscopy

1995 ◽  
Vol 51 (11) ◽  
pp. 1959-1963 ◽  
Author(s):  
Elena Gaggelli ◽  
Nicola Gaggelli ◽  
Antonella Maccotta ◽  
Gianni Valensin ◽  
Domenico Marini ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Hydrogen Bonds ◽  
Water Solution ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen
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