scholarly journals Correction to “Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions”

2019 ◽  
Vol 16 (1) ◽  
pp. 818-819 ◽  
Author(s):  
Petra Kührová ◽  
Vojtěch Mlýnský ◽  
Marie Zgarbová ◽  
Miroslav Krepl ◽  
Giovanni Bussi ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Force Field ◽  
Hydrogen Bonding Interactions

scholarly journals Simulating Absorption Spectra of Flavonoids in Aqueous Solution: A Polarizable QM/MM Study

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5853
Author(s):  
Sulejman Skoko ◽  
Matteo Ambrosetti ◽  
Tommaso Giovannini ◽  
Chiara Cappelli
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Hydrogen Bonding ◽  
Force Field ◽  
Absorption Spectra ◽  
Computational Study ◽  
Md Simulations ◽  
Quantum Mechanical ◽  
Hydrogen Bonding Interactions

We present a detailed computational study of the UV/Vis spectra of four relevant flavonoids in aqueous solution, namely luteolin, kaempferol, quercetin, and myricetin. The absorption spectra are simulated by exploiting a fully polarizable quantum mechanical (QM)/molecular mechanics (MM) model, based on the fluctuating charge (FQ) force field. Such a model is coupled with configurational sampling obtained by performing classical molecular dynamics (MD) simulations. The calculated QM/FQ spectra are compared with the experiments. We show that an accurate reproduction of the UV/Vis spectra of the selected flavonoids can be obtained by appropriately taking into account the role of configurational sampling, polarization, and hydrogen bonding interactions.

scholarly journals Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions

2019 ◽  
Vol 15 (5) ◽  
pp. 3288-3305 ◽  
Author(s):  
Petra Kührová ◽  
Vojtěch Mlýnský ◽  
Marie Zgarbová ◽  
Miroslav Krepl ◽  
Giovanni Bussi ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Force Field ◽  
Hydrogen Bonding Interactions

Modeling hydroxyl and water H atoms

1999 ◽  
Vol 32 (3) ◽  
pp. 563-571 ◽  
Author(s):  
Mario Nardelli
Keyword(s):  
Hydrogen Bonding ◽  
Computer Program ◽  
Force Field ◽  
Force Field Calculations ◽  
Hydrogen Bonding Interactions

The coordinates of hydroxyl (alcohol, phenol,etc.) and water H atoms can be easily calculated, within acceptable approximation, by combined geometric and force-field calculations on the basis of hydrogen-bonding interactions. To perform this kind of calculation the computer programHYDROGENhas been developed.

scholarly journals Folding of the Transmembrane 25-Residues Influenza A M2 and Ala-25 Peptides

2020 ◽  
Author(s):  
Ioannis Stylianakis ◽  
Steve Scheiner ◽  
Isaiah Arkin ◽  
Nikolas Glykos ◽  
Antonios Kolocouris
Keyword(s):  
Hydrogen Bonding ◽  
Force Field ◽  
Influenza A ◽  
Single Point ◽  
Cumulative Effect ◽  
Md Simulations ◽  
Helical Structures ◽  
Hydrogen Bonding Interactions ◽  
Peptide Hydrogen ◽  
Α Helix

<p>The correct balance between hydrophobic London dispersion (LD) and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors we sought a comparison of the influenza A transmembrane M2 protein (M2TM) 25-residues monomer and the 25-Ala (Ala<sub>25</sub>) peptide, used as reference since alanine is the only amino acid forming a standard peptide helix which is stabilized by the backbone peptide hydrogen bonding interactions. Folding molecular dynamics (MD) simulations were performed ing the AMBER99SB-STAR-ILDN force field in trifluoroethanol (TFE) as a membrane mimetic, to study the α-helical stability of M2TM and Ala<sub>25</sub> peptides. It was shown that M2TM peptide did not form a single stable α-helix compared to Ala<sub>25</sub>. Instead appears to be dynamic in nature and quickly inter-converts between an ensemble of various folded helical structures having the highest thermal stability to the N-terminal compared to Ala<sub>25</sub>. Circular dichroism (CD) experiments confirm the stability of the α-helical M2TM. DFT calculations results revealed an extra stabilization for the folding of M2TM from b-strand to the α-helix compared to Ala<sub>25</sub>, due to forces that can't be described from a force field. On a technical level, calculations using D95(d,p) single point at a ONIOM (6-31G,3-21G) minimized geometry, in which the backbone is calculated with 6-31G and alkyl side chains with 3-21G, produced an energy differential for M2TM comparable with full D95(d,p). Natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) calculations were applied to investigate the relative contribution of N-H∙∙∙O as compared to C-H∙∙∙O hydrogen bonding interactions in the M2TM which included 17 lipophilic residues; 26 CH∙∙∙O interactions were identified, as compared to 22 NH∙∙∙O H-bonds. The calculations suggested that CH∙∙∙O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total interaction energy when compared to NH∙∙∙O to the stabilization of the folded α-helix in M2TM compared to Ala<sub>25</sub>.</p>

scholarly journals Folding of the Transmembrane 25-Residues Influenza A M2 and Ala-25 Peptides

2020 ◽  
Author(s):  
Ioannis Stylianakis ◽  
Steve Scheiner ◽  
Isaiah Arkin ◽  
Nikolas Glykos ◽  
Antonios Kolocouris
Keyword(s):  
Hydrogen Bonding ◽  
Force Field ◽  
Influenza A ◽  
Single Point ◽  
Cumulative Effect ◽  
Md Simulations ◽  
Helical Structures ◽  
Hydrogen Bonding Interactions ◽  
Peptide Hydrogen ◽  
Α Helix

<p>The correct balance between hydrophobic London dispersion (LD) and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors we sought a comparison of the influenza A transmembrane M2 protein (M2TM) 25-residues monomer and the 25-Ala (Ala<sub>25</sub>) peptide, used as reference since alanine is the only amino acid forming a standard peptide helix which is stabilized by the backbone peptide hydrogen bonding interactions. Folding molecular dynamics (MD) simulations were performed ing the AMBER99SB-STAR-ILDN force field in trifluoroethanol (TFE) as a membrane mimetic, to study the α-helical stability of M2TM and Ala<sub>25</sub> peptides. It was shown that M2TM peptide did not form a single stable α-helix compared to Ala<sub>25</sub>. Instead appears to be dynamic in nature and quickly inter-converts between an ensemble of various folded helical structures having the highest thermal stability to the N-terminal compared to Ala<sub>25</sub>. Circular dichroism (CD) experiments confirm the stability of the α-helical M2TM. DFT calculations results revealed an extra stabilization for the folding of M2TM from b-strand to the α-helix compared to Ala<sub>25</sub>, due to forces that can't be described from a force field. On a technical level, calculations using D95(d,p) single point at a ONIOM (6-31G,3-21G) minimized geometry, in which the backbone is calculated with 6-31G and alkyl side chains with 3-21G, produced an energy differential for M2TM comparable with full D95(d,p). Natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) calculations were applied to investigate the relative contribution of N-H∙∙∙O as compared to C-H∙∙∙O hydrogen bonding interactions in the M2TM which included 17 lipophilic residues; 26 CH∙∙∙O interactions were identified, as compared to 22 NH∙∙∙O H-bonds. The calculations suggested that CH∙∙∙O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total interaction energy when compared to NH∙∙∙O to the stabilization of the folded α-helix in M2TM compared to Ala<sub>25</sub>.</p>

Theoretical study of hydrogen bonding interactions in substituted nitroxide radicals

2021 ◽  
Author(s):  
Thufail M. Ismail ◽  
Neetha Mohan ◽  
P. K. Sajith
Keyword(s):  
Hydrogen Bonding ◽  
Interaction Energy ◽  
Electrostatic Potential ◽  
Molecular Electrostatic Potential ◽  
Theoretical Study ◽  
Nitroxide Radicals ◽  
Hydrogen Bonding Interactions ◽  
Bonded Complexes ◽  
Hydrogen Bonded

Interaction energy (Eint) of hydrogen bonded complexes of nitroxide radicals can be assessed in terms of the deepest minimum of molecular electrostatic potential (Vmin).

scholarly journals Circular linkage of intramolecular multi-hydrogen bonding frameworks through nucleophilic substitutions of β-dicarbonyls onto cyanuric chloride and subsequent tautomerisation

RSC Advances ◽  
2020 ◽  
Vol 10 (64) ◽  
pp. 39033-39036
Author(s):  
Ayano Awatani ◽  
Masaaki Suzuki
Keyword(s):  
Hydrogen Bonding ◽  
Cyanuric Chloride ◽  
Nucleophilic Substitutions ◽  
Hydrogen Bonding Interactions ◽  
Triazine Derivatives

Triply β-dicarbonyl-embedded 1,3,5-triazine derivatives result in formation of circular linkage of resonance-assisted hydrogen bonding interactions, which can be regarded as well-delocalized resonance hybrids.

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