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.

Synergistic host–guest hydrophobic and hydrogen bonding interactions in the complexation between endo-functionalized molecular tube and strongly hydrophilic guest molecules in aqueous solution

2018 ◽  
Vol 20 (24) ◽  
pp. 16540-16550 ◽  
Author(s):  
Rabindranath Paul ◽  
Sandip Paul
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Guest Molecules ◽  
Hydrogen Bonding Interactions ◽  
Molecular Tube

Molecular dynamics simulation study of the recognition of hydrophilic molecules by an endo-functionalized molecular tube in aqueous solution.

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>

Isolating the role of hydrogen bonding in hydroxyl-functionalized ionic liquids by means of vaporization enthalpies, infrared spectroscopy and molecular dynamics simulations

2019 ◽  
Vol 21 (36) ◽  
pp. 20308-20314 ◽  
Author(s):  
Dzmitry H. Zaitsau ◽  
Jan Neumann ◽  
Thomas Niemann ◽  
Anne Strate ◽  
Dietmar Paschek ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Infrared Spectroscopy ◽  
Ir Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Dispersion Interaction ◽  
Dynamics Simulations

Hydrogen bonding in hydroxyl-functionalized ionic liquids (right) prevents favourable dispersion interaction between cation and anion (left). We analyze this subtle balance of interactions by combining calorimetry, IR spectroscopy and MD simulations.

Bonded Force Constant Derivation of Lysine-Arginine Cross-linked Advanced Glycation End-Products

2018 ◽  
Author(s):  
Anthony Nash ◽  
Nora H de Leeuw ◽  
Helen L Birch
Keyword(s):  
Molecular Dynamics ◽  
Force Constant ◽  
Computational Study ◽  
Force Constants ◽  
Quantum Mechanical ◽  
Advanced Glycation ◽  
Partial Charges ◽  
Cross Links ◽  
Complete Set ◽  
Dynamics Simulations

<div> <div> <div> <p>The computational study of advanced glycation end-product cross- links remains largely unexplored given the limited availability of bonded force constants and equilibrium values for molecular dynamics force fields. In this article, we present the bonded force constants, atomic partial charges and equilibrium values of the arginine-lysine cross-links DOGDIC, GODIC and MODIC. The Hessian was derived from a series of <i>ab initio</i> quantum mechanical electronic structure calculations and from which a complete set of force constant and equilibrium values were generated using our publicly available software, ForceGen. Short <i>in vacuo</i> molecular dynamics simulations were performed to validate their implementation against quantum mechanical frequency calculations. </p> </div> </div> </div>

Molecular Dynamics Study of Aqueous Solution of Polyethylene Oxide: Critical Test of Force Field Models

2013 ◽  
Vol 11 (4) ◽  
pp. 371-383 ◽  
Author(s):  
Yong-Lei Wang ◽  
Rochelle S. Lawrence ◽  
Zhong-Yuan Lu ◽  
Aatto Laaksonen
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Force Field ◽  
Polyethylene Oxide ◽  
Critical Test
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