Unveiling the peculiar hydrogen bonding behavior of solvated N-heterocyclic carbenes

2016 ◽  
Vol 18 (1) ◽  
pp. 126-140 ◽  
Author(s):  
Oldamur Hollóczki
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Force Field ◽  
Practical Importance ◽  
Md Simulations ◽  
Heterocyclic Carbenes ◽  
Mechanical Force

After fitting a molecular mechanical force field for imidazol-2-ylidenes, MD simulations revealed carbene–carbene and three-center hydrogen bonds of carbenes. The practical importance of these structures is also highlighted.

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 Dissolving Cellulose in 1,2,3-Triazolium- and Imidazolium-Based Ionic Liquids with Aromatic Anions

Molecules ◽  
2020 ◽  
Vol 25 (15) ◽  
pp. 3539 ◽  
Author(s):  
Martin Brehm ◽  
Julian Radicke ◽  
Martin Pulst ◽  
Farzaneh Shaabani ◽  
Daniel Sebastiani ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Ionic Liquids ◽  
Hydrogen Bonds ◽  
Md Simulations ◽  
Heterocyclic Carbenes ◽  
Quantitative Prediction ◽  
Lower Amount ◽  
New Class ◽  
Aromatic Anions ◽  
Lower Basicity

We present 1,2,3-triazolium- and imidazolium-based ionic liquids (ILs) with aromatic anions as a new class of cellulose solvents. The two anions in our study, benzoate and salicylate, possess a lower basicity when compared to acetate and therefore should lead to a lower amount of N-heterocyclic carbenes (NHCs) in the ILs. We characterize their physicochemical properties and find that all of them are liquids at room temperature. By applying force field molecular dynamics (MD) simulations, we investigate the structure and dynamics of the liquids and find strong and long-lived hydrogen bonds, as well as significant π–π stacking between the aromatic anion and cation. Our ILs dissolve up to 8.5 wt.-% cellulose. Via NMR spectroscopy of the solution, we rule out chain degradation or derivatization, even after several weeks at elevated temperature. Based on our MD simulations, we estimate the enthalpy of solvation and derive a simple model for semi-quantitative prediction of cellulose solubility in ILs. With the help of Sankey diagrams, we illustrate the hydrogen bond network topology of the solutions, which is characterized by competing hydrogen bond donors and acceptors. The hydrogen bonds between cellulose and the anions possess average lifetimes in the nanosecond range, which is longer than found in common pure ILs.

scholarly journals A detailed picture of a protein–carbohydrate hydrogen-bonding network revealed by NMR and MD simulations

Glycobiology ◽  
2020 ◽  
Author(s):  
Gustav Nestor ◽  
Alessandro Ruda ◽  
Taigh Anderson ◽  
Stefan Oscarson ◽  
Göran Widmalm ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Antiviral Agents ◽  
Md Simulations ◽  
Protein Backbone ◽  
Carbohydrate Ligands ◽  
Hydrogen Bonding Network ◽  
Dynamics Simulations ◽  
Hydroxyl Protons

Abstract Cyanovirin-N (CV-N) is a cyanobacterial lectin with antiviral activity towards HIV and several other viruses. Here, we identify mannoside hydroxyl protons that are hydrogen bonded to the protein backbone of the CV-N domain B binding site, using NMR spectroscopy. For the two carbohydrate ligands Manα(1→2)ManαOMe and Manα(1→2) Manα(1→6)ManαOMe five hydroxyl protons are involved in hydrogen-bonding networks. Comparison with previous crystallographic results revealed that four of these hydroxyl protons donate hydrogen bonds to protein backbone carbonyl oxygens in solution and in the crystal. Hydrogen bonds were not detected between the side chains of Glu41 and Arg76 with sugar hydroxyls, as previously proposed for CV-N binding of mannosides. Molecular dynamics simulations of the CV-N/Manα(1→2)Manα(1→6)ManαOMe complex confirmed the NMR-determined hydrogen-bonding network. Detailed characterization of CV-N/mannoside complexes provides a better understanding of lectin-carbohydrate interactions and opens up to the use of CV-N and similar lectins as antiviral agents.

scholarly journals Preferential N–H⋯:C hydrogen bonding involving ditopic NH-containing systems and N-heterocyclic carbenes

RSC Advances ◽  
2020 ◽  
Vol 10 (69) ◽  
pp. 42164-42171
Author(s):  
Zacharias J. Kinney ◽  
Arnold L. Rheingold ◽  
John D. Protasiewicz
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Heterocyclic Carbenes ◽  
Secondary Amines ◽  
Solution State

Non-traditional hydrogen bonds between a singlet carbene and a series of ditopic secondary amines is detailed. Both the solid- and solution-state metrics reveal the strength of these associations are dependent on the pKa of the NH-containing molecule.

scholarly journals Validating the CHARMM36m Protein Force Field with LJ-PME Reveals Altered Hydrogen Bonding Dynamics under Elevated Pressures

2021 ◽  
Author(s):  
You Xu ◽  
Jing Huang
Keyword(s):  
Hydrogen Bonds ◽  
Force Field ◽  
Md Simulations ◽  
Temperature Phase ◽  
Elevated Pressures ◽  
Wide Range ◽  
Thermodynamic Conditions ◽  
Model Protein ◽  
Temperature And Pressure ◽  
Good Agreement

<p>The pressure-temperature phase diagram is important to our understanding of the physics of biomolecules. Compared to studies on temperature effects, studies of the pressure dependence of protein dynamic are rather limited. Molecular dynamics (MD) simulations with fine-tuned force fields (FFs) offer a powerful tool to explore the influence of thermodynamic conditions on proteins. Here we evaluate the transferability of the CHARMM36m (C36m) protein force field at varied pressures compared with NMR data using ubiquitin as a model protein. The pressure dependences of J couplings for hydrogen bonds and order parameters for internal motion are in good agreement with experiment. We demonstrate that the C36m FF combined with the LJ-PME method is suitable for simulations in a wide range of temperature and pressure. As the ubiquitin remains stable up to 2500 bar, we identify the mobility and stability of different hydrogen bonds in response to pressure. Based on those results, C36m is expected to be applied to more proteins in the future to further investigate protein dynamics under elevated pressures.</p>

scholarly journals Validating the CHARMM36m protein force field with LJ-PME reveals altered hydrogen bonding dynamics under elevated pressures

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
You Xu ◽  
Jing Huang
Keyword(s):  
Hydrogen Bonds ◽  
Force Field ◽  
Md Simulations ◽  
Temperature Phase ◽  
Particle Mesh Ewald ◽  
Elevated Pressures ◽  
Wide Range ◽  
Thermodynamic Conditions ◽  
Model Protein ◽  
Good Agreement

AbstractThe pressure-temperature phase diagram is important to our understanding of the physics of biomolecules. Compared to studies on temperature effects, studies of the pressure dependence of protein dynamic are rather limited. Molecular dynamics (MD) simulations with fine-tuned force fields (FFs) offer a powerful tool to explore the influence of thermodynamic conditions on proteins. Here we evaluate the transferability of the CHARMM36m (C36m) protein force field at varied pressures compared with NMR data using ubiquitin as a model protein. The pressure dependences of J couplings for hydrogen bonds and order parameters for internal motion are in good agreement with experiment. We demonstrate that the C36m FF combined with the Lennard-Jones particle-mesh Ewald (LJ-PME) method is suitable for simulations in a wide range of temperature and pressure. As the ubiquitin remains stable up to 2500 bar, we identify the mobility and stability of different hydrogen bonds in response to pressure. Based on those results, C36m is expected to be applied to more proteins in the future to further investigate protein dynamics under elevated pressures.

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>

scholarly journals Hydrogen Bonds: Raman Spectroscopic Study

2021 ◽  
Vol 22 (10) ◽  
pp. 5380
Author(s):  
Boris A. Kolesov
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Spectroscopic Study ◽  
Raman Spectra ◽  
Temperature Region ◽  
Vibrational Frequency ◽  
Chemical Compounds ◽  
Raman Spectroscopic ◽  
Raman Spectroscopic Study ◽  
Proton Dynamics

The work outlines general ideas on how the frequency and the intensity of proton vibrations of X–H×××Y hydrogen bonding are formed as the bond evolves from weak to maximally strong bonding. For this purpose, the Raman spectra of different chemical compounds with moderate, strong, and extremely strong hydrogen bonds were obtained in the temperature region of 5 K–300 K. The dependence of the proton vibrational frequency is schematically presented as a function of the rigidity of O-H×××O bonding. The problems of proton dynamics on tautomeric O–H···O bonds are considered. A brief description of the N–H···O and C–H···Y hydrogen bonds is given.

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