Site-Specific Hydrogen-Bonding Interaction betweenN-Acetylproline Amide and Protic Solvent Molecules:  Comparisons of IR and VCD Measurements with MD Simulations

2006 ◽  
Vol 110 (50) ◽  
pp. 13355-13365 ◽  
Author(s):  
Kwang-Im Oh ◽  
Jaebeom Han ◽  
Kyung-Koo Lee ◽  
Seungsoo Hahn ◽  
Hogyu Han ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Md Simulations ◽  
Protic Solvent ◽  
Hydrogen Bonding Interaction ◽  
Site Specific ◽  
Bonding Interaction ◽  
Solvent Molecules

On the differential hydration of various forms of glycine in diluted aqueous solutions: a Monte Carlo study

2012 ◽  
Vol 31 (2) ◽  
pp. 295
Author(s):  
Biljana Bujaroska ◽  
Kiro Stojanoski ◽  
Ljupco Pejov
Keyword(s):  
Monte Carlo ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Water Molecules ◽  
Hydrogen Bonding Interaction ◽  
Liquid Environment ◽  
Zwitterionic Form ◽  
Solvent Water ◽  
Bonding Interaction ◽  
Solvent Molecules

Rigid-body Monte Carlo simulations were carried out to study the differential hydration of zwitterionic and neutral forms of glycine in water. To account for the solute polarization by the rather polar liquid environment, initial geometries were chosen as minima on the MP2/aug-cc-pVTZ potential energy surfaces of neutral and zwitterionic glycine continuously solvated by water, implementing the polarizable continuum model (PCM) within the integral equation formalism (IEFPCM). The dynamically changing hydrogen bonding network between the solute and solvent molecules was analyzed imposing distance, energy and angular distribution-based criteria. It was found that, on average, the zwitterionic form of glycine acts as an acceptor of 4.53 hydrogen bonds, while it plays the role of a proton donor in (on average) 2.73 hydrogen bonds with the solvent water molecules. In particular, we have found out that 2.73 solvent water molecules are involved in hydrogen bonding interaction with the ammonium group, acting as proton-acceptors. This is in excellent agreement with the recent experimental neutron diffraction studies, which have indicated that 3.0 water molecules reside in the vicinity of the NH3+ group of aqueous zwitterionic glycine. Neutral form of aqueous glycine, on the other hand, on average donates protons in 1.63 hydrogen bonds with the solvent water molecules, while at the same time it accepts 2.53 hydrogen bonds from the solvent molecules. The greater charge polarization in the zwitterionic form thus makes it much more exposed to hydrogen bonding interaction in polar medium such as water, which is certainly the main reason of the larger stability of this form of glycine in condensed media.

Understanding the mechanism of LCST phase separation of mixed ionic liquids in water by MD simulations

2016 ◽  
Vol 18 (33) ◽  
pp. 23238-23245 ◽  
Author(s):  
Yuling Zhao ◽  
Huiyong Wang ◽  
Yuanchao Pei ◽  
Zhiping Liu ◽  
Jianji Wang
Keyword(s):  
Ionic Liquid ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Phase Separation ◽  
Amino Acid ◽  
Driving Force ◽  
Md Simulations ◽  
Liquid Mixtures ◽  
Hydrogen Bonding Interaction ◽  
Bonding Interaction

Hydrogen bonding interaction between amino acid anions is the driving force for the phase separation of aqueous ionic liquid mixtures.

Radical Enzymes Control the Chemistry of Their Highly Reactive Intermediates Using the Quantum Coulombic Effect

2020 ◽  
Author(s):  
Hossein Khalilian ◽  
Gino A. DiLabio
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Orbital ◽  
Reactive Intermediates ◽  
Hydrogen Bonding Interaction ◽  
Orbital Ordering ◽  
Dynamic Nature ◽  
Radical Intermediate ◽  
Highest Occupied Molecular Orbital ◽  
Bonding Interaction ◽  
Close Proximity

Here, we report an exquisite strategy that the B12 enzymes exploit to manipulate the reactivity of their radical intermediate (Adenosyl radical). Based on the quantum-mechanic calculations, these enzymes utilize a little known long-ranged through space quantum Coulombic effect (QCE). The QCE causes the radical to acquire an electronic structure that contradicts the Aufbau Principle: The singly-occupied molecular orbital (SOMO) is no longer the highest-occupied molecular orbital (HOMO) and the radical is unable to react with neighbouring substrates. The dynamic nature of the enzyme and its structure is expected to be such that the reactivity of the radical is not restored until it is moved into close proximity of the target substrate. We found that the hydrogen bonding interaction between the nearby conserved glutamate residue and the ribose ring of Adenosyl radical plays a crucial role in manipulating the orbital ordering

Radical Enzymes Control the Chemistry of Their Highly Reactive Intermediates Using the Quantum Coulombic Effect

2020 ◽  
Author(s):  
Hossein Khalilian ◽  
Gino A. DiLabio
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Orbital ◽  
Reactive Intermediates ◽  
Hydrogen Bonding Interaction ◽  
Orbital Ordering ◽  
Dynamic Nature ◽  
Radical Intermediate ◽  
Highest Occupied Molecular Orbital ◽  
Bonding Interaction ◽  
Close Proximity

Here, we report an exquisite strategy that the B12 enzymes exploit to manipulate the reactivity of their radical intermediate (Adenosyl radical). Based on the quantum-mechanic calculations, these enzymes utilize a little known long-ranged through space quantum Coulombic effect (QCE). The QCE causes the radical to acquire an electronic structure that contradicts the Aufbau Principle: The singly-occupied molecular orbital (SOMO) is no longer the highest-occupied molecular orbital (HOMO) and the radical is unable to react with neighbouring substrates. The dynamic nature of the enzyme and its structure is expected to be such that the reactivity of the radical is not restored until it is moved into close proximity of the target substrate. We found that the hydrogen bonding interaction between the nearby conserved glutamate residue and the ribose ring of Adenosyl radical plays a crucial role in manipulating the orbital ordering

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