scholarly journals The Mutual Interactions of RNA, Counterions and Water - Quantifying the Electrostatics at the Phosphate-Water Interface

2021 ◽  
Author(s):  
Benjamin Philipp Fingerhut
Keyword(s):  
Water Molecules ◽  
Solvation Dynamics ◽  
Water Interface ◽  
Structure And Dynamics

The structure and dynamics of polyanionic biomolecules, like RNA, is decisively determined by electric interactions with the water molecules and the counterions of the environment. The solvation dynamics of the...

scholarly journals Time-dependent vibrational sum-frequency generation spectroscopy of the air-water interface

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Deepak Ojha ◽  
Naveen Kumar Kaliannan ◽  
Thomas D. Kühne
Keyword(s):  
Sum Frequency Generation ◽  
Time Dependent ◽  
Water Molecules ◽  
Water Interface ◽  
Sum Frequency ◽  
Generation Spectrum ◽  
Structure And Dynamics ◽  
Sum Frequency Generation Spectroscopy ◽  
Air Water Interface ◽  
Frequency Generation

Abstract Vibrational sum-frequency generation spectroscopy is a powerful method to study the microscopic structure and dynamics of interfacial systems. Here we demonstrate a simple computational approach to calculate the time-dependent, frequency-resolved vibrational sum-frequency generation spectrum (TD-vSFG) of the air-water interface. Using this approach, we show that at the air-water interface, the transition of water molecules with bonded OH modes to free OH modes occurs at a time scale of $$\sim$$ ~ 3 ps, whereas water molecules with free OH modes rapidly make a transition to a hydrogen-bonded state within $$\sim$$ ~ 2 ps. Furthermore, we also elucidate the origin of the observed differential dynamics based on the time-dependent evolution of water molecules in the different local solvent environments.

Temperature Dependence of the Air/Water Interface Revealed by Polarization Sensitive Sum-Frequency Generation Spectroscopy

2018 ◽  
Author(s):  
Daniel R. Moberg ◽  
Shelby C. Straight ◽  
Francesco Paesani
Keyword(s):  
Temperature Dependence ◽  
Low Frequency ◽  
Potential Energy Function ◽  
Md Simulations ◽  
Sum Frequency Generation ◽  
Water Molecules ◽  
Water Interface ◽  
Sum Frequency ◽  
Air Water Interface ◽  
Frequency Generation

<div> <div> <div> <p>The temperature dependence of the vibrational sum-frequency generation (vSFG) spectra of the the air/water interface is investigated using many-body molecular dynamics (MB-MD) simulations performed with the MB-pol potential energy function. The total vSFG spectra calculated for different polarization combinations are then analyzed in terms of molecular auto-correlation and cross-correlation contributions. To provide molecular-level insights into interfacial hydrogen-bonding topologies, which give rise to specific spectroscopic features, the vSFG spectra are further investigated by separating contributions associated with water molecules donating 0, 1, or 2 hydrogen bonds to neighboring water molecules. This analysis suggests that the low frequency shoulder of the free OH peak which appears at ∼3600 cm−1 is primarily due to intermolecular couplings between both singly and doubly hydrogen-bonded molecules. </p> </div> </div> </div>

QM/MM Simulations of Organic Phosphorus Adsorption at the Diaspore-Water Interface

2019 ◽  
Author(s):  
Prasanth Babu Ganta ◽  
Oliver Kühn ◽  
Ashour Ahmed
Keyword(s):  
Interaction Energy ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Water Interface ◽  
Mineral Surfaces ◽  
Soil Mineral ◽  
Phosphorus Adsorption ◽  
Covalent Bonds ◽  
Binding Mechanisms

The phosphorus (P) immobilization and thus its availability for plants are mainly affected by the strong interaction of phosphates with soil components especially soil mineral surfaces. Related reactions have been studied extensively via sorption experiments especially by carrying out adsorption of ortho-phosphate onto Fe-oxide surfaces. But a molecular-level understanding for the P-binding mechanisms at the mineral-water interface is still lacking, especially for forest eco-systems. Therefore, the current contribution provides an investigation of the molecular binding mechanisms for two abundant phosphates in forest soils, inositol hexaphosphate (IHP) and glycerolphosphate (GP), at the diaspore mineral surface. Here a hybrid electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) based molecular dynamics simulation has been applied to explore the diaspore-IHP/GP-water interactions. The results provide evidence for the formation of different P-diaspore binding motifs involving monodentate (M) and bidentate (B) for GP and two (2M) as well as three (3M) monodentate for IHP. The interaction energy results indicated the abundance of the GP B motif compared to the M one. The IHP 3M motif has a higher total interaction energy compared to its 2M motif, but exhibits a lower interaction energy per bond. Compared to GP, IHP exhibited stronger interaction with the surface as well as with water. Water was found to play an important role in controlling these diaspore-IHP/GP-water interactions. The interfacial water molecules form moderately strong H-bonds (HBs) with GP and IHP as well as with the diaspore surface. For all the diaspore-IHP/GP-water complexes, the interaction of water with diaspore exceeds that with the studied phosphates. Furthermore, some water molecules form covalent bonds with diaspore Al atoms while others dissociate at the surface to protons and hydroxyl groups leading to proton transfer processes. Finally, the current results confirm previous experimental conclusions indicating the importance of the number of phosphate groups, HBs, and proton transfers in controlling the P-binding at soil mineral surfaces.

Dynamics and metastable surface structure of double atomic layer of water molecules and ions at the interface between KBr(c) and water

2004 ◽  
Vol 76 (1) ◽  
pp. 115-122 ◽  
Author(s):  
K. Ichikawa ◽  
S. Sato ◽  
N. Shimomura
Keyword(s):  
Surface Structure ◽  
Vertical Motion ◽  
Atomic Layer ◽  
Water Molecules ◽  
Potassium Ions ◽  
Force Microscopy ◽  
Structure And Dynamics ◽  
Atomic Force ◽  
Bromide Ions

The metastable surface structure and dynamics of water molecules, cations, and anions at the interface between KBr(001) and water have been demonstrated from the images in situ observed in atomic resolution using atomic force microscopy. The vertical motion of potassium ions, which means their own transfer from the equilibrium sites to the upper height right on the underlying bromide ions, has been observed at the interface. They are used to be located in some steady state stabilized by their interaction with water molecules in the double atomic layer at the interface. The observed water molecules bridge two bromide ions by hydrogen bond; the water molecules are sandwiched by the potassium ions and vice versa.

The structure of a lanthanide complex at an extractant/water interface studied using heterodyne-detected vibrational sum frequency generation

2018 ◽  
Vol 20 (4) ◽  
pp. 2809-2813 ◽  
Author(s):  
Ryoji Kusaka ◽  
Masayuki Watanabe
Keyword(s):  
Lanthanide Complex ◽  
Sum Frequency Generation ◽  
Water Molecules ◽  
Water Interface ◽  
Lower Side ◽  
Sum Frequency ◽  
Frequency Generation

Eu3+ at an extractant/water interface is bound to extractants from the upper side and to water molecules from the lower side, and forms a unique interfacial complex.

scholarly journals Hydration structure and water exchange kinetics at xenotime–water interfaces: implications for rare earth minerals separation

2020 ◽  
Vol 22 (15) ◽  
pp. 7719-7727 ◽  
Author(s):  
Santanu Roy ◽  
Lili Wu ◽  
Sriram Goverapet Srinivasan ◽  
Andrew G. Stack ◽  
Alexandra Navrotsky ◽  
...  
Keyword(s):  
Free Energy ◽  
Water Exchange ◽  
Marcus Theory ◽  
Water Molecules ◽  
Water Interface ◽  
Solvent Exchange ◽  
Energy Landscapes ◽  
Rare Earth Minerals ◽  
Free Energy Landscapes ◽  
Exchange Kinetics

Multilayering of water molecules at the xenotime–water interface and heterogeneous water exchange timescales between these layers obtained by computing 2D-free energy landscapes and employing Marcus theory of solvent exchange.

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