scholarly journals The Relation Between Ejection Mechanism and Ion Abundance in the Electric Double Layer of Drops

2021 ◽  
Author(s):  
Victor Kwan ◽  
Ryan O'Dwyer ◽  
David Laur ◽  
Jiahua Tan ◽  
Styliani Consta
Keyword(s):  
Surface Layer ◽  
Chemical Reactivity ◽  
Critical Role ◽  
Reaction Rates ◽  
Mass Spectrometry Data ◽  
Charged Droplet ◽  
Droplet Deformation ◽  
Ion Evaporation ◽  
Dynamics Simulations ◽  
Evaporation Mechanism

<div> Charged droplets have been associated with distinct chemical reactivity. It is assumed that the composition of the surface layer plays a critical role in enhancing the reaction rates in the droplets relative to their bulk counterparts. We use atomistic modeling to relate the localization of the ions in the surface layer to their ejection propensity. We find that<br>the ion ejection takes place via a two-stage process. Firstly, a conical protrusion emerges as a result of a global droplet deformation that is insensitive to the locations of single ions. The ions are subsequently ejected as they enter the conical regions. The study provides mechanistic insight into the<br> ion-evaporation mechanism, which can be used to revise the commonly used ion-evaporation models. We argue that atomistic molecular dynamics simulations of minute nano-drops, do not sufficiently distinguish the ion-evaporation mechanism from a Rayleigh fission. We explain mass spectrometry data on the charge state of small globular proteins and the existence of super-charged droplet states (above the Rayleigh limit) that have been detected in experiments. <br></div><div><br></div><div><br></div><div><br></div>

scholarly journals The Relation Between Ejection Mechanism and Ion Abundance in the Electric Double Layer of Drops

2021 ◽  
Author(s):  
Victor Kwan ◽  
Ryan O'Dwyer ◽  
David Laur ◽  
Jiahua Tan ◽  
Styliani Consta
Keyword(s):  
Surface Layer ◽  
Chemical Reactivity ◽  
Critical Role ◽  
Reaction Rates ◽  
Mass Spectrometry Data ◽  
Charged Droplet ◽  
Droplet Deformation ◽  
Ion Evaporation ◽  
Dynamics Simulations ◽  
Evaporation Mechanism

<div> Charged droplets have been associated with distinct chemical reactivity. It is assumed that the composition of the surface layer plays a critical role in enhancing the reaction rates in the droplets relative to their bulk counterparts. We use atomistic modeling to relate the localization of the ions in the surface layer to their ejection propensity. We find that<br>the ion ejection takes place via a two-stage process. Firstly, a conical protrusion emerges as a result of a global droplet deformation that is insensitive to the locations of single ions. The ions are subsequently ejected as they enter the conical regions. The study provides mechanistic insight into the<br> ion-evaporation mechanism, which can be used to revise the commonly used ion-evaporation models. We argue that atomistic molecular dynamics simulations of minute nano-drops, do not sufficiently distinguish the ion-evaporation mechanism from a Rayleigh fission. We explain mass spectrometry data on the charge state of small globular proteins and the existence of super-charged droplet states (above the Rayleigh limit) that have been detected in experiments. <br></div><div><br></div><div><br></div><div><br></div>

Atom Condensed Fukui Function for Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide

2019 ◽  
Author(s):  
Javier Oller ◽  
David A. Sáez ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Carbon Dioxide ◽  
Aqueous Solution ◽  
Molecular System ◽  
Chemical Reactivity ◽  
Nucleophilic Attack ◽  
Stable Conformation ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Dynamics Simulations ◽  
Fixation Of Carbon Dioxide

<div><div><div><p>Local reactivity descriptors such as atom condensed Fukui functions are promising computational tools to study chemical reactivity at specific sites within a molecule. Their applications have been mainly focused on isolated molecules in their most stable conformation without considering the effects of the surroundings. Here, we propose to combine QM/MM Born-Oppenheimer molecular dynamics simulations to obtain the microstates (configurations) of a molecular system using different representations of the molecular environment and calculate Boltzmann weighted atom condensed local reac- tivity descriptors based on conceptual DFT. Our approach takes the conformational fluctuations of the molecular system and the polarization of its electron density by the environment into account allowing us to analyze the effect of changes in the molecular environment on reactivity. In this contribution, we apply the method mentioned above to the catalytic fixation of carbon dioxide by crotonyl-CoA carboxylase/reductase and study if the enzyme alters the reactivity of its substrate compared to an aqueous solution. Our main result is that the protein en- vironment activates the substrate by the elimination of solute-solvent hydrogen bonds from aqueous solution in the two elementary steps of the reaction mechanism: the nucleophilic attack of a hydride anion from NADPH on the α, β unsaturated thioester and the electrophilic attack of carbon dioxide on the formed enolate species.</p></div></div></div>

Clustering and Sampling of the c-Met Conformational Space: A Computational Drug Discovery Study

2020 ◽  
Vol 22 (9) ◽  
pp. 635-648 ◽  
Author(s):  
Korosh Mashayekh ◽  
Shahrzad Sharifi ◽  
Tahereh Damghani ◽  
Maryam Elyasi ◽  
Mohammad S. Avestan ◽  
...  
Keyword(s):  
Critical Role ◽  
Scientific Work ◽  
Binding Mode ◽  
Docking Studies ◽  
Conformational Space ◽  
Hydrogen Bond Interactions ◽  
Docking Program ◽  
Dynamics Simulations ◽  
Computational Drug Discovery ◽  
Dynamic Ensembles

Background: c-Met kinase plays a critical role in a myriad of human cancers, and a massive scientific work was devoted to design more potent inhibitors. Objective: In this study, 16 molecular dynamics simulations of different complexes of potent c-Met inhibitors with U-shaped binding mode were carried out regarding the dynamic ensembles to design novel potent inhibitors. Methods: A cluster analysis was performed, and the most representative frame of each complex was subjected to the structure-based pharmacophore screening. The GOLD docking program investigated the interaction energy and pattern of output hits from the virtual screening. The most promising hits with the highest scoring values that showed critical interactions with c-Met were presented for ADME/Tox analysis. Results: The screening yielded 45,324 hits that all of them were subjected to the docking studies and 10 of them with the highest-scoring values having diverse structures were presented for ADME/Tox analyses. Conclusion: The results indicated that all the hits shared critical Pi-Pi stacked and hydrogen bond interactions with Tyr1230 and Met1160 respectively.

Directional manipulation of diffusio-osmosis flow by design of solute-wall and solvent-wall interactions

2021 ◽  
Author(s):  
Xin Wang ◽  
Dengwei Jing
Keyword(s):  
Critical Role ◽  
Liquid Interface ◽  
High Concentration ◽  
Interfacial Layers ◽  
Fluidic Devices ◽  
Wall Interaction ◽  
Dynamics Simulations ◽  
External Forces ◽  
Solid Liquid Interface ◽  
Solid Liquid

Abstract Understanding of the diffusio-osmosis, the flow induced by a solute gradient acting in narrow interfacial layers at nanoscale solid-liquid interface, is of great value in view of the increasing importance of micro- and nano-fluidic devices and self-propelling particle. Here, using molecular dynamics simulations, we develop a numerical method for direct simulation of diffusio-osmosis flows mimicking the realistic experiment without any assumed external forces. It allows us to obtain reliable flow details which is however hard to get in experiments. We found that the solvent-wall interaction, previously overlooked in classical paradigm, plays a critical role in diffusio-osmosis process. In particular, diffusio-osmosis is controlled by the interaction difference between solute-wall and solvent-wall. When solute-than solvent-wall, a surface excess (depletion) of solute particles on solid-liquid interface is formed which induces diffusio-osmosis flow towards low (high) concentration. We modified the classical Derjaguin expression to include the effect of nanoscale hydrodynamics boundary conditions for the accurate prediction of diffusio-osmosis characteristics. Overall, our results provide the clear guidance for controlling fluids flow and manipulating motion of colloids under tunable solute concentrations.

Surface and Near-Surface Atom Dynamics During Low Energy Xe Ion Bombardment of Si and Fcc Surfaces

1990 ◽  
Vol 193 ◽  
Author(s):  
M. V. R. Murty ◽  
H. S. Lee ◽  
Harry A. Atwater
Keyword(s):  
Molecular Dynamics ◽  
Surface Layer ◽  
Ion Bombardment ◽  
Low Energy ◽  
Surface Processes ◽  
Defect Production ◽  
Near Surface ◽  
Qualitative Nature ◽  
Dynamics Simulations ◽  
Atom Dynamics

ABSTRACTSurface and near-surface processes have been studied during low energy Xe ion bombardment of Si (001) and fcc surfaces using molecular dynamics simulations. Defect production is enhanced near the surface of smooth Si (001) surfaces with respect to the bulk in the energy range 20–150 eV, but is not confined exclusively to the surface layer. The extent and qualitative nature of bombardment-induced dissociation of small fcc islands on an otherwise smooth fcc (001) surface is found to depend strongly on island cohesive energy.

scholarly journals The Relation Between Ejection Mechanism and Ion Abundance in the Electric Double Layer of Drops

2021 ◽  
Author(s):  
Victor Kwan ◽  
Ryan O'Dwyer ◽  
David Laur ◽  
Jiahua Tan ◽  
Styliani Consta
Keyword(s):  
Chemical Reactivity ◽  
Double Electric Layer ◽  
Atomistic Simulations ◽  
Excess Charge ◽  
Atomistic Modeling ◽  
Ion Distribution ◽  
Equilibrium Partition ◽  
Equilibrium Process ◽  
Ejection Mechanism ◽  
Ion Evaporation

The composition of outer drop layers has been associated with distinct chemical reactivity. We use atomistic modeling to examine how the composition of the surface excess charge layer (SECL) is related to the ejection mechanisms of ions. Even though the drop disintegration is inherently a non-equilibrium process we find that the equilibrium ion distribution in SECL predicts the ions that are ejected. The escape of the ions in aqueous drops takes place from conical protrusions that are global drop deformations and their appearance is independent of the location of a single ion. Our results are consistent with the equilibrium partition model, which associates the mass spectrum with the distribution of analytes in the drop’s double electric layer. We present evidence that atomistic simulations of minute nano-drops cannot distinguish Rayleigh fission from the ion evaporation mechanism.

scholarly journals The Relation Between Ejection Mechanism and Ion Abundance in the Electric Double Layer of Drops

2021 ◽  
Author(s):  
Victor Kwan ◽  
Ryan O'Dwyer ◽  
David Laur ◽  
Jiahua Tan ◽  
Styliani Consta
Keyword(s):  
Chemical Reactivity ◽  
Double Electric Layer ◽  
Atomistic Simulations ◽  
Excess Charge ◽  
Atomistic Modeling ◽  
Ion Distribution ◽  
Equilibrium Partition ◽  
Equilibrium Process ◽  
Ejection Mechanism ◽  
Ion Evaporation

The composition of outer drop layers has been associated with distinct chemical reactivity. We use atomistic modeling to examine how the composition of the surface excess charge layer (SECL) is related to the ejection mechanisms of ions. Even though the drop disintegration is inherently a non-equilibrium process we find that the equilibrium ion distribution in SECL predicts the ions that are ejected. The escape of the ions in aqueous drops takes place from conical protrusions that are global drop deformations and their appearance is independent of the location of a single ion. Our results agree with the equilibrium partition model, which associates the mass spectrum with the distribution of analytes in the drop’s double electric layer. We present evidence that atomistic simulations of minute nano-drops cannot distinguish Rayleigh fission from the ion evaporation mechanism.

scholarly journals Molecular Determinants of μ-Conotoxin KIIIA Interaction with the Voltage-Gated Sodium Channel Nav1.7

2019 ◽  
Author(s):  
Ian H. Kimball ◽  
Phuong T. Nguyen ◽  
Baldomero M. Olivera ◽  
Jon T. Sack ◽  
Vladimir Yarov-Yarovoy
Keyword(s):  
Computational Modeling ◽  
Rational Design ◽  
Structural Model ◽  
Critical Role ◽  
Structural Data ◽  
Molecular Probes ◽  
Integrative Approach ◽  
In Silico Docking ◽  
Voltage Gated ◽  
Dynamics Simulations

AbstractThe voltage-gated sodium (Nav) channel subtype Nav1.7 plays a critical role in pain signaling, making it an important drug target. Here we studied the molecular interactions between μ-conotoxin KIIIA (KIIIA) and the human Nav1.7 channel (hNav1.7). We developed a structural model of hNav1.7 using Rosetta computational modeling and performed in silico docking of KIIIA using RosettaDock to predict residues forming specific pairwise contacts between KIIIA and hNav1.7. We experimentally validated these contacts using mutant cycle analysis. Comparison between our KIIIA-hNav1.7 model and the recently published cryo-EM structure of KIIIA-hNav1.2 revealed key similarities and differences between channel subtypes with potential implications for the molecular mechanism of toxin block. Our integrative approach, combining structural data with computational modeling, experimental validation, and molecular dynamics simulations will be useful for engineering molecular probes to study Nav channel function, and for rational design of novel biologics targeting specific Nav channels.

scholarly journals The Relation Between Ejection Mechanism and Ion Abundance in the Electric Double Layer of Drops

2021 ◽  
Author(s):  
Victor Kwan ◽  
Ryan O'Dwyer ◽  
David Laur ◽  
Jiahua Tan ◽  
Styliani Consta
Keyword(s):  
Chemical Reactivity ◽  
Double Electric Layer ◽  
Atomistic Simulations ◽  
Excess Charge ◽  
Atomistic Modeling ◽  
Ion Distribution ◽  
Equilibrium Partition ◽  
Equilibrium Process ◽  
Ejection Mechanism ◽  
Ion Evaporation

The composition of outer drop layers has been associated with distinct chemical reactivity. We use atomistic modeling to examine how the composition of the surface excess charge layer (SECL) is related to the ejection mechanisms of ions. Even though the drop disintegration is inherently a non-equilibrium process we find that the equilibrium ion distribution in SECL predicts the ions that are ejected. The escape of the ions in aqueous drops takes place from conical protrusions that are global drop deformations and their appearance is independent of the location of a single ion. Our results are consistent with the equilibrium partition model, which associates the mass spectrum with the distribution of analytes in the drop’s double electric layer. We present evidence that atomistic simulations of minute nano-drops cannot distinguish Rayleigh fission from the ion evaporation mechanism.

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