scholarly journals Modification of Cu(111) Surface with Alkylphosphonic Acids in Aqueous and Ethanol Solution. An Experimental and Theoretical Study

Electrochem ◽  
2022 ◽  
Vol 3 (1) ◽  
pp. 58-69
Author(s):  
Valbonë Mehmeti ◽  
Fetah Podvorica
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Electrochemical Impedance ◽  
Copper Surface ◽  
Ethanol Solution ◽  
Organic Layer ◽  
Copper Corrosion ◽  
Dynamics Simulations ◽  
The Impact ◽  
Alkylphosphonic Acids

Alkylphosphonic acids are well known for their ability to form self-assembled monolayers on hydroxide surfaces. A crucial step to understanding fundamentally how these surfaces are created is the elucidation of the interaction process that leads to such interface creation. In this study, we employed electrochemical impedance spectroscopy (EIS), Monte Carlo and molecular dynamics to understand this process. The interaction with the Cu(111) surface of three different alkylphosphonic acids (hexyl-, octyl- and decylphosphonic acids) is evaluated in an aqueous acidic and in an ethanol solution by Monte Carlo and molecular dynamics simulations, while EIS measurements are used to put in evidence the impact of the layer made in ethanol on copper protection. Nyquist diagrams of copper samples modified with an alkylphosphonic monolayer showed a higher polarization resistance that mitigates the copper corrosion in an aqueous acid medium. The phase–frequency Bode plots had higher and broader phase maxima for a modified copper surface with phosphonic moieties, which confirmed the ability of this organic layer to prevent copper corrosion.

scholarly journals Kinetically corrected Monte Carlo-molecular dynamics simulations of solid electrolyte interphase growth

2021 ◽  
Author(s):  
Joseph W Abbott ◽  
Felix Hanke
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Solid Electrolyte ◽  
Md Simulation ◽  
Solid Electrolyte Interphase ◽  
Lithium Ion ◽  
Organic Layer ◽  
Near Shore ◽  
Definition Of ◽  
Dynamics Simulations

We present a kinetic approach to the Monte Carlo-molecular dynamics (MC-MD) method for simulating reactive liquids using non-reactive forcefields. A graphical reaction representation allows definition of reactions of arbitrary complexity, including their local solvation environment. Reaction probabilities and molecular dynamics (MD) simulation times are derived from ab initio calculations. Detailed validation is followed by studying the development of the solid electrolyte interphase (SEI) in lithium-ion batteries. We reproduce the experimentally observed two-layered structure on graphite, with an inorganic layer close to the anode and an outer organic layer. This structure develops via a near-shore aggregation mechanism.

scholarly journals Inhibition of copper corrosion in chloride solution by caffeine isolated from black tea

2014 ◽  
Vol 33 (1) ◽  
pp. 13 ◽  
Author(s):  
Senka Gudić ◽  
Emeka Emanuel Oguzie ◽  
Ani Radonić ◽  
Ladislav Vrsalović ◽  
Ivana Smoljko ◽  
...  
Keyword(s):  
Chloride Solution ◽  
Electrochemical Impedance ◽  
Black Tea ◽  
Copper Surface ◽  
Uv Spectrophotometry ◽  
Copper Corrosion ◽  
Corrosion Reaction ◽  
Inhibition Performance ◽  
Dynamics Simulations ◽  
Experimental Findings

<p>Caffeine (1,3,7-trimethylxanthine) was isolated from black tea and characterized using different physical methods (determination of melting point, thin layer chromatography, FTIR spectroscopy and UV spectrophotometry). The corrosion inhibition performance of the caffeine isolate on copper corrosion in neutral 0.5 mol L-1 NaCl solution was investigated using potentiodynamic polarization and electrochemical impedance spectroscopy measurements. The obtained results show that caffeine effectively inhibited the corrosion reaction in the chloride solution with inhibition efficiency up to » 92 %. Furthermore, caffeine was found to function essentially as a cathodic inhibitor by adsorption on the copper surface according to the Langmuir adsorption isotherm. The adsorption free energy of » –37 kJ mol<sup>-1</sup> indicates strong adsorption of the caffeine on the metal surface. Quantum chemical computations and molecular dynamics simulations were adapted to understudy the adsorption of a single caffeine molecule as well as a polymeric cluster of caffeine molecules on a model Cu surface at a molecular level and show good agreement with the experimental findings.</p>

Molecular Dynamics Study of Ion Impact Phenomena and Compressive Stress in Thin Films

1993 ◽  
Vol 317 ◽  
Author(s):  
N.A. Marks ◽  
P. Guan ◽  
D.R. Mckenzie ◽  
B.A. PailThorpe
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
Carbon Films ◽  
Loss Mechanism ◽  
Ion Energy ◽  
Lennard Jones ◽  
Impact Phenomena ◽  
Ion Impact ◽  
Dynamics Simulations ◽  
The Impact

ABSTRACTMolecular dynamics simulations of nickel and carbon have been used to study the phenomena due to ion impact. The nickel and carbon interactions were described using the Lennard-Jones and Stillinger-Weber potentials respectively. The phenomena occurring after the impact of 100 e V to 1 keV ions were studied in the nickel simulations, which were both two and three-dimensional. Supersonic focussed collision sequences (or focusons) were observed, and associated with these focusons were unexpected sonic bow waves, which were a major energy loss mechanism for the focuson. A number of 2D carbon films were grown and the stress in the films as a function of incident ion energy was Measured. With increasing energy the stress changed from tensile to compressive and reached a maximum around 50 eV, in agreement with experiment.

scholarly journals Exploiting correlated molecular-dynamics networks to counteract enzyme activity–stability trade-off

2018 ◽  
Vol 115 (52) ◽  
pp. E12192-E12200 ◽  
Author(s):  
Haoran Yu ◽  
Paul A. Dalby
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Dynamic Networks ◽  
Aromatic Aldehydes ◽  
Active Site Residues ◽  
Trade Off ◽  
Highly Correlated ◽  
Dynamics Simulations ◽  
The Impact

The directed evolution of enzymes for improved activity or substrate specificity commonly leads to a trade-off in stability. We have identified an activity–stability trade-off and a loss in unfolding cooperativity for a variant (3M) of Escherichia coli transketolase (TK) engineered to accept aromatic substrates. Molecular dynamics simulations of 3M revealed increased flexibility in several interconnected active-site regions that also form part of the dimer interface. Mutating the newly flexible active-site residues to regain stability risked losing the new activity. We hypothesized that stabilizing mutations could be targeted to residues outside of the active site, whose dynamics were correlated with the newly flexible active-site residues. We previously stabilized WT TK by targeting mutations to highly flexible regions. These regions were much less flexible in 3M and would not have been selected a priori as targets using the same strategy based on flexibility alone. However, their dynamics were highly correlated with the newly flexible active-site regions of 3M. Introducing the previous mutations into 3M reestablished the WT level of stability and unfolding cooperativity, giving a 10.8-fold improved half-life at 55 °C, and increased midpoint and aggregation onset temperatures by 3 °C and 4.3 °C, respectively. Even the activity toward aromatic aldehydes increased up to threefold. Molecular dynamics simulations confirmed that the mutations rigidified the active-site via the correlated network. This work provides insights into the impact of rigidifying mutations within highly correlated dynamic networks that could also be useful for developing improved computational protein engineering strategies.

scholarly journals Systematic Finite-Temperature Reduction of Crystal Energy Landscapes.

2020 ◽  
Author(s):  
Nicholas Francia ◽  
Louise S. Price ◽  
Jonas Nyman ◽  
Sarah (Sally) Price ◽  
Matteo Salvalaglio
Keyword(s):  
Molecular Dynamics ◽  
Finite Temperature ◽  
Structure Prediction ◽  
Lattice Energy ◽  
Biased Sampling ◽  
Energy Landscapes ◽  
Polymorphic Transformations ◽  
Temperature And Pressure ◽  
Dynamics Simulations ◽  
The Impact

<p>Crystal structure prediction methods are prone to overestimate the number of potential polymorphs of organic molecules. In this work, we aim to reduce the overprediction by systematically applying molecular dynamics simulations and biased sampling methods to cluster subsets of structures that can easily interconvert at finite temperature and pressure. Following this approach, we rationally reduce the number of predicted putative polymorphs in CSP-generated crystal energy landscapes. This uses an unsupervised clustering approach to analyze independent finite-temperature molecular dynamics trajectories and hence identify a representative structure of each cluster of distinct lattice energy minima that are effectively equivalent at finite temperature and pressure. Biased simulations are used to reduce the impact of limited sampling time and to estimate the work associated with polymorphic transformations. We demonstrate the proposed systematic approach by studying the polymorphs of urea and succinic acid, reducing an initial set of over 100 energetically plausible CSP structures to 12 and 27 respectively, including the experimentally known polymorphs. The simulations also indicate the types of disorder and stacking errors that may occur in real structures.<br></p>

Sign in / Sign up

Export Citation Format

Share Document