A comparison of the potential energy parameters of aliphatic alkanes: molecular dynamics simulations of triacylglycerols in the alpha phase

2002 ◽  
Vol 31 (2) ◽  
pp. 89-101 ◽  
Author(s):  
Indira Chandrasekhar, Wilfred F. van Gunst
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Molecular Dynamics Simulations ◽  
Alpha Phase ◽  
Energy Parameters ◽  
Dynamics Simulations

Melting at Mg/Al interface in Mg-Al-Mg nanolayer by molecular dynamics simulations

2021 ◽  
Author(s):  
Xue-Qi Lv ◽  
Xiong-Ying Li
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Distribution Function ◽  
Potential Energy ◽  
Density Distribution ◽  
Molecular Dynamics Simulations ◽  
Regional Research ◽  
Melting Temperatures ◽  
Essential Step ◽  
Dynamics Simulations

Abstract The melting at the magnesium/aluminum (Mg/Al) interface is an essential step during the fabrications of Mg-Al structural materials and biomaterials. We carried out molecular dynamics simulations on the melting at the Mg/Al interface in a Mg-Al-Mg nanolayer via analyzing the changes of average atomic potential energy, Lindemann index, heat capacity, atomic density distribution and radial distribution function with temperature. The melting temperatures (T m) of the nanolayer and the slabs near the interface are significantly sensitive to the heating rate (v h) over the range of v h≤4.0 K/ps. The distance (d) range in which the interface affects the melting of the slabs is predicted to be (-98.2, 89.9) Å at v h→0, if the interface is put at d=0 and Mg (Al) is located at the left (right) side of the interface. The (T m) of the Mg (Al) slab just near the interface (e.g., d=4.0 Å) is predicted to be 926.8 K (926.6 K) at v h→0, with 36.9 K (37.1 K) below 963.7 K for the nanolayer. These results highlight the importance of regional research on the melting at an interface in the nanolayers consisting of two different metals.

scholarly journals A [1 + 2] cycloaddition instead of usual [2 + 3] cycloaddition between the B12N12 cluster and methyl azide: Potential energy surface calculations and Born–Oppenheimer molecular dynamics simulations

2020 ◽  
Vol 45 ◽  
pp. 146867831990058
Author(s):  
Parvaneh Pakravan ◽  
Seyyed Amir Siadati
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Molecular Dynamics Simulations ◽  
Energy Surface ◽  
Cycloaddition Reaction ◽  
Reliable Data ◽  
Reaction Channel ◽  
Dynamics Simulations

We have examined here the possibility of functionalization of the B12N12 cluster by methyl azide by means of a [2 + 3] cycloaddition reaction in analogy with the spontaneous functionalization of C20 fullerene using the same reaction. To achieve more reliable data, all possible interactions at different positions and orientations were considered by reaction channel study and potential energy surface calculations. Also, Born–Oppenheimer molecular dynamics simulations were used to find probable species which could emerge during the reactions.

INITIAL ROLL GUIDED STRUCTURAL TRANSITION OF GRAPHENE

NANO ◽  
2014 ◽  
Vol 09 (02) ◽  
pp. 1450024
Author(s):  
Y. F. LI
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Molecular Dynamics Simulations ◽  
Graphene Layer ◽  
Structural Transition ◽  
Small Disturbance ◽  
Combined Action ◽  
Stacking Effect ◽  
Simulation Input ◽  
Dynamics Simulations

Molecular dynamics simulations have been performed to study the initial roll guided structural transition of graphene. The flat graphene is thermodynamic metastable and small disturbance can strike its balance and lead to fold. An initial roll at one end causes the graphene layer to transform into double-fold, multi-fold and scroll spontaneously, depending on the size of the initial roll. This unique phenomenon results from the combined action of the van der Waals interaction and the π–π stacking effect. The potential energy of the final structures decreases with the increase of compact level. This study provides crucial simulation input to help guide to designing the required graphene-based nanostructures.

ON THE STRUCTURAL AND ENERGETIC FEATURES OF SMALL METAL CLUSTERS: Nin, Cun, Pdn, Ptn, AND Pbn; n=3–13

2004 ◽  
Vol 15 (06) ◽  
pp. 917-930 ◽  
Author(s):  
ZUHEIR EL-BAYYARI ◽  
HÜSEYIN OYMAK ◽  
HATICE KÖKTEN
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Molecular Dynamics Simulations ◽  
Energy Function ◽  
Metal Clusters ◽  
Minimum Energy ◽  
Potential Energy Function ◽  
Empirical Potential ◽  
Dynamics Simulations

Using an empirical potential energy function parametrized for each of the Ni , Cu , Pd , Pt , and Pb systems, minimum-energy structures of Ni n, Cu n, Pd n, Pt n, and Pb n (n=3–13) microclusters have been determined by performing molecular-dynamics simulations. The structural and energetic features of the obtained microclusters have been investigated.

Photorelaxation of imidazole and adenine via electron-driven proton transfer along H2O wires

2016 ◽  
Vol 195 ◽  
pp. 237-251 ◽  
Author(s):  
Rafał Szabla ◽  
Robert W. Góra ◽  
Mikołaj Janicki ◽  
Jiří Šponer
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Potential Energy ◽  
Proton Transfer ◽  
Potential Energy Surface ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Energy Surface ◽  
Water Molecules ◽  
Dynamics Simulations

Photochemically created πσ* states were classified among the most prominent factors determining the ultrafast radiationless deactivation and photostability of many biomolecular building blocks. In the past two decades, the gas phase photochemistry of πσ* excitations was extensively investigated and was attributed to N–H and O–H bond fission processes. However, complete understanding of the complex photorelaxation pathways of πσ* states in the aqueous environment was very challenging, owing to the direct participation of solvent molecules in the excited-state deactivation. Here, we present non-adiabatic molecular dynamics simulations and potential energy surface calculations of the photoexcited imidazole–(H2O)5 cluster using the algebraic diagrammatic construction method to the second-order [ADC(2)]. We show that electron driven proton transfer (EDPT) along a wire of at least two water molecules may lead to the formation of a πσ*/S0 state crossing, similarly to what we suggested for 2-aminooxazole. We expand on our previous findings by direct comparison of the imidazole–(H2O)5 cluster to non-adiabatic molecular dynamics simulations of imidazole in the gas phase, which reveal that the presence of water molecules extends the overall excited-state lifetime of the chromophore. To embed the results in a biological context, we provide calculations of potential energy surface cuts for the analogous photorelaxation mechanism present in adenine, which contains an imidazole ring in its structure.

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