van der Waals interactions are critical in Car-Parrinello molecular dynamics simulations of porphyrin-fullerene dyads

2015 ◽  
Vol 36 (9) ◽  
pp. 612-621 ◽  
Author(s):  
Topi Karilainen ◽  
Oana Cramariuc ◽  
Mikael Kuisma ◽  
Kirsi Tappura ◽  
Terttu I. Hukka
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Dynamics Simulations

Van der Waals Attraction and Coalescence of Aqueous Salt Nanodroplets

2003 ◽  
Vol 68 (12) ◽  
pp. 2283-2291 ◽  
Author(s):  
Pavel Jungwirth ◽  
Victoria Buch
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Size Effects ◽  
Relative Velocity ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Van Der Waals Attraction ◽  
Dynamics Simulations ◽  
Precipitation Modeling

Collisions of aqueous salt nanodroplets at zero initial relative velocity are investigated by means of molecular dynamics simulations. The character of the van der Waals interactions, which bring the droplets together and cause coalescence, is described in detail, and the parameters of the droplet-droplet potential are extracted from the collisional trajectories. Concentration and size effects, together with implications for cloud and precipitation modeling are discussed.

Gauging van der Waals interactions in aqueous solutions of 2D MOFs: when water likes organic linkers more than open-metal sites

2021 ◽  
Vol 23 (4) ◽  
pp. 3135-3143
Author(s):  
Mohammad R. Momeni ◽  
Zeyu Zhang ◽  
David Dell'Angelo ◽  
Farnaz A. Shakib
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Layered Architecture ◽  
Open Metal Sites ◽  
Dynamics Simulations

Periodic quantum mechanical calculations combined with classical molecular dynamics simulations are employed to probe stability of layered architecture of 2D MOFs and show how stability and conductivity are affected by the nature of organic linkers.

Phase Transition of Argon in a Nanocavity

2005 ◽  
Author(s):  
Philipp A. E. Schoen ◽  
Dimos Poulikakos
Keyword(s):  
Phase Transition ◽  
Molecular Dynamics ◽  
Phase Diagram ◽  
Molecular Dynamics Simulations ◽  
Van Der Waals ◽  
Van Der Waals Forces ◽  
Constant Volume ◽  
Substrate Interface ◽  
Dynamics Simulations

We performed molecular dynamics simulations of argon liquid enclosed in an infinitely extended channel made out of platinum atoms. It was found that for small temperatures the van der Waals forces at the liquid-substrate interface are increased. Using this fact and the nature of argon, that this liquid thermally contracts if cooled, phase transition of liquid to vapor could also be achieved in this nanocavity of constant volume. However, the phase diagram is altered significantly compared to bulk argon.

scholarly journals THE RANGE OF THE CONTACT INTERACTIONS AND THE KINETICS OF THE GO MODELS OF PROTEINS

2002 ◽  
Vol 13 (09) ◽  
pp. 1231-1242 ◽  
Author(s):  
MAREK CIEPLAK ◽  
TRINH XUAN HOANG
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Van Der Waals ◽  
Contact Interactions ◽  
Residue Contact ◽  
Cutoff Distance ◽  
Dynamics Simulations ◽  
Kinetics Of ◽  
Van Der Waals Radii

We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue–residue contact interactions are selected based on a cutoff distance, Rc. The folding times strongly depend on the value of Rc and nonmonotonically. This indicates a need for a physically determined set of native contacts. One may accomplish it by considering the van der Waals radii of the residual atoms and checking if the atoms overlap. In the second model, non-native attractive contacts are added to the system. This leads to bad foldability. However, for a small number of such extra contacts there is a slight acceleration in the kinetics of folding.

scholarly journals Accurate Simulations of Lipid Monolayers Require a Water Model With Correct Surface Tension

2021 ◽  
Author(s):  
Carmelo Tempra ◽  
O.H. Samuli Ollila ◽  
Matti Javanainen
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Molecular Dynamics Simulations ◽  
Long Range ◽  
Van Der Waals ◽  
Water Model ◽  
Lipid Monolayers ◽  
Experimental Surface ◽  
Water Models ◽  
Dynamics Simulations

Lipid monolayers provide our lungs and eyes their functionality, and serve as proxy systems in biomembrane research. Therefore, lipid monolayers have been studied intensively also using molecular dynamics simulations, which are able to probe their lateral structure and interactions with, e.g., pharmaceuticals or nanoparticles. However, such simulations have struggled in describing the forces at the air–water interface. Particularly the surface tension of water and long-range van der Waals interactions have been considered critical, but their importance in monolayer simulations has been evaluated only separately. Here we combine the recent C36/LJ-PME lipid force field that in- cludes long-range van der Waals forces with water models that reproduce experimental surface tensions to elucidate the importance of these contributions in monolayer simulations. Our results suggest that a water model with correct surface tension is necessary to reproduce experimental surface pressure–area isotherms and monolayer phase behavior, while standard cutoff-based CHARMM36 lipid model with the 4-point OPC water model still provides the best agreement with experiments. Our results emphasize the importance of using high quality water models in applications and parameter development in molecular dynamics simulations of biomolecules.

Molecular Modeling Approach to Investigate the Intercalation of Phthalates and Their Metabolites in DNA Macromolecules

2019 ◽  
Vol 16 (2) ◽  
pp. 373-380 ◽  
Author(s):  
Tatiane P. Rodrigues ◽  
Jorddy N. Cruz ◽  
Tiago S. Arouche ◽  
Tais S. S. Pereira ◽  
Wanessa A. Costa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Docking ◽  
Molecular Modeling ◽  
Molecular Dynamics Simulations ◽  
Binding Free Energy ◽  
Van Der Waals ◽  
Genetic Material ◽  
Ligand Interaction ◽  
Dynamics Simulations

Recent studies have reported that phthalates are capable of causing mutations and other changes in the genetic material. This study aimed to investigate the molecular interactions between phthalate di(2-ethylhexyl) phthalate (DEHP) and its metabolites monobutyl phthalate (MBP) and monoethyl phthalate (MEP), interacting with DNA. The research was conducted using molecular modeling techniques such as molecular docking and molecular dynamics simulations. Molecular docking revealed that the DEHP, MBP, and MEP are able to establish hydrogen interactions with various nucleotide bases. Molecular dynamics simulations revealed that these molecules interacted with the DNA, and the binding free energy results demonstrated that the DNA-ligand interaction has favorable free energy. The values for free binding energy were as follows: DNA–DEHP, –21.66 kcal/mol; DNA–MBP, –17.29 kcal/mol; and DNA–MEP, –20.13 kcal/mol. For these three systems, the contributions of van der Waals, electrostatic, and nonpolar solvation energy were favorable for the interaction. The van der Waals interactions contributed the major energy to the intercalation of the binders.

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