Molecular Dynamics Simulations of Type-sII Hydrogen Clathrate Hydrate Close to Equilibrium Conditions

2007 ◽  
Vol 111 (35) ◽  
pp. 13044-13052 ◽  
Author(s):  
Terry J. Frankcombe ◽  
Geert-Jan Kroes
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Clathrate Hydrate ◽  
Equilibrium Conditions ◽  
Dynamics Simulations

Molecular dynamics simulation of halogen bonding in Cl2, BrCl, and mixed Cl2/Br2 clathrate hydrates

2015 ◽  
Vol 93 (8) ◽  
pp. 864-873 ◽  
Author(s):  
Hana Dureckova ◽  
Tom K. Woo ◽  
Saman Alavi ◽  
John A. Ripmeester
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Van Der Waals ◽  
Halogen Bonding ◽  
Clathrate Hydrate ◽  
Clathrate Hydrates ◽  
Dynamics Simulation ◽  
Water Oxygen ◽  
Dynamics Simulations ◽  
Van Der Waals Radii

Clathrate hydrate phases of dihalogen molecules have properties that differ from those of other guest molecules of similar size. The water oxygen–chlorine distances in the structure I (sI) Cl2 hydrate are smaller than the sum of the van der Waals radii of oxygen and chlorine. Bromine hydrate forms a unique clathrate hydrate structure that is not seen in other guest substances. In mixed Cl2/Br2 structure I hydrate, the water oxygen–bromine distances are also smaller than the sum of the oxygen and bromine van der Waals radii. We previously studied the structure of three dihalogen clathrate hydrates using single crystal X-ray diffraction and described these structural features in terms of halogen bonding between the dihalogen and water molecules. In this work, we perform molecular dynamics simulations of cubic sI Cl2, mixed Cl2/Br2, and BrCl clathrate hydrate phases. We perform quantum chemical computations on the dihalogen molecules to determine the nature of σ-hole near the halogen atoms. We fit the electrostatic potential of the molecules to point charge models including dummy atoms that represent σ-holes adjacent to the halogen molecules. Molecular dynamics simulations are used to determine the lattice constants, radial distribution functions, and guest dynamics in these phases. We determine the effect of guest size and difference in halogen bonding on the properties of the clathrate hydrate phase. Simulations for the Cl2, BrCl, and mixed Cl2/Br2 hydrates are performed with small cages of the sI clathrate hydrate phases completely full or filled with experimental occupancies with Cl2 guests.

Folding Of Trp-Cage Protein In Equilibrium And Nonequilibrium Conditions: Molecular Dynamics Simulations

2015 ◽  
Vol 10 (3) ◽  
pp. 103-109
Author(s):  
Vladimir Andryushchenko ◽  
Sergey Chekmarev
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Native State ◽  
Correct Description ◽  
Equilibrium Conditions ◽  
Physiological Conditions ◽  
Folding Dynamics ◽  
Nonequilibrium Conditions ◽  
Dynamics Simulations ◽  
Kinetics Of

The study of the dynamics of protein folding into its functional (native) state is one of the actual problems of molecular biology. For this, molecular dynamics simulations are widely used. The conditions under which the simulations are performed are important for the correct description of the folding process. In the present paper, we study the folding dynamics of one of the benchmark proteins (Trp-cage) under two conditions – the equilibrium conditions, when the protein repeatedly folds and unfolds, and under nonequilibrium conditions, when an ensemble of trajectories is generated that start in an unfolded sate of the protein and are terminated in the native state, which corresponds to the physiological conditions. It is shown that the behavior of the protein under these conditions is essentially different; in particular, in the case of nonequilibrium conditions an additional metastable state is formed, which leads to a separate folding pathway. The simulations have also shown that the kinetics of Trp-cage are two-state, which corresponds to the experimental results.

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