scholarly journals Isomers and energy landscapes of micro-hydrated sulfite and chlorate clusters

2018 ◽  
Vol 376 (2115) ◽  
pp. 20170154 ◽  
Author(s):  
John C. Hey ◽  
Emily J. Doyle ◽  
Yuting Chen ◽  
Roy L. Johnston
Keyword(s):  
Global Minimum ◽  
Water Clusters ◽  
Structure Optimization ◽  
Theoretical Chemistry ◽  
Hydroxyl Groups ◽  
Energy Landscapes ◽  
Global Minima ◽  
Theme Issue ◽  
Empirical Potential ◽  
Basin Hopping

We present putative global minima for the micro-hydrated sulfite SO 3 2− (H 2 O) N and chlorate ClO 3 − (H 2 O) N systems in the range 3≤ N ≤15 found using basin-hopping global structure optimization with an empirical potential. We present a structural analysis of the hydration of a large number of minimized structures for hydrated sulfite and chlorate clusters in the range 3≤ N ≤50. We show that sulfite is a significantly stronger net acceptor of hydrogen bonding within water clusters than chlorate, completely suppressing the appearance of hydroxyl groups pointing out from the cluster surface (dangling OH bonds), in low-energy clusters. We also present a qualitative analysis of a highly explored energy landscape in the region of the global minimum of the eight water hydrated sulfite and chlorate systems. This article is part of the theme issue ‘Modern theoretical chemistry’.

Global minima for water clusters (H2O)n, n⩽21, described by a five-site empirical potential

2005 ◽  
Vol 415 (4-6) ◽  
pp. 302-307 ◽  
Author(s):  
Tim James ◽  
David J. Wales ◽  
Javier Hernández-Rojas
Keyword(s):  
Water Clusters ◽  
Global Minima ◽  
Empirical Potential

scholarly journals The Effect of Nonnative Interactions on the Energy Landscapes of Frustrated Model Proteins

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Mark T. Oakley ◽  
David J. Wales ◽  
Roy L. Johnston
Keyword(s):  
Genetic Algorithms ◽  
Potential Energy ◽  
Global Minimum ◽  
Energy Surface ◽  
Energy Landscape ◽  
Small Degree ◽  
Energy Landscapes ◽  
Go Model ◽  
Encounter Time ◽  
Basin Hopping

The 46- and 69-residue BLN model proteins both exhibit frustrated folding to β-barrel structures. We study the effect of varying the strength of nonnative interactions on the corresponding energy landscapes by introducing a parameter λ, which scales the potential between the BLN (λ=1) and Gō-like (λ=0) limits. We study the effect of varying λ on the efficiency of global optimisation using basin-hopping and genetic algorithms. We also construct disconnectivity graphs for these proteins at selected values of λ. Both methods indicate that the potential energy surface is frustrated for the original BLN potential but rapidly becomes less frustrated as λ decreases. For values of λ≤0.9, the energy landscape is funnelled. The fastest mean first encounter time for the global minimum does not correspond to the Gō model: instead, we observe a minimum when the favourable nonnative interactions are still present to a small degree.

Structural Exploration of Water, Nitrate/Water, and Oxalate/Water Clusters with Basin-Hopping Method Using a Compressed Sampling Technique

2014 ◽  
Vol 118 (2) ◽  
pp. 508-516 ◽  
Author(s):  
Yi-Rong Liu ◽  
Hui Wen ◽  
Teng Huang ◽  
Xiao-Xiao Lin ◽  
Yan-Bo Gai ◽  
...  
Keyword(s):  
Water Clusters ◽  
Sampling Technique ◽  
Compressed Sampling ◽  
Basin Hopping

GLOBAL MINIMA FOR PdN (N = 5–80) CLUSTERS DESCRIBED BY SUTTON–CHEN POTENTIAL

2007 ◽  
Vol 18 (08) ◽  
pp. 1351-1359 ◽  
Author(s):  
HAYDAR ARSLAN
Keyword(s):  
Monte Carlo ◽  
Energy Surface ◽  
Central Atom ◽  
Low Energy ◽  
Global Minima ◽  
Many Body ◽  
Pd Clusters ◽  
Body Potential ◽  
Basin Hopping ◽  
Theoretical Results

The structure and energetics of Pd N (N = 5–80) clusters have been studied extensively by a Monte Carlo method based on Sutton–Chen many-body potential. The basin-hopping algorithm is used to find the low-energy minima on the potential energy surface for each nuclearity. A variety of structure types (icosahedral, decahedral and fcc closed-packed) are observed for Pd clusters. Some of the icosahedral global minima do not have a central atom. The resulting structures have been compared with the previous theoretical results.

scholarly journals Dynamic simulations of many-body electrostatic self-assembly

2018 ◽  
Vol 376 (2115) ◽  
pp. 20170143 ◽  
Author(s):  
Eric B. Lindgren ◽  
Benjamin Stamm ◽  
Yvon Maday ◽  
Elena Besley ◽  
A. J. Stace
Keyword(s):  
Self Assembly ◽  
Experimental Studies ◽  
Charged Particles ◽  
Theoretical Chemistry ◽  
Many Body ◽  
Single Particles ◽  
Theme Issue ◽  
Dynamic Simulations ◽  
The Subject ◽  
Small Clusters

Two experimental studies relating to electrostatic self-assembly have been the subject of dynamic computer simulations, where the consequences of changing the charge and the dielectric constant of the materials concerned have been explored. One series of calculations relates to experiments on the assembly of polymer particles that have been subjected to tribocharging and the simulations successfully reproduce many of the observed patterns of behaviour. A second study explores events observed following collisions between single particles and small clusters composed of charged particles derived from a metal oxide composite. As before, observations recorded during the course of the experiments are reproduced by the calculations. One study in particular reveals how particle polarizability can influence the assembly process. This article is part of the theme issue ‘Modern theoretical chemistry’.

scholarly journals Investigation of the Structures and Energy Landscapes of Thiocyanate-Water Clusters

Inorganics ◽  
2017 ◽  
Vol 5 (2) ◽  
pp. 20 ◽  
Author(s):  
Lewis Smeeton ◽  
John Hey ◽  
Roy Johnston
Keyword(s):  
Water Clusters ◽  
Energy Landscapes
Sign in / Sign up

Export Citation Format

Share Document