scholarly journals Energy Landscapes, Self-Assembly and Viruses

2005 ◽  
Vol 6 (2) ◽  
pp. 107-110 ◽  
Author(s):  
D. J. Wales

Phenomena such as protein folding, crystallisation, self-assembly, and the observation of magic number clusters in molecular beams are all the result of non-random searches. Analysis of the underlying potential energy surface may provide a unifying framework to explain how such events occur as the result of a guided exploration of the landscape. In particular, icosahedral shells composed of 12 pentagonal pyramids are found to be thermodynamically favourable and kinetically accessible when the pyramids are not too spiky and not too flat. Hence, viruses with icosahedral capsids not only minimise the genetic material required to encode the repeated subunits, but may also utilise the favourable properties of a potential energy surface that effectively directs self-assembly.

Author(s):  
David J. Wales

The potential energy surface (PES) underlies most calculations of structure, dynamics and thermodynamics in molecular science. In this contribution connections between the topology of the PES and observable properties are developed for a coarse–grained model of virus capsid self–assembly. The model predicts that a thermodynamically stable, kinetically accessible icosahedral shell exists for pentameric building blocks of the right shape: not too flat and not too spiky. The structure of the corresponding PES is probably common to other systems where directed searches avoid Levinthal's paradox, such as ‘magic number’ clusters, protein folding and crystallization.


2017 ◽  
Vol 19 (11) ◽  
pp. 7864-7870
Author(s):  
X. J. Zhao ◽  
Wen-Wen Shan ◽  
Hao He ◽  
Xinlian Xue ◽  
Z. X. Guo ◽  
...  

Self-assembly growth of Pd(Pt)n single atomic wires on black phosphorene due to the anisotropic potential energy surface of the substrate.


2001 ◽  
Vol 700 ◽  
Author(s):  
David J. Wales

AbstractThe goal of energy landscape theory is to relate observable thermodynamic and dynamic properties to features of the underlying potential energy surface. Here we illustrate the approach with reference to the annealing of C60 and indicate how it may be used to design improved global optimisation algorithms.


2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>


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