From single atoms to self-assembled quantum single-atomic nanowires: noble metal atoms on black phosphorene monolayers

2017 ◽  
Vol 19 (11) ◽  
pp. 7864-7870
Author(s):  
X. J. Zhao ◽  
Wen-Wen Shan ◽  
Hao He ◽  
Xinlian Xue ◽  
Z. X. Guo ◽  
...  
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Noble Metal ◽  
Self Assembly ◽  
Energy Surface ◽  
Single Atoms ◽  
Atomic Wires ◽  
Metal Atoms ◽  
Black Phosphorene ◽  
Self Assembled

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

scholarly journals Energy Landscapes, Self-Assembly and Viruses

2005 ◽  
Vol 6 (2) ◽  
pp. 107-110 ◽  
Author(s):  
D. J. Wales
Keyword(s):  
Protein Folding ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Self Assembly ◽  
Energy Surface ◽  
Genetic Material ◽  
Magic Number ◽  
Molecular Beams ◽  
Energy Landscapes ◽  
Guided Exploration

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.

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<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>

Rotational de-excitations of C3H+ (1Σ+) by collision with He: new ab initio potential energy surface and scattering calculations

2020 ◽  
Vol 494 (4) ◽  
pp. 5675-5681 ◽  
Author(s):  
Sanchit Chhabra ◽  
T J Dhilip Kumar
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Cross Sections ◽  
Energy Surface ◽  
Molecular Ions ◽  
Basis Set ◽  
Rate Coefficients ◽  
Close Coupling ◽  
Collisional Rate Coefficients

ABSTRACT Molecular ions play an important role in the astrochemistry of interstellar and circumstellar media. C3H+ has been identified in the interstellar medium recently. A new potential energy surface of the C3H+–He van der Waals complex is computed using the ab initio explicitly correlated coupled cluster with the single, double and perturbative triple excitation [CCSD(T)-F12] method and the augmented correlation consistent polarized valence triple zeta (aug-cc-pVTZ) basis set. The potential presents a well of 174.6 cm−1 in linear geometry towards the H end. Calculations of pure rotational excitation cross-sections of C3H+ by He are carried out using the exact quantum mechanical close-coupling approach. Cross-sections for transitions among the rotational levels of C3H+ are computed for energies up to 600 cm−1. The cross-sections are used to obtain the collisional rate coefficients for temperatures T ≤ 100 K. Along with laboratory experiments, the results obtained in this work may be very useful for astrophysical applications to understand hydrocarbon chemistry.

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