New Algorithms for Locating Global Minima of Molecular Clusters: A Progress Report and Test Applications to Water Clusters (H[sub 2]O)[sub n], n≤34

2009 ◽  
Author(s):  
Sergey Kazachenko ◽  
Ajit J. Thakkar ◽  
George Maroulis ◽  
Theodore E. Simos
Keyword(s):  
Water Clusters ◽  
Molecular Clusters ◽  
Progress Report ◽  
Global Minima ◽  
New Algorithms

scholarly journals Resolving the HONO formation mechanism in the ionosphere via ab initio molecular dynamic simulations

2016 ◽  
Vol 113 (17) ◽  
pp. 4629-4633 ◽  
Author(s):  
Rongxing He ◽  
Lei Li ◽  
Jie Zhong ◽  
Chongqin Zhu ◽  
Joseph S. Francisco ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Nitrous Acid ◽  
Water Clusters ◽  
Ab Initio Molecular Dynamics ◽  
Molecular Dynamic Simulations ◽  
Global Minima ◽  
Dynamic Simulations ◽  
Transition State Search ◽  
A Chain

Solar emission produces copious nitrosonium ions (NO+) in the D layer of the ionosphere, 60 to 90 km above the Earth’s surface. NO+ is believed to transfer its charge to water clusters in that region, leading to the formation of gaseous nitrous acid (HONO) and protonated water cluster. The dynamics of this reaction at the ionospheric temperature (200–220 K) and the associated mechanistic details are largely unknown. Using ab initio molecular dynamics (AIMD) simulations and transition-state search, key structures of the water hydrates—tetrahydrate NO+(H2O)4 and pentahydrate NO+(H2O)5—are identified and shown to be responsible for HONO formation in the ionosphere. The critical tetrahydrate NO+(H2O)4 exhibits a chain-like structure through which all of the lowest-energy isomers must go. However, most lowest-energy isomers of pentahydrate NO+(H2O)5 can be converted to the HONO-containing product, encountering very low barriers, via a chain-like or a three-armed, star-like structure. Although these structures are not the global minima, at 220 K, most lowest-energy NO+(H2O)4 and NO+(H2O)5 isomers tend to channel through these highly populated isomers toward HONO formation.

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

Global Geometry Optimization of Molecular Clusters: TIP4P Water

2000 ◽  
Vol 214 (9) ◽  
Author(s):  
B. Hartke
Keyword(s):  
Structural Transition ◽  
Water Clusters ◽  
Geometry Optimization ◽  
Molecular Clusters ◽  
Atomic Clusters ◽  
Water Molecules ◽  
Global Geometry ◽  
Global Cluster ◽  
Cluster Geometry ◽  
Cluster Geometry Optimization

In this paper, we present an extension of our phenotype algorithm for global cluster geometry optimization from atomic clusters to the more difficult molecular clusters. A successful application to the benchmark case of TIP4P water clusters shows that the new method is at least as good as one of the best methods in the literature so far. We point out why the TIP4P water cluster system starts to become very complicated beyond twenty water molecules and follow the traces of a beginning structural transition from clusters with all water molecules at the surface to clathrate-like cages with a truly interior water molecule.

scholarly journals Hydration of Atmospheric Molecular Clusters II: Organic Acid–Water Clusters

2018 ◽  
Vol 122 (43) ◽  
pp. 8549-8556 ◽  
Author(s):  
Jens Vive Kildgaard ◽  
Kurt V. Mikkelsen ◽  
Merete Bilde ◽  
Jonas Elm
Keyword(s):  
Organic Acid ◽  
Water Clusters ◽  
Molecular Clusters ◽  
Acid Water

Global minima of protonated water clusters

2000 ◽  
Vol 324 (4) ◽  
pp. 279-288 ◽  
Author(s):  
Matthew P. Hodges ◽  
David J. Wales
Keyword(s):  
Water Clusters ◽  
Global Minima

scholarly journals PARALLEL OPTIMIZATION TECHNOLOGY FOR ATOMIC-MOLECULAR MORSE CLUSTERS

2022 ◽  
pp. 60-67
Author(s):  
Александр Юрьевич Горнов ◽  
Антон Сергеевич Аникин ◽  
Павел Сергеевич Сороковиков ◽  
Татьяна Сергеевна Зароднюк
Keyword(s):  
Molecular Docking ◽  
Software Package ◽  
Molecular Clusters ◽  
Computational Experiments ◽  
Applied Problem ◽  
Parallel Optimization ◽  
Computing Technology ◽  
Morse Clusters ◽  
New Algorithms

В статье рассматриваются специализированные вычислительные технологии и алгоритмы, используемые для поиска низкопотенциальных атомно-молекулярных кластеров. Проведенные вычислительные эксперименты продемонстрировали достаточно высокую конкурентоспособность новых алгоритмов по сравнению с классическими для функций рассматриваемого типа. С использованием разработанного программного комплекса получены рекордные результаты оптимизации атомно-молекулярных кластеров Морса рекордных размерностей. The paper deals with specialized computing technology and algorithms used for finding low-potential atomic-molecular clusters. The performed computational experiments demonstrated a rather high competitiveness of the new algorithms in comparison with the classical methods for the considerable functions. Using the developed software, the applied problem of molecular docking was solved. Using the developed software package, record results for optimization of atomic-molecular Morse clusters of large dimensions have been obtained.

Global Minima of Protonated Water Clusters (H2O)20H+ Revisited

2012 ◽  
Vol 116 (44) ◽  
pp. 10826-10835 ◽  
Author(s):  
P. Parkkinen ◽  
S. Riikonen ◽  
L. Halonen
Keyword(s):  
Water Clusters ◽  
Global Minima
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