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Searching for Stable Si(n)C(n) Clusters: Combination of Stochastic Potential Surface Search and Pseudopotential Plane-Wave Car-Parinello Simulated Annealing Simulations
To find low energy Si(n)C(n) structures out of hundreds to thousands of isomers we have developed a general method to search for stable isomeric structures that combines Stochastic Potential Surface Search and Pseudopotential Plane-Wave Density Functional Theory Car-Parinello Molecular Dynamics simu...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6270377/ https://www.ncbi.nlm.nih.gov/pubmed/23881049 http://dx.doi.org/10.3390/molecules18078591 |
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author | Duan, Xiaofeng F. Burggraf, Larry W. Huang, Lingyu |
author_facet | Duan, Xiaofeng F. Burggraf, Larry W. Huang, Lingyu |
author_sort | Duan, Xiaofeng F. |
collection | PubMed |
description | To find low energy Si(n)C(n) structures out of hundreds to thousands of isomers we have developed a general method to search for stable isomeric structures that combines Stochastic Potential Surface Search and Pseudopotential Plane-Wave Density Functional Theory Car-Parinello Molecular Dynamics simulated annealing (PSPW-CPMD-SA). We enhanced the Sunders stochastic search method to generate random cluster structures used as seed structures for PSPW-CPMD-SA simulations. This method ensures that each SA simulation samples a different potential surface region to find the regional minimum structure. By iterations of this automated, parallel process on a high performance computer we located hundreds to more than a thousand stable isomers for each Si(n)C(n) cluster. Among these, five to 10 of the lowest energy isomers were further optimized using B3LYP/cc-pVTZ method. We applied this method to Si(n)C(n) (n = 4–12) clusters and found the lowest energy structures, most not previously reported. By analyzing the bonding patterns of low energy structures of each Si(n)C(n) cluster, we observed that carbon segregations tend to form condensed conjugated rings while Si connects to unsaturated bonds at the periphery of the carbon segregation as single atoms or clusters when n is small and when n is large a silicon network spans over the carbon segregation region. |
format | Online Article Text |
id | pubmed-6270377 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-62703772018-12-17 Searching for Stable Si(n)C(n) Clusters: Combination of Stochastic Potential Surface Search and Pseudopotential Plane-Wave Car-Parinello Simulated Annealing Simulations Duan, Xiaofeng F. Burggraf, Larry W. Huang, Lingyu Molecules Article To find low energy Si(n)C(n) structures out of hundreds to thousands of isomers we have developed a general method to search for stable isomeric structures that combines Stochastic Potential Surface Search and Pseudopotential Plane-Wave Density Functional Theory Car-Parinello Molecular Dynamics simulated annealing (PSPW-CPMD-SA). We enhanced the Sunders stochastic search method to generate random cluster structures used as seed structures for PSPW-CPMD-SA simulations. This method ensures that each SA simulation samples a different potential surface region to find the regional minimum structure. By iterations of this automated, parallel process on a high performance computer we located hundreds to more than a thousand stable isomers for each Si(n)C(n) cluster. Among these, five to 10 of the lowest energy isomers were further optimized using B3LYP/cc-pVTZ method. We applied this method to Si(n)C(n) (n = 4–12) clusters and found the lowest energy structures, most not previously reported. By analyzing the bonding patterns of low energy structures of each Si(n)C(n) cluster, we observed that carbon segregations tend to form condensed conjugated rings while Si connects to unsaturated bonds at the periphery of the carbon segregation as single atoms or clusters when n is small and when n is large a silicon network spans over the carbon segregation region. MDPI 2013-07-22 /pmc/articles/PMC6270377/ /pubmed/23881049 http://dx.doi.org/10.3390/molecules18078591 Text en © 2013 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/). |
spellingShingle | Article Duan, Xiaofeng F. Burggraf, Larry W. Huang, Lingyu Searching for Stable Si(n)C(n) Clusters: Combination of Stochastic Potential Surface Search and Pseudopotential Plane-Wave Car-Parinello Simulated Annealing Simulations |
title | Searching for Stable Si(n)C(n) Clusters: Combination of Stochastic Potential Surface Search and Pseudopotential Plane-Wave Car-Parinello Simulated Annealing Simulations |
title_full | Searching for Stable Si(n)C(n) Clusters: Combination of Stochastic Potential Surface Search and Pseudopotential Plane-Wave Car-Parinello Simulated Annealing Simulations |
title_fullStr | Searching for Stable Si(n)C(n) Clusters: Combination of Stochastic Potential Surface Search and Pseudopotential Plane-Wave Car-Parinello Simulated Annealing Simulations |
title_full_unstemmed | Searching for Stable Si(n)C(n) Clusters: Combination of Stochastic Potential Surface Search and Pseudopotential Plane-Wave Car-Parinello Simulated Annealing Simulations |
title_short | Searching for Stable Si(n)C(n) Clusters: Combination of Stochastic Potential Surface Search and Pseudopotential Plane-Wave Car-Parinello Simulated Annealing Simulations |
title_sort | searching for stable si(n)c(n) clusters: combination of stochastic potential surface search and pseudopotential plane-wave car-parinello simulated annealing simulations |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6270377/ https://www.ncbi.nlm.nih.gov/pubmed/23881049 http://dx.doi.org/10.3390/molecules18078591 |
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