Comprehensive genetic algorithm for ab initio global optimisation of clusters

Abstract Cluster, as the aggregate of a few to thousands of atoms or molecules, bridges the microscopic world of atoms and molecules and the macroscopic world of condensed matters. The physical and chemical properties of a cluster are determined by its ground state structure, which is significantly different from its bulk structure and sensitively relies on the cluster size. As a well-known nondeterministic polynomial-time hard problem, determining the ground state structure of a cluster is a challenging task due to the extreme complexity of high-dimensional potential energy surface (PES). Genetic algorithm (GA) is an efficient global optimisation method to explore the PES of clusters. Recently, we have developed a GA-based programme, namely comprehensive genetic algorithm (CGA), and incorporated it with ab initio calculations. Using this programme, the lowest energy structures of a variety of elemental and compound clusters with different types of chemical bonding have been determined, and their physical properties have been investigated and compared with experimental data. In this article, we will describe the technique details of CGA programme and present an overview of its successful applications.

[1]  Peter Schwerdtfeger,et al.  The low lying isomers of the copper nonamer cluster, Cu9 , 2008 .

[2]  Zhi-Pan Liu,et al.  Stochastic Surface Walking Method for Structure Prediction and Pathway Searching. , 2013, Journal of chemical theory and computation.

[3]  Bristowe,et al.  Structures of , 1989, Physical review. B, Condensed matter.

[4]  Yong L. Xiao,et al.  Genetic algorithm: a new approach to the prediction of the structure of molecular clusters , 1993 .

[5]  Bernd Hartke Global geometry optimization of clusters using a growth strategy optimized by a genetic algorithm , 1995 .

[6]  Geometric magic numbers of sodium clusters: Interpretation of the melting behaviour , 2005, cond-mat/0506329.

[7]  Chen Xiaoshuang,et al.  Structural and electronic properties of Sb~n (n=2-10) clusters using density-functional theory (6 pages) , 2005 .

[8]  C. D. Gelatt,et al.  Optimization by Simulated Annealing , 1983, Science.

[9]  R. Johnston,et al.  Nanoalloys: from theory to applications of alloy clusters and nanoparticles. , 2008, Chemical reviews.

[10]  Kresse,et al.  Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. , 1996, Physical review. B, Condensed matter.

[11]  Jijun Zhao,et al.  Tight-binding study of structural and electronic properties of silver clusters , 2001 .

[12]  Sin‐Shong Lin Detection of Large Water Clusters by a Low rf Quadrupole Mass Filter , 1973 .

[13]  Jinlan Wang,et al.  Density-functional study of small and medium-sizedAsnclusters up ton=28 , 2006 .

[14]  M. Springborg,et al.  Isolated and deposited potassium clusters: Energetic and structural properties , 2013 .

[15]  Jijun Zhao,et al.  Structural growth behavior and polarizability of Cd(n)Te(n) (n=1-14) clusters. , 2009, The Journal of chemical physics.

[16]  M. Sierka,et al.  Structural diversity and flexibility of MgO gas-phase clusters. , 2011, Angewandte Chemie.

[17]  Jijun Zhao,et al.  B(80) and other medium-sized boron clusters: core-shell structures, not hollow cages. , 2010, The journal of physical chemistry. A.

[18]  Jijun Zhao,et al.  Genetic Algorithms for the Geometry Optimization of Atomic and Molecular Clusters , 2004 .

[19]  S. Bulusu,et al.  Planar-to-tubular structural transition in boron clusters: B20 as the embryo of single-walled boron nanotubes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Jijun Zhao,et al.  Atomic structures and electronic properties of small Au–Ag binary clusters: Effects of size and composition , 2012 .

[21]  Marek Sierka,et al.  Synergy between theory and experiment in structure resolution of low-dimensional oxides , 2010 .

[22]  Ho,et al.  Molecular geometry optimization with a genetic algorithm. , 1995, Physical review letters.

[23]  L. Ghiringhelli,et al.  Computational design of nanoclusters by property-based genetic algorithms: Tuning the electronic properties of (TiO2 )n clusters , 2015, 1501.05855.

[24]  Leiming Wang,et al.  CB7−: Experimental and Theoretical Evidence against Hypercoordinate Planar Carbon† , 2007 .

[25]  F. Weigend,et al.  Structures of small bismuth cluster cations. , 2012, The Journal of chemical physics.

[26]  Jijun Zhao,et al.  Lowest-energy structures of cationic P2m+1+ (m = 1–12) clusters from first-principles simulated annealing , 2010 .

[27]  Jijun Zhao,et al.  Structural, electronic, and optical properties of medium-sized Lin clusters (n=20, 30, 40, 50) by density functional theory , 2010 .

[28]  J. Doye,et al.  Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms , 1997, cond-mat/9803344.

[29]  M. Hoare Structure and Dynamics of Simple Microclusters , 2007 .

[30]  Jun Li,et al.  Au20: A Tetrahedral Cluster , 2003, Science.

[31]  A. Alexandrova H·(H2O)n clusters: microsolvation of the hydrogen atom via molecular ab initio gradient embedded genetic algorithm (GEGA). , 2010, The journal of physical chemistry. A.

[32]  X. Gong,et al.  Structures of [Ag7(SR)4]- and [Ag7(DMSA)4]-. , 2010, Journal of the American Chemical Society.

[33]  Structures and electronic properties of neutral and anionic Can (n = 2–22) clusters , 2015 .

[34]  Jing Xu,et al.  Al6H18: a baby crystal of γ-AlH3. , 2012, The Journal of chemical physics.

[35]  B. Yakobson,et al.  B80 fullerene: an Ab initio prediction of geometry, stability, and electronic structure. , 2007, Physical review letters.

[36]  J. A. Alonso Electronic and atomic structure, and magnetism of transition-metal clusters. , 2000, Chemical reviews.

[37]  Jijun Zhao,et al.  B80 and B101-103 clusters: remarkable stability of the core-shell structures established by validated density functionals. , 2012, The Journal of chemical physics.

[38]  Jijun Zhao,et al.  Lowest-energy structures and electronic properties of Na-Si binary clusters from ab initio global search. , 2011, The Journal of chemical physics.

[39]  Zeiri Prediction of the lowest energy structure of clusters using a genetic algorithm. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[40]  Hellmut Haberland,et al.  Clusters of Atoms and Molecules II , 1994 .

[41]  Ya-Fan Zhao,et al.  Planar hexagonal B36 as a potential basis for extended single-atom layer boron sheets , 2014, Nature Communications.

[42]  Jinlan Wang,et al.  Structure and electronic properties of Ge n (n=2-25) clusters from density-functional theory , 2001 .

[43]  A. Alexandrova,et al.  Persistent Covalency and Planarity in the B n Al 6 n 2 and LiB n Al 6 n ( n = 0 6 ) Cluster Ions , 2011 .

[44]  S. Yoo,et al.  Stuffed fullerene structures for medium-sized silicon clusters , 2005 .

[45]  M. Kappes,et al.  Structures and energetics of small lead cluster ions. , 2011, The Journal of chemical physics.

[46]  Jijun Zhao,et al.  Design of Three-shell Icosahedral Matryoshka Clusters A@B12@A20 (A = Sn, Pb; B = Mg, Zn, Cd, Mn) , 2014, Scientific Reports.

[47]  Jun Li,et al.  The B35 cluster with a double-hexagonal vacancy: a new and more flexible structural motif for borophene. , 2014, Journal of the American Chemical Society.

[48]  David J Wales,et al.  Symmetrisation schemes for global optimisation of atomic clusters. , 2013, Physical chemistry chemical physics : PCCP.

[49]  Longjiu Cheng,et al.  First principle structural determination of (B2O3)n (n = 1-6) clusters: from planar to cage. , 2013, The Journal of chemical physics.

[50]  C Z Wang,et al.  An adaptive genetic algorithm for crystal structure prediction , 2013, Journal of physics. Condensed matter : an Institute of Physics journal.

[51]  David E. Goldberg,et al.  Genetic Algorithms in Search Optimization and Machine Learning , 1988 .

[52]  Omar P. Vilela Neto,et al.  Theoretical and experimental study of negative LiF clusters produced by fast ion impact on a polycrystalline 7LiF target. , 2009, Journal of Physical Chemistry A.

[53]  Walt A. de Heer,et al.  The physics of simple metal clusters: experimental aspects and simple models , 1993 .

[54]  Timothy S. Zwier,et al.  The Structure of Protonated Water Clusters , 2004, Science.

[55]  Kelling J. Donald,et al.  cluster: Searching for Unique Low Energy Minima of Structures Using a Novel Implementation of a Genetic Algorithm. , 2014, Journal of chemical theory and computation.

[56]  Jinlan Wang,et al.  Nonmetal-metal transition in Zn{sub n} (n=2-20) clusters , 2003 .

[57]  B. Hartke Global geometry optimization of clusters using genetic algorithms , 1993 .

[58]  M. Klein,et al.  Protonated clathrate cages enclosing neutral water molecules: (H+)(H2O)21 and (H+)(H2O)28. , 2005, The Journal of chemical physics.

[59]  R. Johnston,et al.  Global optimization of clusters using electronic structure methods , 2013 .

[60]  Longjiu Cheng,et al.  Geometric and electronic structures of (BeO)(N) (N = 2-12, 16, 20, and 24): rings, double rings, and cages. , 2012, The Journal of chemical physics.

[61]  Anastassia N Alexandrova,et al.  Search for the Lin(0/+1/-1) (n = 5-7) Lowest-Energy Structures Using the ab Initio Gradient Embedded Genetic Algorithm (GEGA). Elucidation of the Chemical Bonding in the Lithium Clusters. , 2005, Journal of chemical theory and computation.

[62]  S. C. O'brien,et al.  C60: Buckminsterfullerene , 1985, Nature.

[63]  Jinlan Wang,et al.  Endohedral Silicon Fullerenes SiN (27 ≤ N ≤ 39) , 2004 .

[64]  B. Delley An all‐electron numerical method for solving the local density functional for polyatomic molecules , 1990 .

[65]  Jijun Zhao,et al.  Ground state structures, electronic and optical properties of medium-sized Nan+ (n = 9, 15, 21, 26, 31, 36, 41, 50 and 59) clusters from ab initio genetic algorithm , 2013 .

[66]  Jijun Zhao,et al.  Structures and Electronic Properties of V3Sin– (n = 3–14) Clusters: A Combined Ab Initio and Experimental Study , 2015 .

[67]  Jijun Zhao,et al.  Discovery of a silicon-based ferrimagnetic wheel structure in V(x)Si(12)(-) (x = 1-3) clusters: photoelectron spectroscopy and density functional theory investigation. , 2014, Nanoscale.

[68]  Xin Yang,et al.  Structure of the Na(x)Cl(x+1) (-) (x=1-4) clusters via ab initio genetic algorithm and photoelectron spectroscopy. , 2004, The Journal of chemical physics.

[69]  Longjiu Cheng,et al.  Theoretical prediction for the structures of gas phase lithium oxide clusters: (Li2O)n (n = 1–8) , 2013 .

[70]  Peter C. Jordan,et al.  Structure of H+(H2O)n clusters near the magic number n=21 , 1993 .

[71]  Rolf Schäfer,et al.  Dopant-induced 2D-3D transition in small Au-containing clusters: DFT-global optimisation of 8-atom Au-Ag nanoalloys. , 2012, Nanoscale.

[72]  David J. Wales,et al.  Global minima of protonated water clusters , 2000 .

[73]  F. Baletto,et al.  Structural properties of nanoclusters: Energetic, thermodynamic, and kinetic effects , 2005 .

[74]  B28: the smallest all-boron cage from an ab initio global search. , 2015, Nanoscale.

[75]  Guanghou Wang,et al.  Atomic structures and covalent-to-metallic transition of lead clusters Pb n ( n = 2 – 22 ) , 2005 .

[76]  R. Ahlrichs,et al.  Theoretical investigation of clusters of phosphorus and arsenic: fascination and temptation of high symmetries. , 2008, Chemistry.

[77]  Asbjörn M. Burow,et al.  Structures and vibrational spectroscopy of partially reduced gas-phase cerium oxide clusters. , 2011, Physical chemistry chemical physics : PCCP.

[78]  R. Johnston,et al.  Nine‐Atom Tin‐Bismuth Clusters: Mimicking Excess Electrons by Element Substitution , 2012 .

[79]  Edoardo Aprà,et al.  Density-functional global optimization of gold nanoclusters , 2006 .

[80]  R. Johnston Evolving better nanoparticles: Genetic algorithms for optimising cluster geometries , 2003 .

[81]  Xunlei Ding,et al.  Density-functional global optimization of (La2O3)n clusters. , 2012, The Journal of chemical physics.

[82]  Roy L. Johnston,et al.  A density functional global optimisation study of neutral 8-atom Cu-Ag and Cu-Au clusters , 2013 .

[83]  Jijun Zhao,et al.  Low-Energy Structures of Binary Pt–Sn Clusters from Global Search Using Genetic Algorithm and Density Functional Theory , 2015, Journal of Cluster Science.

[84]  Jijun Zhao,et al.  Density-functional study of Au n ( n = 2 – 2 0 ) clusters: Lowest-energy structures and electronic properties , 2002 .

[85]  Jijun Zhao,et al.  Magnetic properties of atomic clusters and endohedral metallofullerenes , 2015 .

[86]  First-principles determination of the structure of NaN and NaN- clusters with up to 80 atoms. , 2011, The Journal of chemical physics.

[87]  R. Ahlrichs,et al.  Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory , 1996 .

[88]  Jijun Zhao Density-functional study of structures and electronic properties of Cd clusters , 2001 .

[89]  P. Schwerdtfeger,et al.  From clusters to the solid state: Global minimum structures for cesium clusters Cs n (n=2-20,∞) and their electronic properties , 2008 .

[90]  Extending DFT-based genetic algorithms by atom-to-place re-assignment via perturbation theory: a systematic and unbiased approach to structures of mixed-metallic clusters. , 2014, The Journal of chemical physics.

[91]  Jun Li,et al.  Observation of an all-boron fullerene. , 2014, Nature chemistry.

[92]  Rolf Schäfer,et al.  Bismuth-doped tin clusters: experimental and theoretical studies of neutral Zintl analogues. , 2012, The journal of physical chemistry. A.

[93]  LETTER TO THE EDITOR: Density functional study of beryllium clusters, with gradient correction , 2001 .

[94]  A. Alexandrova,et al.  Persistent Covalency and Planarity in the BnAl6–n2– and LiBnAl6–n– (n = 0–6) Cluster Ions , 2011 .

[95]  Jijun Zhao,et al.  Structural evolution and electronic properties of medium-sized gallium clusters from ab initio genetic algorithm search. , 2012, Journal of nanoscience and nanotechnology.

[96]  Jijun Zhao,et al.  Endohedral Silicon Fullerenes Si N (27 = N = 39) , 2004 .

[97]  Hugh M. Cartwright,et al.  Applications of artificial intelligence in chemistry , 1993 .

[98]  Jijun Zhao,et al.  Lowest-energy structures of (WO3)n (2 ≤ n ≤ 12) clusters from first-principles global search , 2012 .

[99]  B. Delley From molecules to solids with the DMol3 approach , 2000 .

[100]  John H. Holland,et al.  Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence , 1992 .

[101]  L. Wille,et al.  Computational complexity of the ground-state determination of atomic clusters , 1985 .

[102]  F. Weigend,et al.  Structures and properties of neutral gallium clusters: a theoretical investigation. , 2011, The Journal of chemical physics.

[103]  R. Ahlrichs,et al.  Structures of Al(n), its anions and cations up to n = 34: a theoretical investigation. , 2010, The Journal of chemical physics.