TGMin: An efficient global minimum searching program for free and surface‐supported clusters

In this article, we introduce an efficient global‐minimum structural search program named Tsinghua Global Minimum 2 (TGMin‐2), which is the successor of the original TGMin algorithm that was developed in our group in 2011. We have introduced a number of new features and improvements into TGMin‐2, including a symmetric structure generation algorithm that can produce good initial seeds for small‐ and medium‐size clusters, the duplicated structure identification algorithm, and the improved structure adaption algorithm that was implemented in the original TGMin code. To predict the simulated photoelectron spectrum (PE spectrum) automatically, we also implemented a standalone program named AutoPES (Auto Photoelectron Spectroscopy), which can be used to simulate PE spectra and compare them with experimental results automatically. We have demonstrated that TGMin‐2 and AutoPES are powerful tools for studying free and surface‐supported molecules, clusters, and nanoclusters. © 2018 Wiley Periodicals, Inc.

[1]  Yanchao Wang,et al.  Crystal structure prediction via particle-swarm optimization , 2010 .

[2]  Mario Valle,et al.  How to quantify energy landscapes of solids. , 2009, The Journal of chemical physics.

[3]  Paul W Finn,et al.  Ultrafast shape recognition: evaluating a new ligand-based virtual screening technology. , 2009, Journal of molecular graphics & modelling.

[4]  J. G. Snijders,et al.  Electronic Spectra of M(CO)6 (M = Cr, Mo, W) Revisited by a Relativistic TDDFT Approach , 1999 .

[5]  F. Matthias Bickelhaupt,et al.  Chemistry with ADF , 2001, J. Comput. Chem..

[6]  H. Scheraga,et al.  Global optimization of clusters, crystals, and biomolecules. , 1999, Science.

[7]  Satoshi Maeda,et al.  A scaled hypersphere search method for the topography of reaction pathways on the potential energy surface , 2004 .

[8]  Gregory A Voth,et al.  Application of the SCC-DFTB method to hydroxide water clusters and aqueous hydroxide solutions. , 2013, The journal of physical chemistry. B.

[9]  Jun Li,et al.  Manganese-centered tubular boron cluster - MnB16 (-): A new class of transition-metal molecules. , 2016, The Journal of chemical physics.

[10]  S. Papson.  “Model” , 1981 .

[11]  Satoshi Maeda,et al.  Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods. , 2013, Physical chemistry chemical physics : PCCP.

[12]  Jun Li,et al.  [B₃₀]⁻: a quasiplanar chiral boron cluster. , 2014, Angewandte Chemie.

[13]  B. Hammer,et al.  On-the-Fly Machine Learning of Atomic Potential in Density Functional Theory Structure Optimization. , 2018, Physical review letters.

[14]  Bjørk Hammer,et al.  A genetic algorithm for first principles global structure optimization of supported nano structures. , 2014, The Journal of chemical physics.

[15]  J. Perdew,et al.  Density-Functional Theory for Fractional Particle Number: Derivative Discontinuities of the Energy , 1982 .

[16]  Satya Bulusu,et al.  Structures and relative stability of neutral gold clusters: Aun (n=15-19). , 2006, The Journal of chemical physics.

[17]  A. Oganov,et al.  Crystal structure prediction using ab initio evolutionary techniques: principles and applications. , 2006, The Journal of chemical physics.

[18]  Quan Li,et al.  CALYPSO structure prediction method and its wide application , 2016 .

[19]  B. Lundqvist,et al.  Potential--energy surfaces for excited states in extended systems. , 2004, The Journal of chemical physics.

[20]  Zhi-Pan Liu,et al.  Stochastic surface walking method for crystal structure and phase transition pathway prediction. , 2014, Physical chemistry chemical physics : PCCP.

[21]  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.

[22]  Artem R. Oganov,et al.  Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs , 2015, Science.

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

[24]  Yan Tang,et al.  Mechanistic Insights into Propene Epoxidation with O2–H2O Mixture on Au7/α-Al2O3: A Hydroproxyl Pathway from ab Initio Molecular Dynamics Simulations , 2016 .

[25]  Eric J. Bylaska,et al.  Theoretical studies of the global minima and polarizabilities of small lithium clusters , 2016 .

[26]  Bjørk Hammer,et al.  Neural-network-enhanced evolutionary algorithm applied to supported metal nanoparticles , 2018 .

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

[28]  Burke,et al.  Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.

[29]  Pedro J. Ballester,et al.  Ultrafast shape recognition for similarity search in molecular databases , 2007, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[30]  Bruce E. Bursten,et al.  RELATIVISTIC DENSITY FUNCTIONAL STUDY OF THE GEOMETRY, ELECTRONIC TRANSITIONS, IONIZATION ENERGIES, AND VIBRATIONAL FREQUENCIES OF PROTACTINOCENE, PA( ETA 8-C8H8)2 , 1998 .

[31]  R. O. Jones,et al.  The density functional formalism, its applications and prospects , 1989 .

[32]  Jun Li,et al.  Observation and characterization of the smallest borospherene, B28(-) and B28. , 2016, The Journal of chemical physics.

[33]  Jun Li,et al.  Atomic Energies from a Convolutional Neural Network. , 2018, Journal of chemical theory and computation.

[34]  J. G. Snijders,et al.  Implementation of time-dependent density functional response equations , 1999 .

[35]  Jun Li,et al.  Experimental and theoretical evidence of an axially chiral borospherene. , 2015, ACS nano.

[36]  Pekka Pyykkö,et al.  Molecular single-bond covalent radii for elements 1-118. , 2009, Chemistry.

[37]  Stefan Goedecker,et al.  Minima hopping guided path search: an efficient method for finding complex chemical reaction pathways. , 2014, The Journal of chemical physics.

[38]  Nikolaus Hansen,et al.  USPEX - Evolutionary crystal structure prediction , 2006, Comput. Phys. Commun..

[39]  Zhi-Pan Liu,et al.  Double-Ended Surface Walking Method for Pathway Building and Transition State Location of Complex Reactions. , 2013, Journal of chemical theory and computation.

[40]  Jun Li,et al.  Recent progresses of global minimum searches of nanoclusters with a constrained Basin-Hopping algorithm in the TGMin program , 2017 .

[41]  Fabio Pietrucci,et al.  Graph theory meets ab initio molecular dynamics: atomic structures and transformations at the nanoscale. , 2011, Physical review letters.

[42]  Jun Li,et al.  Observation of highly stable and symmetric lanthanide octa-boron inverse sandwich complexes , 2018, Proceedings of the National Academy of Sciences.

[43]  Hui Li,et al.  Experimental realization of two-dimensional boron sheets. , 2015, Nature chemistry.

[44]  Qiang Chen,et al.  B30H8, B39H92−, B42H10, B48H10, and B72H12: polycyclic aromatic snub hydroboron clusters analogous to polycyclic aromatic hydrocarbons , 2013, Journal of Molecular Modeling.

[45]  Tian Jian,et al.  From planar boron clusters to borophenes and metalloborophenes , 2017 .

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

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

[48]  Michele Parrinello,et al.  Generalized neural-network representation of high-dimensional potential-energy surfaces. , 2007, Physical review letters.

[49]  Bjørk Hammer,et al.  Interfacial oxygen under TiO2 supported Au clusters revealed by a genetic algorithm search. , 2013, The Journal of chemical physics.

[50]  M. Engelund,et al.  Delta self-consistent field method to obtain potential energy surfaces of excited molecules on surfaces , 2008 .

[51]  Jun Li,et al.  Theoretical Studies on Hexanuclear Oxometalates [M6L19](q-) (M = Cr, Mo, W, Sg, Nd, U). Electronic Structures, Oxidation States, Aromaticity, and Stability. , 2015, Inorganic chemistry.

[52]  Anastassia N Alexandrova,et al.  SmB 6 − Cluster Anion: Covalency Involving f Orbitals , 2017 .

[53]  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.

[54]  Lutz,et al.  Photodetachment spectroscopy of cold aluminum cluster anions. , 1988, Physical review. A, General physics.

[55]  W. Graham Richards,et al.  Ultrafast shape recognition to search compound databases for similar molecular shapes , 2007, J. Comput. Chem..

[56]  Quan Li,et al.  Materials discovery via CALYPSO methodology , 2014, Journal of physics. Condensed matter : an Institute of Physics journal.

[57]  Jun Li,et al.  TGMin: A global-minimum structure search program based on a constrained basin-hopping algorithm , 2017, Nano Research.

[58]  Yanchao Wang,et al.  Particle-swarm structure prediction on clusters. , 2012, The Journal of chemical physics.

[59]  Pekka Pyykkö,et al.  Molecular double-bond covalent radii for elements Li-E112. , 2009, Chemistry.

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

[61]  Hans Wondratschek,et al.  Bilbao Crystallographic Server. II. Representations of crystallographic point groups and space groups. , 2006, Acta crystallographica. Section A, Foundations of crystallography.

[62]  Satoshi Maeda,et al.  A new global reaction route map on the potential energy surface of H2CO with unrestricted level , 2008 .

[63]  Francisco B. Pereira,et al.  An evolutionary algorithm for global minimum search of binary atomic clusters , 2010 .

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

[65]  Pieter Kruit,et al.  Magnetic field paralleliser for 2π electron-spectrometer and electron-image magnifier , 1983 .

[66]  Zhi-Pan Liu,et al.  Reaction sampling and reactivity prediction using the stochastic surface walking method. , 2015, Physical chemistry chemical physics : PCCP.

[67]  Satoshi Maeda,et al.  Toward Predicting Full Catalytic Cycle Using Automatic Reaction Path Search Method: A Case Study on HCo(CO)3-Catalyzed Hydroformylation. , 2012, Journal of chemical theory and computation.

[68]  Yanming Ma,et al.  Structure Prediction of Atoms Adsorbed on Two-Dimensional Layer Materials: Method and Applications , 2015 .

[69]  Tetsuya Taketsugu,et al.  Exploring transition state structures for intramolecular pathways by the artificial force induced reaction method , 2014, J. Comput. Chem..

[70]  Tom Ziegler,et al.  The performance of time-dependent density functional theory based on a noncollinear exchange-correlation potential in the calculations of excitation energies. , 2005, The Journal of chemical physics.

[71]  Jun Li,et al.  PrB7- : A Praseodymium-Doped Boron Cluster with a PrII Center Coordinated by a Doubly Aromatic Planar η7 -B73- Ligand. , 2017, Angewandte Chemie.

[72]  Tian Jian,et al.  B 26 - : The smallest planar boron cluster with a hexagonal vacancy and a complicated potential landscape , 2017 .

[73]  Satoshi Maeda,et al.  A new method for constructing multidimensional potential energy surfaces by a polar coordinate interpolation technique , 2003 .

[74]  Dmitry Yu. Zubarev,et al.  Global minimum structure searches via particle swarm optimization , 2007, J. Comput. Chem..

[75]  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.

[76]  Li Zhu,et al.  CALYPSO: A method for crystal structure prediction , 2012, Comput. Phys. Commun..

[77]  Xiaojun Wu,et al.  Predicting two-dimensional boron-carbon compounds by the global optimization method. , 2011, Journal of the American Chemical Society.

[78]  Tom Ziegler,et al.  Time-dependent density functional theory based on a noncollinear formulation of the exchange-correlation potential. , 2004, The Journal of chemical physics.

[79]  Lev Kantorovich,et al.  Quantum Theory of the Solid State: An Introduction , 2004 .

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

[81]  Si-Da Huang,et al.  Material discovery by combining stochastic surface walking global optimization with a neural network† †Electronic supplementary information (ESI) available: Derivation for the gradient of J σ with respect to NN parameters. DFT calculation setups. Parameters of atom-centered symmetry functions for ge , 2017, Chemical science.

[82]  Bjørk Hammer,et al.  Combining Evolutionary Algorithms with Clustering toward Rational Global Structure Optimization at the Atomic Scale. , 2017, Journal of chemical theory and computation.

[83]  Zhi-Pan Liu,et al.  From Atoms to Fullerene: Stochastic Surface Walking Solution for Automated Structure Prediction of Complex Material. , 2013, Journal of chemical theory and computation.

[84]  Satoshi Maeda,et al.  Global reaction route mapping on potential energy surfaces of C2H7+ and C3H9+ , 2007 .

[85]  Lai‐Sheng Wang,et al.  Photoelectron spectroscopy of size-selected boron clusters: from planar structures to borophenes and borospherenes , 2016 .

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

[87]  K. Müller,et al.  Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space , 2015, The journal of physical chemistry letters.