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.

Structure Prediction for Surface-Induced Phases of Organic Monolayers: Overcoming the Combinatorial Bottleneck.

Structure determination and prediction pose a major challenge to computational material science, demanding efficient global structure search techniques tailored to identify promising and relevant candidates. A major bottleneck is the fact that due to the many combinatorial possibilities, there are too many possible geometries to be sampled exhaustively. Here, an innovative computational approach to overcome this problem is presented that explores the potential energy landscape of commensurate organic/inorganic interfaces where the orientation and conformation of the molecules in the tightly packed layer is close to a favorable geometry adopted by isolated molecules on the surface. It is specifically designed to sample the energetically lowest lying structures, including the thermodynamic minimum, in order to survey the particularly rich and intricate polymorphism in such systems. The approach combines a systematic discretization of the configuration space, which leads to a huge reduction of the combinatorial possibilities with an efficient exploration of the potential energy surface inspired by the Basin-Hopping method. Interfacing the algorithm with first-principles calculations, the power and efficiency of this approach is demonstrated for the example of the organic molecule TCNE (tetracyanoethylene) on Au(111). For the pristine metal surface, the global minimum structure is found to be at variance with the geometry found by scanning tunneling microscopy. Rather, our results suggest the presence of surface adatoms or vacancies that are not imaged in the experiment.

Hybridizing rapidly exploring random trees and basin hopping yields an improved exploration of energy landscapes.

The number of local minima of the potential energy landscape (PEL) of molecular systems generally grows exponentially with the number of degrees of freedom, so that a crucial property of PEL exploration algorithms is their ability to identify local minima, which are low lying and diverse. In this work, we present a new exploration algorithm, retaining the ability of basin hopping (BH) to identify local minima, and that of transition based rapidly exploring random trees (T-RRT) to foster the exploration of yet unexplored regions. This ability is obtained by interleaving calls to the extension procedures of BH and T-RRT, and we show tuning the balance between these two types of calls allows the algorithm to focus on low lying regions. Computational efficiency is obtained using state-of-the art data structures, in particular for searching approximate nearest neighbors in metric spaces. We present results for the BLN69, a protein model whose conformational space has dimension 207 and whose PEL has been studied exhaustively. On this system, we show that the propensity of our algorithm to explore low lying regions of the landscape significantly outperforms those of BH and T-RRT.

Global Materials Structure Search with Chemically Motivated Coordinates.

Identification of relevant reaction pathways in ever more complex composite materials and nanostructures poses a central challenge to computational materials discovery. Efficient global structure search, tailored to identify chemically relevant intermediates, could provide the necessary first-principles atomistic insight to enable a rational process design. In this work we modify a common feature of global geometry optimization schemes by employing automatically generated collective curvilinear coordinates. The similarity of these coordinates to molecular vibrations enhances the generation of chemically meaningful trial structures for covalently bound systems. In the application to hydrogenated Si clusters, we concomitantly observe a significantly increased efficiency in identifying low-energy structures and exploit it for an extensive sampling of potential products of silicon-cluster soft landing on Si(001) surfaces.

Study of Cl(-)(H2O)n (n = 1-4) using basin-hopping method coupled with density functional theory.

Cl(-)(H2O)n (n = 1-4) clusters were investigated using a basin-hopping (BH) algorithm coupled with density functional theory (DFT). Structures, energetics, thermodynamics, vertical detachment energies, and vibrational frequencies were obtained from high-level ab initio calculations. Through comparisons with previous theoretical and experimental data, it was demonstrated that the combination of the BH method and DFT could accurately predict the global and local minima of Cl(-)(H2O)n (n = 1-4). Additionally, to optimize larger Cl(-)(H2O)n (n > 4) clusters, several popular density functionals as well as DF-LMP2 (Schütz et al., J. Chem. Phys. 2004, 121, 737) (second-order Møller-Plesset perturbation theory using local and density fitting approximations) were tested with appropriate basis sets through comparisons with MP2 optimized results. DF-LMP2 will be used in future studies because its overall performance in describing the relative binding energies and the geometrical parameters of Cl(-)(H2O)n (n = 1-4) was outstanding in this study.

Protein structure prediction: assembly of secondary structure elements by basin-hopping.

The prediction of protein tertiary structure from primary structure remains a challenging task. One possible approach to this problem is the application of basin-hopping global optimization combined with an all-atom force field. In this work, the efficiency of basin-hopping is improved by introducing an approach that derives tertiary structures from the secondary structure assignments of individual residues. This approach is termed secondary-to-tertiary basin-hopping and benchmarked for three miniproteins: trpzip, trp-cage and ER-10. For each of the three miniproteins, the secondary-to-tertiary basin-hopping approach successfully and reliably predicts their three-dimensional structure. When it is applied to larger proteins, correctly folded structures are obtained. It can be concluded that the assembly of secondary structure elements using basin-hopping is a promising tool for de novo protein structure prediction.

Microsolvation of lithium cation in xenon clusters: An octahedral growth pattern.

The structural and energetic proprieties for the Li + Xen (n = 1-18) clusters are investigated using both Basin-Hopping combined with Potential Model description (BH-PM) and DFT methods. A structural transition from tetrahedral (4 coordination) form to octahedral (6 coordination) one is observed for n = 6. Above this size, all structures have an octahedral core. The cubic-face-centered arrangement for xenon atoms is detected for Li + Xe14. To the best of our knowledge, the Li + Xen (n = 1-18) clusters are studied in the present work for the first time using the DFT theoretical approach. The M062X functional combined with aug-cc-pVDZ (for Li) and def2-TZVP (for Xe) basis sets reproduces accurately the CCSD(T) potential energy curve of Li + Xe system. Atom-Centered Density Matrix Propagation (ADMP) molecular dynamic calculations have been carried. Moreover, we investigate the larger sizes n = 31-35, 44, and 55 for the first time using the BH-PM theoretical approach. The closing of the first and second octahedron shells are proved for the n = 6 and 34 sizes, respectively. The relative stabilities of the Li + Xen molecules are also studied by computing the total energy, the binding energy per atoms for each size n. Then, the second energy difference between the size n and its two near neighbors allows identifying the magic number series. Our present data are analyzed, discussed and compared with the available theoretical and experimental data.

Efficiency of tabu-search-based conformational search algorithms.

Efficient conformational search or sampling approaches play an integral role in molecular modeling, leading to a strong demand for even faster and more reliable conformer search algorithms. This article compares the efficiency of a molecular dynamics method, a simulated annealing method, and the basin hopping (BH) approach (which are widely used in this field) with a previously suggested tabu-search-based approach called gradient only tabu search (GOTS). The study emphasizes the success of the GOTS procedure and, more importantly, shows that an approach which combines BH and GOTS outperforms the single methods in efficiency and speed. We also show that ring structures built by a hydrogen bond are useful as starting points for conformational search investigations of peptides and organic ligands with biological activities, especially in structures that contain multiple rings.

Minimal Design Principles for Icosahedral Virus Capsids.

The geometrical structures of single- and multiple-shell icosahedral virus capsids are reproduced as the targets that minimize the cost corresponding to relatively simple design functions. Capsid subunits are first identified as building blocks at a given coarse-grained scale and then represented in these functions as point particles located on an appropriate number of concentric spherical surfaces. Minimal design cost is assigned to optimal spherical packings of the particles. The cost functions are inspired by the packings favored for the Thomson problem, which minimize the electrostatic potential energy between identical charged particles. In some cases, icosahedral symmetry constraints are incorporated as external fields acting on the particles. The simplest cost functions can be obtained by separating particles in disjoint nonequivalent sets with distinct interactions, or by introducing interacting holes (the absence of particles). These functions can be adapted to reproduce any capsid structure found in real viruses. Structures absent in Nature require significantly more complex designs. Measures of information content and complexity are assigned to both the cost functions and the capsid geometries. In terms of these measures, icosahedral structures and the corresponding cost functions are the simplest solutions.

Search for Global Minimum Structures of P 2 n + 1 + (n = 1-15) Using xTB-Based Basin-Hopping Algorithm.

A new program for searching global minimum structures of atomic clusters using basin-hopping algorithm based on the xTB method was developed here. The program can be performed with a much higher speed than its replacement directly based on DFT methods. Considering the structural varieties and complexities in finding their global minimum structures, phosphorus cluster cations were studied by the program. The global minimum structures of cationic P 2 n + 1 + (n = 1-15) clusters are determined through the unbiased structure searching method. In the last step, further DFT optimization was performed for the selected isomers. For P 2 n + 1 + (n = 1-4, 7), the found global minimum structures are in consistent with the ones previously reported; while for P 2 n + 1 + (n = 5, 6, 8-12), newly found isomers are more energy-favorable than those previously reported. And those for P 2 n + 1 + (n = 13-15) are reported here for the first time. Among them, the most stable isomers of P 2 n + 1 + (n = 4-6, 9) are characterized by their C3v, Cs, C2v and Cs symmetry, in turn. But those of P 2 n + 1 + (n = 7, 8, 10-12), no symmetry has been identified. The most stable isomers of P 29 + and P 31 + are characterized by single P-P bonds bridging units inside the clusters. Further analysis shows that the pnicogen bonds play an important role in the stabilization of these clusters. These results show that the new developed program is effective and robust in searching global minimum structures for atom clusters, and it also provides new insights into the role of pnicogen bonds in phosphorus clusters.

Solvation of lithium ion in helium clusters: Structural properties and relative stabilities.

Structural study and relative stabilities of Li+-doped helium clusters Li+Hen (n = 1-18) has been reported in this work using two theoretical protocols. The first one is based on the basin-hopping optimization technique, where the total energy of each cluster is described by an additive model describing Li+-He and He-He interactions. The second one is the DFT calculations, in which the initial structures are generated by ABCluster algorithm and CALYPSO software. The CSA shape was found where the first solvation shell is completed at n = 10. The relative stabilities of Li+Hen (n = 1-18) clusters have been discussed based on the variation of the binding energy, second-order difference in energy, fragmentation energy and HOMO-LUMO energy gap as a function of the cluster size. The results showed that Li+He10 is the most stable cluster. The dipole moment is calculated and showed the polar character of the Li+Hen clusters. Finally, the interatomic interactions have been examined topologically by the means of AIM and non-covalent reduced density gradient (NC-RDG) analyses.

Influence of Softness on the Stability of Binary Colloidal Crystals.

Mixtures of two types of nanoparticles can self-assemble into a wide variety of binary colloidal crystals (also called binary nanoparticle superlattices), which are interesting for their structural diversity and potential applications. Although so-called packing models-which usually treat the particles as "hard" with only excluded volume interactions-seem to explain many reported dense crystalline phases, these models often fail to predict the right structure. Here, we examine the role of soft repulsive interparticle interactions on binary colloidal crystals comprising two sizes of spherical particles; such "softness" can arise due to ligand shells or screened electrostatics. We determine the ground state phase diagram of binary systems of particles interacting with an additive inverse power law potential using a basin hopping algorithm to calculate the enthalpy of an extremely large pool of candidate structures. We find that a surprisingly small amount of softness can destabilize dense packings in favor of less densely packed structures, which provides further evidence that considerations beyond packing are necessary for describing many of the observed phases of binary colloidal crystals. Importantly, we find that several of the phases stabilized by softness, which are characterized by relatively few interparticle contacts and a tendency for local icosahedral order, are more likely to be observed experimentally than those predicted by packing models. We also report a previously unknown dense AB4 phase and conduct free energy calculations to examine how the stability of several crystals will vary with temperature. Our results further our understanding of why particular binary colloidal crystals form and will be useful as a reference for experimentalists working with softly repulsive colloids.

Aptasensor designed via the stochastic tunneling-basin hopping method for biosensing of vascular endothelial growth factor.

The Systematic Evolution Ligands by Exponential Enrichment (SELEX) is common used for selection of high affinity single-stranded DNA (ssDNA) aptamer with target protein. However, we do not know what the most stable configuration of the selected aptamer bound with target protein is. Therefore, a systematic search process using the stochastic tunneling-basin hopping (STUN-BH) method is proposed to find the most stable configuration of the ssDNA aptamer specific for vascular endothelial growth factor (VEGF) capture (AptVEGF; 5'-TGTGGGGGTGGACGGGCCGGGTAGA-3'). After the most stable configuration was obtained by the STUN-BH method, molecular dynamics (MD) simulation was carried out to investigate the thermal stability of AptVEGF/VEGF at 300 K in both vacuum and water. All molecular simulations were conducted with the large-scale atomic/molecular massively parallel simulator (LAMMPS), and the AMBER99SB force field was used to describe the atomic interactions for the current AptVEGF/VEGF system. The three most stable AptVEGF/VEGF configurations obtained by the STUN-BH method indicated that AptVEGF residues exhibit greater affinity for VEGF surface loop fragments as compared with surface alpha helix and beta sheet fragments. Results indicated that after the first AptVEGF (AptVEGF I) occupies most of the VEGF loop fragment, the second AptVEGF (AptVEGF II) is adsorbed by the rest of the VEGF loop fragment and the VEGF Chain B beta sheet fragment, resulting in a 24.8% reduction in binding strength as compared to that of AptVEGF I. Furthermore, when AptVEGF I and AptVEGF II chains were stably adsorbed by VEGF, the third AptVEGF (AptVEGF III) chain can only partially attach to VEGF, as confirmed by real AptVEGF-VEGF binding experiments. Lastly, we demonstrated that the aptasensor constructed according to MD simulation is highly sensitive for VEGF with a linear detection range of 10 pg/mL-10 ng/mL.

Interaction of Gold Clusters with a Hydroxylated Surface.

We explore the interaction between gold nanoclusters and a fully hydroxylated surface, Mg(OH)2's basal plane, by using a density functional theory-enabled local basin-hopping technique for global-minimum search. We find strong interaction of gold nanoclusters with the surface hydroxyls via a short bond between edge Au atoms and O atoms of the -OH groups. We expect that this strong interaction is ubiquitous on hydroxylated support surfaces and helps the gold nanoclusters against sintering, thereby contributing to their CO-oxidation activity at low temperatures.