Yan Su

Nonstandard cages in the formation process of methane clathrate: Stability, structure, and spectroscopic implications from first-principles

Endohedral CH(4)@(H(2)O)(n) (n = 16, 18, 20, 22, 24) clusters with standard and nonstandard cage configurations containing four-, five-, six-, seven-membered rings were generated by spiral algorithm and were systematically explored using DFT-D methods. The geometries of all isomers were optimized in vacuum and aqueous solution. In vacuum, encapsulation of methane molecules can stabilize the hollow (H(2)O)(n) cage by 2.31~5.44 kcal/mol; but the endohedral CH(4)@(H(2)O)(n) cages are still less stable than the pure (H(2)O)(n) clusters. Aqueous environment could promote the stabilities of the hollow (H(2)O)(n) cages as well as the CH(4)@(H(2)O)(n) clusters, and the CH(4)@(H(2)O)(n) clusters possess larger stabilization energies with regard to the pure (H(2)O)(n) clusters except for n = 24. The lowest energy structures of the CH(4)@(H(2)O)(20) and CH(4)@(H(2)O)(24) cages are identical to the building units in the crystalline sI clathrate hydrate. All of the low-energy cages (including both regular and irregular ones) have large structural similarity and can be connected by dimer-insertion operation and Stone-Wales transformation. Our calculation also showed that in the range of cluster size n = 16-24, the relative energies of cage isomers tend to decrease with increasing number of the adjacent pentagons in the oxygen skeleton structures. In addition to the regular endohedral CH(4)@(H(2)O)(20) and CH(4)@(H(2)O)(24) cage structures, some nonstandard CH(4)@(H(2)O)(n) (n = 18, 20, 22, 24) cages have lower energies and might appear during nucleation process of methane hydrate. For the methane molecules in these low-energy cage isomers, we found that the C-H symmetric stretching frequencies show a red-shift trend and the (13)C NMR chemical shifts generally move toward negative values as the cavity size increases. These theoretical results are comparable to the available experimental data and might help experimental identification of the endohedral water cages during nucleation.

Low-Energy Structures of Binary Pt–Sn Clusters from Global Search Using Genetic Algorithm and Density Functional Theory

The low-energy structures of PtnSnn (nxa0=xa01–10) and Pt3mSnm (mxa0=xa01–5) clusters have been determined using genetic algorithm incorporated with density functional theory. Platinum and tin atoms tend to mix with each other due to the energetically favorable Pt–Sn bonds. However, due to the larger atomic radius of Sn atoms, we find segregation of Sn atoms on the surface of PtnSnn clusters. This leaves one or two Pt atoms available for reaction and for larger clusters segregation of Sn could block the Pt sites. For Pt3mSnm clusters, Sn atoms are well separated in the cluster structures and prefer to form sharp vertices leaving triangular faces of three Pt atoms available for reactivity. The electronic properties such as highest occupied molecular orbital–lowest unoccupied molecular orbital gap, distribution of frontier orbitals, Mayer bond order, Mülliken atomic charge, and the density of states are discussed. Significant hybridization between the d orbitals of Pt and the p orbitals of Sn is revealed. These theoretical results provide the general trends for the structural and bonding characteristics of the Pt–Sn alloy clusters and help understand their catalytic behavior.

Storage capacity and vibration frequencies of guest molecules in CH4 and CO2 hydrates by first-principles calculations.

Using first-principle calculations at B97-D/6-311++G(2d,2p) level, we systematically explore the gas capacity of five standard water cavities (5(12), 4(3)5(6)6(3), 5(12)6(2), 5(12)6(4), and 5(12)6(8)) in clathrate hydrate and study the inclusion complexes to infer general trends in vibrational frequencies of guest molecules as a function of cage size and number of guest molecules. In addition, the Raman spectra of hydrates from CO2/CH4 gases are simulated. From our calculations, the maximum cage occupancy of the five considered cages (5(12), 4(3)5(6)6(3), 5(12)6(2), 5(12)6(4), and 5(12)6(8)) is one, one, two, three, and seven for both CH4 and CO2 guest molecules, respectively. Meanwhile, the optimum cage occupancy are one, one, one, two, and four for CO2 molecules and one, one, two, three, and five for CH4 molecules, respectively. Both the C-H stretching frequency of CH4 and the C-O stretching frequency of CO2 gradually decrease as size of the water cages increases. Meanwhile, the C-H stretching frequency gradually increases as the amount of CH4 molecules in the water cavity (e.g., 5(12)6(8)) increases.

Design of Three-shell Icosahedral Matryoshka Clusters A@B12@A20 (A = Sn, Pb; B = Mg, Zn, Cd, Mn)

We propose a series of icosahedral matryoshka clusters of A@B12@A20 (A = Sn, Pb; B = Mg, Zn, Cd), which possess large HOMO-LUMO gaps (1.29 to 1.54u2005eV) and low formation energies (0.06 to 0.21u2005eV/atom). A global minimum search using a genetic algorithm and density functional theory calculations confirms that such onion-like three-shell structures are the ground states for these A21B12 binary clusters. All of these icosahedral matryoshka clusters, including two previously found ones, i.e., [As@Ni12@As20]3− and [Sn@Cu12@Sn20]12−, follow the 108-electron rule, which originates from the high Ih symmetry and consequently the splitting of superatom orbitals of high angular momentum. More interestingly, two magnetic matryoshka clusters, i.e., Sn@Mn12@Sn20 and Pb@Mn12@Pb20, are designed, which combine a large magnetic moment of 28 µB, a moderate HOMO-LUMO gap, and weak inter-cluster interaction energy, making them ideal building blocks in novel magnetic materials and devices.

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.

Structures and Electronic Properties of V3Sin- (n=3-14) Clusters: A Combined Ab Initio and Experimental Study

The anionic silicon clusters doped with three boron atoms, B3Sin- (n = 4-10), have been generated by laser vaporization and investigated by anion photoelectron spectroscopy. The vertical detachment energies (VDEs) and adiabatic detachment energies (ADEs) of these anionic clusters are determined. The lowest energy structures of B3Sin- (n = 4-10) clusters are globally searched using genetic algorithm incorporated with density functional theory (DFT) calculations. The photoelectron spectra, VDEs, ADEs of these B3Sin- clusters (n = 4-10) are simulated using B3LYP/6-311+G(d) calculations. Satisfactory agreement is found between theory and experiment. Most of the lowest-energy structures of B3Sin- (n = 4-10) clusters can be derived by using the squashed pentagonal bipyramid structure of B3Si4- as the major building unit. Analyses of natural charge populations show that the boron atoms always possess negative charges, and that the electrons transfer from the 3s orbital of silicon and the 2s orbital of boron to the 2p orbital of boron. The calculated average binding energies, second-order differences of energies, and the HOMO-LUMO gaps show that B3Si6- and B3Si9- clusters have relatively high stability and enhanced chemical inertness. In particular, the B3Si9- cluster with high symmetry (C3v) stands out as an interesting superatom cluster with a magic number of 40 skeletal electrons and a closed-shell electronic configuration of 1S21P61D102S22P61F14 for superatom orbitals.

Stability and Vibrations of Guest Molecules in the Type II Clathrate Hydrate: A First-Principles Study of Solid Phase

Natural gas mixtures are inclusion compounds composed of major light hydrocarbon gaseous molecules (CH4, C2H6, C3H6, and C3H8). Previous ab initio calculations were mainly limited by the cluster models. For the first time, we report first-principles calculations on the stability and vibrational properties of the gas molecules inside the crystalline lattice of type II clathrate. In accordance with our calculations, the larger the size of guest molecule, the more stable the clathrate hydrate for small-sized alkane guest molecules (CnHm, n ≤ 3, m ≤ 8). The interaction energy per guest molecule gradually increases as the number of guest molecules increase for both sII pure and sII mixed hydrates. In addition, the vibrational frequencies of guest molecules trapped in sII hydrate are also simulated. The C-C stretching frequency shows a blue shift as the amount of guest molecules increase. Our theoretical results prove to be valuable insight for identifying the types of guest molecules from experimental spectroscopic data.

Which Density Functional Should Be Used to Describe Protonated Water Clusters

Protonated water cluster is one of the most important hydrogen-bond network systems. Finding an appropriate DFT method to study the properties of protonated water clusters can substantially improve the economy in computational resources without sacrificing the accuracy compared to high-level methods. Using high-level MP2 and CCSD(T) methods as well as experimental results as benchmark, we systematically examined the effect of seven exchange-correlation GGA functionals (with BLYP, B3LYP, X3LYP, PBE0, PBE1W, M05-2X, and B97-D parametrizations) in describing the geometric parameters, interaction energies, dipole moments, and vibrational properties of protonated water clusters H+(H2O)2-9,12. The overall performance of all these functionals is acceptable, and each of them has its advantage in certain aspects. X3LYP is the best to describe the interaction energies, and PBE0 and M05-2X are also recommended to investigate interaction energies. PBE0 gives the best anharmonic frequencies, followed by PBE1W, B97-D and BLYP methods. PBE1W, B3LYP, B97-D, and X3LYP can yield better geometries. The capability of B97-D to distinguish the relative energies between isomers is the best among all the seven methods, followed by M05-2X and PBE0.

Ab initio global optimization of clusters

Due to the complexity of high-dimensional potential energy surface, determining the ground state structure of a cluster is challenging. In recent years, there has been significant progress in the development of ab initio global optimization methods, such as genetic algorithm, basin hopping, topological methods, particle swarm optimization, tabu search, and minima hopping. The essential idea is to avoid being trapped in local minimum and to explore the entire region of potential energy surface. All these methods show remarkable performance in finding the ground state structures of various kinds of clusters. In this chapter, we present an overview of these methods.

Structures, Stabilities, and Spectra Properties of Fused CH4 Endohedral Water Cage (CH4)m(H2O)n Clusters from DFT‑D Methods

In order to understand the cage fusion behavior during the nucleation processes of methane hydrate (MH), methane-encapsulated double-cage clusters (CH4)2(H2O)n (n = 30-43) and several multicage structures with three or more cages were studied employing DFT-D methods. We find that almost all the lowest-energy double-cage structures can be constructed by merging the most stable structures of the monocage clusters CH4(H2O)n (n = 18-24). Double-cage structures can achieve higher stability through sharing a hexagon than a pentagon, which may be applicable to larger fused cage clusters. The preference of hexagons during cage fusion should be favorable for the appearance of the cages including hexagons such as the 5(12)6(2), 5(12)6(4) cages during the MH nucleation process. The symmetric C-H stretching modes of methane molecules in the double-cage structures show a clear trend of red shift with increasing size of the composing monocages. Compared with the case of monocages, the stretching frequencies of methane molecules in double-cage structures shift slightly, indicating variation of monocage configuration when cage fusion occurs. The larger multicage structures are found to possess higher fusion energies through sharing more polygons. Their thermodynamic stabilities do not simply increase with the number of fused monocages and are affected by the spatial arrangement of the building cages.