ABSTRACT
A cluster is a special matter level above a single atom and between macroscopic and microscopic matter, and it is an important bridge to understanding the relationship between the structure and function of matter. Here, we perform a comprehensive theoretical study of 2D planar Aun (n = 1-12) clusters doped with both magnesium and germanium. Two interesting results are found, namely the rapid 3D "roll-up" structural growth of the GeMgAun (n = 1-12) cluster ground state isomers, and the relative "alienation" of the different sizes of the Aun (n = 1-12) cluster framework towards the Ge atom, and the relative "affinity" towards the Mg atom. This study will not only enrich the data on gold-based clusters but will also provide a simple and clear theoretical guide for the 3D structuring of planar clusters, i.e. the doping of different classes of "affinition" and "alienatation" atoms.
ABSTRACT
Structure, stability, charge transfer, chemical bonding, and spectroscopic properties of Ga atom-doped neutral Mgn (n = 2-12) clusters have been systematically investigated by CALYPSO and density functional theory. All cluster structures are based on "tetrahedral" and "yurt-like" growth except for GaMg2. The ground state isomer of GaMg8 with high symmetry structure is predicted to be the best-fit candidate for the "magic" cluster because of its excellent stability. Natural bond orbital calculations reveal that Ga and Mg atoms play the role of electron acceptor and donor in all ground state isomers, while the orbitals in both Ga and Mg are sp-hybridized. Most importantly, chemical bonding studies based on atom-in-molecular theory have shown that the lowest-energy state of GaMg4 is so special, in that it has not only the critical size for the appearance of Mg-Mg covalent bonds, but also the only cluster that has both Ga-Mg covalent and non-covalent bonds. Finally, theoretical calculations of IR and Raman spectra of all ground state isomers indicate that the spectra of these clusters are observable in the low-frequency band, and thus they can be identified by spectroscopic experiments. Furthermore, the bond heterogeneity of the Ga-Mg in the GaMg4 ground state isomer has also been specifically investigated, including the fixed GaMg4 structure with Mg atoms added in different directions, as well as ab initio molecular dynamics sampling at different temperatures.
ABSTRACT
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. In this study, we conducted a comparative analysis of the structural genes of SARS-CoV-2 and other CoVs. We found that the sequence of the E gene was the most evolutionarily conserved across 200 SARS-CoV-2 isolates. The E gene and M gene sequences of SARS-CoV-2 and NC014470 CoV were closely related and fell within the same branch of a phylogenetic tree. The absolute diversity of E gene and M gene sequences of SARS-CoV-2 isolates was similar to that of common CoVs (C-CoVs) infecting other organisms. The absolute diversity of the M gene sequence of the KJ481931 CoV that can infect humans was similar to that of SARS-CoV-2 and C-CoVs infecting other organisms. The M gene sequence of KJ481931 CoV (infecting humans), SARS-CoV-2 and NC014470 CoV (infecting other organisms) were closely related, falling within the same branch of a phylogenetic tree. Patterns of variation and evolutionary characteristics of the N gene and S gene were very similar. These data may be of value for understanding the origins and intermediate hosts of SARS-CoV-2.
ABSTRACT
Using CALYPSO crystal search software, the structural growth mechanism, relative stability, charge transfer, chemical bonding and optical properties of AuMgn (n = 2-12) nanoclusters were extensively investigated based on DFT. The shape development uncovers two interesting properties of AuMgn nanoclusters contrasted with other doped Mg-based clusters, in particular, the planar design of AuMg3 and the highly symmetrical cage-like of AuMg9. The relative stability study shows that AuMg10 has the robust local stability, followed by AuMg9. In all nanoclusters, the charge is transferred from the Mg atoms to the Au atoms. Chemical bonding properties were confirmed by ELF analysis that Mg-Mg formed covalent bonds in nanoclusters larger than AuMg3. Static polarizability and hyperpolarizability calculations strongly suggest that AuMg9 nanocluster possesses interesting nonlinear optical properties. Boltzmann distribution weighted average IR and Raman spectroscopy studies at room temperature verify that these nanoclusters are identifiable by spectroscopic experiments. Finally, the average bond distance and average nearest neighbor distance were fully investigated.
ABSTRACT
Using CALYPSO method to search new structures of neutral and anionic beryllium-doped magnesium clusters followed by density functional theory (DFT) calculations, an extensive study of the structures, electronic and spectral properties of Be2 Mgn Q (Q = 0, -1; n = 2-11) clusters is performed. Based on the structural optimization, it is found that the Be2 Mgn Q (Q = 0, -1) clusters are shown by tetrahedral-based geometries at n = 2-6 and tower-like-based geometries at n = 7-11. The calculations of stability indicate that Be2 Mg5 Q=0 , Be2 Mg5 Q=-1 , and Be2 Mg8 Q=-1 clusters are "magic" clusters with high stability. The NCP shows that the charges are transferred from Mg atoms to Be atoms. The s- and p-orbitals interactions of Mg and Be atoms are main responsible for their NEC. In particular, chemical bond analysis including molecular orbitals (MOs) and chemical bonding composition for magic clusters to further study their stability. The results confirmed that the high stability of these clusters is due to the interactions between the Be atom and the Mg5 or Mg8 host. Finally, theoretical calculations of infrared and Raman spectra of the ground state of Be2 Mgn Q (Q = 0, -1; n = 1-11) clusters were performed, which will be absolutely useful for future experiments to identify these clusters.
ABSTRACT
By using CALYPSO searching method and Density Functional Theory (DFT) method at the B3LYP/6-311G (d) level of cluster method, a systematic study of the structures, stabilities, electronic and spectral properties of Si2 Mg n Q (n = 1-11; Q = 0, ±1) clusters of silicon-magnesium sensor material, is performed. According to the calculations, it was found that when n > 4, most stable isomers in Si2 Mg n Q (n = 1-11; Q = 0, ±1) clusters of silicon-magnesium sensor material are three-dimensional structures. Interestingly, although large size Si2 Mg n Q clusters show cage-like structures, silicon atoms are not in the center of the cage, but tend to the edge. The Si2 Mg 1 , 5 , 6 , 8 - 1 and Si2 Mg 13 , 4 , 7 , 9 , 10 + 1 clusters obviously differ to their corresponding neutral structures, which are in good agreement with the calculated values of VIP, AIP, VEA, and AEA. |VIP-VEA| values reveal that the hardness of Si2Mgn clusters decreases with the increase of magnesium atoms. The relative stabilities of neutral and charged Si2 Mg n Q (n = 1-11; Q = 0, ±1) clusters of silicon-magnesium sensor material is analyzed by calculating the average binding energy, fragmentation energy, second-order energy difference and HOMO-LUMO gaps. The results reveal that the Si2 Mg 3 0 , Si2 Mg 3 - 1 , and Si2 Mg 3 + 1 clusters have stronger stabilities than others. NCP and NEC analysis results show that the charges in Si2 Mg n Q (n = 1-11; Q = 0, ±1) clusters of silicon-magnesium sensor material transfer from Mg atoms to Si atoms except for Si2 Mg 1 + 1 , and strong sp hybridizations are presented in Si atoms of Si2 Mg n Q clusters. Finally, the infrared (IR) and Raman spectra of all ground state of Si2 Mg n Q (n = 1-11; Q = 0, ±1) clusters of silicon magnesium sensor material are also discussed.
