Structural and dynamical properties of 13-atom Cu–Co mixed clusters

In this paper, the geometric structures and the melting-like processes of the 13-atom pure copper, pure cobalt cluster and their 13-atom mixed clusters are investigated and compared by the molecular dynamics method. The calculation shows that the pure copper and cobalt clusters have the standard icosahedral structures and the mixed clusters take on the deformed icosahedral structures. The quantitative analysis shows that the deformations are slight. Moreover, an element similarity function is introduced by which the contribution of the compositions of the clusters to the deformation of the mixed clusters is analyzed and discussed. With the increase of the temperature, the migrating and recombination of the atoms on the surface of the clusters are observed, indicating the starting of the transition from solid-like to liquid-like state for the clusters. Through the calculating of the relative root-mean-squared pair separation fluctuation and monitoring the dynamical structures of the clusters, it is found that the mixed clusters experience a multi-step process in the transition.

Tracking Fecal Bacterial Dispersion from Municipal Wastewater to Peri-Urban Farms during Monsoon Rains in Hue City, Vietnam

Disease outbreaks attributed to monsoon flood-induced pathogen exposure are frequently reported, especially in developing cities with poor sanitation. Contamination levels have been monitored in past studies, yet the sources, routes, and extents of contamination are not always clear. We evaluated pollution from municipal wastewater (MWW) discharge and investigated fecal contamination by Escherichia coli (E. coli) in three agricultural fields on the outskirts of Hue City, Vietnam. After E. coli concentration was determined in irrigation water (IRW), MWW, soil, vegetables (VEG), and manure, its dispersion from MWW was tracked using multilocus sequence typing (MLST) and phylogenetic analyses during the wet and dry seasons. IRW was severely contaminated; 94% of the samples were positive with E. coli exceeding the stipulated standards, while VEG contamination was very low in both seasons. The confirmed total number of isolates was comparable between the seasons; however, results from MLST and phylogenetic clustering revealed more links between the sites and samples to MWW during the wet season. The wet season had four mixed clusters of E. coli isolates from multiple locations and samples linked to MWW, while only one mixed cluster also linking MWW to IRW was observed during the dry season. The most prevalent sequence type (ST) complex 10 and two others (40 and 155) have been associated with disease outbreaks, while other STs have links to major pathotypes. Irrigation canals are significant routes for E. coli dispersion through direct links to the urban drainage-infested river. This study clarified the genotype of E. coli in Hue city, and the numerous links between the samples and sites revealed MWW discharge as the source of E. coli contamination that was enhanced by flooding.

Molecular dynamics reveals formation path of benzonitrile and other molecules in conditions relevant to the interstellar medium

Polycyclic aromatic hydrocarbons and polycyclic aromatic nitrogen heterocycles are believed to be widespread in different areas of the interstellar medium. However, the astronomical detection of specific aromatic molecules is extremely challenging. As a result, only a few aromatic molecules have been identified, and very little is known about how they are formed in different areas of the interstellar medium. Recently, McGuire et al. [Science 359, 202–205 (2018)] detected the simple aromatic molecule benzonitrile in Taurus Molecular Cloud-1. Although benzonitrile has been observed, the molecular mechanism for its formation is still unknown. In this study, we use quantum chemistry and ab initio molecular dynamics to model ionization processes of van der Waals clusters containing cyanoacetylene and acetylene molecules. We demonstrate computationally that the clusters' ionization leads to molecular formation. For pure cyanoacetylene clusters, we observe bond formation among two and three monomer units, whereas in mixed clusters, bond formation can also occur in up to four units. We show that the large amount of energy available to the system after ionization can lead to barrier crossing and the formation of complex molecules. Our study reveals the rich chemistry that is observed upon ionization of the clusters, with a wide variety of molecules being formed. Benzonitrile is among the observed molecules, and we study the potential energy path for its formation. These results also offer insights that can guide astronomers in their search for aromatic molecules in the interstellar medium.

$$\hbox {Ag}_{m} \hbox {Rh}_n$$ clusters with $$m+n\le 55$$

Using a combination of genetic algorithms for the unbiased structure optimization and a Gupta many-body potential for the calculation of the energetic properties of a given structure, we determine the putative total-energy minima for all $$\hbox {Ag}_{m} \hbox {Rh}_n$$ Ag m Rh n clusters with a total number of atoms $$m+n$$ m + n up to 55. Subsequently, we use various descriptors to analyze the obtained structural and energetic properties. With the help of a similarity function, we show that the pure Ag and Rh clusters are structurally similar for sizes up to around 20 atoms. The same approach gives that the mixed clusters tend to possess a larger structural similarity with the pure Rh clusters than with the pure Ag clusters. However, for clusters with $$m\simeq n\ge 25$$ m ≃ n ≥ 25 , other structures dominate. The effective coordination numbers for the Ag and Rh atoms as well as the radial distributions of those atoms indicate that there is a tendency towards segregation with Rh atoms forming an inner part and the Ag atoms forming a shell. Only few clusters, all with a fairly large total number of atoms, are found to be particularly stable.

Molecular Growth upon Ionization of Van Der Waals Clusters Containing HCCH and HCN is a Pathway to Prebiotic Molecules

The growth mechanisms of organic molecules in an ionizing environment such as the interstellar medium are not completely understood. Here we examine by means of ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) computations the possibility of bond formation and molecular growth upon ionization of Van der Waals clusters of pure HCN clusters, and mixed clusters of HCN and HCCH, both of which are widespread in the interstellar medium. Ionization of van der Waals clusters can potentially lead to growth in low temperature and low-density environments. Our results show, that upon ionization of the pure HCN clusters, strongly bound stable structures are formed that contain NH bonds, and growth beyond pairwise HCN molecules is seen only in a small percentage of cases. In contrast, mixed clusters, where HCCH is preferentially ionized over HCN, can grow up to 3 or 4 units long with new carbon-carbon and carbon-nitrogen covalent bonds. Moreover, cyclic molecules formed, such as the radical cation of pyridine, which is a prebiotic molecule. The results presented here are significant as they provide a feasible pathway for molecular growth of small organic molecules containing both carbon and nitrogen in cold and relatively denser environments such as in dense molecular clouds but closer to the photo-dissociation regions, and protoplanetary disks. In the mechanism we propose, first, a neutral van der Waals cluster is formed. Once the cluster is formed it can undergo photoionization which leads to chemical reactivity without any reaction barrier.

Molecular Growth upon Ionization of Van Der Waals Clusters Containing HCCH and HCN is a Pathway to Prebiotic Molecules

The growth mechanisms of organic molecules in an ionizing environment such as the interstellar medium are not completely understood. Here we examine by means of ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) computations the possibility of bond formation and molecular growth upon ionization of Van der Waals clusters of pure HCN clusters, and mixed clusters of HCN and HCCH, both of which are widespread in the interstellar medium. Ionization of van der Waals clusters can potentially lead to growth in low temperature and low-density environments. Our results show, that upon ionization of the pure HCN clusters, strongly bound stable structures are formed that contain NH bonds, and growth beyond pairwise HCN molecules is seen only in a small percentage of cases. In contrast, mixed clusters, where HCCH is preferentially ionized over HCN, can grow up to 3 or 4 units long with new carbon-carbon and carbon-nitrogen covalent bonds. Moreover, cyclic molecules formed, such as the radical cation of pyridine, which is a prebiotic molecule. The results presented here are significant as they provide a feasible pathway for molecular growth of small organic molecules containing both carbon and nitrogen in cold and relatively denser environments such as in dense molecular clouds but closer to the photo-dissociation regions, and protoplanetary disks. In the mechanism we propose, first, a neutral van der Waals cluster is formed. Once the cluster is formed it can undergo photoionization which leads to chemical reactivity without any reaction barrier.