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

2021 ◽  
Vol 118 (19) ◽  
pp. e2101371118
Author(s):  
Jeeno Jose ◽  
Alon Zamir ◽  
Tamar Stein
Keyword(s):  
Molecular Dynamics ◽  
Interstellar Medium ◽  
Bond Formation ◽  
Ab Initio Molecular Dynamics ◽  
Complex Molecules ◽  
Van Der Waals Clusters ◽  
Aromatic Molecules ◽  
Polycyclic Aromatic ◽  
The Rich ◽  
Mixed Clusters

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.

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

2020 ◽  
Author(s):  
Tamar Stein ◽  
Partha P. Bera ◽  
Timothy J. Lee ◽  
Martin Head-Gordon
Keyword(s):  
Interstellar Medium ◽  
Density Functional ◽  
Organic Molecules ◽  
Chemical Reactivity ◽  
Van Der Waals ◽  
Ab Initio Molecular Dynamics ◽  
Covalent Bonds ◽  
Van Der Waals Clusters ◽  
Prebiotic Molecule ◽  
Mixed Clusters

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.

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

2020 ◽  
Author(s):  
Tamar Stein ◽  
Partha P. Bera ◽  
Timothy J. Lee ◽  
Martin Head-Gordon
Keyword(s):  
Interstellar Medium ◽  
Density Functional ◽  
Organic Molecules ◽  
Chemical Reactivity ◽  
Van Der Waals ◽  
Ab Initio Molecular Dynamics ◽  
Covalent Bonds ◽  
Van Der Waals Clusters ◽  
Prebiotic Molecule ◽  
Mixed Clusters

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.

STRUCTURE AND STABILITY OF ENDOHEDRAL Cn@C60

2010 ◽  
Vol 24 (12) ◽  
pp. 1255-1266 ◽  
Author(s):  
REENA DEVI ◽  
RANJAN KUMAR
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Free Space ◽  
Chemical Reactivity ◽  
Bond Formation ◽  
Carbon Cluster ◽  
Ab Initio Molecular Dynamics ◽  
Carbon Clusters ◽  
The Stability ◽  
Dynamics Simulations

We report ab initio molecular dynamics simulations of carbon clusters in free space and inside C 60 using SIESTA. We have studied the stability and geometries of small carbon clusters consisting of 2–12 carbon atoms inside the C 60 molecule and in free space by optimizing the atomic geometries. We have found that the C – C bond length is in agreement with the 1.40 and 1.45 values reported earlier. We find that the clusters inside the C 60 are more stable than clusters in free space. Binding energy per carbon atom initially increases with number of carbon atoms in the cluster and then decreases after maximizing for the 9-atom cluster. For more than 9 carbon atoms in the cluster inside C 60, C atoms of the cluster start forming bond with the C 60 cage and the C 60 structure gets distorted. We have done calculations for charge transfer and chemical reactivity. The calculations of ionization potential and electron affinity show that clusters in free space are less reactive compared with C n@ C 60. Charge transfer calculations show that the bond formation of C atoms with the C 60 cage is accompanied with a transfer of charge from carbon cluster to C 60.

scholarly journals Detection of the aromatic molecule benzonitrile (c-C6H5CN) in the interstellar medium

Science ◽  
2018 ◽  
Vol 359 (6372) ◽  
pp. 202-205 ◽  
Author(s):  
Brett A. McGuire ◽  
Andrew M. Burkhardt ◽  
Sergei Kalenskii ◽  
Christopher N. Shingledecker ◽  
Anthony J. Remijan ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Polycyclic Aromatic Hydrocarbon ◽  
Interstellar Medium ◽  
Aromatic Hydrocarbon ◽  
Aromatic Hydrocarbons ◽  
Nitrogen Heterocycles ◽  
Aromatic Molecules ◽  
Polycyclic Aromatic ◽  
Hydrocarbon Formation ◽  
The Universe

Polycyclic aromatic hydrocarbons and polycyclic aromatic nitrogen heterocycles are thought to be widespread throughout the universe, because these classes of molecules are probably responsible for the unidentified infrared bands, a set of emission features seen in numerous Galactic and extragalactic sources. Despite their expected ubiquity, astronomical identification of specific aromatic molecules has proven elusive. We present the discovery of benzonitrile (c-C6H5CN), one of the simplest nitrogen-bearing aromatic molecules, in the interstellar medium. We observed hyperfine-resolved transitions of benzonitrile in emission from the molecular cloud TMC-1. Simple aromatic molecules such as benzonitrile may be precursors for polycyclic aromatic hydrocarbon formation, providing a chemical link to the carriers of the unidentified infrared bands.

scholarly journals Chemical Properties of Interstellar Polycyclic Aromatic Molecules

1987 ◽  
Vol 120 ◽  
pp. 545-546 ◽  
Author(s):  
Alain Omont
Keyword(s):  
Interstellar Medium ◽  
Chemical Properties ◽  
Physical And Chemical Properties ◽  
Substantial Evidence ◽  
Interstellar Molecules ◽  
Aromatic Molecules ◽  
Polycyclic Aromatic ◽  
Physical And Chemical ◽  
And Chemical Properties

There is substantial evidence of the presence of polycyclic aromatic molecules, mainly hydrocarbons (PAH's) in the interstellar medium (Léger and Puget, 1984, Allamandola et al. 1985, Léger and d'Hendecourt in these proceedings). They should contain typically NC = 20–100 carbon atoms, and they can contain perhaps 1–10% of the total interstellar carbon. I have recently discussed in detail their physical and chemical properties (Omont, 1986), which should be intermediate between that of conventional interstellar molecules and grains.

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Liqun Cao ◽  
Jinzhe Zeng ◽  
Mingyuan Xu ◽  
Chih-Hao Chin ◽  
Tong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Large Scale ◽  
Methane Combustion ◽  
Combustion Method ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Computational Time ◽  
Combustion Mechanism ◽  
Daily Lives

Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system.

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