Engineering topics
Bera, Partha P.
Publications and source records attributed to Bera, Partha P..
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.
The Production and Potential Detection of Hexamethylenetetramine-Methanol in Space
Numerous laboratory studies of astrophysical ice analogues have shown that their exposure to ionizing radiation leads to the production of large numbers of new, more complex compounds, many of which are of astrobiological interest. We show here that the irradiation of astrophysical ice analogues containing H2O, CH3OH, CO, and NH3 yields quantities of hexamethylenetetramine-methanol (hereafter HMT-methanol; C7N4H14O) that are easily detectible in the resulting organic residues. This molecule differs from simple HMT, which is known to be abundant in similar ice photolysis residues, by the replacement of a peripheral H atom with a CH2OH group. As with HMT, HMT-methanol is likely to be an amino acid precursor. HMT has tetrahedral (T(d)) symmetry, whereas HMT-methanol has C1 symmetry. We report the computed expected infrared spectra for HMT and HMT-methanol obtained using ab initio quantum chemistry methods and show that there is a good match between the observed and computed spectra for regular HMT. Since HMT-methanol lacks the high symmetry of HMT, it produces rotational transitions that could be observed at longer wavelengths, although establishing the exact positions of these transitions may be challenging. It is likely that HMT-methanol represents an abundant member of a larger family of functionalized HMT molecules that may be present in cold astrophysical environments.
Cation, Anion, and Radical Isomers of C4H4N: Computational Characterization and Implications for Astrophysical and Planetary Environments
Nitrogen-containing ions and molecules in the gas phase have been detected in non-Earth environments such as dark molecular clouds and more recently in the atmosphere of Saturn's moon Titan. These molecules may serve as precursors to larger heterocyclic structures that provide the foundation of complex biological molecules. On Titan, molecules of m/z 66 have been detected by the Cassini mission, and species of the empirical formula C 4 H 4 N may contribute to this signature. We have characterized seven isomers of C 4 H 4 N in anionic, neutral radical, and cationic states using density functional theory. Structures were optimized using the range-separated hybrid ωB97X-V with the cc-pVTZ and aug-cc-pVTZ basis sets. Anionic and radical C4H4N favor cyclic structures with aromatic and quasi-aromatic electron arrangements, respectively. Interestingly, ionization from the radical surface to the cation induces significant changes in structural stability, and the global minimum for positively charged isomers is CH 2 CCHCNH + , a pseudo-linear species reminiscent of cyanoallene. Select formation pathways to these structures from Titan's existing or postulated gas-phase species, reactions that are also relevant for other astrophysical environments, are discussed. By characterizing C 4 H 4 N isomers, we have identified energetically stable anionic, radical, and cationic structures that may be present in Titan's atmosphere and dark molecular clouds.
Mechanisms for the Formations of the Thymine Under Astrophysical Conditions and Implications for the Origin of Life
Nucleobases are the carriers of the genetic information in ribonucleic acid and deoxyribonucleic acid (DNA) for all life on Earth. Their presence in meteorites clearly indicates that compounds of biological importance can form via non-biological processes in extraterrestrial environments. Recent experimental studies have shown that the pyrimidine-based nucleobases uracil and cytosine can be easily formed from the ultraviolet irradiation of pyrimidine in H2O-rich ice mixtures that simulate astrophysical processes. In contrast, thymine, which is found only in DNA, is more difficult to form under the same experimental conditions, as its formation usually requires a higher photon dose. Earlier quantum chemical studies confirmed that the reaction pathways were favorable provided that several H2O molecules surrounded the reactants. However, the present quantum chemical study shows that the formation of thymine is limited because of the inefficiency of the methylation of pyrimidine and its oxidized derivatives in an H2O ice, as supported by the laboratory studies. Our results constrain the formation of thymine in astrophysical environments and thus the inventory of organic molecules delivered to the early Earth and have implications for the role of thymine and DNA in the origin of life.
Energy and Spectroscopic Characterization of the Isomers of C4H3-, C6H3-, and C6H5-
Organic and inorganic molecules, neutral and ions have been observed in the interstellar medium. A few anions of organic molecules have also been observed recently. The Cassini spacecraft in the upper atmosphere of Titan has observed anions of large organic molecules. In this project we have studied the physical and spectroscopic properties of C4H3-, C6H3-, and C6H5-. We have optimized the geometrical structures of all low-lying isomers of the anions, calculated rotational, and harmonic vibrational frequencies of the anions mentioned above using the B3LYP density functional along with the augmented correlation consistent polar valence triple zeta (aug-cc-pVTZ) basis set. We have found many low-lying isomers on the potential energy surface of these anions.
Association Mechanisms of Unsaturated C2 Hydrocarbons with Their Cations: Acetylene and Ethylene
The ion-molecule association mechanism of acetylene and ethylene with their cations is investigated by ab initio quantum chemical methods to understand the structures, association energies, and the vibrational and electronic spectra of the products. Stable puckered cyclic isomers are found as the result of first forming less stable linear and bridge isomers. The puckered cyclic complexes are calculated to be strongly bound, by 87, 35 and 56 kcal/mol for acetylene-acetylene cation, ethylene-ethylene cation and acetylene-ethylene cation, respectively. These stable complexes may be intermediates that participate in further association reactions. There are no association barriers, and no significant inter-conversion barriers, so the initial linear and bridge encounter complexes are unlikely to be observable. However, the energy gap between the bridged and cyclic puckered isomers greatly differs from complex to complex: it is 44 kcal/mol in C4H4 +, but only 6 kcal/mol in C4H8 +. The accurate CCSD(T) calculations summarized above are also compared against less computationally expensive MP2 and density functional theory (DFT) calculations for structures, relative energies, and vibrational spectra. Calculated vibrational spectra are compared against available experiments for cyclobutadiene cation. Electronic spectra are also calculated using time-dependent DFT.
A Group Increment Scheme for Infrared Absorption Intensities of Greenhouse Gases
A molecule's absorption in the atmospheric infrared (IR) window (IRW) is an indicator of its efficiency as a greenhouse gas. A model for estimating the absorption of a fluorinated molecule within the IRW was developed to assess its radiative impact. This model will be useful in comparing different hydrofluorocarbons and hydrofluoroethers contribution to global warming. The absorption of radiation by greenhouse gases, in particular hydrofluoroethers and hydrofluorocarbons, was investigated using ab initio quantum mechanical methods. Least squares regression techniques were used to create a model based on this data. The placement and number of fluorines in the molecule were found to affect the absorption in the IR window and were incorporated into the model. Several group increment models are discussed. An additive model based on one-carbon groups is found to work satisfactorily in predicting the ab initio calculated vibrational intensities.
Initiating Molecular Growth in the Interstellar Medium via Dimeric Complexes of Observed Ions and Molecules
A feasible initiation step for particle growth in the interstellar medium (ISM) is simulated by means of ab quantum chemistry methods. The systems studied are dimer ions formed by pairing nitrogen containing small molecules known to exist in the ISM with ions of unsaturated hydrocarbons or vice versa. Complexation energies, structures of ensuing complexes and electronic excitation spectra of the encounter complexes are estimated using various quantum chemistry methods. Moller-Plesset perturbation theory (MP2, Z-averaged perturbation theory (ZAP2), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)), and density functional theory (DFT) methods (B3LYP) were employed along with the correlation consistent cc-pVTZ and aug-cc-pVTZ basis sets. Two types of complexes are predicted. One type of complex has electrostatic binding with moderate (7-20 kcal per mol) binding energies, that are nonetheless significantly stronger than typical van der Waals interactions between molecules of this size. The other type of complex develops strong covalent bonds between the fragments. Cyclic isomers of the nitrogen containing complexes are produced very easily by ion-molecule reactions. Some of these complexes show intense ultraviolet visible spectra for electronic transitions with large oscillator strengths at the B3LYP, omegaB97, and equations of motion coupled cluster (EOM-CCSD) levels. The open shell nitrogen containing carbonaceous complexes especially exhibit a large oscillator strength electronic transition in the visible region of the electromagnetic spectrum.
Differences in Electronic Structure of Global Warming Molecules Lead to Different Molecular Properties. Reply to Wallington et al.
No abstract available
Identifying the Molecular Origin of Global Warming
We have investigated the physical characteristics of greenhouse gases (GHGs) to assess which properties are most important in determining the efficiency of a GHG. Chlorofluorcarbons (CFCs), hydrofluorocarbons (HFCs), perfluorocarbons (PFCs), nitrogen fluorides, and various other known atmospheric trace molecules have been included in this study. Compounds containing the halogens F or Cl have in common very polar X-F or X-Cl bonds, particularly the X-F bonds. It is shown that as more F atoms bond to the same central atom, the bond dipoles become larger as a result of the central atom becoming more positive. This leads to a linear increase in the total or integrated XF bond dipole derivatives for the molecule, which leads to a non-linear (quadratic) increase in infrared (IR) intensity. Moreover, virtually all of the X-F bond stretches occur in the atmospheric IR window as opposed to X-H stretches, which do not occur in the atmospheric window. It is concluded that molecules possessing several F atoms will always have a large radiative forcing parameter in the calculation of their global warming potential. Some of the implications for global warming and climate change are discussed.