Partha P. Bera

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. Chlorofluorocarbons (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 X-F bond dipole derivatives for the molecule, which leads to a nonlinear (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.

The deprotonated guanine-cytosine base pair

Awareness of the harmful effects of radiation has increased interest in finding the mechanisms of DNA damage. Radical and anion formation among the DNA base pairs are thought to be important steps in such damage [Collins, G. P. (2003) Sci. Am. 289 (3), 26–27]. Energetic properties and optimized geometries of 10 radicals and their respective anions derived through hydrogen abstraction from the Watson-Crick guanine–cytosine (G-C) base pair have been studied using reliable theoretical methods. The most favorable deprotonated structure (dissociation energy 42 kcal·mol−1, vertical detachment energy 3.79 eV) ejects the proton analogous to the cytosine glycosidic bond in DNA. This structure is a surprisingly large 12 kcal·mol−1 lower in energy than any of the other nine deprotonated G-C structures. This system retains the qualitative G-C structure but with the H···O2 distance dramatically reduced from 1.88 to 1.58 Å, an extremely short hydrogen bond. The most interesting deprotonated G-C structure is a “reverse wobble” incorporating two N-H···N hydrogen bonds. Three different types of relaxation energies (4.3–54 kcal·mol−1) are defined and reported to evaluate the energy released via different mechanisms for the preparation of the deprotonated species. Relative energies, adiabatic electron affinities (ranging from 1.93 to 3.65 eV), and pairing energies are determined to discern which radical will most alter the G-C properties. The most stable deprotonated base pair corresponds to the radical with the largest adiabatic electron affinity, 3.65 eV. This value is an enormous increase over the electron affinity (0.60 eV) of the closed-shell G-C base pair.

Thymine and Other Prebiotic Molecules Produced from the Ultraviolet Photo-Irradiation of Pyrimidine in Simple Astrophysical Ice Analogs

The informational subunits of RNA or DNA consist of substituted N-heterocyclic compounds that fall into two groups: those based on purine (C₅H₄N₄) (adenine and guanine) and those based on pyrimidine (C₄H₄N₂) (uracil, cytosine, and thymine). Although not yet detected in the interstellar medium, N-heterocycles, including the nucleobase uracil, have been reported in carbonaceous chondrites. Recent laboratory experiments and ab initio calculations have shown that the irradiation of pyrimidine in ices containing H₂O, NH₃, or both leads to the abiotic production of substituted pyrimidines, including the nucleobases uracil and cytosine. In this work, we studied the methylation and oxidation of pyrimidine in CH₃OH:pyrimidine, H₂O:CH₃OH:pyrimidine, CH₄:pyrimidine, and H₂O:CH₄:pyrimidine ices irradiated with UV photons under astrophysically relevant conditions. The nucleobase thymine was detected in the residues from some of the mixtures. Our results suggest that the abundance of abiotic thymine produced by ice photolysis and delivered to the early Earth may have been significantly lower than that of uracil. Insofar as the delivery of extraterrestrial molecules was important for early biological chemistry on early Earth, these results suggest that there was more uracil than thymine available for emergent life, a scenario consistent with the RNA world hypothesis.

Design strategies to minimize the radiative efficiency of global warming molecules

A strategy is devised to screen molecules based on their radiative efficiency. The methodology should be useful as one additional constraint when determining the best molecule to use for an industrial application. The strategy is based on the results of a recent study where we examined molecular properties of global warming molecules using ab initio electronic structure methods to determine which fundamental molecular properties are important in assessing the radiative efficiency of a molecule. Six classes of perfluorinated compounds are investigated. For similar numbers of fluorine atoms, their absorption of radiation in the IR window decreases according to perfluoroethers > perfluorothioethers ≈ sulfur/carbon compounds > perfluorocarbons > perfluoroolefins > carbon/nitrogen compounds. Perfluoroethers and hydrofluorethers are shown to possess a large absorption in the IR window due to (i) the C─O bonds are very polar, (ii) the C-O stretches fall within the IR window and have large IR intensity due to their polarity, and (iii) the IR intensity for C-F stretches in which the fluorine atom is bonded to the carbon that is bonded to the oxygen atom is enhanced due to a larger C─F bond polarity. Lengthening the carbon chain leads to a larger overall absorption in the IR window, though the IR intensity per bond is smaller. Finally, for a class of partially fluorinated compounds with a set number of electronegative atoms, the overall absorption in the IR window can vary significantly, as much as a factor of 2, depending on how the fluorine atoms are distributed within the molecule.

Are isomers of the vinyl cyanide ion missing links for interstellar pyrimidine formation

In the interstellar medium (ISM) there are many regions where the formation of molecules is kinetically driven rather than thermochemically, which can lead to the formation of many isomers even though some may be fairly higher in energy relative to the molecular global minimum. Recent laboratory experiments where noble gas cations are reacted with pyrimidine favored the formation of C(3)H(3)N(+), but the molecular structure(s) of this fragment was not determined. Microscopic reversibility means that pyrimidine could form under interstellar conditions should the required C(3)H(3)N(+) reactant be detected in the ISM. Hence C(3)H(3)N(+) could be a strong candidate for involvement in the formation of heterocyclic biomolecules such as pyrimidine in the ISM. In this study, we have investigated the low energy isomers of the acrylonitrile ion (C(3)H(3)N(+)) using density functional theory as well as high levels of ab initio theory, namely, the singles and doubles coupled-cluster theory that includes a perturbational correction for connected triple excitations, denoted as CCSD(T). An automated stochastic search procedure, Kick, has been employed to find isomers on the ground state doublet potential energy surface. Several new structures, along with all the previously reported minima, have been found. The global minimum H(2)CCCNH(+) is energetically much lower than either H(2)CC(H)CN(+), the acrylonitrile ion, or HCC(H)NCH(+), the most likely intermediate of the reaction between HCCH(+) and HCN. These isomers are connected to the global minimum via several transition states and intermediates. The results indicate that not only the global minimum but also several higher energy isomers of the C(3)H(3)N(+) ion could be important in interstellar pyrimidine formation. The isomeric molecules have the necessary CCNC backbone needed for the reaction with HCN to form the cyclic pyrimidine framework. The structural and rotational parameters of all the isomers studied in this work have been predicted at the CCSD(T) level of theory with the anticipation that it will expedite their laboratory as well as astronomical identification.

Photochemistry and Photophysics of n-Butanal, 3-Methylbutanal, and 3,3-Dimethylbutanal: Experimental and Theoretical Study

Dilute mixtures of n-butanal, 3-methylbutanal, and 3,3-dimethylbutanal in synthetic air, different N(2)/O(2) mixtures, and pure nitrogen (up to 100 ppm) were photolyzed with fluorescent UV lamps (275-380 nm) at 298 K. The main photooxidation products were ethene (n-butanal), propene (3-methylbutanal) or i-butene (3,3-dimethylbutanal), CO, vinylalcohol, and ethanal. The photolysis rates and the absolute quantum yields were found to be dependent on the total pressure of synthetic air but not of nitrogen. At 100 Torr, the total quantum yield Φ(100) = 0.45 ± 0.01 and 0.49 ± 0.07, whereas at 700 Torr, Φ(700) = 0.31 ± 0.01 and 0.36 ± 0.03 for 3-methylbutanal and 3,3-dimethybutanal, respectively. Quantum yield values for n-butanal were reported earlier by Tadić et al. (J. Photochem. Photobiol. A2001143, 169-179) to be Φ(100) = 0.48 ± 0.02 and Φ(700) = 0.32 ± 0.01. Two decomposition channels were identified: the radical channel RCHO → R + HCO (Norrish type I) and the molecular channel CH(3)CH(CH(3))CH(2)CHO → CH(2)CHCH(3) + CH(2)═CHOH or CH(3)C(CH(3))(2)CH(2)CHO → CHC(CH(3))CH(3) + CH(2)═CHOH, (Norrish type II) having the absolute quantum yields of 0.123 and 0.119 for 3-methybutanal and 0.071 and 0.199 for 3,3-dimethylbutanal at 700 Torr of synthetic air. The product ethenol CH(2)═CHOH tautomerizes to ethanal. We have performed ab initio and density functional quantum (DFT) chemical computations of both type I and type II processes starting from the singlet and triplet excited states. We conclude that the Norrish type I dissociation produces radicals from both singlet and triplet excited states, while Norrish type II dissociation is a two-step process starting from the triplet excited state, but is a concerted process from the singlet state.

Characterization of the Azirinyl Cation and Its Isomers

The azirinyl cation (C2H2N(+)) and its geometrical isomers could be present in the interstellar medium. The C2H2N(+) isomers are, however, difficult to identify in interstellar chemistry because of the lack of high-resolution spectroscopic data from laboratory experiments. Ab initio quantum chemical methods were used to characterize the structures, relative energies, and spectroscopic and physical properties of the low energy isomers of the azirinyl cation. We have employed second-order Møller-Plesset perturbation theory (MP2), second-order Z-averaged perturbation theory (ZAPT2), and coupled cluster theory with singles and doubles with perturbative triples CCSD(T) methods along with large correlation consistent basis sets such as cc-pVTZ, cc-pCVTZ, cc-pVQZ, cc-pCVQZ, and cc-pV5Z. Harmonic vibrational frequencies, dipole moments, rotational constants, and proton affinities for the lowest energy isomers were calculated using the CCSD(T) method. Azirinyl cation, a cyclic isomer, is lowest in energy at all levels of theory employed. Azirinyl cation is followed by the cyanomethyl cation (H2CCN)(+), isocyanomethyl cation (H2CNC)(+), and a quasilinear HCCNH(+) cation, which are 13.8, 17.3, and 21.5 kcal mol(-1) above the cyclic isomer, respectively, at the CCSD(T)/cc-pV5Z level of theory. The lowest three isomers all have C2v symmetry and (1)A1 ground electronic states. The quasilinear HCCNH(+) cation has a Cs symmetry planar structure, and a (3)A″ electronic ground state, unlike what some previous work suggested.

Formation and stability of C6H3+isomers

The stability of the five main isomers of C6H3(+) was investigated using quantum chemical calculations. The cyclic isomers are stabilized by two complementary aromatic effects, first 6-electron π aromaticity, and second a more unusual three-center two-electron σ aromaticity. Two cyclic isomers sit at the bottom of the potential energy surface with energies very close to each other, with a third cyclic isomer slightly higher. The reaction barriers for the interconversion of these isomers, as well as to convert to low-energy linear isomers, are found to be very high with transition states that break both the π and the σ aromaticities. Finally, possibilities for forming the cyclic isomers via association reactions are discussed.

Relative energies, structures, vibrational frequencies, and electronic spectra of pyrylium cation, an oxygen-containing carbocyclic ring isoelectronic with benzene, and its isomers.

We have studied relative energies, structures, rotational, vibrational, and electronic spectra of the pyrylium cation, an oxygen-containing six-membered carbocyclic ring, and its six isomers, using ab initio quantum chemical methods. Isoelectronic with benzene, the pyrylium cation has a benzenoid structure and is the global minimum on the singlet potential energy surface of C5H5O(+). The second lowest energy isomer, the furfuryl cation, has a five membered backbone akin to a sugar, and is only 16 kcal mol(-1) above the global minimum computed using coupled cluster theory with singles, doubles, and perturbative triple excitations (CCSD(T)) with the correlation consistent cc-pVTZ basis set. Other isomers are 25, 26, 37, 60, and 65 kcal mol(-1) above the global minimum, respectively, at the same level of theory. Lower level methods such as density functional theory (B3LYP) and second order Møller-Plesset perturbation theory performed well when tested against the CCSD(T) results. The pyrylium and furfuryl cations, although separated by only 16 kcal mol(-1), are not easily interconverted, as multiple bonds must be broken and formed, and the existence of more than one transition state is likely. Additionally, we have also investigated the asymptotes for the barrierless ion-molecule association of molecules known to exist in the interstellar medium that may lead to formation of the pyrylium cation.

Reply to Wallington et al.: Differences in electronic structure of global warming molecules lead to different molecular properties.

The comment by Wallington et al. (1) is not germane to our studies (2, 3), contributes to further confusion on the use of the radiative forcing (RF) and radiative efficiency (RE) terms, and misses a fundamental point: differences in electronic structure lead to different molecular properties.