Saumitra Saha

Coexistence of 1,3-butadiene conformers in ionization energies and Dyson orbitals

The minimum-energy structures on the torsional potential-energy surface of 1,3-butadiene have been studied quantum mechanically using a range of models including ab initio Hartree-Fock and second-order Møller-Plesset theories, outer valence Greens function, and density-functional theory with a hybrid functional and statistical average orbital potential model in order to understand the binding-energy (ionization energy) spectra and orbital cross sections observed by experiments. The unique full geometry optimization process locates the s-trans-1,3-butadiene as the global minimum structure and the s-gauche-1,3-butadiene as the local minimum structure. The latter possesses the dihedral angle of the central carbon bond of 32.81 degrees in agreement with the range of 30 degrees-41 degrees obtained by other theoretical models. Ionization energies in the outer valence space of the conformer pair have been obtained using Hartree-Fock, outer valence Greens function, and density-functional (statistical average orbital potentials) models, respectively. The Hartree-Fock results indicate that electron correlation (and orbital relaxation) effects become more significant towards the inner shell. The spectroscopic pole strengths calculated in the Greens function model are in the range of 0.85-0.91, suggesting that the independent particle picture is a good approximation in the present study. The binding energies from the density-functional (statisticaly averaged orbital potential) model are in good agreement with photoelectron spectroscopy, and the simulated Dyson orbitals in momentum space approximated by the density-functional orbitals using plane-wave impulse approximation agree well with those from experimental electron momentum spectroscopy. The coexistence of the conformer pair under the experimental conditions is supported by the approximated experimental binding-energy spectra due to the split conformer orbital energies, as well as the orbital momentum distributions of the mixed conformer pair observed in the orbital cross sections of electron momentum spectroscopy.

The attachment of amino fragment to purine: inner-shell structures and spectra

The impact of the amino fragment (-NH(2)) attachment on the inner-shell structures and spectra of unsubstituted purine and the purine ring of adenine are studied. Density functional theory calculations, using the LB94/TZ2P//B3LYP/TZVP model, reveal significant site-dependent electronic structural changes in the inner shell of the species. A condensed Fukui function indicates that all of the N and C sites, except for N((1)) and C((5)), demonstrate significant electrophilic reactivity (f(-) > 0.5 in |e|) in the unsubstituted purine. Once the amino fragment binds to the C((6)) position of purine to form adenine, the electrophilic reactivity of these N and C sites is greatly reduced. As expected, the C((6)) position experiences substantial changes in energy and charge transfer, owing to the formation of the C-NH(2) bond in adenine. The present study reveals that the N1s spectra of adenine inherit the N1s spectra of the unsubstituted purine, whereas the C1s spectra experience significant changes although purine and adenine have geometrically similar carbon frames. The findings also indicate that the attachment of the NH(2) fragment to purine exhibits deeply rooted influences to the inner-shell structures of DNA/RNA bases. The present study suggests that some fragment-based methods may not be applicable to spectral analyses in the inner shell.

Intramolecular proton transfer in adenine imino tautomers

The electronic structural impact on intramolecular proton transfer in the cis- and trans-imino N7 and N9 tautomers of adenine (A) has been studied quantum mechanically, using density functional theory (B3LYP/TZVP, SAOP/TZ2P, LB94/TZ2P) and Green function (OVGF/TZVP) models. It is found that proton transfer does not significantly change isotropic properties but has profound impact on electron distributions of the species through anisotropic properties. The relative energies with respect to the canonical A tautomer (amino-9H), ΔE, for imino 7Hcis, imino 7Htrans, imino 9Hcis and imino 9Htrans are calculated as 16.15, 16.43, 18.46 and 13.80 kcal mol− 1 (B3LYP/TZVP model) and some minor changes in perimeters of the purine ring is also observed. The Hirshfeld atomic charges indicate that whether a proton attached to N(7) or N(9) causes a significant local charge redistribution. However, these charges are insensitive to cis–trans proton transfer. Condensed Fukui function reveals N(10) and C(8) as the most electrophilic reactive site among N- and C-atom sites, respectively. We also found that proton transfer significantly alters in-plane σ orbitals, rather than out of plane π orbitals including the frontier orbital 6a″. Moreover, orbital based responses to various proton transfers are presented: the orbital 29a′ (HOMO-1) is a signature orbital differentiating all the four tautomers. Orbital 27a′ is a site (N(7) and N(9)) sensitive orbital, whereas orbital 22a′ is only sensitive to proton orientation on the imino group = N–H.

Calculation of Gamma Spectra for Positron Annihilation on Molecules

Calculations of gamma spectra for positron annihilation for a selection of molecules, including methane and its fluoro-substitutes, ethane, propane, butane and benzene are presented. The contribution to the -spectra from individual molecular orbitals is obtained from electron momentum distributions calculated using the density functional theory (DFT) based B3LYP/TZVP model. For positrons thermalised to room temperature, the calculation, in its simplest form, effectively treats the positron as a plane wave and gives positron annihilation  spectra linewidths that are broader (30–40%) than experiment, although the main chemical trends are reproduced. The main physical reason for this is the neglect of positron repulsion from the nuclei. We show that this effect can be incorporated through momentum-dependent correction factors, determined from positron-atom calculations, e.g., many-body perturbation theory. Inclusion of these factors in the calculation gives linewidths that are in improved agreement with experiment.

An experimental and theoretical study into the valence electronic structure of bicyclo[2.2.1]hepta-2,5-dione

The results from an electron momentum spectroscopy (EMS) study of the outer valence electronic region of bicyclo[2.2.1]hepta-2,5-dione (C7H8O2 )a re reported for the first time. The measured binding energy spectra are presented for the azimuthal angles 0 ◦ ,1 0 ◦ and 0 ◦ +1 0 ◦ , respectively, and are compared to new He(I) photoelectron spectroscopy results, which are measured as a part of this work. These experimental data are compared further with results from theoretical computations, using various methods including Hartree–Fock, density functional and an outer valence Green’s function theory. Measured orbital momentum distributions are compared on an orbital by orbital basis against those obtained by calculations which employ the plane-wave impulse approximation. These calculations use orbital wavefunctions obtained from Hartree–Fock and density functional theory with a couple of generalized gradient approximation exchange correlation (XC) functionals and the DGauss triple zeta valence polarization basis set. Agreement between the measured and calculated momentum distributions was found to be only fair. Nonetheless, the orbital momentum distributions of the molecule still provide an orbital based assessment of the XC functionals of the density functional theory employed, and an understanding of the chemical bonding mechanisms within the species. Finally, the spectroscopic strengths calculated using outer valence Green’s function theory are compared against those derived from our EMS measurements. (Some figures in this article are in colour only in the electronic version)