Ionization energy and electronic structure of polycytidine

Future of computational molecular spectroscopy-from supporting interpretation to leading the innovation

Molecular spectroscopy measures transitions between discrete molecular energies which follow quantum mechanics. Structural information of a molecule is encoded in the spectra, which can be only decoded using quantum mechanics and therefore computational molecular spectroscopy becomes essential. In this review perspective, the role evolution of computational molecular spectroscopy has been discussed with several joint theory and experiment spectroscopic studies in the past decades, which includes rotational (microwave), vibrational and electronic spectroscopy (valence and core) of molecules. With the development in high resolution and computerized synchrotron sourced spectroscopy, spectral measurements and computational molecular spectroscopy need to be integrated for materials development. Contemporary computational molecular spectroscopy is, therefore, more than merely supporting interpretation but leading the innovation. Future development of molecular spectroscopy lies to identify the niche to integrate experimental and computational molecular spectroscopy. It also requires to engineer molecular spectroscopic databases that function according to the universal approaches of computing, such as those in a Turing machine, to be realized in a chemical and/or spectroscopic programable manner (digital twinning research) in the future.

Band Edge Energetics of Heterostructured Nanorods: Photoemission Spectroscopy and Waveguide Spectroelectrochemistry of Au-Tipped CdSe Nanorod Monolayers

Conduction and valence band energies (ECB, EVB) for CdSe nanorods (NRs) functionalized with Au nanoparticle (NP) tips are reported here, referenced to the vacuum scale. We use (a) UV photoemission spectroscopy (UPS) to measure EVB for NR films, utilizing advanced approaches to secondary electron background correction, satellite removal to enhance spectral contrast, and correction for shifts in local vacuum levels; and (b) waveguide-based spectroelectrochemistry to measure ECB from onset potentials for electron injection into NR films tethered to ITO. For untipped CdSe NRs, both approaches show EVB = 5.9-6.1 eV and ECB = 4.1-4.3 eV. Addition of Au tips alters the NR band edge energies and introduces midgap states, in ways that are predicted to influence the efficiency of these nanomaterials as photoelectrocatalysts. UPS results show that Au tipping shifts EVB closer to vacuum by up to 0.4 eV, shifts the apparent Fermi energy toward the middle of the band gap, and introduces additional states above EVB. Spectroelectrochemical results confirm these trends: Au tipping shifts ECB closer to vacuum, by 0.4-0.6 eV, and introduces midgap states below ECB, which are assigned as metal-semiconductor interface (MSI) states. Characterization of these band edge energies and understanding the origins of MSI states is needed to design energy conversion systems with proper band alignment between the light absorbing NR, the NP catalyst, and solution electron donors and acceptors. The complementary characterization protocols presented here should be applicable to a wide variety of thin films of heterogeneous photoactive nanomaterials, aiding in the identification of the most promising material combinations for photoelectrochemical energy conversion.

Unsaturated didehydrodeoxycytidine drugs. 1. Impact of C=C positions in the sugar ring

The chemical names of a pair of recently synthesized antitumor drugs are given in the present study as 1',2'-didehydro-3',4'-deoxycytidine and 3',4'-didehydro-2',4'-deoxycytidine. The order of stabilities, geometries, and ionization potentials of the unsaturated sugar-modified cytidine derivatives is investigated quantum mechanically. Our density functional theory calculations based on the B3LYP/6-311++G** model reveal that 3',4'-didehydro-2',4'-deoxycytidine (SD-C2) is slightly more stable than its isomer, 1',2'-didehydro-3',4'-deoxycytidine, by an energy of 5.28 kJ x mol(-1) in isolation. The isomers structurally differ by only the C=C location in the sugar ring. However, the compounds exhibit an unusual orientation with a less puckered sugar ring; that is, 3',4'-didehydro-2',4'-deoxycytidine is determined to be a beta-nucleoside, which is a C1'-endo, north conformer with an anticlinal sugar ring, whereas 1',2'-didehydro-3',4'-deoxycytidine is neither an alpha-nucleoside nor a beta-nucleoside but is a C4'-endo, south conformer with an antiperiplanar sugar ring. The present study further indicates that the C=C double bond location imposes significant effects on their ionization potentials (IPs) and other important molecular properties such as molecular electrostatic potential (MEP). In addition, inner shell binding energy spectral variations with respect to the C=C bond exhibit more site dependence. The valence shell binding energy spectral changes are, on the other hand, significant and delocalized. The latter indicates that such changes in valence space are not isolated effects but are within the entire nucleoside. Finally, the present study suggests that the nearly 0.6 eV difference in the first ionization potentials (highest occupied molecular orbital) of the isomers is sufficiently large to identify them by further spectroscopic measures.