Showing papers by "Qadir K. Timerghazin published in 2008"

Structure and stability of HSNO, the simplest S-nitrosothiol

Abstract: High-level ab initio calculations employing the CCSD and CCSD(T) coupled cluster methods with a series of systematically convergent correlation-consistent basis sets have been performed to obtain accurate molecular geometry and energetic properties of the simplest S-nitrosothiol (RSNO), HSNO. The properties of the S–N bond, which are central to the physiological role of RSNOs in the storage and transport of nitric oxide, are highlighted. Following corrections for quadruple excitations, core-valence correlation and relativistic effects, the CCSD(T) method extrapolated to the complete basis set (CBS) limit yielded values of 1.85 A and 29.2 kcal mol−1 for the S–N bond length and the dissociation energy for homolysis of the S–N bond, respectively, in the energetically most stable trans-conformer of HSNO. The properties of the S–N bond strongly depend on the basis-set size and the inclusion of triple, and, to a lesser extent, quadruple excitations in the coupled cluster expansion. CCSD calculations systematically underestimate the S–N equilibrium distance and S–N bond dissociation energy by 0.05–0.07 A and 6–7 kcal mol−1, respectively. The significant differences between the CCSD(T) and CCSD descriptions of HSNO, the high values of the coupled clusterT1 (0.027) and D1 (0.076) diagnostics, as well as the instability of the reference restricted Hartree–Fock (RHF) wavefunction indicate that the electronic structure of the SNO group possesses multireference character. Previous quantum-chemical data on RSNOs are reexamined based on the new insight into the SNO electronic structure obtained from the present high-level calculations on HSNO.

Electronic Structure of the Acetonitrile and Acetonitrile Dimer Anions: A Topological Investigation†

Abstract: Acetonitrile molecules are known for their intriguing ability to accommodate an excess electron in either a diffuse dipole-bound orbital, away from the valence electrons, or in its valence orbitals, depending on the environment. In this work, we report a computational investigation of the monomer and dimer acetonitrile anions, with the main goal of gaining further insight into the unusual electronic structure of these species. To this end, the topology of the electron density distribution has been examined in detail with the quantum theory of atoms in molecules (AIM). The excess electron is found to affect the topology of the electron density very differently for two dipole-bound-electron isomers of the acetonitrile dimer anion: for the head-to-tail isomer, the electron density simply decays away from the atomic nuclei, and the presence of the excess electron only manifests itself in the Laplacian of the electron density as a very diffuse region of “dipole-bound” charge concentration; in contrast, for th...

Computational prediction of absorbance maxima for a structurally diverse series of engineered green fluorescent protein chromophores.

Abstract: By virtue of its self-sufficiency to form a visible wavelength chromophore within the confines of its tertiary structure, the Aequorea victoria green fluorescent protein (GFP) is single-handedly responsible for the ever-growing popularity of fluorescence imaging of recombinant fusion proteins in biological research. Engineered variants of GFP with altered excitation or emission wavelength maxima have helped to expand the range of applications of GFP. The engineering of the GFP variants is usually done empirically by genetic modifications of the chromophore structure and/or its environment in order to find variants with new photophysical properties. The process of identifying improved variants could be greatly facilitated if augmented or guided by computational studies of the chromophore ground and excited-state properties and dynamics. In pursuit of this goal, we now report a thorough investigation of computational methods for prediction of the absorbance maxima for an experimentally validated series of e...