Ozone model for bonding of an O_2 to heme in oxyhemoglobin

Several rather different models of the Fe-O_2 bond in oxyhemoglobin have previously been proposed, none of which provide a satisfactory explanation of several properties. We propose a new model for the bonding of an O_2 to the Fe of myoglobin and hemoglobin and report ab initio generalized valence bond and configuration interaction calculations on FeO_2 that corroborate this model. Our model is based closely upon the bonding in ozone which recent theoretical studies have shown to be basically a biradical with a singlet state stabilized by a three-center four-electron pi bond. In this model, the facile formation and dissociation of the Fe-O_2 bond is easily rationalized since the O_2 always retains its triplet ground state character. The ozone model leads naturally to a large negative electric field gradient (in agreement with Mossbauer studies) and to z-polarized (perpendicular to the heme) charge transfer transitions. It also suggests that the 1.3 eV transition, present in HbO_2 and absent in HbCO, is due to a porphyrin-to-Fe transition, analogous to that of ferric hemoglobins (e.g., HbCN)

Shapes and Dynamics from the Time-Dependent Mean Field

Explaining observed properties in terms of underlying shape degrees of freedom is a well--established prism with which to understand atomic nuclei. Self--consistent mean--field models provide one tool to understand nuclear shapes, and their link to other nuclear properties and observables. We present examples of how the time--dependent extension of the mean--field approach can be used in particular to shed light on nuclear shape properties, particularly looking at the giant resonances built on deformed nuclear ground states, and at dynamics in highly-deformed fission isomers. Example calculations are shown of $^{28}$Si in the first case, and $^{240}$Pu in the latter case.Comment: 9 pages, 5 figures, to appear in proceedings of International Workshop "Shapes and Dynamics of Atomic Nuclei: Contemporary Aspects" (SDANCA-15), 8-10 October 2015, Sofia, Bulgari

Cause of the charge radius isotope shift at the \emph{N}=126 shell gap

We discuss the mechanism causing the `kink' in the charge radius isotope shift at the N=126 shell closure. The occupation of the 1$i_{11/2}$ neutron orbital is the decisive factor for reproducing the experimentally observed kink. We investigate whether this orbital is occupied or not by different Skyrme effective interactions as neutrons are added above the shell closure. Our results demonstrate that several factors can cause an appreciable occupation of the 1$i_{11/2}$ neutron orbital, including the magnitude of the spin-orbit field, and the isoscalar effective mass of the Skyrme interaction. The symmetry energy of the effective interaction has little influence upon its ability to reproduce the kink.Comment: 4 pages, 4 figures, to be submitted to proceedings of INPC 201

Lancifodilactone G : insights about an unusually stable enol

From quantum mechanics calculations we confirm that the naturally occurring enol lancifodilactone G is stable over the keto form (by 2.6 kcal/mol in water), the only known stable aliphatic enol (devoid of conjugated or bulky aromatics and lacking a 1,3-diketone structural motif known to stabilize enols). We determine architectural elements responsible for the enol stabilization and find a mechanism for keto-enol conversion in solution. In addition, we correct previously reported computational results that were performed on the misinterpreted structure demonstrating that the enol form of this natural product is more stable than previously thought

Theoretical interpretation of scanning tunneling microscopy images: Application to the molybdenum disulfide family of transition metal dichalcogenides

We have performed ab initio quantum mechanical calculations to describe scanning tunneling microscopy (STM) images of MoS_2 and MoTe_2. These results indicate that the interpretation of the STM images of these and related materials depends sensitively on experimental conditions. For example, determining whether the maximum tunneling current correlates to the top atom (S or Te) or to the second‐layer atom (Mo) requires information on the tip‐sample separation. Based on these results we discuss some STM experimental procedures which would allow assignment of the chemical identity of STM spots with greater certainty

DREIDING: A generic force field for molecular simulations

We report the parameters for a new generic force field, DREIDING, that we find useful for predicting structures and dynamics of organic, biological, and main-group inorganic molecules. The philosophy in DREIDING is to use general force constants and geometry parameters based on simple hybridization considerations rather than individual force constants and geometric parameters that depend on the particular combination of atoms involved in the bond, angle, or torsion terms. Thus all bond distances are derived from atomic radii, and there is only one force constant each for bonds, angles, and inversions and only six different values for torsional barriers. Parameters are defined for all possible combinations of atoms and new atoms can be added to the force field rather simply. This paper reports the parameters for the "nonmetallic" main-group elements (B, C, N, 0, F columns for the C, Si, Ge, and Sn rows) plus H and a few metals (Na, Ca, Zn, Fe). The accuracy of the DREIDING force field is tested by comparing with (i) 76 accurately determined crystal structures of organic compounds involving H, C, N, 0, F, P, S, CI, and Br, (ii) rotational barriers of a number of molecules, and (iii) relative conformational energies and barriers of a number of molecules. We find excellent results for these systems