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)

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

Early Onset of Kinetic Roughening due to a Finite Step Width in Hematin Crystallization

The structure of the interface of a growing crystal with its nutrient phase largely determines the growth dynamics. We demonstrate that hematin crystals, crucial for the survival of malaria parasites, transition from faceted to rough growth interfaces at increasing thermodynamic supersaturation Δμ. Contrary to theoretical predictions and previous observations, this transition occurs at moderate values of Δμ. Moreover, surface roughness varies nonmonotonically with Δμ, and the rate constant for rough growth is slower than that resulting from nucleation and spreading of layers. We attribute these unexpected behaviors to the dynamics of step growth dominated by surface diffusion and the loss of identity of nuclei separated by less than the step width w. We put forth a general criterion for the onset of kinetic roughening using w as a critical length scale.National Institutes of Health (U.S.) (Grant 1R21AI126215-01)National Science Foundation (U.S.) (Grant DMR-1710354)United States. National Aeronautics and Space Administration (Grant NNX14AD68G)United States. National Aeronautics and Space Administration (Grant NNX14AE79G)Robert A. Welch Foundation (Grant E-1794