Atomizer residue contributions

Comparison of Predicted and Measured Atomizer Solids Residue Contributions... 

In the ionic model, the energy of an inorganic solid is assumed to be the sum of all the potentials, C/y, between atoms i and j. These consists of two terms, a classical electrostatic potential, C/y,eiectrostatio determined by the charges on the atoms, and a quantum mechanical term, C/,y,Fermi> that includes the repulsion that prevents individual atoms from collapsing into each other as well as any residual contributions from covalent bonding (eqn (2.1)) ... 

The catalytic triad consists of the side chains of Asp, His, and Ser close to each other. The Ser residue is reactive and forms a covalent bond with the substrate, thereby providing a specific pathway for the reaction. His has a dual role first, it accepts a proton from Ser to facilitate formation of the covalent bond and, second, it stabilizes the negatively charged transition state. The proton is subsequently transferred to the N atom of the leaving group. Mutations of either of these two residues decrease the catalytic rate by a factor of 10 because they abolish the specific reaction pathway. Asp, by stabilizing the positive charge of His, contributes a rate enhancement of 10. ... 

Carbon has six electrons around the atomic core as shown in Fig. 2. Among them two electrons are in the K-shell being the closest position from the centre of atom, and the residual four electrons in the L-shell. TTie former is the Is state and the latter are divided into two states, 2s and 2p. The chemical bonding between neighbouring carbon atoms is undertaken by the L-shell electrons. Three types of chemical bonds in carbon are single bond contributed from one 2s electron and three 2p electrons to be cited as sp bonding, double bond as sp and triple bond as sp from the hybridised atomic-orbital model. 

With data averaged in point group m, the first refinements were carried out to estimate the atomic coordinates and anisotropic thermal motion parameters IP s. We have started with the atomic coordinates and equivalent isotropic thermal parameters of Joswig et al. [14] determined by neutron diffraction at room temperature. The high order X-ray data (0.9 < s < 1.28A-1) were used in this case in order not to alter these parameters by the valence electron density contributing to low order structure factors. Hydrogen atoms of the water molecules were refined isotropically with all data and the distance O-H were kept fixed at 0.95 A until the end of the multipolar refinement. The inspection of the residual Fourier maps has revealed anharmonic thermal motion features around the Ca2+ cation. Therefore, the coefficients up to order 6 of the Gram-Charlier expansion [15] were refined for the calcium cation in the scolecite. 

However, the active site is only a conceptual tool and the assignment of the active-site atoms is more or less arbitrary. It is not possible to know beforehand which residues and protein interactions that will turn out to be important for the studied reaction. Hybrid QM/MM methods have been used to extend the active site only models by incorporating larger parts of the protein matrix in studies of enzymatic reactions [19-22], The problem to select active-site residues appears both for active-site and QM/MM models, but in the latter, explicit effects of the surrounding protein (i.e. atoms outside the active-site selection) can at least be approximately evaluated. As this and several other contributions in this volume show, this is in many cases highly desirable. 

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