Binding molecular

Helmut Grubmiiller, Berthold Heymann, and Paul Tavan. Ligand binding Molecular mechanics calculation of the streptavidin-biotin rupture force. Science, 271(5251) 997-999, 1996. 

STUDY OF MAGNETIC CLUSTERS USING A TIGHT BINDING MOLECULAR DYNAMICS APPROACH... 

In the present work, we report on a new semi-empirical theoretical approach which allows us to perform spin and symmetry unconstrained total energy calculations for clusters of transition metal atoms in a co .putationally efficient way. Our approach is based on the Tight Binding Molecular Dynamics (TBMD) method. 

A. N. Andriotis, N. Lathiotakis and M. Menon, Magnetic properties of Ni and Fe clusters A tight binding molecular optimization study , Chem. Phys. Lett, (in press (1996)). ... 

KirchhofF, F., Mehl, M.J., Papanicolaou, N.I., Papaconstantopoulos, D.A. and Khan, F.S. (2001) Dynamical properties of Au from tight-binding molecular-dynamics simulations. Physical Review B -Condensed Matter, 63,195101-1-195101-7. 

We saw previously that a major factor in inhibiting the bimolecular termination reaction was the presence of sufficiently bulky ligands so that a monomeric dioxygen adduct could be isolated 135). A number of synthetic metal porphyrins 239) have been prepared recently which satisfy the above requirement, and bind molecular oxygen we shall now proceed to discuss these. 

For molecules and molecular ions, such as the cations of 8-methyl-N5-deazapterin and 8-methyl-pterin, the charge distribution (which is represented in MD simulations by a set of discrete atomic charges) will be dependent on the chosen quantum chemical model. Differences in the charge distributions of these cations may influence both the relative binding and solvation thermodynamics. Consequently, we studied the relative solvation thermodynamics of similar DHFR-binding molecular ions.30 Atomic charges... 

Tight-binding Molecular Dynamics of Shock Waves in Methane. 

Tight Binding Molecular Dynamics Study of Ni Clusters. 

Amongst metal complexes able to reversibly bind molecular dioxygen one should recall the previously mentioned trigonal-bipyramidal Co(II) complexes with bis(salicylideneimine-3-propyl)amine, [Co(R-X-saldpt)] (Chapter 5, Section 5), Scheme 3. 

Interest in metal complexes able to bind molecular dinitrogen is mainly due to a desire to understand and reproduce in the laboratory the so-called nitrogen fixation reaction. This process, which in nature is catalysed by the metalloprotein nitrogenases, reduces the inert dinitrogen molecule to the metabolically useful NH3 ... 

Cogoni, M., Uberuaga, B.P., Voter, A.F., Colombo, L. Diffusion of small self-interstitial clusters in silicon temperature-accelerated tight-binding molecular dynamics simulations. Phys. Rev. B 2005, 71(12), 121203-1-1. 

Mechanism of Action An antidote that binds molecularly to digoxin in the extracellular space. Therapeutic Effect Makes digoxin unavailable for binding at its site of action on cells in the body. 

Cobalt(II)-Schiff-base complexes with a nitrogenous base are also well known to bind molecular oxygen in an organic solvent at room temperature. 

Basdo etall00 found that the attachment of Fe(II)(TPP) to a rigid modified silica gel support produced an efficient oxygen carrier. The silica gel used contained a 3-imidazolylpropyl group bonded to the surface atoms of silicon. This then reacted with Fe(lI)(TPP)(B)2, and the axial base was removed by heating the silica gel. The five-coordinate Fe(II)(TPP) complex 41 was prepared. The open coordination site could reversibly bind molecular oxygen. It was concluded that... 

Baldwin et al102 synthesized the Fe(II) complex of capped porphyrin 43. This Fe(II) porphyrin complex was reported to bind molecular oxygen in pyridine at 25 °C, the life of the oxygenated complex being about 20 h. 

The reaction with 8 only occurred in stoichiometric ratios, hence we searched for a way to use copper-based molecular clips as true oxygenation catalysts. To this end the host molecule was altered by changing the pyrazole ligands for pyridine to obtain a model system that could mimic dicopper proteins, which can bind molecular oxygen between the copper centers in a bridging fashion [16]. After the binding of two Cu ... 

Several low-spin mono- and dicobalt (II) complexes of simple amines in solutions were reported to bind molecular oxygen reversibly (7). The best known example of the binuclear peroxy complexes is [(H3N)5-Co-02-Co(NH3)5]5+ (8). In aqueous solutions no definitive evidence for mono-... 

Recent investigations provide new insight on the structural chemistry of dissolved organic matter (DOM) in freshwater environments and the role of these structures in contaminant binding. Molecular models of DOM derived from allochthonous and autochthonous sources show that short-chain, branched, and alicyclic structures are terminated by carboxyl or methyl groups in DOM from both sources. Allochthonous DOM, however, had aromatic structures indicative of tannin and lignin residues, whereas the autochthonous DOM was characterized by aliphatic alicyclic structures indicative of lipid hydrocarbons as the source. DOM isolated from different morphoclimatic regions had minor structural differences. 

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