Complex molecular modeling

The formation of dimeric products is unique for the case of boron, because analogous complexes with other elements are all monomeric [95]. This can be attributed to the small covalent radius of the boron atom and its tetrahedral geometry in four-coordinate boron complexes. Molecular modeling shows that bipyramidal-trigonal and octahedral coordination geometries are more favorable for the formation of monomeric complexes with these ligands. 

These conclusions are not altered in going over to more complex molecular models, since the utilization of the laws of conservation of momentum are not dependent on the nature of the molecular forces. 

Complexity - molecular models are complex with respect to the depth and amount of information they represent. This will be particularly problematic for novices, whereas experts can easily decode the infonnation in a model and understand interrelations between different types of representations. 

In the fully loaded polymer, the diameter of the individual complexes ( 14 Al is significandy greater than the unit repeat distance along the polymeric backbone (5-6 A). Because of the relatively large excluded volume of the complexes, molecular modeling studies (which treat the complexes as di-cationic spheres of diameter 14 A) show that the polymers adopt extended stmctures. In energy minimized structures the intemuclear separation is 21 A and the average separation distance between the peripheries of adjacent complexes is 7 A. ... 

Conformational free energy simulations are being widely used in modeling of complex molecular systems [1]. Recent examples of applications include study of torsions in n-butane [2] and peptide sidechains [3, 4], as well as aggregation of methane [5] and a helix bundle protein in water [6]. Calculating free energy differences between molecular states is valuable because they are observable thermodynamic quantities, related to equilibrium constants and... 

Since the early 20th century, chemists have represented molecular information by molecular models. The human brain comprehends these representations of graphical models with 3D relationships more effectively than numerical data of distances and angles in tabular form. Thus, visualization makes complex information accessible to human understanding easily and directly through the use of images. 

The modeling of inorganic compounds in general is gaining more and more interest [25-28]. The authors of MOMEC addressed this in a monograph describing how molecular modeling techniques can be applied to metal complexes and how the results can be interpreted [29]. The current force field parameter set is available on the author s web site. 

The strength of this bonding depends on the kind of ether Simple ethers form relatively weak complexes with metal ions but Charles J Pedersen of Du Pont discovered that cer tain polyethers form much more stable complexes with metal ions than do simple ethers Pedersen prepared a series of macrocyclic polyethers cyclic compounds contain mg four or more oxygens m a ring of 12 or more atoms He called these compounds crown ethers, because their molecular models resemble crowns Systematic nomencla ture of crown ethers is somewhat cumbersome and so Pedersen devised a shorthand description whereby the word crown is preceded by the total number of atoms m the ring and is followed by the number of oxygen atoms... 

Wiegand, G., ef al. Crysfal strucfure analysis and molecular model of a complex of cifrafe synthase with oxaloacetate and S-acetonyl-coenzyme A. 

Fig. 4.13. Space-lilling molecular model depicting a metal cation complexed by 1 R-crown-6.

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