Geometry, refinement

Siam, K., V. J. Klimkowski, C. Van Alsenoy, J. D. Ewbank, andL. Schafer. 1987. Ab Initio Geometry Refinement of Some Selected Structures of the Model Dipeptide N-Acetyl N -Methyl Serine Amide. J. Mol. Struct. (Theochem) 152, 261-270. 

Caminati, W., A. C. Fantoni, L. Schafer, K. Siam, and C. Van Alsenoy. 1986. Conformational and Structural Analysis of Methyl Hydrazinocarboxylate by Microwave Spectroscopy and Ab Initio Geometry Refinements. J. Am. Chem. Soc. 108,4364 1367. 

Fig. 7.17 Bend structure resulting from the HF/4-21G geometry refinement of a type-II bend of N-formyl pentaglycine amide. The torsional angles in this structure are not common in proteins due to the effects of the end groups on the dihedral angles in the bend.

Baerlocher Ch., Hepp A., and Meier W. M. (1977). DLS—76. A program for Simulation of Crystal Structures by Geometry Refinement Zurich Institut of Crystallography and Petrography ETH. 

The practical approaches for protein geometry refinement rely on iterative local linearizations of the full nonlinear optimization problem. The procedure is to step along the potential surface in a direction that decreases the energy. Such iterative approaches in Cartesian coordinates may be symbolized by... 

Model building, in which molecular structure is represented by experimental data as input and this structure is manipulated with use of stereochemical rules. This includes computer graphics and distance geometry refinement. 

In general, these variations of the geometry may have a distinct effect on the local stress. It means that at a certain level of geometry refinement the model becomes rmstable in a sense of a system (geometrical input)—(mechanical output). This understanding poses the question of how sophisticated should a model be ... 

A number of refinements and applications are in the literature. Corrections may be made for discreteness of charge [36] or the excluded volume of the hydrated ions [19, 37]. The effects of surface roughness on the electrical double layer have been treated by several groups [38-41] by means of perturbative expansions and numerical analysis. Several geometries have been treated, including two eccentric spheres such as found in encapsulated proteins or drugs [42], and biconcave disks with elastic membranes to model red blood cells [43]. The double-layer repulsion between two spheres has been a topic of much attention due to its importance in colloidal stability. A new numeri-... 

A molecular dynamics simulation nsnally starts with a molecular structure refined by geometry optimization, but wnthont atomic velocities. To completely describe the dynamics of a classical system con lain in g X atom s, yon m nsl define 6N variables. These correspond to ilX geometric coordinates (x, y, and /) and iSX variables for the velocities of each atom in the x, y, and /. directions. 

The greatest value of molecular dynamic simulations is that they complement and help to explain existing data for designing new experiments. The simulations are increasingly useful for structural refinement of models generated from NMR, distance geometry, and X-ray data. 

Use the HyperChem Model Builder to construct an approximate geometry. If you want to look at the relative energies of a set of molecules, you may want to carry out the calculations using fully optimized molecular geometries. These geometry optimization calculations can use either molecular mechanics or quantum mechanics to further refine the molecular geometry beyond that given by the Model Builder. 

Model Builder to get a reasonable starting geometry, with the possibility of refining the geometry by semi-empirical calculations before submitting it to ab initio computation. 

Second, the structures should satisfy the a priori information used in the refinement in the form of the energy parameters. Programs like PROCHECK-NMR check for deviation from expected geometries and close non-bonded contacts. 

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