Complex refinement

We now consider separately each function used to calculate the terms that go to make up the total strain energy. We have restricted our discussion here to the simplest forms of the functions. With the greater approximations involved in modeling metal complexes, refinements of the functions are often an unneccessary elaboration. A full account of possible functions is given in Chapter 2, Section 2.2. When the use of other functions is indicated, these can be parameterized by application of the general philosophies of force field development outlined below. 

Schreuder HA, Prick PA, Wierenga RK, Vriend G, Wilson KS, Hoi WG, Drenth J. Crystal structure of the p-hydroxybenzoate hydroxylase-substrate complex refined at 1.9 A resolution. Analysis of the enzyme-substrate and enzyme-product complexes. J. Mol. Biol. 1989 208 679-696. 

It is important to emphasize that all conventional motor fuels—petroleum gasolines and diesel—are produced by complex refining processes. These fuels are mixtures and contain hundreds of organic compounds. None is a single, pure substance. Similarly, almost all biomass-based liquid motor fuels contain numerous organic compounds, but in some cases can consist of relatively few compounds, as in the case of the methyl esters of fatty acids in biodiesel. The exceptions are the lower molecular weight alcohols and a few derivatives that can be used directly as neat motor fuels. They can easily be manufactured from biomass feedstocks as individual compounds. 

Complex Refinement Structures. Flowsheets are refined across various hierarchical abstraction levels and depicted in specific representation formats. In the context of the IMPROVE project, we are mainly interested in two of the three commonly used flowsheet variants the abstract flow diagram (AFD) and the process flow diagram (PFD). Thus, the flowsheet editor supports the full hierarchy of complex stepwise refinement operations from AFD to PFD and assures a set of consistency constrains in order to preserve their semantic correctness. 

ICM Full-Atom Ligand-Receptor Complex Refinement and Scoring... 

Soft receptors are an easy and efficient way to model a certain degree of protein flexibility. Their major disadvantage is certainly a substantial lack of accuracy. Usually, soft docking is the initial step of an induced fit workflow before a complex refinement occurs. 

Induced fit docking approaches usually integrate a complex refinement stage. 

Y. Bourne, P. Rouge, and C. Cambillau, J. Biol. Chem., 267,197 H992). X-Ray Structure of a Biantennary Octasaccharide—Lectin Complex Refined at 2.3-A Resolution. 

Naphthalene chemistry differs fundamentally from benzene chemistry in that two isomers can be produced by monosubstitution, facilitating the formation of byproducts. Furthermore, in comparison with benzene, naphthalene is more reactive in electrophilic substitution, so that this type of reaction can be carried out under relatively mild conditions. Naphthalene chemistry is therefore characterized by especially-optimized reaction procedures and complex refining processes. Increased reactivity and substitution capacity offer advantages which can be used, for example, in dyestuffs production, where the naphthalene moiety serves as a carrier for a variety of auxochromic groups. 

Recent ab initio studies have refocused their attention upon resolving questions such as the binding energy of the complex, refinement of the details of the molecular geometry such as the equilibrium orientation of the proton acceptor molecule, and reasons why the O O distance in the dimer is substantially longer than in condensed phases [120-123]. 

C p - lodo - N - dimethylaniline - hydrochloride - hydroiodide - iodine < complex (refined as space group no. 15)... 

C Tetrahydroselenophene - iodine complex (refined as space group no. 62)... 

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