Complexation molecular mechanisms

Ab initio calculations for activated complex molecular mechanics parameters reported in paper No additional parameters necesary... 

Bygott, A.M.T. Sargeson. A.M. Critical evaluation of metal complex molecular mechanics. Part 1. Cobalt(IIT) hexaamines. Inorg. Chem. 1998, 37, 4795-4806. 

Lehnert N, Praneeth VKK, Paulat F (2006) Electronic structure of iron(II)-porphyrin nitroxyl complexes molecular mechanism of fungal nitric oxide reductase (P450nor). J Comput Chem 27 1338-1351... 

In the modelling of structures of host-guest complexes, molecular mechanics, particularly when allied with molecular graphics, has proved to be particularly useful. Molecular mechanics has the virtue of being simple to understand and easy to program. The technique can be applied to a large number of atoms without excessive computer power. It is now available in several relatively cheap and easy to use packages on many hardware platforms. Paradoxically its main drawback is caused by its virtues. Results can be obtained easily from the software but are very often unsatisfactory because the parameters provided are either inaccurate or not applicable to the systems under study. This problem is common with commercial software where parameters are often added... 

Dimethyl- (4) and diethyl-2,6-naphthalene-carboxylate (5) also exhibited fluorescence modiflcations by formation of higher-order complexes with a- and j6-CD [5,8]. The intensity greatly increased by addition of ot-CD, whereas the addition of j8-CD caused a small increase of 5 emission and had no effect on that of 4. In all the cases, except for 4 in presence of j6-CD, the fluorescence variations as a function of [CD] gave evidence for a 2 1 stoichiometry. Van T Hoff plots for the formation of the complexes pointed to an enthalpy-driven complexation. Molecular mechanics calculations indicated that in the 2 1 P-CD-5 complex the guest is well shielded from the solvent and stabilized by H-bonding between the faced j6-CD, while in the 2 1 ot-CD-5 it is partially exposed to the aqueous medium. 

The complexity of polymeric systems make tire development of an analytical model to predict tlieir stmctural and dynamical properties difficult. Therefore, numerical computer simulations of polymers are widely used to bridge tire gap between tire tlieoretical concepts and the experimental results. Computer simulations can also help tire prediction of material properties and provide detailed insights into tire behaviour of polymer systems. A simulation is based on two elements a more or less detailed model of tire polymer and a related force field which allows tire calculation of tire energy and tire motion of tire system using molecular mechanisms, molecular dynamics, or Monte Carlo teclmiques 1631. 

The molecular mechanism of ion enliancement proved to be both subtle and complex. The complexity of the... 

Singh, U.C., Kollman, P.A. A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems Applications to the CH3CI 4- Cl exchange reaction and gas phase protonation of polyethers. J. Comput. Chem. 7 (1986) 718-730. 

Singh U C and P A Kollman 1986. A Combined Ab Initio Quantum Mechanical and Molecule Mechanical Method for Carrying out Simulations on Complex Molecular Systems Applicatior to the CHsQ + Cr Exchange Reaction and Gas Phase Protonation of Polyethers. Journal Computational Chemistry 7 718-730. 

The molecular mechanics force helds available are AMBER95 and CFIARMM. The molecular mechanics and dynamics portion of the code is capable of performing very sophisticated calculations. This is implemented through a large number of data hies used to hold different types of information along with keywords to create, use, process, and preprocess this information. This results in having a very hexible program, but it makes the input for simple calculations unnecessarily complex. QM/MM minimization and dynamics calculations are also possible. 

MacroModel (we tested Version 6.5) is a powerful molecular mechanics program. The program can be run from either its graphic interface or an ASCII command file. The command file structure allows very complex simulations to be performed. The XCluster utility permits the analysis and filtering of a large number of structures, such as Monte Carlo or dynamics trajectories. The documentation is very thorough. 

Absorption, metaboHsm, and biological activities of organic compounds are influenced by molecular interactions with asymmetric biomolecules. These interactions, which involve hydrophobic, electrostatic, inductive, dipole—dipole, hydrogen bonding, van der Waals forces, steric hindrance, and inclusion complex formation give rise to enantioselective differentiation (1,2). Within a series of similar stmctures, substantial differences in biological effects, molecular mechanism of action, distribution, or metaboHc events may be observed. Eor example, (R)-carvone [6485-40-1] (1) has the odor of spearrnint whereas (5)-carvone [2244-16-8] (2) has the odor of caraway (3,4). 

Once the model of a ligand-receptor complex is built, its stability should be evaluated. Simple molecular mechanics optimization of the putative ligand-receptor complex leads only to the identification of the closest local minimum. However, molecular mechanics optimization of molecules lacks two crucial properties of real molecular systems temperature and, consequently, motion. Molecular dynamics studies the time-dependent evolution of coordinates of complex multimolecular systems as a function of inter- and intramolecular interactions (see Chapter 3). Because simulations are usually performed at nonnal temperature (—300 K), relatively low energy barriers, on the order of kT (0.6 kcal), can... 

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