Molecular covalent-bonding methods

Incorporating Chiral Molecular Catalysts In Nanoreactors through Covalent-Bonding Methods... 

Parallel molecular dynamics codes are distinguished by their methods of dividing the force evaluation workload among the processors (or nodes). The force evaluation is naturally divided into bonded terms, approximating the effects of covalent bonds and involving up to four nearby atoms, and pairwise nonbonded terms, which account for the electrostatic, dispersive, and electronic repulsion interactions between atoms that are not covalently bonded. The nonbonded forces involve interactions between all pairs of particles in the system and hence require time proportional to the square of the number of atoms. Even when neglected outside of a cutoff, nonbonded force evaluations represent the vast majority of work involved in a molecular dynamics simulation. 

The UHE wave function can also apply to singlet molecules. Usually, the results are the same as for the faster RHEmethod. That is, electrons prefer to pair, with an alpha electron sharing a molecular space orbital with a beta electron. Use the UHE method for singlet states only to avoid potential energy discontinuities when a covalent bond is broken and electrons can unpair (see Bond Breaking on page 46). 

An interpenetrating polymer network (IPN) is defined as a material comprising two or more networks which are at least partly interlaced on a molecular scale, hut not covalently bonded to each other. These networks caimot he separated unless chemical bonds are broken. Two possible methods exist for preparing them, as follows ... 

In our simulations of histone modifying enzymes, the computational approaches centered on the pseudobond ab initio quantum mechanical/molecular mechanical (QM/MM) approach. This approach consists of three major components [20,26-29] a pseudobond method for the treatment of the QM/MM boundary across covalent bonds, an efficient iterative optimization procedure which allows for the use of the ab initio QM/MM method to determine the reaction paths with a realistic enzyme environment, and a free energy perturbation method to take account... 

In the methods surveyed here, a specific interaction between target and ligand is created and then preserved so that the target can be identified. Two of the three approaches reviewed depend on forming a covalent bond between the molecular partners, but the first does not. 

In this chapter, the basic ideas related to the molecular orbital approach to covalent bonds have been presented. Other applications of the molecular orbital method will be discussed in Chapters 5 and 17. 

At shorter distances, particularly those characteristic of H-bonded and other charge-transfer complexes, the concepts of partial covalency, resonance, and chemical forces must be extended to intramolecular species. In such cases the distinction between, e.g., the covalent bond and the H-bond may become completely arbitrary. The concept of supramolecular clusters as fundamental chemical units presents challenges both to theory and to standard methods of structural characterization. Fortunately, the quantal theory of donor-acceptor interactions follows parallel lines for intramolecular and intermolecular cases, allowing seamless description of molecular and supramolecular bonding in a unified conceptual framework. In this sense, supramolecular aggregation under ambient thermal conditions should be considered a true chemical phenomenon. 

Murphy et al. [34,45] have parameterized and extensively tested a QM/MM approach utilizing the frozen orbital method at the HF/6-31G and B3LYP/6-31G levels for amino acid side chains. They parameterized the van der Waals parameters of the QM atoms and molecular mechanical bond, angle and torsion angle parameters (Eq. 3, Hqm/mm (bonded int.)) acting across the covalent QM/MM boundary. High-level QM calculations were used as a reference in the parameterization and the molecular mechanical calculations were performed with the OPLS-AA force... 

The result of the integration will be less sensitive to the exact position of the boundary when the density in the boundary area is small, which means that integration over the deformation density is preferable. Because covalently bonded atoms overlap significantly, the method is suitable for obtaining ionic or molecular charges but not for separation of atoms in a molecule. It should not be used for the latter purpose. 

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