Bond breaking/formation, simulation

There are many factors governing the choice of active space. An important consideration is the nature of the chemical problem that is to be addressed. For example, if a chemical reaction is to be studied, then all orbitals involved in bond breaking/formation must be considered. If, instead, excited state properties are of interest, for example in the simulation of absorption processes, then orbitals whose occupations differ significantly between the ground and excited state must be included. This can be particularly important in coordination complexes, where excitation processes may involve a change in the oxidation state of the metal ion. However, some general points with regard to the choice of active space orbitals can be made ... 

Quantum mechanical calculation of molecular dynamics trajectories can simulate bond breaking and formation. Although you do not see the appearance or disappearance of bonds, you can plot the distance between two bonded atoms. Adistance exceeding a theoretical bond length suggests bond breaking. 

Despite advent of theoretical methods and techniques and faster computers, no single theoretical method seems to be capable of reliable computational studies of reactivities of biocatalysts. Ab initio quantum mechanical (QM) methods may be accurate but are still too expensive to apply to large systems like biocatalysts. Semi-empirical quantum methods are not as accurate but are faster, but may not be fast enough for long time simulation of large molecular systems. Molecular mechanics (MM) force field methods are not usually capable of dealing with bond-breaking and formation... 

When addressing problems in computational chemistry, the choice of computational scheme depends on the applicability of the method (i.e. the types of atoms and/or molecules, and the type of property, that can be treated satisfactorily) and the size of the system to be investigated. In biochemical applications the method of choice - if we are interested in the dynamics and effects of temperature on an entire protein with, say, 10,000 atoms - will be to run a classical molecular dynamics (MD) simulation. The key problem then becomes that of choosing a relevant force field in which the different atomic interactions are described. If, on the other hand, we are interested in electronic and/or spectroscopic properties or explicit bond breaking and bond formation in an enzymatic active site, we must resort to a quantum chemical methodology in which electrons are treated explicitly. These phenomena are usually highly localized, and thus only involve a small number of chemical groups compared with the complete macromolecule. 

The previous two sections of this review deal with classical simulation methods. A description of the activation of adsorbates by acidic sites, together with any bond breaking or bond formation that may take place, is the realm of quantum mechanical (QM) simulations. These types of calculations are particularly well-suited to zeolite-adsorbate systems when the cluster approximation is used. The active acidic site in the zeolite is modeled by a molecular cluster, formed by cutting out a small portion of... 

Ab initio MD studies were carried out to help understand the elementary processes that occur at the metal-solution interface [77]. At temperatures less than 300 K, acetic acid decomposed on Pd, leaving an adsorbed acetate intermediate along with a proton in solution. Above 300 K, however, surface acetate recombines with a proton in solution to form acetic acid. Acetic acid is then displaced from the surface by water. Once the acetic acid finds its way into solution, it redissociates to form acetate and protons in solution that are now more efficiently stabilized by water. A series of snapshots that portray some of the images from the simulation is shown in Figure 13. These results were further corroborated with a more conventional transition-state search approach, which showed that desorption of acetate from the surface was an activated process. The process is quite complicated, involving the simultaneous breaking of the acetate-metal bond, the formation of an... 

Seven CH2N2O2 species have been formed at around 200 fs of simulation time. These results are similar to those identified in thermal decomposition experiments. [51,53] A further N-NO2 bond breaking then follows the decomposition (1) and (2) above. From (1), this leads to the formation of CH2N and NO2. These pathways are remarkably similar to those predicted previously by Melius from the decomposition of nitramines at fast heating rates. [70]... 

The first factor means that the approach to equilibrium will be slow, although the initial rate of bond formation in a fluid of monomers may be high. The second factor means that the fluctuations required to give an accurate statistical measure of the equilibrium composition and other properties will occur over very long simulation times. As equilibrium is approached, there is an effective slowing down of the system as bond formation and bond breaking both become rare events. The idea of RCMC is... 

Monte Carlo simulations using classical potentials are not adequate to describe chemical processes like bond formation and bond breaking which occur in chemisorption. 

ReaxFF. ReaxFF allows for bond breaking and bond formation in MD simulation so that thermal decomposition can be modeled as has been shown recently for polydi-methylsiloxane [9]. ReaxxFF includes terms for traditional bonded potentials as well as nonbonded potentials (i.e., van der Waals and Coulombic). Bond breaking and bond formation are handled through a bond order/bond distance relationship. Parameterization is through high-level DFT calculations (B3LYP/6-311++G ). 

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