Dynamics with Specific Reaction Parameters

Direct Dynamics with Specific Reaction Parameters 

In the original application,the SRP method was applied to the following reaction  

In this particular example, a neglect of the diatomic differential overlap 

In MCMM, the Born-Oppenheimer PES is estimated as being the lowest eigenvalue of the 2x2 potential matrix V  

Using a suitable quantum mechanical electronic structure method, the energy, gradient, and Hessian can be calculated at an arbitrary geometry, q, which is called an interpolation point or a Shepard point. Near q Vii(q), V(q), and V22(q) may be expanded as a Taylor series, yielding 

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Direct Dynamics with Specific Reaction Parameters... 

Gonzalez-Lafont, A. Truong, T. N. Truhlar, D. G. Direct dynamics calculations with neglect of diatomic differential overlap molecular orbital theory with specific reaction parameters, J. Phys. Chem. 1991, 95,4618-4627. 

Gonzalez-Lafont, A., Truong, T.N. and Truhlar, D.G. (1991) Direct Dynamics Calculations with Neglect of Diatomic Differential Overlap Molecular Orbital Theory with Specific Reaction Parameters, J. Phys. Chem. 95, 4618-4627. 

A promising recent development concerns the use of semiempirical NDDO methods with specific reaction parameters (NDDO-SRP) [144-147] in direct dynamics calculations. In these studies the parameters in the standard AMI method are carefully adjusted to optimize the potential surface for an individual reaction or a set of related reactions (typically allowing parameter variations up to 10% from the original values). When adjusting with respect to experimental data, NDDO-SRP is required to reproduce the exothermicity and the barrier (or rate constant) of the reaction investigated. Under these circumstances NDDO-SRP then predicts reasonable transition structures and force fields for the reaction which is consistent with previous experience [48,49]. Direct dynamics calculations on such NDDO-SRP surfaces have provided very encourag-... 

Semiempirical direct dynamics was used to study trimethylene s unimo-lecular dynamics and the thermal stereomutation of cyclopropane.The semiempirical model used in these simulations is AMI with specific reaction parameters (SRPs see discussion of semiempirical electronic structure theory in the section on BO direct dynamics) chosen to fit the CASSCF PES. In choosing the SRPs, the AMI barrier for propene formation was lowered by... 

Dynamics Calculations with NDDO (Neglect of Diatomic Differential Overlap) Molecular Orbital Theory with Specific Reaction Parameters. 

ABSTRACT. Laser and molecular beam techniques allow detailed study of many dynamical properties of single reactive collisions. The chemical scope of these methods is now very wide and includes internal state preparation of reactants, change of collision energies, state detection of products, and thus determination of state-to-state reaction rates. The great impact of laser spectroscopy on knowledge in the field of structure, molecular energy transfer and the mechanism of elementary chemical reactions is illustrated by two selected examples, i.e. studies in which laser-induced fluorescence (LIF) has been used to determine the specific impact parameter dependence of the Ca + HF -> CaF(X) + H reaction and the product state distributions for the reaction of metastable Ca with SF5. 

The major reasons for using intrinsic fluorescence and phosphorescence to study conformation are that these spectroscopies are extremely sensitive, they provide many specific parameters to correlate with physical structure, and they cover a wide time range, from picoseconds to seconds, which allows the study of a variety of different processes. The time scale of tyrosine fluorescence extends from picoseconds to a few nanoseconds, which is a good time window to obtain information about rotational diffusion, intermolecular association reactions, and conformational relaxation in the presence and absence of cofactors and substrates. Moreover, the time dependence of the fluorescence intensity and anisotropy decay can be used to test predictions from molecular dynamics.(167) In using tyrosine to study the dynamics of protein structure, it is particularly important that we begin to understand the basis for the anisotropy decay of tyrosine in terms of the potential motions of the phenol ring.(221) For example, the frequency of flips about the C -C bond of tyrosine appears to cover a time range from milliseconds to nanoseconds.(222)... 

As discussed by M. Shapiro and R Brumer in the book Quantum Control of Molecular Processes, there are two general control strategies that can be applied to harness and direct molecular dynamics optimal control and coherent control. The optimal control schemes aim to find a sef of external field parameters that conspire - through quantum interferences or by incoherent addition - to yield the best possible outcome for a specific, desired evolution of a quantum system. Coherent control relies on interferences, constructive or destructive, that prohibit or enhance certain reaction pathways. Both of these control strategies meet with challenges when applied to molecular collisions. 

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