Proton transfer quantum methods

Comparison of Barrier Heights (BH) in kcal mol for the Proton Transfer in Malonaldehyde Computed by Different Quantum Chemical Methods... 

Most of the AIMD simulations described in the literature have assumed that Newtonian dynamics was sufficient for the nuclei. While this is often justified, there are important cases where the quantum mechanical nature of the nuclei is crucial for even a qualitative understanding. For example, tunneling is intrinsically quantum mechanical and can be important in chemistry involving proton transfer. A second area where nuclei must be described quantum mechanically is when the BOA breaks down, as is always the case when multiple coupled electronic states participate in chemistry. In particular, photochemical processes are often dominated by conical intersections [14,15], where two electronic states are exactly degenerate and the BOA fails. In this chapter, we discuss our recent development of the ab initio multiple spawning (AIMS) method which solves the elecronic and nuclear Schrodinger equations simultaneously this makes AIMD approaches applicable for problems where quantum mechanical effects of both electrons and nuclei are important. We present an overview of what has been achieved, and make a special effort to point out areas where further improvements can be made. Theoretical aspects of the AIMS method are... 

Another development that we will undertake in the near fumre is development of algorithms for non-BO calculations of molecules with 7i-electrons (the CH radical is an example of such a system). We also contemplate development of methods for describing systems where only the light nuclei (apart from electrons) are treated as quantum particles, and the other heavier nuclei are described either classically or by using a low-level approximation. This development would move us closer to cosidering the quantum dynamics of such reactions as inter- and intramolecular proton transfer. 

The study of chemical reactions requires the definition of simple concepts associated with the properties ofthe system. Topological approaches of bonding, based on the analysis of the gradient field of well-defined local functions, evaluated from any quantum mechanical method are close to chemists intuition and experience and provide method-independent techniques [4-7]. In this work, we have used the concepts developed in the Bonding Evolution Theory [8] (BET, see Appendix B), applied to the Electron Localization Function (ELF, see Appendix A) [9]. This method has been applied successfully to proton transfer mechanism [10,11] as well as isomerization reaction [12]. The latter approach focuses on the evolution of chemical properties by assuming an isomorphism between chemical structures and the molecular graph defined in Appendix C. 

We have examined the proton transfer reaction AH-B A -H+B in liquid methyl chloride, where the AH-B complex corresponds to phenol-amine. The intermolecular and the complex-solvent potentials have a Lennard-Jones and a Coulomb component as described in detail in the original papers. There have been other quantum studies of this system. Azzouz and Borgis performed two calculations one based on centroid theory and another on the Landau-Zener theory. The two methods gave similar results. Hammes-Schiffer and Tully used a mixed quantum-classical method and predicted a rate that is one order of magnitude larger and a kinetic isotope effect that is one order of magnitude smaller than the Azzouz-Borgis results. 

The expansion in the power of computers and theoretical methods has made it possible to investigate the mechanism of action of enzymes by combinations of quantum-mechanical and molecular-mechanical calculations. A study of two possible mechanisms for dihydrofolate reductase catalysis was consistent with indirect proton transfer from aspartate to N-5 of the pterin as has been suggested for many years by crystallographic evidence <2003PCB14036>. This conclusion is also consistent with the outcome of a study that directly measured the of the active site aspartate in the Lactobacillus casei enzyme <1999B8038>. Observations of chemical shifts of... 

In the final exploration of the quantum chemistry unit students use a computational chemistry package (eg. Spartan, Gaussian, CaChe, etc.) to calculate the ground state energies, molecular orbitals, and in some cases the excited state energies, of two proton transfer tautomers. Calculations are performed at several different levels of theory, and use both semi-empirical and ab initio methods. Several different basis sets are compared in the ab initio calculations. The students use the results of these calculations to estimate the likelihood of excited state proton transfer. The calculations require CPU time ranging from a couple of minutes to a couple of hours on the PCs available to the students in the laboratory. 

The nature of the methanol-zeolite interaction has been shown to be sensitive to a number of parameters and as such has proved to be a good benchmark for judging the reliability of quantum chemical methods. Not only are there a number of possible modes whereby one and two molecules interact with an acidic site (245), the barrier to proton transfer is small and sensitive to calculation details. Recent first-principles simulations (236-238) suggest that the nature of adsorbed methanol may be sensitive to the topology of the zeolite pore. The activation and reaction of methane, ethane, and isobutane have been characterized by using reliable methods and models, and realistic activation energies for catalytic reactions have been obtained. 

The rate coefficient of a reactive process is a transport coefficient of interest in chemical physics. It has been shown from linear response theory that this coefficient can be obtained from the reactive flux correlation function of the system of interest. This quantity has been computed extensively in the literature for systems such as proton and electron transfer in solvents as well as clusters [29,32,33,56,71-76], where the use of the QCL formalism has allowed one to consider quantum phenomena such as the kinetic isotope effect in proton transfer [31], Here, we will consider the problem of formulating an expression for a reactive rate coefficient in the framework of the QCL theory. Results from a model calculation will be presented including a comparison to the approximate methods described in Sec. 4. 

The ET processes under discussion here correspond by definition to pure ET, in which molecular or medium coordinates may shift (the polaron response) [17], but no overall bonding rearrangements occur. More complex ET processes accompanied by such rearrangements (e.g., coupled electron/proton transfer and dissociative ET) are of great current interest, and many theoretical approaches have been formulated to deal with them, including quantum mechanical methods based on DC treatment of solvent [31,32],... 

In terms of photophysics, electron transfer reactions create an additional non-radiative pathway, so reducing the observed emission lifetimes and quantum yields in A-L-B dyads in comparison with a model compound. However, there are other processes, such as molecular rearrangements, proton transfer and heavy-atom effects, which may decrease the radiative ability of a compound. One of the most important experimental methods for studying photoinduced processes is emission spectroscopy. Emission is relatively easy to detect and emission intensities and lifetimes are sensitive to competing processes. Studying parameters such as emission quantum yields and lifetimes for a given supramolecular species and associated... 

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