Proton transfer, computational methods

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

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 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. 

A study of the chiral discrimination in diaziridine clusters has been carried out using DFT computational methods [38]. The most stable neutral structure corresponds to that with the monomers in alternated chirality. The proton transfer within the neutral diaziridine chain proceeds with high TS barriers. The protonation of the fist diaziridine of the chain tends to produce a spontaneous proton transfer from the first monomer to the second (Fig. 3.18). The studied processes of proton transfer in the charged system show small barriers. The proton transfer in the neutral or protonated systems produces an inversion of the chirality of the monomers as the process evolves along the chain producing chirality waves. Finally, the calculated ORP of the clusters is very dependent on the cluster size, cyclic or helix shape, and on the number of monomers that form the cluster. 

Recently, there has been considerable interest in determining thermochemical properties, such as the AH°( and EA values of carbenes, notably the halo- and dihalomethylenes, and both experimental and computational methods were applied to this end. One thorough ICR investigation produced heats of formation for CF2, CC12, CC1F, CFH and CC1H, from estimates of the thermochemistry of the proton transfer reaction of equation 44 where X and Y are F and/or Cl, and B is a base of known gas-phase basicity323. 

In the previous papers, we applied QM/MM-ER to various systems to examine the efficiency of the method [19,63,64,38,65,66], Here, we present the results of a few applications. At first, we employ the QM/MM-ER approach to compute solvation free energy of a QM water molecule described by DFT in an MM water solvent [19]. Second, the method is utilized to compute free energy change associated with a proton transfer in glycine in aqueous solution [64], The results are compared with those obtained by experiments and the accuracy and efficiency of the QM/MM-ER approach is discussed. 

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