A combined quantum mechanical (QM) and molecular mechanical (MM) potential has been developed for the study of reactions in condensed phases. For the quantum mechanical calculations semiempirical methods of the MNDO and AM1 type are used, while the molecular mechanics part is treated with the CHARMM force field. Specific prescriptions are given for the interactions between the QM and MM portions of the system; cases in which the QM and MM methodology is applied to parts of the same molecule or to different molecules are considered. The details of the method and a range of test calculations, including comparisons with ab initio and experimental results, are given. It is found that in many cases satisfactory results are obtained. However, there are limitations to this type of approach, some of which arise from the AM1 or MNDO methods themselves and others from the present QM/MM implementation. This suggests that it is important to test the applicability of the method to each particular case prior to its use. Possible areas of improvement in the methodology are discussed.

A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

Electrostatic Basis for Enzyme Catalysis

We present an approach to couple ab initio quantum mechanical geometry optimiuzations with molecular mechanical optimizations, with the added capability to carry out molecular dynamics simulations of the systems to earch for new local minima. The approach is applied to the aqueous solution CH3Cl + Cl− exchange reaction and the gas phase protonation of polyethers.

A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers

Formation of a short (less than 2.5 angstroms), very strong, low-barrier hydrogen bond in the transition state, or in an enzyme-intermediate complex, can be an important contribution to enzymic catalysis. Formation of such a bond can supply 10 to 20 kilocalories per mole and thus facilitate difficult reactions such as enolization of carboxylate groups. Because low-barrier hydrogen bonds form only when the pKa's (negative logarithm of the acid constant) of the oxygens or nitrogens sharing the hydrogen are similar, a weak hydrogen bond in the enzyme-substrate complex in which the pKa's do not match can become a strong, low-barrier one if the pKa's become matched in the transition state or enzyme-intermediate complex. Several examples of enzymatic reactions that appear to use this principle are presented.

https://science.sciencemag.org/content/sci/269/5220/102.full.pdf

Low-barrier hydrogen bonds and enzymic catalysis

Simulation of Enzyme Reactions Using Valence Bond Force Fields and Other Hybrid Quantum/Classical Approaches

Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches

Quantum mechanical and molecular mechanical studies on a model for the dihydroxyacetone phosphate-glyceraldehyde phosphate isomerization catalyzed by triose phosphate isomerase (TIM)

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Quantum mechanical and molecular mechanical studies on a model for the dihydroxyacetone phosphate-glyceraldehyde phosphate isomerization catalyzed by triose phosphate isomerase (TIM)

Quantum mechanical and molecular mechanical studies on a model for the dihydroxyacetone phosphate-glyceraldehyde phosphate isomerization catalyzed by triose phosphate isomerase (TIM)