On the Treatment of Link Atoms in Hybrid Methods

Abstract

Several coupling models and link atom options are investigated for combined quantum-chemical and classical approaches. Ab initio, density functional, and semiempirical methods are used for the quantum-chemical region, whereas the classical region is described by the AMBER force field. Numerical results are reported for the proton affinities of alcohols and ethers. Recommendations for link atoms are given based on these results and theoretical analysis

QM/MM: what have we learned, where are we, and where do we go from here?

“…In this contribution, we will briefly review the current status of the most popular methods for QM/MM calculations, including their advantages and disadvantages. There are many reviews of QM/MM methods available in literature [49,58,59,65,66,74,75,81,95,113,119]. The present study will put a special emphasis on very general link atom methods and various ways to treat the charge near the boundary.…”

“…An improved eliminated-groupcharge scheme [58] takes advantage of this feature by deleting the atomic charges for the whole group that contains the M1 atom. This ensures that the net charge of the SS does not change.…”

Mechanisms and Free Energies of Enzymatic Reactions

“…All computational studies of atomic scale dynamics must begin with a potential energy surface, and the most promising approach to calculating this surface is to treat the enzyme active site by electronic structure methods [11][12][13][14][15][16][17][18][19] that include the electronic polarization of the reactive species by the dynamical fluctuations of the enzyme-solvent environment through effective sampling of the enzyme conformational space. Although a review necessarily involves only a very limited selection of the reactions that enzymes catalyze in the cell, we can nevertheless conclude 7 that each enzyme has its unique characteristics, and enzymes use all possible means to achieve the ultimate objective of reducing the free energy of activation.…”

Multiscale Modeling of Hydrogen Embrittlement

“…For many molecular systems that are of interest in chemistry and biochemistry, one can partition the QM/MM system by cutting chemical bonds linking the QM and MM parts and then saturate the dangling bonds at the boundary of QM region by so-called link atoms [41,43,44]. This procedure and the similar ones can be justified because of the presence of well-defined and localized chemical bonds in such molecular systems.…”