The description of the phosphate group and its reactions with nitrogen species appears to
be challenging using semi-empirical quantum chemical methods, and this holds for DFTB3 …

During the second half of the 20th century, following structural biology hallmark works on
DNA and proteins, biochemists shifted their questions from “what does this molecule look …

A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions
catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined …

Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the
modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method …

Understanding enzyme catalysis is one of the grand challenges of both experimental and
computational biochemistry. The last decade has witnessed dramatic growth in both the …

In the last years, we have developed a computationally efficient approximation to density
functional theory, the so called self-consistent charge density functional tight-binding …

QM/MM simulations have become an indispensable tool in many chemical and biochemical
investigations. Considering the tremendous degree of success, including recognition by a …

There are two key requirements for reliably simulating enzyme reactions: one is a
reasonably accurate potential energy surface to describe the bond-forming/breaking …

In recent years, a number of quantum mechanical–molecular mechanical (QM/MM) enzyme
studies have investigated the dependence of reaction energetics on the size of the QM …

Structural and energetic changes are two important characteristic properties of a chemical
reaction process. In the condensed phase, studying these two properties is very challenging …