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Quantum chemical methods allow one to investigate chemical aspects that are often difficult to evaluate using only experimental approaches. In particular, the continuous increase in reliability and speed of quantum chemical methods has recently allowed the investigation of very complex molecular systems, such as biological macromolecules. In this contribution, we present applications of quantum chemical...
Vibrational spectroscopy of biomolecules like enzymes, nucleic acids, carbohydrates, lipids, and their components, is in most cases the vibrational spectroscopy of large molecules in aqueous solution or in vivo. Since large molecules in solution are likely to yield conventional infrared (IR) and Raman spectra with many close-lying peaks, spectroscopic techniques which filter out information selectively...
The basic concepts of Car–Parrinello molecular dynamics (CPMD) and its application to biological systems are reviewed. In Car–Parrinello simulations the electronic structure is calculated on the fly, i.e., during the course of simulations the potential is adjusted according to the chemical events occurring in the system. This allows for more unbiased simulations of chemical processes, as opposed to...
Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus on biomolecular systems. We provide a detailed overview of the methodology of QM/MM calculations and their use within optimization and simulation schemes. A tabular survey of recent applications, mostly to enzymatic reactions,...
Transition path sampling is a computational method for the simulation of rare but important events occurring in complex systems. Based on a statistical mechanics in trajectory space, transition path sampling can be applied to identify mechanisms and determine rate constants. Here we review the basic ideas and algorithms of transition path sampling and discuss some recent applications of this methodology...
Molecular motors are adenosine tri-phosphate (ATP) hydrolysis-driven, cellular proteins responsible for a wide variety of different tasks, such as transport, energy metabolism, and DNA processing. Their operation cycle spans a wide range of length and time scales, from the localized and fast chemical reaction in the catalytic site(s) to the large scale and much slower conformational motions involved...
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