In serine proteases (SPs), the Hbond between His57 and Asp102 and that between Gly193 and the transition state intermediate play a crucial role in enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes represen
Ab initio molecular dynamics calculations to study catalysis
✍ Scribed by K. Schwarz; E. Nusterer; P. Margl; P. E. Blöchl
- Publisher
- John Wiley and Sons
- Year
- 1997
- Tongue
- English
- Weight
- 251 KB
- Volume
- 61
- Category
- Article
- ISSN
- 0020-7608
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✦ Synopsis
The modern versions of the density functional theory DFT , especially those using the Ž . Ž . generalized gradient approximation GGA , have reached almost chemical accuracy and thus can be applied to study problems of real chemical interest such as catalysis. The Ž . important equations for the DFT, the local density approximation LDA , and GGA are Ž .
given. The full-potential linearized augmented plane wave method LAPW is used to check the accuracy of GGA in solids. The basic concepts of the ab initio molecular Ž . dynamics MD method by Car and Parrinello and its recent implementation using the Ž . projector augmented Wave PAW method which use a similar augmentation as LAPW are described. PAW applications to ferrocene and beryllocene are summarized, which illustrate that vibrational or fluxional behavior are well described. Sodalite, an aluminosilicate, is discussed as a generic zeolite in comparison with gmelinite. A study of the dynamics of such a system allows the determination of, e.g., the proton stretch vibrations which can be related to infrared spectra. This is illustrated for the OH stretch vibration of the acid site in silicon-rich sodalite. With this methodology, we are able to study the interaction of methanol trapped inside the cage structure of silicon-rich sodalite and to gain new insight into crucial steps of catalytic reactions, namely, the hydrogenbonding and the possible protonation in this system, or a proton-exchange reaction. The strategies for parallelizing the PAW code are outlined.
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