Ab initio molecular dynamics: Theory and Implementation

CH=CH 2 using Cl(CO) 2 20 , or Sakakura–Tanaka functionalization 382 . As in thereal laboratory, side reactions can occur also in the virtual laboratory, such as e.g.the β–hydrogen elimination as an unpredicted reaction path 383 . A digression onusing finite–temperature ab initio dynamics in homogeneous catalysis research canbe found in Ref. 697 .Zeolites often serve as catalysists as well and are at the same time ideal candidatesfor finite–temperature ab initio simulations in view of their chemical complexity.A host of different studies 559,100,268,614,545,206,560,598,207,315,208,209,546 contributedgreatly to the understanding of these materials and the processes occurringtherein such as the initial stages of the methanol to gasoline conversion 599 . Heterogenouscatalysts are often poisoned, which was for instance studied in the caseof hydrogen dissociation on the Pd(100) surface in the presence adsorbed sulfurlayers 257 .5.11 Biophysics and BiochemistryApplications of ab initio molecular dynamics to molecules and processes of interestin life sciences begin to emerge 18,113 . Investigations related to these interests areinvestigations of the crystal structure of a hydrated RNA duplex (sodium guanylyl–3’–5’–cytidine nona–hydrate) 311 , structure models for the cytochrom P450 enzymefamily 547,548,549 , nanotubular polypeptides 112 , a synthetic biomimetic model ofgalactose oxidase 523 , aspects of the process of vision in form of the 11–cis toall–trans isomerization in rhodopsin 67,68,474 , interconversion pathways of the protonatedβ–ionone Schiff base 615 , or of the binding properties of small moleculesof physiological relevance such as O 2 , CO or NO to iron–porphyrines and its complexes527,528,529 .Proton transport throught water wires is an important biophysical process inthe chemiosmotic theory for biochemical ATP production. Using the ab initiopath integral technique 395,399,644,404 the properties of linear water wires with anexcess proton were studied at room temperature 419 . Amino acids are importantingredients as they are the building blocks of polypeptides, which in turn formchannels and pores for ion exchange. Motivated by their ubiquity, glycine andalanine as well as some of their oligopeptides and helical (periodic) polypeptideswere studied in great detail 323 .5.12 OutlookAb initio molecular dynamics is by now not only a standard tool in academic researchbut also becomes increasingly attractive to industrial researchers. Analysisof data bases, see caption of Fig. 1 for details, uncovers that quite a few companiesseem to be interested in this methodology. Researchers affiliated to Bayer, Corning,DSM, Dupont, Exxon, Ford, Hitachi, Hoechst, Kodak, NEC, Philips, Pirelli, Shell,Toyota, Xerox and others cite the Car–Parrinello paper Ref. 108 or use ab initiomolecular dynamics in their work. This trend will certainly be enhanced by theavailability of efficient and general ab initio molecular dynamics packages which arecommercially available.126