Ab initio molecular dynamics: Theory and Implementation

properties of fullerenes 19,17,451 , the growth process of nanotubes 127,62,72 , or theelectrical conductivity of nanowires 38,272 became of great interest.5.8 Complex and Floppy MoleculesThe determination of the structure of a RNA duplex including its hydration water311 , investigations of geometry and electronic structure of porphyrins and porphyrazines356 , and the simulation of a bacteriochlorophyll crystal 381 are someapplications to large molecules. Similarly, the “carboplatin” complex 623 – a drugwith large ligands – as well as the organometallic complex Alq(3) 148 – an electroluminescentmaterial used in organic light–emitting diodes – were investigated withrespect to structural, dynamical and electronic properties.The organometallic compound C 2 H 2 Li 2 has an unexpected ground–state structurethat was found by careful ab initio simulated annealing 521 . In addition, thiscomplex shows at high temperatures intramolecular hydrogen migration that ismediated via a lithium hydride unit 521 . Ground–state fluxionality of protonatedmethane CH + 5 397,408 including some isotopomers 409 and of protonated acetyleneC 2 H + 3 400 was shown to be driven by quantum effects. The related dynamicalexchange of atoms in these molecules can also be excited by thermal fluctuations630,85,401 . In addition it was shown that CH + 5 is three–center two–electronbonded and that this bonding topology does not qualitatively change in the presenceof strong quantum motion 402 . The fluxional behavior of the protonated ethanemolecular ion C 2 H + 7 was investigated by ab initio molecular dynamics as well 172 .The neutral and ionized SiH 5 and Si 2 H 3 species display a rich dynamical behaviorwhich was seen during ab initio molecular dynamics simulations 246 . Thelithium pentamer Li 5 was found to perform pseudorotational motion on a timescale of picoseconds or faster at temperatures as low as 77 K 231 . Using ab initioinstanton dynamics the inversion splitting of the NH 3 , ND 3 , and PH 3 moleculesdue to the umbrella mode was estimated 325 . Similarly, a semiclassical ab initiodynamics approach as used to compute the tunneling rate for intramolecular protontransfer in malonaldehyde 47 . Ab initio simulated annealing can be used toexplore the potential energy landscape and to locate various minima, such as forinstance done for protonated water clusters 673 . Molecular dynamics simulations ofthe trimethylaluminum Al(CH 3 ) 3 have been carried out in order to investigate theproperties of the gas–phase dimer 29 . The structures and vibrational frequenciesof tetrathiafulvalene in different oxidation states was probed by ab initio moleculardynamics 324 . Implanted muons in organic molecules (benzene, 3–quinolylnitronyl nitroxide, para–pyridyl nitronyl nitroxide, phenyl nitronyl nitroxide andpara–nitrophenyl nitronyl nitroxide) were investigated using approximate ab initiopath integral simulations that include the strong quantum broadening of themuonium 656,657 .5.9 Chemical Reactions and TransformationsEarly applications of ab initio molecular dynamics were devoted to reactive scatteringin the gas phase such as CH 2 + H 2 → CH 4 669 or H − + CH 4 → CH 4 +H − 365 . The “on–the–fly” approach can be compared to classical trajectory cal-124