Ab initio MD simulations

Furthermore, the electrical conductivities of liquid Na-Sn alloys for the five compositions are determined with the Kubo-Greenwood scheme, using the trajectories from our ab initio MD simulations. The calculated values reproduce the measured strong variation of the conductivity with the Na (or Sn) concentration very well. The small (semimetallic) conductivity of the alloys with nearly equimolar composition can be explained by the position of the Fermi energy between the occupied sp-band of tin and the sp-band of sodium. 

In addition, for the sodium-antimony alloy, where the Zintl anions are Sb spiral chains, ab initio MD simulations are in progress. 

Tab. 1.1 Comparison of the properties of quantum chemical electronic structure calculations (QC methods), classical molecular dynamics (Classical MD) based on empirical force fields and first-principles molecular dynamics (ab initio MD) simulations.

In order to reconcile this discrepancy, dynamics effect was examined by means of ab initio MD simulations at (U)B3LYP/6-31G. 44 Trajectories were initiated at the TS for the denitrogenation from 27 (R = Z = H) to 31 with 353 K Boltzmann distribution for the reaction coordinate translation. Out of 10 trajectories, 1 went back to the reactant, 8 gave 31, and 1 led directly to 29. Thus, the trajectory calculations reproduced experimental trend reported in the literature,45 namely spiropentane is the major product for the reaction of the parent 4-spirocyclopropane-l-pyrazoline. 

Ab initio MD simulations were not practical until the last decades of the 20th century due to their computational cost. In addition to rapid increase in computational power of modern computers, the factor of great importance for expansion of the ab initio molecular dynamics was a novel, practical scheme proposed by Car and Parinello.1 This methodology gave rise to a growing interest in ab initio MD and thus, quickly dominated the field. 

Quantum-mechanical approaches appear ideally suited to provide an understanding of the underlying molecular intercictions of the Asp dyad. Here, we present results from our ab initio MD simulations [100]. This investigation, which focuses on the free enzyme, is divided in two steps. First, we attempt to determine the protonation state of the Asp... 

Figure 13 Snapshots from an ab initio MD simulation (T = 300 K) of acetic acid on Pd(l 11) in the presence of water, (a) Acetate forms at the surface along with an H5O2+ intermediate adjacent to the acetate layer (b) acetate species and protons react at the surface to form acetic acid (c) water displaces acetic acid from the surface (d) water adsorbs to the surface (e) acetic acid rotates in solution toward the water layer (f) acetic acid dissociates in solution to form acetate anions and protons in solution. (Adapted from Ref. [77].)...

Paddison, Eikerling and coworkers performed quantum chemical calculations and ab initio MD simulations of crystal hydrates [89-91], The studies reveal the strong influence of the acid functional group on proton mobility at low humidity they show how chemical modifications of side chain entities can make the dissociation of the acid more complete. 

In the simulations that are referred to as first-principles molecular dynamics (FPMD), or ab initio MD, simulations, the motions of the nuclei are... 

This method can be employed to treat most molecules, however, for larger, highly flexible species, the conformational space may be too large for convergence to occur. Ab initio MD simulations (Carr Parinello, CPMD), which are based on Newtonian dynamics and where the interaction potential is handled quantum mechanically/ tend to be important for the treatment of large systems. 

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