Ab-initio molecular simulation

The ab initio molecular simulation was carried out in the NPT ensemble with version 3.9.1 of CPMD [29]. In the calculation, 20 water and one acetic acid molecules were simulated in a periodic cubic cell under an ambient condition of a constant pressure 1 bar, a constant temperature 300 K, and density of 1.0 gem-3. The starting structure was constructed in a simple flexible cubic cell with a length of 8.8794 A, by randomly adding 11 water molecules to an optimized hydration compound composed of a single acetic acid molecule and 9 water molecules. 

Blum et al. suggested the application of numerically tabulated atom-centered orbitals (NAOs) in AIMD. These basis sets are implemented in the ab initio molecular simulations package FHI-aims. In benchmark calculations the authors showed an 0(N) scalability and a good parallelization [38]. 

Atta-Fynn R, Bylaska EJ and de Jong WA 2013 Importance of counteranions on the hydration structure of the curium ion. The Journal of Physical Chemistry Letters 4(13), 2166-2170. Atta-Fynn R, Johnson DF, Bylaska EJ, llton ES, Schenter GK and De Jong WA 2012b Structure and hydrolysis of the u (iv), u (v), and u (vi) aqua ions from ab initio molecular simulations. 

Figure Al.3.30. Theoretical frequency-dependent conductivity for GaAs and CdTe liquids from ab initio molecular dynamics simulations [42].

Applications of Ab-Initio Molecular Dynamics Simulations in Chemistry and Polymer Science... 

The full ab-initio molecular dynamics simulation revealed the insertion of ethylene into the Zr-C bond, leading to propyl formation. The dynamics simulations showed that this first step in ethylene polymerisation is extremely fast. Figure 2 shows the distance between the carbon atoms in ethylene and between an ethylene carbon and the methyl carbon, from which it follows that the insertion time is only about 170 fs. This observation suggests the absence of any significant barrier of activation at this stage of the polymerisation process, and for this catalyst. The absence or very small value of a barrier for insertion of ethylene into a bis-cyclopentadienyl titanocene or zirconocene has also been confirmed by static quantum simulations reported independently... 

Sandre E and A Pasturel 1997. An Introduction to Ab-Initio Molecular Dynamics Schemes. Molecu Simulation 20 63-77. 

Rothlisberger and M Parrinello 1997. Ab Initio Molecular Dynamics Simulation of Liquid Hydroge Fluoride. Journal of Chemical Physics 106 4658-4664. 

AB INITIO MOLECULAR DYNAMICS SIMULATIONS OF LIQUID ALLOYS ... 

A successful tool to describe and interpret experimental findings of liquids is to perform ab initio molecular dynamics (MD) simulations for the particular systems. We performed such simulations for 5 different compositions of NaSn - ranging from 20% to 80% of sodium - applying the Car-Parrinello technique [5]. 

Computer simulations therefore have several inter-related objectives. In the long term one would hope that molecular level simulations of structure and bonding in liquid crystal systems would become sufficiently predictive so as to remove the need for costly and time-consuming synthesis of many compounds in order to optimise certain properties. In this way, predictive simulations would become a routine tool in the design of new materials. Predictive, in this sense, refers to calculations without reference to experimental results. Such calculations are said to be from first principles or ab initio. As a step toward this goal, simulations of properties at the molecular level can be used to parametrise interaction potentials for use in the study of phase behaviour and condensed phase properties such as elastic constants, viscosities, molecular diffusion and reorientational motion with maximum specificity to real systems. Another role of ab initio computer simulation lies in its interaction... 

Ab initio molecular orbital calculations are being used to study the reactions of anionic nucleophiles with carbonyl compounds in the gas phase. A rich variety of energy surfaces is found as shown here for reactions of hydroxide ion with methyl formate and formaldehyde, chloride ion with formyl and acetyl chloride, and fluoride ion with formyl fluoride. Extension of these investigations to determine the influence of solvation on the energy profiles is also underway the statistical mechanics approach is outlined and illustrated by results from Monte Carlo simulations for the addition of hydroxide ion to formaldehyde in water. 

M. Odelius, M. Kadi, J. Davidsson, and A. N. Tarnovsky, Photodissociation of diiodomethane in acetonitrile solution and fragment recombination into iso-diiodomethane studied with ab initio molecular dynamics simulations. J. Chem. Phys. 121(5), 2208-2214 (2004). 

The measurement of these angles for a series of [PdClj(NHC) P(OR)3 ] complexes permitted to evidence the remarkable flexibility of NHCs due to rotations aronnd the iV-substituent bonds [82]. This flexibility, captured by the allows NHCs to respond actively to the steric requirements of co-ligands. This is further confirmed by ab initio molecular dynamics simulations aimed at understanding the variability of ( )j and in a series of NHCs containing Ru-complexes relevant to olefin metathesis [83]. 

In addition to enhancing surface reactions, water can also facilitate surface transport processes. First-principles ab initio molecular dynamics simulations of the aqueous/ metal interface for Rh(l 11) [Vassilev et al., 2002] and PtRu(OOOl) alloy [Desai et al., 2003b] surfaces showed that the aqueous interface enhanced the apparent transport or diffusion of OH intermediates across the metal surface. Adsorbed OH and H2O molecules engage in fast proton transfer, such that OH appears to diffuse across the surface. The oxygen atoms, however, remained fixed at the same positions, and it is only the proton that transfers. Transport occurs via the symmetric reaction... 

Vassilev P, Hartnig C, Koper MTM, Frechard F, van Santen RA. 2001. Ab initio molecular dynamics simulation of liquid water and water-vapor interface. J Chem Phys 115 9815-9820. 

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