Simulation density functional theory

Among the electronic stracture methods to be used in AIMD simulations, density functional theory (DPT) [27], because of accuracy and favorable scaling with the number of atoms, is the reconunended method to model organometallic systems. Extensive research has been dedicated to test and improve the performance of DPT when dealing with transition metal systems, and dedicated reviews cover recent developments [28-30]. 

The entropically driven disorder-order transition in hard-sphere fluids was originally discovered in computer simulations [58, 59]. The development of colloidal suspensions behaving as hard spheres (i.e., having negligible Hamaker constants, see Section VI-3) provided the means to experimentally verify the transition. Experimental data on the nucleation of hard-sphere colloidal crystals [60] allows one to extract the hard-sphere solid-liquid interfacial tension, 7 = 0.55 0.02k T/o, where a is the hard-sphere diameter [61]. This value agrees well with that found from density functional theory, 7 = 0.6 0.02k r/a 2 [21] (Section IX-2A). 

Handy, N.C. Density functional theory. In Quantum mechanical simulation methods for studying biological systems, D. Bicout and M. Field, eds. Springer, Berlin (1996) 1-35. 

The dynamic mean-field density functional method is similar to DPD in practice, but not in its mathematical formulation. This method is built around the density functional theory of coarse-grained systems. The actual simulation is a... 

In 1985 Car and Parrinello invented a method [111-113] in which molecular dynamics (MD) methods are combined with first-principles computations such that the interatomic forces due to the electronic degrees of freedom are computed by density functional theory [114-116] and the statistical properties by the MD method. This method and related ab initio simulations have been successfully applied to carbon [117], silicon [118-120], copper [121], surface reconstruction [122-128], atomic clusters [129-133], molecular crystals [134], the epitaxial growth of metals [135-140], and many other systems for a review see Ref. 113. 

Fig. 10(a) presents a comparison of computer simulation data with the predictions of both density functional theories presented above [144]. The computations have been carried out for e /k T = 7 and for a bulk fluid density equal to pi, = 0.2098. One can see that the contact profiles, p(z = 0), obtained by different methods are quite similar and approximately equal to 0.5. We realize that the surface effects extend over a wide region, despite the very simple and purely repulsive character of the particle-wall potential. However, the theory of Segura et al. [38,39] underestimates slightly the range of the surface zone. On the other hand, the modified Meister-Kroll-Groot theory [145] leads to a more correct picture. 

In this chapter we have largely relied on computational chemistry, in particular on density-functional theory. Quantum mechanical calculations of a macroscopic piece of metal with various species adsorbed on it are as yet impossible, but it is possible to obtain realistic results on simplified systems. One approach is to simulate the metal by a cluster of 3-30 atoms on which the molecule adsorbs and then describe all the involved orbitals. Many calculations have been performed on this basis with many useful results. Obviously, the cluster must be sufficiently large that the results do not represent an artefact of the particular cluster size chosen, which can be verified by varying the cluster size. 

Forda, M.J., Hoft, R.C. and Gale, J.D. (2006) Adsorption and dimerisation of thiol molecules on Au(lll) using a Z-matrix approach in density functional theory. Molecular Simulation, 32, 1219-1225. 

Ab initio methods allow the nature of active sites to be elucidated and the influence of supports or solvents on the catalytic kinetics to be predicted. Neurock and coworkers have successfully coupled theory with atomic-scale simulations and have tracked the molecular transformations that occur over different surfaces to assess their catalytic activity and selectivity [95-98]. Relevant examples are the Pt-catalyzed NO decomposition and methanol oxidation. In case of NO decomposition, density functional theory calculations and kinetic Monte Carlo simulations substantially helped to optimize the composition of the nanocatalyst by alloying Pt with Au and creating a specific structure of the PtgAu7 particles. In catalytic methanol decomposition the elementary pathways were identified... 

While in previous ab initio smdies the reconstructed surface was mostly simulated as Au(lll), Feng et al. [2005] have recently performed periodic density functional theory (DFT) calculations on a realistic system in which they used a (5 x 1) unit cell and added an additional atom to the first surface layer. In their calculations, the electrode potential was included by charging the slab and placing a reference electrode (with the counter charge) in the middle of the vacuum region. From the surface free energy curves, which were evaluated on the basis of experimentally measured capacities, they concluded that there is no necessity for specific ion adsorption [Bohnen and Kolb, 1998] and that the positive surface charge alone would be sufficient to lift the reconstmction. 

Further studies were carried out with halocarbene amides 34 and 357 Although again no direct spectroscopic signatures for specifically solvated carbenes were found, compelling evidence for such solvation was obtained with a combination of laser flash photolysis (LFP) with UV-VIS detection via pyridine ylides, TRIR spectroscopy, density functional theory (DFT) calculations, and kinetic simulations. Carbenes 34 and 35 were generated by photolysis of indan-based precursors (Scheme 4.7) and were directly observed by TRIR spectroscopy in Freon-113 at 1635 and 1650 cm , respectively. The addition of small amounts of dioxane or THF significantly retarded the rate of biomolecular reaction with both pyridine and TME in Freon-113. Also, the addition of dioxane increased the observed lifetime of carbene 34 in Freon-113. These are both unprecedented observations. 

Termath, V., Sauer, J., 1997, Ab Initio Molecular Dynamics Simulation of H502+ and H703+ Gas Phase Clusters Based on Density Functional Theory , Mol. Phys., 91, 963. 

Van Bavel, A. P., Hermse, C. G. M., Hopstaken, M. J. P. et al. (2004) Quantifying lateral adsorbate interactions by kinetic Monte-Carlo simulations and density-functional theory NO dissociation on Rh(100) , Phys. Chem. Chem. Phys., 6, 1830. 

Equation (4-5) can be directly utilized in statistical mechanical Monte Carlo and molecular dynamics simulations by choosing an appropriate QM model, balancing computational efficiency and accuracy, and MM force fields for biomacromolecules and the solvent water. Our group has extensively explored various QM/MM methods using different quantum models, ranging from semiempirical methods to ab initio molecular orbital and valence bond theories to density functional theory, applied to a wide range of applications in chemistry and biology. Some of these studies have been discussed before and they are not emphasized in this article. We focus on developments that have not been often discussed. 

That classical calculation may be a density functional theory (DFT) ab initio simulation. An ab initio treatment may be important to handle charge redistribution effects in the condensed phase. 

Schwegler, E. Grossman, J. C. Gygi, F. Galli, G., Towards an assessment of the accuracy of density functional theory for first principles simulations of water II, J. Chem. Phys. 2004,121, 5400-5409... 

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