Ab-initio simulations

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. 

Ab initio Simulating MeCN (the Onsager Model), semiempirical The COSMO Model, MOPAPC 93 keywords NSPA = 60, EPS = 35.9, TS, PRECISE. 

Hofer, T.S., Tran, H.T., Schwenk, C.S. and Rode, B.M. (2004) Characterization of dynamics and reactivities of solvated ions by ab initio simulations. Journal of Computational Chemistry, 25, 211—217. 

Monatomic Gold Wires with Single Molecules An Ab Initio Simulation. Physical Review Letters, 89, 186402-1-186402-4. 

These results show that the electrochemical measurements can, via ab initio simulations, be linked to phenomena at the atomic level, such as structural and electronic effects and, in this case, binding energies on the surfaces. 

Figure 4.5 The trajectory of water molecules during an ab initio simulation of the electrode/ electrolyte interface. The disentanglement and then reorganization of water molecules into bilayers can be clearly seen as time progresses [Taylor, 2009b].

Markwick PRL, Doltsinis NL (2007) Ultrafast repair of irradiated DNA nonadiabatic ab initio simulations of the guanine-cytosine photocycle. J Chem Phys 126 175102... 

How important the breakdown of the Born-Oppenheimer approximation is in limiting our ability to carry out ab initio simulations of chemical reactivity at metal surfaces is the central topic of this review. Stated more provocatively, do we have the correct theoretical picture of heterogeneous catalysis. This review will restrict itself to a consideration of experiments that have begun to shed light on this important question. The reader is directed to other recent review articles, where aspects of this field of research not mentioned in this article are more fully addressed.10-16... 

The coupled DFT/MM formalism can be regarded as an intermediate approximation between ab initio molecular dynamics, and classical molecular mechanics. Being so, the range of its applicability extends to problems not treatable by molecular mechanics, chemical reactions for instance. The possibility of restricting quantum-mehcanical treatment to well-localized regions also makes it computationally advantageous over supermolecule ab initio simulations. It is important to note that this formalism does not differ whether applied to study biochemical reactions or to study reactions taking place in an other microscopic environment. This makes it possible to test any implementation on problems for which there... 

In an ab initio simulation, the electronic structure problem is solved for each nuclear configuration, and forces are computed using the Hellmann-Feynman theorem. 

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. 

Ab initio simulations of water using classical propagation generally lead to an overstructured liquid compared with experiment. 

Treating water as a rigid molecule in ab initio simulations leads to a destructuring of the fluid relative to classical flexible water. 

The radial distribution functions in ab initio simulations agree with experiment if the temperature is raised by roughly 50 K, consistent with results from the... 

A quasichemical theory, using ab initio simulation (rPBE functional) to generate data for the computation of the various contributions to the free energy, yields an estimate for the excess chemical potential of water very close to the experimental value. 

The QM/MM and ab initio methodologies have just begun to be applied to challenging problems involving ion channels [73] and proton motion through them [74]. Reference [73] utilizes Hartree-Fock and DFT calculations on the KcsA channel to illustrate that classical force fields can fail to include polarization effects properly due to the interaction of ions with the protein, and protein residues with each other. Reference [74] employs a QM/MM technique developed in conjunction with Car-Parrinello ab initio simulations [75] to model proton and hydroxide ion motion in aquaporins. Due to the large system size, the time scale for these simulations was relatively short (lOps), but the influences of key residues and macrodipoles on the short time motions of the ions could be examined. 

We can expect to see future research directed at QM/MM and ab initio simulation methods to handle these electronic structure effects coupled with path integral or approximate quantum free energy methods to treat nuclear quantum effects. These topics are broadly reviewed in [32], Nuclear quantum effects for the proton in water have already received some attention [30, 76, 77]. Utilizing the various methods briefly described above (and other related approaches), free energy calculations have been performed for a wide range of problems involving proton motion [30, 67-69, 71, 72, 78-80]. 

Methods similar to those discussed in this chapter have been applied to determine free energies of activation in enzyme kinetics and quantum effects on proton transport. They hold promise to be coupled with QM/MM and ab initio simulations to compute accurate estimates of nulcear quantum effects on rate constants in TST and proton transport rates through membranes. 

Warkentin and co-workers continued studies on gas-phase pyrolysis of oxadiazoline derivatives. DFT calculations and ab initio simulations of PE spectra were used in the interpretation of the experimental results <2006CJC546>. 

The discrepancies in the reported conductance data of Au-alkanedithiol-Au junctions attracted our attention, and we decided to carry out an in-depth experimental study of the charge transport properties of Au-a,oo-alkanedithiol-Au molecule junctions in a non-conducting solvent. The combination with quantum chemistry ab initio simulations yielded a detailed view of this archetype of molecular junctions, and helped to resolve the puzzle on the role of microscopic geometries at the contacts and in the molecular conformation. 

Comparison of the experimental data with the trends predicted from quantum chemistry ab initio simulations demonstrated that the multiple conductance values of Au-alkanedithiol-Au junctions could be attributed to different Au-sulfur coordination geometries and to different conformations of the alkyl chain. In particular, the medium conductance corresponds to an all-trans conformation of the alkyl chain, with each sulfur atom coordinated in atop position to a single... 

Kalibaeva G, Vuilleumier R, Meloni S, Alavi A, Ciccotti G, and Rosei R. Ab initio simulation of carbon clustering on an Ni (111) Surface A model of the poisoning of nickel-based catalysts. J Phys Chem B 2006 110 3638-3646. 

The density functional calculations were performed using the Vienna Ab Initio Simulation Package (VASP). ° The spin-polarized generalized gradient approximation, Perdue—Wang exchange correlation function, and ultrasoft pseudopotentials were used. ... 

Abstract Special theoretical tools are needed to carry out ab initio simulations of... 

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