Quantum-chemical modeling

The main purpose of quantum-chemical modeling in materials simulation is to obtain necessary input data for the subsequent calculations of thermodynamic and kinetic parameters required for the next steps of multiscale techniques. Quantum-chemical calculations can also be used to predict various physical and chemical properties of the material in hand (the growing film in our case). Under quantum-chemical, we mean here both molecular and solid-state techniques, which are now implemented in numerous computer codes (such as Gaussian [25], GAMESS [26], or NWCHEM [27] for molecular applications and VASP [28], CASTEP [29], or ABINIT [30] for solid-state applications). 

While quantum-chemical calculations related to gas-phase reactions or bulk properties have become now a matter of routine, calculations of local properties and, in particular, surface reactions are still a matter of art. There is no simple and consistent way of adequately constructing a model of a surface impurity or reaction site. We will briefly consider here three main approaches (1) molecular models, (2) cluster models, and (3) periodic slab models. 

In molecular models, a surface site is modeled using an analogous molecular reaction. This is the simplest approach, which requires the least amount of computational resources. The selection of a molecule that can more or less adequately reproduce the properties of the surface site under study determines the success or failure of the approach. This approach was used in Ref. [20] in the multiscale simulation of zirconium and hafnium oxide film growth. 

In cluster models, a surface site is modeled using a surface fragment (cluster) that contains the surface site of interest and its nearest environment. The further procedure depends on the substrate type. 

In the case of ionic materials, the cluster simulating a surface site must be embedded in the surrounding matrix. The problem of embedding has been discussed in numerous papers, and many embedding recipes and techniques have been proposed [41 48]. 

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QUANTUM-CHEMICAL MODELLING OL PROCESSES OF INTERACTION OF ACTIVE FORMS OF OXYGEN WITH PHOSPHOLIPIDES... 

It is well known and accepted that the quality of the methods as well as of the underlying models has great effect on the results of scientific research, This is especially applicable to quantum chemical model calculations. If the method is adequate to the subject of investigation, and the model is well adapted, then a good modelling of macroscopic processes on a microscopic level can be expected. That is why it is of importance to... 

Essential assertions can be obtained by examining the following results of quantum chemical model calculations from the point of view of reaction theory 5> 7 72 73). 

The description of reactive intermediates, which are short-lived species, is the main field of application of quantum chemical model calculations, due to the fact that the intermediates are difficult to observe and characterize. For example, the influence of structure on the stability of various carbenium ions — which have been used as models of the cationic chain end — and the delocalization of the positive charge were treated on this basis. 

The results from quantum chemical model calculations described above represent a valuable tool for solving reaction theoretical problems. In the field of cationic polymerization, for instance, the following problems could be dealt with ... 

The competing reactions are isomerization of the cationic chain end, transfer reactions to monomer, counterion and solvent, and also termination reactions. The actual process of propagation depends on the concrete interactions between the reactants present in the polymerizing system. A synopsis of interactions expected is given in Table 7. For the most important of them quantum chemical model calculations were carried out. 

Scheme 5.22 Quantum-chemical model system of the lipase-catalyzed Michael addition of methanethiol to acrolein [110],...

Theoretical chemistry works on models. My point of view on models in chemistry - and quantum chemistry in partieidar - has been expressed elsewhere [6] this view closely corresponds to that expressed by other eolleagues [7-11]. 1 suggested a partition of a quantum chemical model into three eomponents, and in my scientific practice I have always taken into consideration the presenee and interplay of these three components. The consideration of the evolution of the whole quantum ehemistiy suggests me now the introduction of a fourth component of the models. My revised partition of quantum chemical models may be put in the following form... 

The introduction of the last eomponents in quantum chemical models makes easier the analysis of the second methodological point I will consider here. 

QuantlogP, developed by Quantum Pharmaceuticals, uses another quantum-chemical model to calculate the solvation energy. As in COSMO-RS, the authors do not explicitly consider water molecules but use a continuum solvation model. However, while the COSMO-RS model simpUfies solvation to interaction of molecular surfaces, the new vector-field model of polar Uquids accounts for short-range (H-bond formation) and long-range dipole-dipole interactions of target and solute molecules [40]. The application of QuantlogP to calculate log P for over 900 molecules resulted in an RMSE of 0.7 and a correlation coefficient r of 0.94 [41]. 

Besides these generalities, little is known about proton transfer towards an electrode surface. Based on classical molecular dynamics, it has been suggested that the ratedetermining step is the orientation of the HsO with one proton towards the surface [Pecina and Schmickler, 1998] this would be in line with proton transport in bulk water, where the proton transfer itself occurs without a barrier, once the participating molecules have a suitable orientation. This is also supported by a recent quantum chemical study of hydrogen evolution on a Pt(lll) surface [Skulason et al., 2007], in which the barrier for proton transfer to the surface was found to be lower than 0.15 eV. This extensive study used a highly idealized model for the solution—a bilayer of water with a few protons added—and it is not clear how this simplification affects the result. However, a fully quantum chemical model must necessarily limit the number of particles, and this study is probably among the best that one can do at present. 

Nazmutdinov RR, Shapnik MS. 1996. Contemporary quantum chemical modelling of electrified interfaces. Electrochim Acta 41 2253-2265. 

FIG. 6 Quantum chemical model of the CT complex of a polyanion and water. (From Ref. 33. Copyright 1996 Elsevier Science B.V., Amsterdam.)... 

Having all the essential building blocks of the DeNO, mechanism well established and verified spectroscopically, quantum chemical modeling may be then used for providing a molecular rational for the observed structure-reactivity relationships. The first mechanistic cycle of the DeNO reaction, where NO reacting with Cu Z center is transformed into N20, involves the following steps ... 

Broclawik, E., Datka, J., Gil, B. et al. (2000) T-O-T skeletal vibration in CuZSM-5 zeolite IR study and quantum chemical modeling, Phys. Chem. Chem. Phys., 2, 401. 

This section concerns unsubstituted planar polyenes C H, , n even and m = n+2(l—r), r being the number of rings, i.e. 7r-sy sterns with all atoms, C and H, in a common plane. Low man on the totem pole of quantum-chemical models adequate for such polyenes (and, of course, for aromatic 7r-sy sterns) is the Hiickel (HMO) treatment2 which assumes strict orthogonality between the molecular [Pg.199]

For molecules and molecular ions, such as the cations of 8-methyl-N5-deazapterin and 8-methyl-pterin, the charge distribution (which is represented in MD simulations by a set of discrete atomic charges) will be dependent on the chosen quantum chemical model. Differences in the charge distributions of these cations may influence both the relative binding and solvation thermodynamics. Consequently, we studied the relative solvation thermodynamics of similar DHFR-binding molecular ions.30 Atomic charges... 

T. Kugler, M. Logdlun, and W.R. Saneck, Photoelectron spectroscopy and quantum chemical modeling applied to polymer surfaces and interfaces in light-emitting devices, Acc. Chem. Res., 32 225-234, 1999. 

J. R. Alvarez-Idaboy, R. Gonzalez-Jonte, A. Hernandez-Laguna, Y. G. Smeyers, Reaction Mechanism of the Acyl-Enzyme Formation in /3-Lactam Hydrolysis by Means of Quantum Chemical Modeling , J. Mol. Struct. 2000, 204, 13 - 28. 

The structure effects on rate in the catalytic dehydration of alcohols on acidic catalysts also have been elucidated by quantum-chemical modeling of the adsorption complex in a series of alcohols R CH(OH)-CH3, using a proton as a simple model of the catalyst 69). It has been found that the protonation of the hydroxyl group causes an increasing weakening of the C—O bond in the order R = CHj, C2H5, /-C3H7, This corresponds... 

As pointed out in the preface, a wide variety of different procedures or models have been developed to calculate molecular structure and energetics. These have generally been broken down into two categories, quantum chemical models and molecular mechanics models. 

The opening chapter in this section outlines a number of different classes of Quantum Chemical Models and provides details for a few specific models. It anticipates issues relating to cosf and capability (to be addressed in detail in Section II). Similar treatment of Molecular Mechanics Models is provided in the second chapter in this section. 

Important quantities which come out of molecular mechanics and quantum chemical models are typically related in terms of numbers , e.g., the heat of a chemical reaction, or in terms of simple diagrams, e.g., an equilibrium structure. Other quantities, in particular those arising from quantum chemical models, may not be best expressed in this way, e.g., the distribution of electrons in molecules. Here computer graphics provides a vessel. This is addressed in the concluding chapter in this section. Graphical Models. 

These terms were introduced by John Pople, who in 1998 received the Nobel Prize in Chemistry for his work in bringing quantum chemical models into widespread use. 

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