Atomization description

Martin M G and J I Siepmann 1999. Novel Configurational-bias Monte Carlo Method for Blanche Molecules. Transferable Potentials for Phase Equilibria. 2. United-atom Description of Branchi Alkanes. Journal of Physical Chemistry 103 4508-4517. 

Basis Set [Applicable Atoms] Description Basis Fimctions 1st row hydrogen atoms atoms Default Function Types ... 

One of the most important reasons for man s progress in understanding and controlling his environment is his ability to communicate knowledge to the next generation. It isn t necessary for each twentieth century scientist to invent the atomic description of matter. This was invented by John Dalton in the nineteenth century, and Dalton recorded his ideas in the scientific literature together with the observations that led him to the model. By study of this and subsequent literature a modern scientist can appraise the nature of the description, the facts it will explain, and the limitations. He is quickly able to approach the frontiers of knowledge—the frontiers defined by the limitations in our accepted models of the behavior of matter. 

The mapping procedure provides an explicit connection between an atomistic model of a polymer chain and the corresponding coarse-grained model. For PE, we use an united atom description for the CH2 groups, resulting in a potential of the following type [146,182,183] ... 

Garcia, A.E. Onuchic, J.N., Folding a protein in a computer An atomic description of the folding/unfolding of protein A, Proc. Natl Acad. Sci. USA 2003,100, 13898-13903... 

Polarization Functions. Functions of higher angular quantum than required for the Ground State atomic description. Added to a Basis Set to allow displacement of Valence Basis Functions away from atomic positions. 

Narrow bands arise when the overlap of the atomic wave functions is small (as for 5 f s). In this case, the dispersion E(k) is strongly reduced and the bandwidth W becomes very small (zero, in the case of no overlap). The electron charge density, caused by these wave functions, is high in the core region of Fig. 12, and the quasi-particles spend most of their life there, nearly bound to the atom. In case the charge density is all confined within the core region (as for 4f in lanthanides), then the bond description loses its meaning and the atomic description holds. 

Here we shall briefly discuss i. the of (11) ii. the parameters allowing to choose between a band or an atomic description. 

Atom description in QSAR models development and use of an atom level index, 22, 1 Autoradiographic investigations of cholinergic and other receptors in the motor endplate, 3, 81 The Binding of drugs to blood plasma macromolecules Recent advances and therapeutic... 

Optimization of the basis set for atoms inevitably introduces some bias towards the atomic description, although this effect is seldom noticeable in basis sets of the traditional types described in Sec. 4.2. Bias towards the atoms can appear, however, if very small ANO sets (or, presumably, cc sets) are used. An ANO set contracted to split-valence plus polarization, [3s 2p Id], is probably too contracted to provide a good description of molecular binding. In particular, the d NO may be quite different in shape from what is required to describe polarization and correlation in the molecule. At least two d orbitals should be included to properly allow for these effects. Hence ANO or cc basis sets smaller than, say, [4s 3p 2d] should probably not be used for molecular calculations. 

The first computational investigations of phospholipids were undertaken using purely statistical methods to describe overall properties. In the 1980s the simulation of molecules and their behavior using an explicit atomic description was extended to large systems such as proteins and lipids. To simulate the static and dynamic behav-... 

Masgrau L, A Roujeinikova, LO Johannissen, J Basran, KE Ranaghan, P Hothi, AJ Mulholland, MJ Sutcliffe, NS Scrutton, D Leys (2006) Atomic description of an enzyme reaction dominated by proton tunnelling. Science 312 237-241... 

Figure 6.8. Correlation of molecular orbitals in a two-centre system for equal nuclear charges. The united atom descriptions are shown on the left, with the molecular orbital descriptions on the right.

In the (notional and best avoided in practice) formation of NaCl from a sodium atom and a chlorine atom, descriptions like this abound in textbooks an electron is transferred from the valency shell of the sodium atom to the valency shell of the chlorine atom . 

ADAS is centred on generalized collisional-radiative (GCR) theory. The theory recognizes relaxation time-scales of atomic processes and how these relate to plasma relaxation times, metastable states, secondary collisions etc. Attention to these aspects - rigorously specified in generalized collisional-radiative theory - allow an atomic description suitable for modeling and analyzing spectral emission from most static and dynamic plasmas in the fusion and astrophysical domains [3,4]. 

The resemblance between LCAO bands and nearly-frec-electron bands is an assertion that at the observed interatomic distances in solids both the metallic and the atomic descriptions are tenable. This would certainly not be true at very large spacing, where the electronic states are truly atomic and the frce-electron description has no relevance. It is also not true at sufficiently high density, where the LCAO description has no relevance. The assertion applies only near the observed spacing. 

For convenience, we first discuss this problem for the case that an atomic description of the liquid is satisfactory. The sum is over all atoms of type a. This density is zero for the case that there are no atoms of type a (n = 0), so for the cases making a nonzero contribution, we distinguish a specific one of those atoms of type a present, say the first with location, and use Eq. (3.24). Thus we can write... 

The most successful X-ray scattering model beyond the simple, but widely used spherical-atom description consists of an expansion of atom-centered spherical harmonic functions (2). The radial dependence in this multipole model is given flexibility by the introduction of a radial parameter k, which scales the radial coordinate ... 

For metal surfaces the d s state will dominate the atomic description even if other states are dominant for the isolated atoms. This means that for both iron and cobalt surfaces, a barrierless dissociation over on-top sites is expected. For metal clusters with more than a single atom at least one atom is expected to be in the d s state, which means that a dissociation mechanism with a low barrier should exist in principle for all these iron, cobalt and nickel clusters. For the single metal atoms the low spin coupling between the d- and the s-hole was found to be important to reduce the repulsion to. The same type of spin-coupling is also important for clusters and surfaces. For clusters the spin-coupling will in general require a small excitation energy, which can cause the appearence of small barriers in the reaction with (8). 

Figure 1 Examples of lipids found commonly and used in cells, (a) DPPC (b) 1-palmitoyl-2-(1-pyrenedecanoyl)-sn-glycero-3-phosphocholine (PyrPC) (c) Palmitoyl-SM (d) Cholesterol (e) Dipalmitoylphosphatidylethanolamine (f) 1,2-di-0-palmitoyl-3-0-fi-D-galactosyl-sn-glycerol (DPGALA). Of these lipids, PyrPC is a pyrene-linked lipid probe and DPGALA is a glycolipid. The first four lipids are represented by a united-atom description, and the last two lipids are represented by a full-atom description.

The most popular technique to deal with lipid systems has by far been classical molecular dynamics (MD) (28, 30). In MD, all interactions are classic, and the time evolution of the system is described by integrating Newton s equations of motion. The particles can represent atoms or clusters of atoms the most typical choice is the full-atom description in which all atoms including hydrogens are described explicitly, and the united-atom description in which each methyl and methylene group is described by a single particle. The particle-particle interactions are usually determined from QM calculations and tuned even more in an iterative manner by fitting system properties to experiments until simulation results and experimental data match sufficiently well. Usually, the largest system sizes are hundreds... 

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