Atom-based

Alternative descriptions of quantum states based on a knowledge of the electronic charge density equation Al.3.14 have existed since the 1920s. For example, the Thomas-Femii description of atoms based on a knowledge of p (r)... 

The power of optical spectroscopies is that they are often much better developed than their electron-, ion- and atom-based counterparts, and therefore provide results that are easier to interpret. Furtlienuore, photon-based teclmiques are uniquely poised to help in the characterization of liquid-liquid, liquid-solid and even solid-solid interfaces generally inaccessible by other means. There has certainly been a renewed interest in the use of optical spectroscopies for the study of more realistic systems such as catalysts, adsorbates, emulsions, surfactants, self-assembled layers, etc. 

Atoms not explicitly included in the trajectory must be generated. The position at which an atom may be placed is in some sense arbitrary, the approach being analogous to the insertion of a test particle. Chemically meaningful end states may be generated by placing atoms based on internal coordinates. It is required, however, that an atom be sampled in the same relative location in every configuration. An isolated molecule can, for example, be inserted into... 

GENSTAR [67] atom-based, grows molecules in situ based on an enzyme contact model ... 

Molecular clynainics sim illations calculate future position s and velocities of atoms, based on their current positions and velocities. A sim Illation first determ in es the force on each atom (lY) as a function of time, ct ual to the negative gradient of the polen tial en ergy (ct]uation 2 I ),... 

The builder works very well. It has an atom-based mode in which the user chooses the element and hybridization. There are also libraries of functional... 

A molecular system at room temperature is accurately characterized by its motion. Molecular dynamics simulations calculate the future positions and velocities of atoms based upon their current values. You can obtain qualitative and quantitative data from HyperChem molecular dynamics simulations. 

Table 1. Summary of Atomizers Based on Source of Energy...

Hollow Sprays. Most atomizers that impart swid to the Hquid tend to produce a cone-shaped hoUow spray. Although swid atomizers can produce varying degrees of hoUowness in the spray pattern, they aU seem to exhibit similar spray dynamic features. For example, detailed measurements made with simplex, duplex, dual-orifice, and pure airblast atomizers show similar dynamic stmctures in radial distributions of mean droplet diameter, velocity, and Hquid volume flux. Extensive studies have been made (30,31) on the spray dynamics associated with pressure swid atomizers. Based on these studies, some common features were observed. Test results obtained from a pressure swid atomizer spray could be used to iUustrate typical dynamic stmctures in hoUow sprays. The measurements were made using a phase Doppler spray analyzer. 

The energy functions for folding simulations include atom-based potentials from molecular mechanics packages [164] such as CHARMM [81], AMBER [165], and ECEPP... 

T Lazaridis, G Archontis, M Karplus. Enthalpic contribution to protein stability Atom-based calculations and statistical mechanics. Adv Protein Chem 47 231-306, 1995. 

Fig. 20. Schematic representation of the unrolled major groove of the MPD 7 helix showing the first hydration shell, consisting of all solvent molecules that are directly associated with base edge N and O atoms. Base atoms are labeled N4,04, N6,06 and N7 solvent peaks are numbered. Interatomic distances are given in Aup to 3,5 A represented by unbroken lines, between 3,5-4,1 A by dotted lines. The eight circles connected by double-lines represent the image of a spermine molecule bound to phosphate groups P2 and P22. There are 20 solvent molecules in a first hydration layer associated with N- and O-atoms l58)...

The rapid rise in computer power over the last ten years has opened up new possibilities for modelling complex chemical systems. One of the most important areas of chemical modelling has involved the use of classical force fields which represent molecules by atomistic potentials. Typically, a molecule is represented by a series of simple potential functions situated on each atom that can describe the non-bonded interaction energy between separate atomic sites. A further set of atom-based potentials can then be used to describe the intramolecular interactions within the molecule. Together, the potential functions comprise a force field for the molecule of interest. 

The rapid rise in computer speed over recent years has led to atom-based simulations of liquid crystals becoming an important new area of research. Molecular mechanics and Monte Carlo studies of isolated liquid crystal molecules are now routine. However, care must be taken to model properly the influence of a nematic mean field if information about molecular structure in a mesophase is required. The current state-of-the-art consists of studies of (in the order of) 100 molecules in the bulk, in contact with a surface, or in a bilayer in contact with a solvent. Current simulation times can extend to around 10 ns and are sufficient to observe the growth of mesophases from an isotropic liquid. The results from a number of studies look very promising, and a wealth of structural and dynamic data now exists for bulk phases, monolayers and bilayers. Continued development of force fields for liquid crystals will be particularly important in the next few years, and particular emphasis must be placed on the development of all-atom force fields that are able to reproduce liquid phase densities for small molecules. Without these it will be difficult to obtain accurate phase transition temperatures. It will also be necessary to extend atomistic models to several thousand molecules to remove major system size effects which are present in all current work. This will be greatly facilitated by modern parallel simulation methods that allow molecular dynamics simulations to be carried out in parallel on multi-processor systems [115]. 

In this chapter, we describe substructure-based logP calculation approaches comprising fragmental and atom-based methods property-based approaches are discussed in Chapter 15. 

Atom-based methods [40, 57-68] cut molecules down to single atoms and commonly do not apply correction rules. According to Eq. (9) they work by summing the products of the contribution of an atom type i times the frequency of its presence in a query molecule ... 

The group of Grippen [40, 61-63] has described the development of a purely atom-based procedure, which exclusively applies atomic contributions and avoids correction factors ... 

I 14 Prediction of Log with Substructure-based Methods Tab. 14.3 Atom-based methods. 

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