Atom pairs

The structure of a fluid is characterized by the spatial and orientational correlations between atoms and molecules detemiiued through x-ray and neutron diffraction experiments. Examples are the atomic pair correlation fiinctions (g, g. . ) in liquid water. An important feature of these correlation functions is that... 

The analysis of recent measurements of the density dependence of has shown, however, that considering only the variation of solvent structure in the vicinity of the atom pair as a fiinction of density is entirely sufficient to understand tire observed changes in with pressure and also with size of the solvent molecules [38]. Assuming that iodine atoms colliding with a solvent molecule of the first solvation shell under an angle a less than (the value of is solvent dependent and has to be found by simulations) are reflected back onto each other in the solvent cage, is given by... 

Additionally, to optimize task 4, we applied a conventional, atom pair interaction based multiple-time-step scheme to the force computation within Ihe innermost distance class. Here, for atom pairs closer than 5 A, the Coulomb sum is calculated every step, and for all other atom pairs the Coulomb sum is extrapolated every second step from previously explicitly calculated forces. 

Table 6-3 shows an example of a molecule parsed into atom pairs and topological... 

Table 6.3. Sample molecules acetone and isobutene described by atom pair (ap) descriptors.

Mixtures containing up to several thousand distinct chemical entities are often synthesized and tested in mix-and-split combinatorial chemistry. The descriptor representation of a mixture may be approximated as the descriptor average of its individual component molecules, e.g., using atom-pair and topological torsion descriptors. 

The atom pair, ap, and topological torsion, tt, descriptors are selected for illustrative purposes in the similarity searching context. 

The connection table of the query object (similarity probe) is processed to obtain the set of atom pairs, and then the database file is scanned to evaluate the similarity between the query and each of the database structures. The maximum number of structures that the program will select is specified, as well as the minimum similarity score that a database compoimd must show to be selected. Within these limits, the program will select from the database the structures that are most similar (with the highest similarity value) to the query and will create an output file of compoimd numbers and similarity values, sorted by decreasing similarity, for the selected compounds. 

In this case, only two parameters (k and Iq) per atom pair are needed, and the computation of a quadratic function is less expensive. Therefore, this type of expression is used especially by biomolecular force fields (AMBER, CHARMM, GROMOS) dealing with large molecules like proteins, lipids, or DNA. 

Atom pairs, topological torsions 2D structure See Section 12.9.3... 

Carhart R E, D H Smith and R Venkataraghavan 1985. Atom Pairs as Molecular Features in Structure Activity Studies Definition and Applications. Journal of Chemical Information and Computer Scienc 25 64-73. 

In the sodium atom pairs of 3/2 states result from the promotion of the 3s valence electron to any np orbital with n > 2. It is convenient to label the states with this value of n, as n P 1/2 and n f 3/2, the n label being helpful for states that arise when only one electron is promoted and the unpromoted electrons are either in filled orbitals or in an x orbital. The n label can be used, therefore, for hydrogen, the alkali metals, helium and the alkaline earths. In other atoms it is usual to precede the state symbols by the configuration of the electrons in unfilled orbitals, as in the 2p3p state of carbon. 

Since empirical force fields do not accurately estimate the true interatomic forces, it is difficult a priori to say how accurate the fast multipole approximation to the exact Coulomb potential and forces (exact in terms of the sum over partial charges) should be. Probably a good rule is to make sure that at each atom the approximate electrostatic force is within a few percent relative error of the true electrostatic force, obtained by explicitly summing over all atom pairs, i.e., IF — FJ < 0.05 F , for all atoms i, where F is the... 

Bahar et al. [46] have used this kind of approach to predict the B-factors of 12 X-ray structures. Elements in the Hessian corresponding to atom pairs separated by a distance of less than 7 A are set to zero, and the remainder have the same value dependent on a single adjustable parameter. Generally B-factor predictions for the a-carbons compare very well with the B-factors measured by X-ray crystallography. Figure 1 shows the result for the subunit A of endodeoxyribonuclease I complexed with actin. 

The second step concerns distance selection and metrization. Bound smoothing only reduces the possible intervals for interatomic distances from the original bounds. However, the embedding algorithm demands a specific distance for every atom pair in the molecule. These distances are chosen randomly within the interval, from either a uniform or an estimated distribution [48,49], to generate a trial distance matrix. Unifonn distance distributions seem to provide better sampling for very sparse data sets [48]. 

The assignment of resonances in Table 14.2 results from summation of substituent effects as listed in Table 14.1. The data refer to conformer I for conformer II the C atoms pairs C-l/C-2, C-3/C-6, C-4/C-5 and C-7/C-8 change places. 

The technique of INS is probably the least used of those described here, because of experimental difficulties, but it is also one of the physically most interesting. Ions of He" of a chosen low energy in the range 5-10 eV approach a metal surface and within an interaction distance of a fraction of a nanometer form ion-atom pairs with the nearest surface atoms. The excited quasi molecule so formed can de-excite by Auger neutralization. If unfilled levels in the ion fall outside the range of filled levels of the solid, as for He", an Auger process can occur in which an electron from the va-... 

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