Nonhydrogen atom

They compared the PME method with equivalent simulations based on a 9 A residue-based cutoflF and found that for PME the averaged RMS deviations of the nonhydrogen atoms from the X-ray structure were considerably smaller than in the non-PME case. Also, the atomic fluctuations calculated from the PME dynamics simulation were in close agreement with those derived from the crystallographic temperature factors. In the case of DNA, which is highly charged, the application of PME electrostatics leads to more stable dynamics trajectories with geometries closer to experimental data [30]. A theoretical and numerical comparison of various particle mesh routines has been published by Desemo and Holm [31]. 

For the purposes of the following discussion small molecules are considered to have fewer than 200 nonhydrogen atoms. Macromolecules, primarily proteins, polynucleic acids, and vimses, can have many thousands of atoms. 

Information on the electronic configuration of each nonhydrogen atom is incorporated in the second order atomic index (S ) of the atom. 

Aldehydes up to a chain length of four nonhydrogen atoms are tolerated as acceptors. 2-Hydroxyaldehydes are relatively good acceptors, and the D-isomers are preferred over the t-isomers [180]. Reactions that lead to thermodynamically unfavorable structures may proceed with low stereoselectivity at the reaction center [181]. Recently, a single-point mutant aldolase was found 2.5 times more effective than the wild type in accepting unphosphorylated glyceraldehyde [182,183]. 

The CASE approach is quite different. CASE decomposes a molecule into all possible fragments from two to ten heavy (nonhydrogen) atoms. With a statistical technique, these are then classified into biophores (allied to toxicity) and biophobes (not allied to toxicity). These are then combined into an equation ... 

The geometry of nitromethane (1) is characterized by the equivalence of the two NO bonds, the single bond character of the CN bond, the coplanarity of the four nonhydrogen atoms, and a value of the zONO angle larger than 120°. The geometry of aci-nitromethane (4) is characterized by the nonequivalence of two NO bonds, the double bond character of the... 

Thus, in each molecule, there are two sets of E-state values one for all nonhydrogen atoms and the second for the hydrogen atoms. The HS values are zero for atoms without hydrogens. 

Percentage of structures with an RM S deviation of the nonhydrogen atoms less than 0.3 A. 

Quasielastic (Rayleigh) scattering of the 46.5 keV Mossbauer radiation was used to examine the liquid dynamics of glycerol [245, 246] and the harmonic vibrations of the nonhydrogen atoms in polycrystalline myoglobin [247] as a function of temperature. The y-quanta emitted by the Mossbauer source are... 

Figure 4. A perspective drawing of C.jH NjSi.B, with nonhydrogen atoms represented by thermal vibration ellipsoids drawn to encompass 50% of their electron density hydrogen atoms are represented by arbitrarily small spheres which are in no way representative of their true thermal motion.

Figure 2. ORTEP drawing of the nonhydrogen atoms of one of the two crystal-lographically independent Th[(CHS)5C5]2[p-CO(CH2C(CHs)s)CO]Cl molecules in the unit cell of 5. The stereochemistry of the second molecule differs from this one primarily in the orientation of the t-butyl groups. All atoms are represented by thermal-vibration ellipsoids drawn to encompass 50% of the electron density...

Intramolecular distances in theophylline monohydrate involving nonhydrogen atoms [20]... 

DN2Sy Triplet index from distance matrix, square of graph order ( of nonhydrogen atoms), and distance sum operation y — 1-5... 

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