Nonhydrogen atoms drawing

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...

Fig. 2. Stereo drawing of all nonhydrogen atoms of basic pancreatic trypsin inhibitor. The main chain is shown with heavy lines and side chains with thin lines.

With the experience we have gained so far. it should be fairly easy to draw a structure for any formula. It is also possible to crudely estimate the stability of the compound represented by this structure. As an example, let s show the structure for the compound with the formula C2HeO. We quickly discover that there are two ways to assemble these atoms, depending on whether we start with a C—C—O or a C—O—C arrangement of the nonhydrogen atoms. 

In the survey of nucleoside and nucleotide crystal structures [62], there are five clear examples of C(6)H 0(50 hydrogen bonds of which three are three-centered (Thble 10.2). All are in pyrimidine nucleosides. For the purine nucleosides and nucleotides, there are insufficient structure determinations with hydrogen atoms located from X-ray data to draw any conclusions. However, in many nucleoside and nucleotide crystal structures, the nonhydrogen atom C- 0(50 distances are... 

Figure 6. Perspective drawing of the independent ascorbate anions A and B. Distances and angles for the nonhydrogen atoms are included in the drawing. (Reproduced, with permission, from Ref. 13. ...

Figure 6a. A stereo a-carbon stick drawing of fine lysozyme (from Bruccoleri et al. 1986), where the size of a circle associated with each a-carbon indicates die rms shift of the atoms in each residue resulting from the bending of the system from the minimized 0° structure to the 30° closed structure. The rotation of the lobes is removed from the calculation, so only relative shifts are considered here. In the drawing of the inhibitor, all nonhydrogen atoms are drawn, but no scaled cricles are used because the rms shifts for the inhibitor were quite large and they obscured the cleft Their diameter in the drawing would be approximately the width of the cleft In addition to plotting lines between each sequential a-carbons, four additional lines are drawn between a-carbons of residues involved in disulfide bridges. The sizes of the circles are scaled such that a rms shift of lA for a residue will result in a circle with diameter of 1cm.

Fig. 2. ORTEP drawing of the (CH3)2NPP2 molecule with 50% thermal motion ellipsoids for the nonhydrogen atoms. Bond lengths (in Angstroms) and angles (in degrees) are given with standard deviations expressed in units of the last significant figure 212).

The 1,5-interaction between two nonhydrogen atoms on and N or CO (Newman strain) constitutes the most important repulsive interaction in proteins. One first draws the formal C = N double bond in the Newman projection with up and N down. At ( ) = 0 both carbonyl... 

Figure 1. ORTEP drawing of the [Co(en)2(SCH2-CH2NH2) Cu(CHsC N2]2 cation. The 50% thermal prohahility ellipsoids are shown for all nonhydrogen atoms. Unlabeled atoms are related to the labeled ones by the crystallographic center of inversion (25).

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