International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F. ch. 24.3, p. 666

Section 24.3.3.8. Use of the CSD software system: an example

F. H. Allena* and V. J. Hoya

aCambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
Correspondence e-mail:  allen@ccdc.cam.ac.uk

24.3.3.8. Use of the CSD software system: an example

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The preceding sections can only give a flavour of the extensive search, analysis and visualization capabilities of Quest3D, ConQuest, Vista and Pluto, which are fully documented in manuals available online via the web address given below, or in printed form from the CCDC.

In this section, we illustrate the application of the CSD system to one specific example: a CSD-based analysis to examine the O—H···O hydrogen-bonding ability of the keto oxygen of Fig. 24.3.3.2[link]. This example illustrates a number of key features of the software system. The example is constructed in terms of Quest3D terminology, but identical facilities are available in the ConQuest program.

  • (1) Draw the two component substructures: the keto group and the O—H donor group. Constrain the total coordination number of C1, C3 (Fig. 24.3.3.2)[link] to be 4, thus defining them as C(sp3) atoms.

    [Figure 24.3.3.2]

    Figure 24.3.3.2 | top | pdf |

    The keto···hydroxyl fragment described in the example of CSDS usage (see Section 24.3.3.8[link]), illustrating the parameters DOH, AH, THETA and PHI used to describe the hydrogen-bonded system.

  • (2) Define a non-bonded contact between keto O1 and hydroxy donor H1. Require that this contact (DOH) is less than 2.62 Å, the sum of van der Waals radii, after normalization of the H-atom position to correspond to a standard O—H bond length as determined by neutron diffraction [X-ray location of H atoms is imprecise – X—H distances are usually foreshortened – so the system will reposition H atoms along the X—H vector and at an X—H distance that corresponds to the mean value from neutron diffraction experiments (Allen et al., 1987[link])].

  • (3) Define the geometrical parameters shown in Fig. 24.3.3.2,[link] comprising the H···O distance (DOH), the O—H···O angle (AH), and the angles THETA and PHI that describe the angle of approach of H to the putative lone-pair plane of the keto oxygen atom. THETA is the angle of approach of the donor H atom to the plane of the keto group, PHI is the angle of rotation of the projection of the O···H vector in that plane; THETA = 0°, PHI = ±120° would correspond to H-atom approach along an O-atom lone-pair direction. The search is further constrained so that hits are only accepted if AH > 90°.

  • (4) At this stage, the 3D-CONSTRAIN menu will show a graphic which closely resembles Fig. 24.3.3.2[link]. Test 1 is now defined.

  • (5) Since there will be large numbers of examples of keto-O···H—O hydrogen bonds in the CSD, a secondary constraint based on the crystallographic R factor is applied so that examples are only located in the more precise structure determinations. To do this, we access the NUMERIC search menu to define RFACT < 0.075 as test 2.

  • (6) Enter the QUEST menu, which summarizes all current tests, select the organic structures only bit screen, and complete the full query by combining test 1 and test 2 via a Boolean .AND. operator.

Searches can be performed interactively or allowed to run to completion without further intervention from the user. In interactive mode, Quest3D presents each hit as it is located, as illustrated in Fig. 24.3.3.3,[link] and can then display the 1D bibliographic information, a 2D structural diagram, the 3D molecular structure, or a 3D packing diagram by toggling between display options. For an intermolecular search, as exemplified here, the non-bonded contact that triggered the hit is clearly identified. For the example described above, a file of the four user-defined geometrical parameters (DOH, AH, THETA, PHI) for each hit is created for use by Vista.

[Figure 24.3.3.3]

Figure 24.3.3.3 | top | pdf |

A typical Quest3D graphics screen showing how search hits are visualized and manipulated.

Vista displays the geometrical parameters in the form of an interactive spreadsheet; the user may include or exclude specific substructures on the basis of numerical criteria during the data analysis, e.g. to focus on a specific range of DOH values, exclude outlying observations etc. Hyperlinking between Vista and the master CSD file means that all of the database information of Fig. 24.3.1.1[link] is immediately available during a Vista session, either by clicking on a particular fragment in the spreadsheet or on a particular data point in a histogram or scattergram. Use of Vista is illustrated for the >C=O···H—O example in Figs. 24.3.3.4,[link] 24.3.3.5[link] and 24.3.3.6[link].

[Figure 24.3.3.4]

Figure 24.3.3.4 | top | pdf |

A Vista histogram of the hydrogen-bond distance, DOH, showing a sharp peak in the range 1.8–2.2 Å, well below the sum of van der Waals radii (2.62 Å). This peak can be isolated in Vista to obtain an estimate of the mean O···H separation in >C=O···H—O systems.

[Figure 24.3.3.5]

Figure 24.3.3.5 | top | pdf |

A Vista scatterplot of the hydrogen-bond length (DOH) versus the O—H···O angle (AH). The plot shows a major clustering of observations having short DOH values and hydrogen-bond linearity (AH = 180°): stronger hydrogen bonds prefer to be linear.

[Figure 24.3.3.6]

Figure 24.3.3.6 | top | pdf |

A Vista polar scatterplot of THETA versus PHI, the angles that define the direction of approach of the donor H atom to the >C=O plane. There are clear indications of lone-pair directionality: H prefers an in-plane approach to O (THETA = 0°), with preferred PHI values in the range 120–135°.

References

First citationAllen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). Tables of bond lengths determined by X-ray and neutron diffraction. Part 1. Bond lengths in organic compounds. J. Chem. Soc. Perkin Trans. 2, pp. S1–S19.Google Scholar








































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