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3.2 QUEST3D: Worked Examples


Example 1: A Basic Fragment Search

Objectives

Steps Required

Example 1 Query

where Hal = F or Cl or Br or I

Menu Commands Required

1. Red boxes highlight:

Click in drawing area of BUILD menu to place a C atom, move to new position, click again to create:

Red cross shows that you are in DRAW mode. Any new atom that is added will be bonded to this "active" atom.

2. Deactivate DRAW mode:

In move mode no atom is active.

3. Add ketone group:

4. Create acetyl group:

5. Create halogen substituent:

6. Fragment is now complete:

Connectivity bit-screens (search keys) now displayed in text area:
Total Number of Screens Set = 36
(The more specific the fragment the larger number of screens set. A good practice is to run a preliminary search where the fragment is non-specific, and then run a more specific search if needed, so that no entries are missed.)

7. Initiate search of the CSD:

Display of Hits

Hits and Results

Selection of Hits

Continuing the Search

The journal file: ex1.jnl

COMM These are comments in the QUEST initialisation file. This file may
COMM contain QUEST commands, such as terminal type, that are always entered.
COMM For more information enter "HELP INITIALISATION FILES" within QUEST.
COMM
COMM Type "HELP LATEST NEWS" for a summary of new features. More detailed
COMM release notes now distributed with the software. Type "HELP RELEASE NOTES"
COMM for more information.
COMM
COMM Set better PRINT style:
PRINT 10
T1 *CONN
NFRAG   1
AT1 O 1                                            :XY   202   365
AT2 C 3                                            :XY   400   469
AT3 C 2                                            :XY   609   394
AT4 7A 1                                           :XY   798   458
AT5 O 1                                            :XY   389   636
BO 1 2 1
BO 2 3 1
BO 3 4 1
BO 2 5 2
END
QUEST T1
---------+---------+---------+---------+---------+---------+---------+---------+
ABRAHE
Acetyl-bromoacetyl-dihydroenmein
absolute configuration
C24 H31 Br1 O8
M.Natsume,Y.Iitaka
Acta Crystallogr., 20, 197,1966
---------+---------+---------+---------+---------+---------+---------+---------+
ACEBEN
3-Acetoxy-2-benzoyl-9,12 bis(iodoacetoxy)-10,14,17,17-tetramethyl-1,15-dihydroxy
      -6-oxatetracyclo(11.3.1.0$3,10!.0$4.7!)heptadec-13-en-11-one
absolute configuration
C33 H38 I2 O12
M.C.Wani,H.L.Taylor,M.E.Wall,P.Coggon,A.T.McPhail
J.Am.Chem.Soc., 93, 2325,1971
---------+---------+---------+---------+---------+---------+---------+---------+

The bibliographic information given in the journal file, is the same as in the display menus.


Example 2: Fragment Search with 2D-Constraints

2D-Constraints add Chemical Detail to Search Fragments

Handling of Hydrogen Atoms (Notes)

Atom Substitution commands in 2D-CONSTRAIN sub-menu

Example 2 Query

where:

	7A	=	F or Cl or Br or I
	NL	=	C or N or O
	R	=	Any atom, except H
	NL cannot be coordinated by cyclic bonds
	Bond C..O can be either single or double

No fragment atom can be directly bonded to another fragment atom

Menu Commands Required

1. Draw acetyl fragment as shown in Ex.1:

2. Add cyclopentane ring to drawing area:

3. Connect cyclopentane and acetyl groups:

4. Change O(acetyl) to NL = C,N,O:

5. Define C2-O5 to be single or double bond:

6. Select 2D-CONSTRAIN to obtain sub-menu, then:

7. Specify CH1 at C6

8. Specify R substitution at C7:

9. Specify sp3 hybridisation at C7, C9, C10:

10. Require that NL cannot be connected to atoms outside the fragment by cyclic bonds:

11. Require that bonding pattern coded is exact - no other links allowed (see extra notes):

12. Fragment now complete:

Total Number of Screens Set = 33

Initiate the CSD Search

Selection of Hits

Results in ex2.jnl

ANYCLA
5alpha-Androst-2-en-17beta-yl chloroacetate
C21 H31 Cl1 O2
W.L.Duax,M.G.Erman,J.F.Griffin,M.E.Wolff
Cryst.Struct.Commun., 5, 775,1976

 Authors' cell dimensions
     a        b        c    alpha     beta    gamma
 12.8910  22.600   6.5280   90.0     90.0     90.0                       

 C1          .02830          .13832          .45000                            
 C2          .13710          .15075          .52650                            
 C3          .15640          .17640          .69980                            
 C4          .07420          .19738          .84400                            
 C5         -.03350          .19734          .74590                            
 C6         -.11770          .20898          .90670                            
 C7         -.22470          .21186          .80750                            
 C8         -.24970          .15556          .68750                            
 C9         -.16350          .14447          .52420                            
 C10        -.05510          .13957          .62360                            
 C11        -.19010          .09170          .38290                            
 C12        -.30020          .09575          .28880                            
 C13        -.38210          .10500          .45280                            
 C14        -.35460          .16041          .57930                            
 C15        -.45170          .17325          .70290                            
 C16        -.54140          .15090          .56180                            
 C17        -.48800          .12469          .37570                            
 C18        -.39330          .04927          .58780                            
 C19        -.04360          .08525          .75440                            
 C20        -.62140          .08860          .16290                            
 C21        -.66720          .03431          .06730                            
 Cl21       -.80330          .03641          .06400                            
 O17        -.54300          .07559          .28450                            
 O20        -.65290          .13754          .13440                            
 H1          .00300          .17000          .34400                            
 H1'         .02600          .10600          .39400                            
........
 H211       -.64300          .03000         -.11700                            

Extra Notes

NO-CYCLIC-ROUTES and NO-LINKS

This example has made use of these two commands. They are powerful tools for constraining the environment of your fragment.

Atom Substitution at C7

In this example, substitution at C7 was required to be:

The first two of these criteria are established by use of MIN-CONNECTIONS = 3. (The two ring C atoms plus one other, undefined, non-H substituent.)

However, this is not sufficient to establish C7 as sp3: would still satisfy mca=3. Hence, TOTAL-COORD-NO = 4 is also required to specify the sp3 centre at C7.


Example 3: Geometric Parameters and 3D-Constraints

Geometric Parameters may be defined in QUEST3D and:

3D-CONSTRAIN sub-menu commands (see Exs. 3, 4, 5)

Example 3 Query

where: Tr = any transition element, and the coordination of Tr is exactly 4.

Menu Commands Required

1. Draw fragment in BUILD menu:

2. Specify TR as 4-coordinate:

3. Enter the 3D-CONSTRAIN sub-menu:

4. Define TR1-Cl2 distance as a parameter:

5. Define other parameters in a similar way so that summary area eventually looks like:

	TRCL1 1 2
	TRCL2 1 3
	TRN1 1 4
	TRN2 1 7
	CC 5 6
	CLTRCL 2 1 3
	NTRN 4 1 7

6. Finally define torsion angle:

7. Require that specific element symbol of TR is tabulated for each hit (Vol.2, p.3-8):

8. Define mean TR-CL and TR-N bond lengths:

9. Define histograms and scattergrams:

Initiate the CSD Search

As we are only interested in organometallic structures, select also: ONLY-ORGANOMETALS

Display and Selection of Hits

Results and Sumary File ex3.sum

  1. Question header:

    This includes:

  2. Tabulation of parameters for hit entries:
     Nfrag  Refcode     TRCL   TRCL2    TRN1    TRN2      CC  CLTRCL    NTRN      T1
         1  ACHPTA     2.286   2.291   2.061   2.026   1.496  93.578  82.705  51.554
         2  ACHPTA     2.283   2.291   2.014   2.042   1.517  91.488  84.801 -54.911
         3  ACHPTA     2.297   2.309   2.014   2.017   1.513  91.397  82.283 -47.006
         4  AMBUPD     2.315   2.318   2.029   2.031   1.535  95.313  83.525 -53.291
     ....
        40  YAGBEN     2.302   2.325   2.085   2.024   1.531  92.028  83.630  52.827
    

    (The final 3 parameters for this search are listed in a separate table.)

  3. Mean statistics for each hit
     Nent   34                                                                      
            Nobs          40      40      40      40      40      40      40      40
            Mean       2.289   2.285   2.068   2.045   1.505  96.757  84.353  12.978
            SDSample   0.037   0.036   0.037   0.035   0.029  10.634   2.456  53.174
            SDMean     0.006   0.006   0.006   0.006   0.005   1.681   0.388   8.408
            Minimum    2.183   2.198   1.980   1.980   1.417  86.331  73.150 -62.304
            Maximum    2.335   2.325   2.174   2.120   1.566 128.521  88.912  68.044
    

  4. 4.Histograms and scatterplots, if requested: (See VISTA, Ch.4, for alternative plots)

Example 4: More Geometric Definitions

Torsion Angle Definition

Torsion angle A-X-Y-F is defined as the angle by which A-X must be rotated to overlie Y-F

Torsion Angle Selection - Enantiomer commands in 3D-CONSTRAIN sub-menu

As torsion angles range in value from 0 to +/-180[ring] the following commands can be important for torsion angle selection:

ENANTIOMER NOINVERT:	Fragment not inverted (DEFAULT) (Vol.2, p.3-25).
ENANTIOMER INVERT:	Fragment inverted (Vol.2, p.3-24).
ENANTIOMER NORMAL:	Fragment only inverted if space-group is centrosymmetric (Vol.2, p.3-27).
In most cases the default setting is used. See Extra Notes below.

Example 4 Query

Where: C1 and C2 atoms are acyclic (i.e. not part of a ring) and are substituted by 1 or 2 H atoms.

Menu Commands Required

1. Draw fragment using BUILD menu:

2. Specify the C atoms to be acyclic:

3. Specify H attachment:

4. Enter 3D-CONSTRAIN sub-menu:

5. Define centroid of the phenyl rings:

6. Define phenyl planes in similar way:

7. Define required parameters:

8. Constrain the search so only structures where the phenyl groups are cis are selected:

9. Define the absolute value of T1, i.e. 0 to 90:

10. Tabulate the R-factor for each hit:

Initiate the CSD Search

Display and Selection of Hits

Results and Summary File ex4.sum

The table of parameters and mean statistics will resemble:

 Nfrag  Refcode     DIST    PANG      T1    TOR1   *RFAC                
     1  BEJMAE     4.900 125.125  69.407  69.407   0.054                
     2  BOBYEW     5.077  80.718 -70.535  70.535   0.025                
     3  BOYNOS     4.594  61.752 -53.686  53.686   0.079                
     4  BUKMEZ     4.933  43.973  72.581  72.581   0.066                
     5  BUMGUL     4.549 129.363   1.649   1.649   0.089                
  .....
    41  VUKGEN     4.659  46.401  64.293  64.293   0.021 
 Nent   34                                                                      
        Nobs          41      41      41      41      41 
        Mean       4.608  85.641  -2.671  54.695   0.060                
        SDSample   0.222  35.938  57.763  16.660   0.022                
        SDMean     0.035   5.613   9.021   2.602   0.004                
        Minimum    4.227  32.882 -73.414   1.649   0.021                
        Maximum    5.077 145.557  77.519  77.519   0.098                

Extra Notes on Torsion Angle Selection

As mentioned in the introduction the choice of ENANTIOMER command (and torsion angle range) are important when selecting on torsion angles although, as in this example usually the default ENANT NOIN is normally used. There are, however, two other alternatives to obtain the same results as above:

  1. Above example:

  2. Use absolute torsion angle value:

  3. Allow inversion of fragment:

EXHAUSTIVE and OVERLAP Commands

Both commands are located in 3D-CONSTRAIN sub-menu, and govern the selection of search fragments in an entry:

EXHAUSTIVE: When highlighted (default) the search finds all occurrences in an entry of the search fragment which passes the search test(s). If EXHAUSTIVE is not highlighted, the search will find a maximum of NFRAG fragments in an entry, as set by NUMBER-OF-FRAGS command in 2D-CONSTRAIN sub-menu, the default is 1. (Vol.2, p.3-29)

OVERLAP: When highlighted (default) the search allows overlap of atoms in occurrences of the search fragment, i.e. fragments in different search hits can have atoms in common. If OVERLAP is not highlighted the search fragments are required to be separate from each other, i.e. to have no atoms in common. (Vol.2, p.3-63)

In most searches (as in all the searches described in this manual) the default settings are used, as this means all possible fragments are located.

See Vol.1, p.7-17 to 7-21 for further information.


Example 5: Search for Non-bonded Interactions

Fragments Involving Non-bonded Contacts

QUEST3D can locate fragments containing one or more intramolecular and/or intermolecular non-bonded contacts defined using distance criteria. Contacts can involve:

Full details of non-bonded search capabilities are given in Vol.1, p.7-23 to 7-53 and Vol.2, p.3-34 to 3-59.

Non-bonded Search Commands (3D-CONSTRAIN sub-menu)

Example 5 Query

Special Notes

Intramolecular Contacts: Shortest Path

In locating intramolecular non-bonded contacts (INTRA or INTRA + INTER options) QUEST3D will take account of limits placed on the shortest path of covalent bonds that links two atoms in the molecule. Thus:

has a shortest path (S-PATH) of 5 bonds.

Minimum and maximum S-PATH values can be input via the NON-BONDED CONTACT command. Default values are min. = 4, max.= 999.

Normalization of Hydrogen Positions (H-NORMALIZE in SEARCH menu)

In X-ray analyses (but not neutron studies), the position of a proton is usually too close to that of its bonded atom (due to asphericity in the electron -density distribution) although the bonded vector direction may be acceptable.

The H-NORMALIZE command will reposition H atoms along the X-H bonded vector at distances that correspond to mean X-H inter-nuclear separations obtained in neutron studies for X = C, N, O. Distances are taken from J. Chem. Soc. Perkin 2 (1987) pp. S1 - S19.

Lone-pair Directionality in H-bond studies (*LP2, *LP3 in 3D-CONSTRAIN sub-menu)

The direction of approach of donor H atoms to an acceptor atom A can be quantified in terms of the spherical polar angle [theta] and [phi] made by the A...H vector with respect to some reference plane that represents the equatorial plane of the sphere. (Vol.2, pp.3-10 to 3-13)

For H-bonding studies it is convenient to take this plane as that which is assumed to contain the lone pairs on the acceptor A. The QUEST3D commands *LP2, *LP3 will calculate [theta], [phi] for two common situations: an sp2-hybridized acceptor (e.g. O in ) or an sp3-hybridized acceptor (e.g. O in C-O-C).

The DEFINE *LP2, *LP3 commands on the 3D-CONSTRAIN sub-menu require the user to specify (click) on four atoms (i, j, k, n in the constructs below) to define the reference plane. Two parameter names, e.g. THETA, PHI must also be provided.

*LP2

*LP3

Menu Commands Required

1. Draw bonded fragments using BUILD menu:

2. Constrain N to be 3-coordinate:

3. Specify non-bonded search criteria:

4. Define intermolecular O...H # 2.1Å:

5. Define required distances and angles:

6. Define the atom labels of O and H:

7. Calculate direction of approach of N-H to O:

8. Take absolute values of THETA and PHI:

9. Define histograms and scattergram:

Initiate the CSD Search

Searching of Database

The first residue selected for the Non-bonded Contact (carbonyl group) is the reference molecule, where the complete molecule is displayed. The second residue selected (amine group) is the non-bonded residue, where only the search fragment is displayed. (For an intramolecular contact simply one molecule is displayed with the non-bonded contact highlighted.)

Display of the H-bond Network

PACK commands are located in the 3D display menu:

Selection of Hits

Results and Summary File ex5.sum

  Nfrag  Refcode     O..H    O..N     OHN     COH    LAB4    LAB5   THETA     PHI
      1  ACMPIM10   1.863   2.871 176.467 143.474      O1    H13%   4.833-143.751
      2  AEMPYC     1.923   2.922 169.643 126.025     O12     H1% -22.623-129.581
      3  BANKIK     1.931   2.940 177.232 169.310      O1     H2%   2.721-169.659
      4  BARCOX     1.818   2.819 170.794 124.976      O3     H9%  21.101 127.911
      5  BARYOI     1.955   2.955 170.273 126.014      O7     H5%  -0.301-126.014
 ......
     81  YABSAV     2.003   2.985 163.722 158.220      O4      H7 -11.139 161.163
  Nent   72                                                                      
         Nobs          81      81      81      81      81      81      81      81
         Mean       1.928   2.890 161.086 141.167   0.000   0.000   1.641 -41.054
         SDSample   0.096   0.084  10.622  17.162   0.000   0.000  22.560 144.183
         SDMean     0.011   0.009   1.180   1.907   0.000   0.000   2.507  16.020
         Minimum    1.725   2.704 126.554 111.817   0.000   0.000 -52.786-178.896
         Maximum    2.100   3.055 177.232 177.833   0.000   0.000  67.649 174.900

The final 2 parameters are listed in a continuation table:

  Nfrag  Refcode   PTHETA    PPHI                                                
      1  ACMPIM10   4.833 143.751                                                
      2  AEMPYC    22.623 129.581                                                
      3  BANKIK     2.721 169.659                                                
      4  BARCOX    21.101 127.911                                                
      5  BARYOI     0.301 126.014                                                
 ......
     81  YABSAV    11.139 161.163                                                
  Nent   72                                                                      
         Nobs          81      81                                                
         Mean      17.344 147.953                                                
         SDSample  14.392  18.210                                                
         SDMean     1.599   2.023                                                
         Minimum    0.000 120.429                                                
         Maximum   67.649 178.896                                                

It is advisable to use the absolute values of THETA and PHI, as in most cases the sign is unimportant due to the symmetry of the fragment.

Historgrams and Scattergrams

 Histogram   1 for parameter O..H  
   1.720 TO  1.740     1 *
   1.740 TO  1.760     2 **
   1.760 TO  1.780     2 **
   1.780 TO  1.800     3 ***
   1.800 TO  1.820     5 *****
   1.820 TO  1.840     4 ****
   1.840 TO  1.860     4 ****
   1.860 TO  1.880     7 *******
   1.880 TO  1.900     3 ***
   1.900 TO  1.920     6 ******
   1.920 TO  1.940     5 *****
   1.940 TO  1.960     6 ******
   1.960 TO  1.980     7 *******
   1.980 TO  2.000     5 *****
   2.000 TO  2.020     7 *******
   2.020 TO  2.040     3 ***
   2.040 TO  2.060     3 ***
   2.060 TO  2.080     2 **
   2.080 TO  2.100     5 *****
   2.100 TO  2.120     1 *
 
 Histogram   2 for parameter OHN   
   125.0 TO  127.5     1 *
   127.5 TO  130.0     0 
   130.0 TO  132.5     1 *
   132.5 TO  135.0     0 
   135.0 TO  137.5     1 *
   137.5 TO  140.0     1 *
   140.0 TO  142.5     0 
   142.5 TO  145.0     0 
   145.0 TO  147.5     3 ***
   147.5 TO  150.0     2 **
   150.0 TO  152.5     8 ********
   152.5 TO  155.0     4 ****
   155.0 TO  157.5     8 ********
   157.5 TO  160.0     6 ******
   160.0 TO  162.5     2 **
   162.5 TO  165.0    10 **********
   165.0 TO  167.5    11 ***********
   167.5 TO  170.0     5 *****
   170.0 TO  172.5     8 ********
   172.5 TO  175.0     4 ****
   175.0 TO  177.5     6 ******
 
 Scattergram for O..H   along X-axis versus OHN    up Y-axis
   185.0 +                                   
         I                                   
         I     11    1 1 2 1  1              
         I  1  1 111 11      2    1          
   170.0 +    1   11  2   1   1  1    1      
         I1  1   11 1 11 111 21 12     1     
         I           1      1 1     1   1    
         I  1    2    2   1    1 111    1    
   155.0 +          1    1 1   11 1     11   
         I              1    1  11 1  1      
         I                   1   1   1       
         I                                   
   140.0 +                    1          1   
         I                                   
         I                              1    
         I                            1      
         +----+----+----+----+----+----+----+
            1.780     1.900     2.020     2.140

Note: VISTA (see Ch.4) has extensive postscript editing features for output of histograms and scattergrams and allows ranges of parameters to be selected.


Example 6: Text Searches

Available Search Fields

Example 6.1: Author Name

Locate all entries published by STONE.

  1. Enter the TEXT sub-menu

  2. Encode the TEST:

  3. Initiate the search:

  4. Examine hits:

  5. Notes:

Example 6.2: Compound Name

Locate all entries containing the character string BUTADIENE.

  1. Enter the TEXT sub-menu as at 1. above

  2. Encode the test:

  3. Initiate the search

  4. Examine hits:

Notes

Warning

Reassurance!


Example 7: Numeric Searches

Available Search Fields

Search tests

Example 7.1: Year of publication (integer)

Locate all entries published from 1992 onwards.

  1. Enter the NUMERIC sub-menu:

  2. Encode the test:

  3. Initiate the search:

  4. Examine hits:

  5. Notes:

Example 7.2: Crystallographic R-factor (real)

Locate all entries with R#4% (0.04).

  1. Enter the NUMERIC sub-menu as in 1. above

  2. Encode the test:

  3. Initiate the search:

  4. Examine hits:

  5. Notes:


Example 8: Element and Formula Searches

Available Search Fields

	*FORMULA	On TEXT sub-menu. Tests complete formula using CSD syntax (Vol.2,
			p.11-12). Use only in special circumstances.
	ELEMENTS	Sub-menu called from SEARCH menu. Locates individual elements or
			groups of elements. (Vol.2, p.10-11.)
	FORMULAE	Command on SEARCH menu. Locates element symbol/element count
			combinations. (Vol.2, p.10-15.)
	[BUILD]		[Chemical fragment searches can be an effective alternative: 
			examples are given below.]

Example 8.1: Element Search

Locate all entries containing Palladium.

  1. Enter the ELEMENTS sub-menu:

  2. Encode the test:

  3. Initiate the search:

  4. Notes:

  5. Alternative coding via BUILD menu:

  6. or Define further chemical attributes of Pd:

Example 8.2: Formula Search

Locate entries containing 2 - 4 Os atoms.

  1. Encode the test:

  2. Initiate the search

  3. Notes:

Example 8.3: Residue Search

Locate alpha-cyclodextrin, a residue of formula C36 H60 O30.

  1. Encode the test:

  2. Initiate search as in 2. above

  3. Alternative coding via TEMPLATES in BUILD menu:


Example 9: Cell Paramter Searches

Available Search Fields

Full cell-parameter searches are conducted by comparison of reduced-cell parameters.

Example 9.1: Cell Parameter Search

Locate Primitive Monoclinic cells with dimensions:

a=6.638 b=7.550 c=23.180 beta=95.98

  1. Enter the REDUCED-CELL sub-menu:

  2. Encode the test:

  3. Initiate the search:

Notes


Example 10: Amino-acid Sequences in CSD Peptides

Available Information

Simple TEXT Search

Use of PEPTIDE-SEQ sub-menu

To encode the sequence TEST you may need to:


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