Chapter 29. Directives controlling the choice of the probe

There are two different methods of choosing your Probe or Probes:

  1. The properties of the Probe may be selected by entering the Probe's Symbol. This is the recommended method, and it is only necessary to enter the Symbol for the Probe somewhere before IEND in the list of Control Directives. Thus for a phenolic hydroxyl Probe you would simply enter: OH on a line by itself somewhere before IEND. When you use directive POSI (in order to define explicit grid points at which you want the GRID energy to be calculated), you may enter the names of several different Probes one after the other in the list of Control Directives thus:

         POSI 1.23 27.86   1.     Note that the input on 
         POSI 45.9 1.1 117.03     each line is free-format, 
         POSI     0.9 -1.  67.    so do not use Tabs to 
         OH                       format the lines.  Note 
         O1                       also that POSI and the 
         O                        Probe Symbols must be 
         OES                      entered before the line 
         OC2                      with:       IEND 
    The Grid energy will then be computed at each point for each Probe. The maximum number of Probes is defined by Parameter MAXPRO and the maximum number of grid points by MAXPOS. The list may not include multi-atom Probes. Similarly, if you are studying several Targets one after the other as a Set, you may enter several Probe Symbols in the list of Directives.

  2. The properties of a Probe may be defined one by one, as described in Section 31.3 for the Probe. This is a very flexible method of input for a single-atom Probe. The Energy Variables are its Van der Waals Radius, Polarisability, Charge etc. They are described in detail below.

29.1. Table of single-atom probes which can be called by their symbol

The following Symbols may be included in the Directives list for Programme GRID, in order to define a single-atom Probe.

C3Methyl CH3 groupC1=sp2 CH aromatic or vinyl
    
N:#sp N with lone pairN:=sp2 N with lone pair
N:sp3 N with lone pairN-:Anionic tetrazole N
    
N1Neutral flat NH eg amideN1+sp3 amine NH cation
N1=sp2 Amine NH cationN1:sp3 NH with lone pair
NH=sp2 NH with lone pairN1#sp NH with one hydrogen
    
N2Neutral flat NH2 eg amideN2+sp3 amine NH2 cation
N2=sp2 Amine NH2 cationN2:sp3 NH2 with lone pair
    
N3+sp3 amine NH3 cationNM3trimethyl-ammonium cation
    
O1Alkyl hydroxy OH groupOHPhenol or carboxy OH
O-sp2 phenolate oxygenOsp2 carbonyl oxygen
O::sp2 carboxy oxygen atomO=O of sulphate/sulphonamide
OESsp3 ester oxygen atomOC2Ether or furan oxygen
OSO of sulphone / sulphoxideONOxygen of nitro group
OH2Water  
    
PO4PO4 phosphate dianionPO4HPO4H phosphate anion
    
S1Neutral SH group  
    
FOrganic fluorine atomF-Fluoride anion
CLOrganic chlorine atomCL-Chloride anion
BROrganic bromine atomBR-Bromide anion
IOrganic iodine atomI-Iodide anion
    
LI+Lithium cationNA+Sodium cation
K+Potassium cationRB+Rubidium cation
CS+Caesium cationMG+2Magnesium cation
CA+2Calcium cationSR+2Strontium cation
ZN+2Zinc cationCU+2Cupric copper cation
FE+2Ferrous iron cationFE+3Ferric iron cation
    
BOTHThe Amphipatic ProbeDRYThe Hydrophobic Probe

29.2. Table of multi-atom probes which can be called by their symbol

The following Symbols may be included in the Directives list for Programme GRID, in order to define a multi-atom Probe.

COO-Aliphatic anionic carboxy group
AR.COO-Aromatic anionic carboxy group
  
CONH2Aliphatic neutral amide group
AR.CONH2Aromatic neutral amide group
  
CONHRAliphatic neutral amide group*
AR.CONHRAromatic neutral amide group*
  
AMIDINEAliphatic cationic amidine group
AR.AMIDINEAromatic cationic amidine group
  
M-DIAMINEMeta-diamino-benzene

* The NH moiety of these Multi-Atom Probes can be either cis or trans with respect to the carbonyl oxygen, and this MUST be specified by the User. The appropriate indicator should be included in the list of Directives before IEND and the job-title like this:

. 
. 
. 
AR.CONHR 
CIS 
. 
. 
IEND 
Title of the job 

If the CIS or TRANS indicator is not specified, the Multi-Atom Probe will behave as if it had a complete NH2 moiety

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