| GRID manual | ||
|---|---|---|
| <<< Previous | Next >>> | |
Chapter 29. Directives controlling the choice of the probe
There are two different methods of choosing your Probe or Probes:
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:
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.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: IENDThe 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.
| C3 | Methyl CH3 group | C1= | sp2 CH aromatic or vinyl |
| N:# | sp N with lone pair | N:= | sp2 N with lone pair |
| N: | sp3 N with lone pair | N-: | Anionic tetrazole N |
| N1 | Neutral flat NH eg amide | N1+ | sp3 amine NH cation |
| N1= | sp2 Amine NH cation | N1: | sp3 NH with lone pair |
| NH= | sp2 NH with lone pair | N1# | sp NH with one hydrogen |
| N2 | Neutral flat NH2 eg amide | N2+ | sp3 amine NH2 cation |
| N2= | sp2 Amine NH2 cation | N2: | sp3 NH2 with lone pair |
| N3+ | sp3 amine NH3 cation | NM3 | trimethyl-ammonium cation |
| O1 | Alkyl hydroxy OH group | OH | Phenol or carboxy OH |
| O- | sp2 phenolate oxygen | O | sp2 carbonyl oxygen |
| O:: | sp2 carboxy oxygen atom | O= | O of sulphate/sulphonamide |
| OES | sp3 ester oxygen atom | OC2 | Ether or furan oxygen |
| OS | O of sulphone / sulphoxide | ON | Oxygen of nitro group |
| OH2 | Water | ||
| PO4 | PO4 phosphate dianion | PO4H | PO4H phosphate anion |
| S1 | Neutral SH group | ||
| F | Organic fluorine atom | F- | Fluoride anion |
| CL | Organic chlorine atom | CL- | Chloride anion |
| BR | Organic bromine atom | BR- | Bromide anion |
| I | Organic iodine atom | I- | Iodide anion |
| LI+ | Lithium cation | NA+ | Sodium cation |
| K+ | Potassium cation | RB+ | Rubidium cation |
| CS+ | Caesium cation | MG+2 | Magnesium cation |
| CA+2 | Calcium cation | SR+2 | Strontium cation |
| ZN+2 | Zinc cation | CU+2 | Cupric copper cation |
| FE+2 | Ferrous iron cation | FE+3 | Ferric iron cation |
| BOTH | The Amphipatic Probe | DRY | The 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 |
| CONH2 | Aliphatic neutral amide group |
| AR.CONH2 | Aromatic neutral amide group |
| CONHR | Aliphatic neutral amide group* |
| AR.CONHR | Aromatic neutral amide group* |
| AMIDINE | Aliphatic cationic amidine group |
| AR.AMIDINE | Aromatic cationic amidine group |
| M-DIAMINE | Meta-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
| <<< Previous | Home | Next >>> |
| Control directives | Up | Comments |