Technical Documentation => Chemical Structures

Chemical Structures


Validation - Stereochemistry - Racemates - More Stereo Centers - Stereobond, Down Bonds - Metal Complexes - Nitro Groups - Polymers
Hydrochlorids of Amines - Aromatic Systems - Ferrocenes and Metallocenes - Mesomers, pi-systems - Tautomers - Specialities

Description

SciDex stores structure information in three categories:
- molecule (attribute to the whole molecule),
- atom
- bond

Molecule Attributes

ST Stereo chemistry. Values are: 'rac' for racemates 'chir' for enantiomers
INFO Information text, which will be written in the upper left corner of the drawing.
CL  Colour used for all atoms and bonds, which have no CL attribute themselves.
CO Comment: any text.
E Energy of formation.
UQ Unique ID. A text string to make a unique registration of a structure, e.g. to make planar chirality or stereo attributes, which are not found by SciDex.
V1 to V4 Numerical values for user defined purpose.

Atom Attributes

SY Symbol of the chemical element.Valid symbols are: H ..Mt (the first 109 elements) A, Q, M1, M2, X (wild cards) * (marker for polymer repeating sides)
LB Label, which is used in the drawing to represent the atom. No other attributes of the atom will be written, if a label is given to an atom.
CL Colour used for this atom.
CO Comment: any text.
UQ  Unique ID. A text string to make a unique description of a atom. This can be used to reduce the symmetry of an molecule.
HCO Hydrogen count of the atom.
CHG  Charge of the atom.
RAD Radical description of the atom.
ISO Isotope mass, e.g. 13 for Carbon atoms.
d NMR NMR chemical shift of the atom in ppm. If the atom has a colour, than all other atoms with the same symbol and the same colour will get this value. The value can be exact or an interval, e.g.:1.2 or 1.1-1.2 or <1.2
ST Stereo attribute yes or no.This attribute is used for the internal R/S calculation. no forces SciDex to ignore the stereo center, yes forces the calculation for nitrogen atoms with three substituents.
V1 to V4 Numerical values for user defined purpose.
  Further, X,Y and Z co-ordinates are stored for the atom. SciDex stores Z co-ordinates, but did not use them for the drawing. Z co-ordinates are used to calculate stereo attributes.

Bond Attributes

BO Bond order.
CL Colour used for this bond.
CO Comment: any text.
J NMR coupling constant in Hz. The value can be exact or an interval, e.g.:1.2 or 1.1-1.2 or <1.2
ST Stereo attribute yes or no.This attribute is used for the internal E/Z calculation of double bonds. no forces SciDex to ignore the E/Z of a bond (e.g. fast rotation/inversion), yes forces the calculation of E/Z for double bond.
V1 až V4 Numerical values for user defined purpose.

Bond Orders

  • Single bond
  • Double bond E/Z isomers are defined by the angles of the attached single bonds.
  • Triple bond.
  • Quadruple bond Attention: many other drawing programs cannot handle this type of bonds. SciDex converts this bond to triple bonds, if the other program cannot handle this type of bonds.
  • , , , Stereo bond Up stereo bond (single bond only). Down stereo bond (single bond only).Attention: the definition of down bonds is tricky!
  • Undefined stereo bond Single bond to a undefined stereo center
  • Coordinative bond
  • Non bonding relation or interaction Can be used to mark 3J couplings etc.

Attention:

1. SciDex bond types are not known to all chemical drawing programs.
2. SciDex do support all drawing types used to define the chemical needs, but not all types used for the graphical display used by other drawing programs.


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