Software-driven complete elimination of hydrogens from chemical structures

Procedure:

• Start the webpage nmrshiftdb.org

• Perform a search e.g. by molecular formula - I used c5 h10 cl2
  
  

• Select a structure from the resulting hitlist - I selected the first one

• Select now "Additional Data"
  
  

• What can we learn here ?
  

  • Its 1,5-dichloropentane
  • The molecular formula is C5 H10 Cl2
  • The molecular formula can be found again in the INCHI
  • The INCHIKEY is "IPVYZLACGWVYRC-YTTNPODESA-N"
  • Using "IPVYZLACGWVYRC" as query for a google-search leads to webpages dealing with 1,5-dichloropentane

• All correct, simply perfect - lets download the structure as MOLfile using "Get this molecule as mdl molfile file"
  

  1,5-dichloropentane
    CDK     09062309122D
  nmrshiftdb2 20096878
    7  6  0  0  0  0  0  0  0  0999 V2000
      5.7900   -0.3200    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
      4.9000   -0.7400    0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
      3.9600   -0.3200    0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
      3.0700   -0.7400    0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
      2.1600   -0.3200    0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
      1.2400   -0.7400    0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
      0.3200   -0.3200    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1  2  1  0  0  0  0 
    2  3  1  0  0  0  0 
    3  4  1  0  0  0  0 
    4  5  1  0  0  0  0 
    5  6  1  0  0  0  0 
    6  7  1  0  0  0  0 
  M  END
  

  
  
  

• Now recalculate the INCHI starting from this MOLfile

  * Input_File: "answer_1.mol"
  Structure: 1
  InChI=1/C5Cl2/c6-4-2-1-3-5-7
  AuxInfo=1/0/N:4,3,5,2,6,1,7/E:(2,3)(4,5)(6,7)/CRV:1.2,2.2,3.2,4.2,5.2/rA:7nClC2C2C2C2C2Cl/rB:s1;s2;s3;s4;s5;s6;/rC:5.79,-.32,0;4.9,-.74,0;3 column.96,-.32,0;3.07,-.74,0;2.16,-.32,0;1.24,-.74,0;.32,-.32,0;
  

• Now the molecular formula is C5 Cl2 - formerly C5 H10 Cl2

• According to the MOLfile description the 6^th column (marked "vvv" in the description below) in the atom block behind the atom symbol holds the valence; in this example every carbon has a valence of "2"
  
  

  

• Editing the MOLfile leads to an updated version:
  

  1,5-dichloropentane
    CDK     09062309122D
  nmrshiftdb2 20096878
    7  6  0  0  0  0  0  0  0  0999 V2000
      5.7900   -0.3200    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
      4.9000   -0.7400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
      3.9600   -0.3200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
      3.0700   -0.7400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
      2.1600   -0.3200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
      1.2400   -0.7400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
      0.3200   -0.3200    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1  2  1  0  0  0  0 
    2  3  1  0  0  0  0 
    3  4  1  0  0  0  0 
    4  5  1  0  0  0  0 
    5  6  1  0  0  0  0 
    6  7  1  0  0  0  0 
  M  END
  

  giving again C5H10Cl2

  * Input_File: "answer_1_corrected.mol"
  Structure: 1
  InChI=1/C5H10Cl2/c6-4-2-1-3-5-7/h1-5H2
  AuxInfo=1/0/N:4,3,5,2,6,1,7/E:(2,3)(4,5)(6,7)/rA:7nClCCCCCCl/rB:s1;s2;s3;s4;s5;s6;/rC:5.79,-.32,0;4.9,-.74,0;3.96,-.32,0;3.07,-.74,0;2.16,-.32,0;1.24,-.74,0;.32,-.32,0;
  
  

Summary:

• I want to download this molecule (= 1,5-dichloropentane) as MOLfile

• According to my selection "Get this molecule as mdl molfile file" I expect a correct MOLfile holding the selected structure for further usage

  
  
  

• I got a MOLfile which has to be corrected before further usage

• The MOLfile is a defacto-standard since some 4 decades and should be well-known therefore