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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 03:11:39 UTC

Update Date

2022-03-07 02:57:02 UTC

HMDB ID

HMDB0041505

Secondary Accession Numbers

HMDB41505

Metabolite Identification

Common Name

5-Hydroxy-2-benzyl-1,3-dioxane

Description

5-Hydroxy-2-benzyl-1,3-dioxane belongs to the class of organic compounds known as 1,3-dioxanes. These are organic compounds containing 1,3-dioxane, an aliphatic six-member ring with two oxygen atoms in ring positions 1 and 3. Based on a literature review very few articles have been published on 5-Hydroxy-2-benzyl-1,3-dioxane.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0041505
     RDKit          3D
5-Hydroxy-2-benzyl-1,3-dioxane
 28 29  0  0  0  0  0  0  0  0999 V2000
   -4.0404    1.1610   -0.0581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3361   -0.0254   -0.2385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5687    0.1158   -1.5598 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7228    1.2112   -1.3891 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6965    0.8136   -0.5295 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4798    0.4308   -1.3969 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6467   -0.0145   -0.5952 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8089   -1.3400   -0.2566 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8814   -1.7749    0.4849 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8530   -0.8906    0.9268 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6800    0.4333    0.5818 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6067    0.8776   -0.1619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0572   -0.2842    0.2101 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2784   -0.1658    0.8422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4912    1.7421    0.5188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0102   -0.8997   -0.2734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9385   -0.7982   -1.6579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2675    0.2538   -2.3939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3808    1.6537    0.1206 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7883    1.3449   -1.9494 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1594   -0.3211   -2.1367 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0767   -2.0665   -0.5787 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0100   -2.8220    0.7527 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7038   -1.2306    1.5139 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4025    1.1596    0.8980 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4665    1.9220   -0.4363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4669   -1.1534    1.3507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3086    0.6674    1.5707 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
  5 13  1  0
 13 14  1  0
 14  2  1  0
 12  7  1  0
  1 15  1  0
  2 16  1  0
  3 17  1  0
  3 18  1  0
  5 19  1  0
  6 20  1  0
  6 21  1  0
  8 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  0
 12 26  1  0
 14 27  1  0
 14 28  1  0
M  END


  Mrv0541 05061312432D          

 14 15  0  0  0  0            999 V2000
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    5.7750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  9  4  2  0  0  0  0
  9  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  6  1  0  0  0  0
 12 10  1  0  0  0  0
 13  7  1  0  0  0  0
 13 11  1  0  0  0  0
 14  8  1  0  0  0  0
 14 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0041505

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1COC(CC2=CC=CC=C2)OC1

> <INCHI_IDENTIFIER>
InChI=1S/C11H14O3/c12-10-7-13-11(14-8-10)6-9-4-2-1-3-5-9/h1-5,10-12H,6-8H2

> <INCHI_KEY>
SCBQUBIXYNMXER-UHFFFAOYSA-N

> <FORMULA>
C11H14O3

> <MOLECULAR_WEIGHT>
194.2271

> <EXACT_MASS>
194.094294314

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
20.53908359088127

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-benzyl-1,3-dioxan-5-ol

> <ALOGPS_LOGP>
1.01

> <JCHEM_LOGP>
1.3860249679999999

> <ALOGPS_LOGS>
-1.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.668730493985223

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3810972819308622

> <JCHEM_POLAR_SURFACE_AREA>
38.69

> <JCHEM_REFRACTIVITY>
52.26510000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.14e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-benzyl-1,3-dioxan-5-ol

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0041505
     RDKit          3D
5-Hydroxy-2-benzyl-1,3-dioxane
 28 29  0  0  0  0  0  0  0  0999 V2000
   -4.0404    1.1610   -0.0581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3361   -0.0254   -0.2385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5687    0.1158   -1.5598 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7228    1.2112   -1.3891 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6965    0.8136   -0.5295 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4798    0.4308   -1.3969 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6467   -0.0145   -0.5952 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8089   -1.3400   -0.2566 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8814   -1.7749    0.4849 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8530   -0.8906    0.9268 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6800    0.4333    0.5818 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6067    0.8776   -0.1619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0572   -0.2842    0.2101 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2784   -0.1658    0.8422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4912    1.7421    0.5188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0102   -0.8997   -0.2734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9385   -0.7982   -1.6579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2675    0.2538   -2.3939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3808    1.6537    0.1206 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7883    1.3449   -1.9494 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1594   -0.3211   -2.1367 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0767   -2.0665   -0.5787 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0100   -2.8220    0.7527 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7038   -1.2306    1.5139 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4025    1.1596    0.8980 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4665    1.9220   -0.4363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4669   -1.1534    1.3507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3086    0.6674    1.5707 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
  5 13  1  0
 13 14  1  0
 14  2  1  0
 12  7  1  0
  1 15  1  0
  2 16  1  0
  3 17  1  0
  3 18  1  0
  5 19  1  0
  6 20  1  0
  6 21  1  0
  8 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  0
 12 26  1  0
 14 27  1  0
 14 28  1  0
M  END

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001   8.470   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  11.550   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   9.240   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000  10.780   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334  11.550   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       2.667  10.780   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.334   8.470   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    9                                                       
CONECT    5    3    9                                                       
CONECT    6    9   11                                                       
CONECT    7   10   13                                                       
CONECT    8   10   14                                                       
CONECT    9    4    5    6                                                  
CONECT   10    7    8   12                                                  
CONECT   11    6   13   14                                                  
CONECT   12   10                                                            
CONECT   13    7   11                                                       
CONECT   14    8   11                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

COMPND    HMDB0041505
HETATM    1  O1  UNL     1      -4.040   1.161  -0.058  1.00  0.00           O  
HETATM    2  C1  UNL     1      -3.336  -0.025  -0.238  1.00  0.00           C  
HETATM    3  C2  UNL     1      -2.569   0.116  -1.560  1.00  0.00           C  
HETATM    4  O2  UNL     1      -1.723   1.211  -1.389  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.697   0.814  -0.529  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.480   0.431  -1.397  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.647  -0.014  -0.595  1.00  0.00           C  
HETATM    8  C6  UNL     1       1.809  -1.340  -0.257  1.00  0.00           C  
HETATM    9  C7  UNL     1       2.881  -1.775   0.485  1.00  0.00           C  
HETATM   10  C8  UNL     1       3.853  -0.891   0.927  1.00  0.00           C  
HETATM   11  C9  UNL     1       3.680   0.433   0.582  1.00  0.00           C  
HETATM   12  C10 UNL     1       2.607   0.878  -0.162  1.00  0.00           C  
HETATM   13  O3  UNL     1      -1.057  -0.284   0.210  1.00  0.00           O  
HETATM   14  C11 UNL     1      -2.278  -0.166   0.842  1.00  0.00           C  
HETATM   15  H1  UNL     1      -3.491   1.742   0.519  1.00  0.00           H  
HETATM   16  H2  UNL     1      -4.010  -0.900  -0.273  1.00  0.00           H  
HETATM   17  H3  UNL     1      -1.939  -0.798  -1.658  1.00  0.00           H  
HETATM   18  H4  UNL     1      -3.268   0.254  -2.394  1.00  0.00           H  
HETATM   19  H5  UNL     1      -0.381   1.654   0.121  1.00  0.00           H  
HETATM   20  H6  UNL     1       0.788   1.345  -1.949  1.00  0.00           H  
HETATM   21  H7  UNL     1       0.159  -0.321  -2.137  1.00  0.00           H  
HETATM   22  H8  UNL     1       1.077  -2.067  -0.579  1.00  0.00           H  
HETATM   23  H9  UNL     1       3.010  -2.822   0.753  1.00  0.00           H  
HETATM   24  H10 UNL     1       4.704  -1.231   1.514  1.00  0.00           H  
HETATM   25  H11 UNL     1       4.403   1.160   0.898  1.00  0.00           H  
HETATM   26  H12 UNL     1       2.466   1.922  -0.436  1.00  0.00           H  
HETATM   27  H13 UNL     1      -2.467  -1.153   1.351  1.00  0.00           H  
HETATM   28  H14 UNL     1      -2.309   0.667   1.571  1.00  0.00           H  
CONECT    1    2   15
CONECT    2    3   14   16
CONECT    3    4   17   18
CONECT    4    5
CONECT    5    6   13   19
CONECT    6    7   20   21
CONECT    7    8    8   12
CONECT    8    9   22
CONECT    9   10   10   23
CONECT   10   11   24
CONECT   11   12   12   25
CONECT   12   26
CONECT   13   14
CONECT   14   27   28
END

HMDB0041505
     RDKit          3D
5-Hydroxy-2-benzyl-1,3-dioxane
 28 29  0  0  0  0  0  0  0  0999 V2000
   -4.0404    1.1610   -0.0581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3361   -0.0254   -0.2385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5687    0.1158   -1.5598 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7228    1.2112   -1.3891 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6965    0.8136   -0.5295 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4798    0.4308   -1.3969 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6467   -0.0145   -0.5952 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8089   -1.3400   -0.2566 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8814   -1.7749    0.4849 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8530   -0.8906    0.9268 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6800    0.4333    0.5818 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6067    0.8776   -0.1619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0572   -0.2842    0.2101 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2784   -0.1658    0.8422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4912    1.7421    0.5188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0102   -0.8997   -0.2734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9385   -0.7982   -1.6579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2675    0.2538   -2.3939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3808    1.6537    0.1206 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7883    1.3449   -1.9494 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1594   -0.3211   -2.1367 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0767   -2.0665   -0.5787 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0100   -2.8220    0.7527 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7038   -1.2306    1.5139 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4025    1.1596    0.8980 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4665    1.9220   -0.4363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4669   -1.1534    1.3507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3086    0.6674    1.5707 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
  5 13  1  0
 13 14  1  0
 14  2  1  0
 12  7  1  0
  1 15  1  0
  2 16  1  0
  3 17  1  0
  3 18  1  0
  5 19  1  0
  6 20  1  0
  6 21  1  0
  8 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  0
 12 26  1  0
 14 27  1  0
 14 28  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2-(Phenylmethyl)-1,3-dioxan-5-ol, 9ci	HMDB
2-Benzyl-1,3-dioxan-5-ol	HMDB

Chemical Formula

C₁₁H₁₄O₃

Average Molecular Weight

194.2271

Monoisotopic Molecular Weight

194.094294314

IUPAC Name

2-benzyl-1,3-dioxan-5-ol

Traditional Name

2-benzyl-1,3-dioxan-5-ol

CAS Registry Number

4740-79-8

SMILES

OC1COC(CC2=CC=CC=C2)OC1

InChI Identifier

InChI=1S/C11H14O3/c12-10-7-13-11(14-8-10)6-9-4-2-1-3-5-9/h1-5,10-12H,6-8H2

InChI Key

SCBQUBIXYNMXER-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,3-dioxanes. These are organic compounds containing 1,3-dioxane, an aliphatic six-member ring with two oxygen atoms in ring positions 1 and 3.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Dioxanes

Sub Class

1,3-dioxanes

Direct Parent

1,3-dioxanes

Alternative Parents

Substituents

Benzenoid
Monocyclic benzene moiety
Meta-dioxane
Secondary alcohol
Oxacycle
Acetal
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0041505)
Cytoplasm (HMDB: HMDB0041505)

Source

Exogenous

Exogenous (HMDB: HMDB0041505)

Food

Food (HMDB: HMDB0041505)

Process

Not Available

Role

Industrial application

Food and nutrition

Food additive

Flavoring agent

Flavoring Agent (HMDB: HMDB0041505)

Biological role

Nutrient (HMDB: HMDB0041505)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	324.00 to 326.00 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	33260 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	0.850 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	11.4 g/L	ALOGPS
logP	1.01	ALOGPS
logP	1.39	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	13.67	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	38.69 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.27 m³·mol⁻¹	ChemAxon
Polarizability	20.54 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	144.601	31661259
DarkChem	[M-H]-	141.509	31661259
DeepCCS	[M+H]+	142.869	30932474
DeepCCS	[M-H]-	139.479	30932474
DeepCCS	[M-2H]-	176.496	30932474
DeepCCS	[M+Na]+	152.034	30932474
AllCCS	[M+H]+	144.5	32859911
AllCCS	[M+H-H2O]+	140.2	32859911
AllCCS	[M+NH4]+	148.6	32859911
AllCCS	[M+Na]+	149.7	32859911
AllCCS	[M-H]-	146.2	32859911
AllCCS	[M+Na-2H]-	146.6	32859911
AllCCS	[M+HCOO]-	147.2	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.	4.29 minutes	32390414
Predicted by Siyang on May 30, 2022	11.6286 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.54 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	27.6 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1870.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	353.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	145.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	200.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	105.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	394.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	539.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	71.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1066.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	416.0 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1100.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	292.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	371.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	340.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	231.6 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	10.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Hydroxy-2-benzyl-1,3-dioxane	OC1COC(CC2=CC=CC=C2)OC1	2487.1	Standard polar	33892256
5-Hydroxy-2-benzyl-1,3-dioxane	OC1COC(CC2=CC=CC=C2)OC1	1560.5	Standard non polar	33892256
5-Hydroxy-2-benzyl-1,3-dioxane	OC1COC(CC2=CC=CC=C2)OC1	1593.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Hydroxy-2-benzyl-1,3-dioxane,1TMS,isomer #1	C[Si](C)(C)OC1COC(CC2=CC=CC=C2)OC1	1712.3	Semi standard non polar	33892256
5-Hydroxy-2-benzyl-1,3-dioxane,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1COC(CC2=CC=CC=C2)OC1	1940.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9400000000-6316a9054c341aabbebd	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane GC-MS (1 TMS) - 70eV, Positive	splash10-0006-9300000000-1050eee78bccdf602ae2	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane 10V, Positive-QTOF	splash10-0002-3900000000-0c762837f1283d8b1a00	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane 20V, Positive-QTOF	splash10-0a6u-9400000000-c51f1715a0548b36508f	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane 40V, Positive-QTOF	splash10-0006-9200000000-5e8fa90ede7febbe8afc	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane 10V, Negative-QTOF	splash10-0006-0900000000-189d60f72db0ef141045	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane 20V, Negative-QTOF	splash10-006x-6900000000-4de2f1c3ea3029113d3b	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane 40V, Negative-QTOF	splash10-0006-9000000000-22475781c3b810fc2535	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane 10V, Negative-QTOF	splash10-0006-3900000000-b6ff3afc18591a922850	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane 20V, Negative-QTOF	splash10-0006-9000000000-5a8ec3435d84e76c2d19	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane 40V, Negative-QTOF	splash10-0006-9000000000-0407e543fff4a883d87e	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane 10V, Positive-QTOF	splash10-0002-1900000000-d32694b2f21c2326a7ef	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane 20V, Positive-QTOF	splash10-0006-9400000000-b50cb09ab6438ec84957	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2-benzyl-1,3-dioxane 40V, Positive-QTOF	splash10-0f6x-9400000000-81397dc1ef602d50d3f1	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB021477

KNApSAcK ID

Not Available

Chemspider ID

70841

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

78476

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1548491

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for 5-Hydroxy-2-benzyl-1,3-dioxane (HMDB0041505)

MOL for HMDB0041505 (5-Hydroxy-2-benzyl-1,3-dioxane)

3D MOL for HMDB0041505 (5-Hydroxy-2-benzyl-1,3-dioxane)

3D SDF for HMDB0041505 (5-Hydroxy-2-benzyl-1,3-dioxane)

3D-SDF for HMDB0041505 (5-Hydroxy-2-benzyl-1,3-dioxane)

PDB for HMDB0041505 (5-Hydroxy-2-benzyl-1,3-dioxane)

3D PDB for HMDB0041505 (5-Hydroxy-2-benzyl-1,3-dioxane)

SMILES for HMDB0041505 (5-Hydroxy-2-benzyl-1,3-dioxane)

INCHI for HMDB0041505 (5-Hydroxy-2-benzyl-1,3-dioxane)

Structure for HMDB0041505 (5-Hydroxy-2-benzyl-1,3-dioxane)

3D Structure for HMDB0041505 (5-Hydroxy-2-benzyl-1,3-dioxane)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra