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Showing metabocard for Silica (HMDB0035659)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 20:40:07 UTC
Update Date2023-02-21 17:24:51 UTC
HMDB IDHMDB0035659
Secondary Accession Numbers
  • HMDB35659
Metabolite Identification
Common NameSilica
DescriptionSilica, also known as (sio2)N or [sio2], belongs to the class of inorganic compounds known as metalloid oxides. These are inorganic compounds containing an oxygen atom of an oxidation state of -2, in which the heaviest atom bonded to the oxygen is a metalloid. Silica is found, on average, in the highest concentration within common hazelnuts (Corylus avellana) and cottonseeds (Gossypium). Silica has also been detected, but not quantified in, oats (Avena sativa). This could make silica a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on Silica.
Structure
Data?1677000291
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0035659 (Silica)


  Mrv0541 02241221522D          

  3  2  0  0  0  0            999 V2000
    1.6500    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 Si  0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  2  0  0  0  0
M  END
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3D MOL for HMDB0035659 (Silica)

HMDB0035659
     RDKit          3D
Silica
  3  2  0  0  0  0  0  0  0  0999 V2000
    1.5660   -0.0553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0006    0.1106   -0.0000 Si  0  0  0  0  0  4  0  0  0  0  0  0
   -1.5654   -0.0553   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  2  0
M  END
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3D SDF for HMDB0035659 (Silica)


  Mrv0541 02241221522D          

  3  2  0  0  0  0            999 V2000
    1.6500    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 Si  0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0035659

> <DATABASE_NAME>
hmdb

> <SMILES>
O=[Si]=O

> <INCHI_IDENTIFIER>
InChI=1S/O2Si/c1-3-2

> <INCHI_KEY>
VYPSYNLAJGMNEJ-UHFFFAOYSA-N

> <FORMULA>
O2Si

> <MOLECULAR_WEIGHT>
60.0843

> <EXACT_MASS>
59.966755777

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
3.2811468900078617

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
silanedione

> <JCHEM_LOGP>
-0.6577999999999999

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-8.532702804224158

> <JCHEM_POLAR_SURFACE_AREA>
34.14

> <JCHEM_REFRACTIVITY>
2.8858

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
silica

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0035659 (Silica)

HMDB0035659
     RDKit          3D
Silica
  3  2  0  0  0  0  0  0  0  0999 V2000
    1.5660   -0.0553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0006    0.1106   -0.0000 Si  0  0  0  0  0  4  0  0  0  0  0  0
   -1.5654   -0.0553   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  2  0
M  END
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PDB for HMDB0035659 (Silica)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       3.080   0.000   0.000  0.00  0.00           O+0
HETATM    2 Si   UNK     0       4.620   0.000   0.000  0.00  0.00          Si+0
HETATM    3  O   UNK     0       6.160   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2                                                            
MASTER        0    0    0    0    0    0    0    0    3    0    4    0
END
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3D PDB for HMDB0035659 (Silica)

COMPND    HMDB0035659
HETATM    1  O1  UNL     1       1.566  -0.055   0.000  1.00  0.00           O  
HETATM    2 SI1  UNL     1      -0.001   0.111  -0.000  1.00  0.00          SI  
HETATM    3  O2  UNL     1      -1.565  -0.055  -0.000  1.00  0.00           O  
CONECT    1    2    2
CONECT    2    3    3
END
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SMILES for HMDB0035659 (Silica)

O=[Si]=O
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INCHI for HMDB0035659 (Silica)

InChI=1S/O2Si/c1-3-2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(SiO2)NChEBI
[SiO2]ChEBI
KieselsaeureanhydridChEBI
Silica, amorphousChEBI
Silicic anhydrideChEBI
SiliziumdioxidChEBI
SiO2ChEBI
e551HMDB
Silicon dioxideHMDB
Silicon(IV) oxide (sio2)HMDB
Quso g32HMDB
TridymiteHMDB
g32, QusoHMDB
Quso g-32HMDB
Aerosil 380HMDB
380, AerosilHMDB
AerosilHMDB
CristobaliteHMDB
Dioxide, siliconHMDB
Quso g 32HMDB
SilicaChEBI
Chemical FormulaO2Si
Average Molecular Weight60.0843
Monoisotopic Molecular Weight59.966755777
IUPAC Namesilanedione
Traditional Namesilica
CAS Registry Number7631-86-9
SMILES
O=[Si]=O
InChI Identifier
InChI=1S/O2Si/c1-3-2
InChI KeyVYPSYNLAJGMNEJ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as metalloid oxides. These are inorganic compounds containing an oxygen atom of an oxidation state of -2, in which the heaviest atom bonded to the oxygen is a metalloid.
KingdomInorganic compounds
Super ClassMixed metal/non-metal compounds
ClassMetalloid organides
Sub ClassMetalloid oxides
Direct ParentMetalloid oxides
Alternative Parents
Substituents
  • Metalloid oxide
  • Inorganic oxide
  • Inorganic salt
  • Inorganic metalloid salt
Molecular FrameworkNot Available
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point1716 - 1736 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility48440 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-0.66ChemAxon
pKa (Strongest Basic)-8.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area34.14 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity2.89 m³·mol⁻¹ChemAxon
Polarizability3.28 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1277.1 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid551.6 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid237.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid445.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid288.6 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid427.9 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid557.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)772.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid883.2 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid315.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid991.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid380.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid463.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate846.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA490.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water357.6 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
SilicaO=[Si]=O755.9Standard polar33892256
SilicaO=[Si]=O226.0Standard non polar33892256
SilicaO=[Si]=O399.9Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB004246
KNApSAcK IDC00002479
Chemspider ID22683
KEGG Compound IDC16459
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkSilicon dioxide
METLIN IDNot Available
PubChem Compound24261
PDB IDNot Available
ChEBI ID30563
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1282321
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Yamamoto K, Granger DL, Brehmer W, Azuma I, Ribi E: Inhibition of pulmonary granuloma formation in mice by treatment with Mycobacterial protoplasm and immuno-suppressants and its relation to protection against aerosol infection with virulent Mycobacterium tuberculosis. Zentralbl Bakteriol Mikrobiol Hyg A. 1981;250(1-2):127-41. [PubMed:6797153 ]
  2. Peluso MR, Schneeman BO: A food-grade silicon dioxide is hypocholesterolemic in the diet of cholesterol-fed rats. J Nutr. 1994 Jun;124(6):853-60. [PubMed:8207542 ]
  3. Bhushan R, Reena, Chauhan RS: Separation of some antihistamines on impregnated TLC silica plates. Biomed Chromatogr. 1989 Jan;3(1):46-7. [PubMed:2706366 ]
  4. Gozal E, Ortiz LA, Zou X, Burow ME, Lasky JA, Friedman M: Silica-induced apoptosis in murine macrophage: involvement of tumor necrosis factor-alpha and nuclear factor-kappaB activation. Am J Respir Cell Mol Biol. 2002 Jul;27(1):91-8. [PubMed:12091251 ]
  5. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .