605-23-2

Basic information

• Product Name: THYMINE-BETA-D-ARABINOFURANOSIDE
• Synonyms: THYMINE-BETA-D-ARABINOFURANOSIDE;THYMINE 1-BETA-D-ARABINOFURANOSIDE;1-BETA-D-ARABINOFURANOSYLTHYMINE;ARABINOFURANOSYL-5-METHYLURACIL;ARA-T;1-beta-d-arabinofuranosyl-thymin;3h)-pyrimidinedione,1-beta-d-arabinofuranosyl-5-methyl-4(1h;arabinosylthymine
• CAS NO: 605-23-2
• Molecular Formula: C₁₀H₁₄N₂O₆
• Molecular Weight: 258.23
• EINECS: 210-083-7
• Mol File: 605-23-2.mol
• Article Data: 11

Chemical Properties

• Appearance: /
• Density: 1.576g/cm³
• Refractive Index: 1.618
• Storage Temp.: 2-8°C
• CAS DataBase Reference: THYMINE-BETA-D-ARABINOFURANOSIDE(CAS DataBase Reference)
• NIST Chemistry Reference: THYMINE-BETA-D-ARABINOFURANOSIDE(605-23-2)
• EPA Substance Registry System: THYMINE-BETA-D-ARABINOFURANOSIDE(605-23-2)

Safety Data

• WGK Germany: 2
• RTECS: XP2100200
• Hazardous Substances Data: 605-23-2(Hazardous Substances Data)

Usage

Chemical Properties

White to off-white powder

InChI:InChI=1/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7+,9-/m1/s1

Synthetic route

O-2,2'-cyclo-5-methyluridine (22423-26-3) → thymine arabinoside (605-23-2)

Conditions	Yield
With ammonium hydroxide at 70℃; for 14h;	100%
With sodium hydroxide at 22℃; for 2h; Rate constant;
With sodium hydroxide at 37℃;

5-(p-tolylthiomethyl)-1-β-D-arabinofuranosyluracil (88054-44-8) → thymine arabinoside (605-23-2)

Conditions	Yield
With nickel In ethanol Heating;	66%

2,2'-anhydro-5'-O-tert-butyldiphenylsilyl-3'-O-ethylphosphonoacetyl-5-methyluridine → 5'-O-tert-butyldiphenylsilyl-O2-2'-anhydro-5-methyluridine (171763-19-2) + 1-(5-O-tert-butyldiphenylsilyl-β-D-arabinofuranosyl)thymine + thymine arabinoside (605-23-2)

Conditions	Yield
With potassium hydroxide In 1,4-dioxane; water at 20℃; for 0.333333h; Hydrolysis; Alkaline hydrolysis;	A 65% B 25% C n/a

5-Methyluridine (1463-10-1) → thymine arabinoside (605-23-2)

Conditions	Yield
With bis(phenyl) carbonate; copper; sodium hydrogencarbonate In N,N-dimethyl-formamide at 140 - 150℃; for 45h;	50%
With hydrogenchloride; O-acetylsalicyloyl chloride 1.) nitromethane, 20 deg C, 15 h, 2.) water, dioxane, 100 deg C, 2.5 h; Yield given. Multistep reaction;
With hydrogenchloride; O-acetylsalicyloyl chloride 2.) water, dioxane; Yield given. Multistep reaction;
Multi-step reaction with 2 steps 1: pyridine 2: aufeinanderfolgende Behandlung des Reaktionsprodukts mit methanol.NH3 und mit wss.H2SO4 View Scheme

2-((3aR,5R,6R,6aS)-6-Hydroxy-5-hydroxymethyl-2-imino-tetrahydro-furo[2,3-d]oxazol-3-ylmethyl)-acrylic acid ethyl ester; hydrobromide → O-2,2'-cyclo-5-methyluridine (22423-26-3) + thymine arabinoside (605-23-2)

Conditions	Yield
With potassium tert-butylate In tert-butyl alcohol at 25℃; for 20h;	A 32% B 14%

methanesulfonyl chloride (124-63-0) + 1-(5'-O-trityl-β-D-ribofuranosyl)thymine (101796-28-5) → thymine arabinoside (605-23-2)

Conditions	Yield
aufeinanderfolgende Behandlung des Reaktionsprodukts mit methanol.NH3 und mit wss.H2SO4;

trimethylaluminum (75-24-1) + 1-((2R,3S,4R,5R)-3,4-Bis-trimethylsilanyloxy-5-trimethylsilanyloxymethyl-tetrahydro-furan-2-yl)-5-bromo-4-trimethylsilanyloxy-1H-pyrimidin-2-one (111582-87-7) → thymine arabinoside (605-23-2)

Conditions	Yield
With water; ammonium chloride; triphenylphosphine 1) THF, reflux, 12 h, 2) MeOH, reflux, 3 h; Yield given. Multistep reaction;

trimethylaluminum (75-24-1) + 1-((2R,3S,4R,5R)-3,4-Bis-trimethylsilanyloxy-5-trimethylsilanyloxymethyl-tetrahydro-furan-2-yl)-5-iodo-4-trimethylsilanyloxy-1H-pyrimidin-2-one (111582-88-8) → thymine arabinoside (605-23-2)

Conditions	Yield
With water; ammonium chloride; triphenylphosphine 1) THF, reflux, 24 h, 2) MeOH, reflux, 3 h; Yield given. Multistep reaction;

β-D-arabinofuranose (25545-03-3) → thymine arabinoside (605-23-2)

Conditions	Yield
Multi-step reaction with 4 steps 1: 96 percent 2: 95 percent / N,N-dimethyl-acetamide / Ambient temperature 3: 32 percent / potassium tert-butoxide / 2-methyl-propan-2-ol / 20 h / 25 °C 4: 100 percent / aq. ammonia / 14 h / 70 °C View Scheme
Multi-step reaction with 3 steps 1: 96 percent 2: 95 percent / N,N-dimethyl-acetamide / Ambient temperature 3: 14 percent / potassium tert-butoxide / 2-methyl-propan-2-ol / 20 h / 25 °C View Scheme

2-amino-β-D-arabinofurano[1',2':4,5]-oxazoline (27963-98-0) → thymine arabinoside (605-23-2)

Conditions	Yield
Multi-step reaction with 3 steps 1: 95 percent / N,N-dimethyl-acetamide / Ambient temperature 2: 32 percent / potassium tert-butoxide / 2-methyl-propan-2-ol / 20 h / 25 °C 3: 100 percent / aq. ammonia / 14 h / 70 °C View Scheme
Multi-step reaction with 2 steps 1: 95 percent / N,N-dimethyl-acetamide / Ambient temperature 2: 14 percent / potassium tert-butoxide / 2-methyl-propan-2-ol / 20 h / 25 °C View Scheme

2-((3aR,5R,6R,6aS)-6-Hydroxy-5-hydroxymethyl-2-imino-tetrahydro-furo[2,3-d]oxazol-3-ylmethyl)-acrylic acid ethyl ester; hydrobromide → thymine arabinoside (605-23-2)

Conditions	Yield
Multi-step reaction with 2 steps 1: 32 percent / potassium tert-butoxide / 2-methyl-propan-2-ol / 20 h / 25 °C 2: 100 percent / aq. ammonia / 14 h / 70 °C View Scheme

araU (3083-77-0) → thymine arabinoside (605-23-2)

Conditions	Yield
Multi-step reaction with 3 steps 1: H2O / 0.25 h / Heating 2: ethanol / 0.25 h / Heating 3: 66 percent / Raney-Ni / ethanol / Heating View Scheme

1-((2R,3S,4S,5R)-3,4-Dihydroxy-5-hydroxymethyl-tetrahydro-furan-2-yl)-5-pyrrolidin-1-ylmethyl-1H-pyrimidine-2,4-dione (88054-41-5) → thymine arabinoside (605-23-2)

Conditions	Yield
Multi-step reaction with 2 steps 1: ethanol / 0.25 h / Heating 2: 66 percent / Raney-Ni / ethanol / Heating View Scheme

Inosine (58-63-9) → thymine arabinoside (605-23-2)

Conditions	Yield
Multi-step reaction with 3 steps 1: Escherichia coli purine nucleoside phosphorylase 2: 45 percent / uridine phosphorylase 3: 1.) acetylsalicyloyl chloride, 2.) 0.5 N HCl / 2.) water, dioxane View Scheme
Multi-step reaction with 2 steps 1: 45 percent / BM-11 E. coli cells, 0.015 M potassium phosphate buffer (pH 7.25); 1.) 60 deg C, 2 h, 2.) 4 deg C, 18 h 2: 1.) acetylsalicylic chloroanhydride, 2.) 0.5 N HCl / 1.) nitromethane, 20 deg C, 15 h, 2.) water, dioxane, 100 deg C, 2.5 h View Scheme

α-D-ribofuranosyl-1-phosphate (18646-11-2) → thymine arabinoside (605-23-2)

Conditions	Yield
Multi-step reaction with 2 steps 1: 45 percent / uridine phosphorylase 2: 1.) acetylsalicyloyl chloride, 2.) 0.5 N HCl / 2.) water, dioxane View Scheme

1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose (6974-32-9) → thymine arabinoside (605-23-2)

Conditions	Yield
Multi-step reaction with 3 steps 1: 93 percent / SnCl4 / 1,2-dichloro-ethane / 48 h / 20 °C 2: 80 percent / 1 N sodium methylate / methanol / 3 h / 20 °C 3: 1.) acetylsalicylic chloroanhydride, 2.) 0.5 N HCl / 1.) nitromethane, 20 deg C, 15 h, 2.) water, dioxane, 100 deg C, 2.5 h View Scheme

2',3',5'-tri-O-benzoyluridine (3180-76-5) → thymine arabinoside (605-23-2)

Conditions	Yield
Multi-step reaction with 2 steps 1: 80 percent / 1 N sodium methylate / methanol / 3 h / 20 °C 2: 1.) acetylsalicylic chloroanhydride, 2.) 0.5 N HCl / 1.) nitromethane, 20 deg C, 15 h, 2.) water, dioxane, 100 deg C, 2.5 h View Scheme

thymin (65-71-4) → thymine arabinoside (605-23-2)

Conditions	Yield
Multi-step reaction with 2 steps 1: 45 percent / BM-11 E. coli cells, 0.015 M potassium phosphate buffer (pH 7.25); 1.) 60 deg C, 2 h, 2.) 4 deg C, 18 h 2: 1.) acetylsalicylic chloroanhydride, 2.) 0.5 N HCl / 1.) nitromethane, 20 deg C, 15 h, 2.) water, dioxane, 100 deg C, 2.5 h View Scheme
Multi-step reaction with 4 steps 1: ammonium sulfate / 2 h / Heating 2: 93 percent / SnCl4 / 1,2-dichloro-ethane / 48 h / 20 °C 3: 80 percent / 1 N sodium methylate / methanol / 3 h / 20 °C 4: 1.) acetylsalicylic chloroanhydride, 2.) 0.5 N HCl / 1.) nitromethane, 20 deg C, 15 h, 2.) water, dioxane, 100 deg C, 2.5 h View Scheme

2,4-bis(trimethylsiloxy)-5-methylpyrimidine (7288-28-0) → thymine arabinoside (605-23-2)

Conditions	Yield
Multi-step reaction with 3 steps 1: 93 percent / SnCl4 / 1,2-dichloro-ethane / 48 h / 20 °C 2: 80 percent / 1 N sodium methylate / methanol / 3 h / 20 °C 3: 1.) acetylsalicylic chloroanhydride, 2.) 0.5 N HCl / 1.) nitromethane, 20 deg C, 15 h, 2.) water, dioxane, 100 deg C, 2.5 h View Scheme

1,3-Dichloro-1,1,3,3-tetraisopropyldisiloxane (69304-37-6) + thymine arabinoside (605-23-2) → 1-[3,5-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-β-D-arabinofuranosyl]thymine (161602-00-2)

Conditions	Yield
With pyridine at 22 - 25℃; for 20h;	93%
With pyridine at 20℃;

thymine arabinoside (605-23-2) → Phosphoric acid mono-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-2-ylmethyl] ester (21052-26-6)

Conditions	Yield
With tris(p-nitrophenyl)phosphate at 50℃; Erwina herbicola 47/3 cells;	46%

Propargylic aldehyde (624-67-9) + thymine arabinoside (605-23-2) → 3-(3-oxoprop-1-enyl)-2'β-hydroxythymidine (90029-89-3)

Conditions	Yield
With triethylamine In N,N-dimethyl-formamide at -78℃; for 2h;	28%

4,4'-dimethoxytrityl chloride (40615-36-9) + thymine arabinoside (605-23-2) → 1-{(2R,3S,4S,5R)-5-[Bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-3,4-dihydroxy-tetrahydro-furan-2-yl}-5-methyl-1H-pyrimidine-2,4-dione

Conditions	Yield
With pyridine

bis(trifluoromethyl)mercury (371-76-6) + thymine arabinoside (605-23-2) → 1-β-D-arabinofuranosyl-4-O-(difluoromethyl)thymine (102302-70-5)

Conditions	Yield
With 1,1,1,3,3,3-hexamethyl-disilazane; sodium iodide 1.) 120 deg C; 2.) THF, reflux; Yield given. Multistep reaction;

acetic anhydride (108-24-7) + thymine arabinoside (605-23-2) → 5-methyl-1-(tri-O-acetyl-β-D-arabinofuranosyl)-1H-pyrimidine-2,4-dione (22423-27-4)

Conditions	Yield
With dmap at 20℃;

thymine arabinoside (605-23-2) → 1-β-D-arabinofuranosyl-4-thio-5-methyluracil

Conditions	Yield
Multi-step reaction with 3 steps 1: 4-dimethylaminopyridine / 20 °C 2: Lawesson's reagent / dioxane / Heating 3: NH3 / methanol / 3 h / 20 °C View Scheme

thymine arabinoside (605-23-2) → 5-methyl-4-thioxo-1-(tri-O-acetyl-β-D-arabinofuranosyl)-3,4-dihydro-1H-pyrimidin-2-one (22423-28-5)

Conditions	Yield
Multi-step reaction with 2 steps 1: 4-dimethylaminopyridine / 20 °C 2: Lawesson's reagent / dioxane / Heating View Scheme

thymine arabinoside (605-23-2) → 1-[2-O-octanoyl-3,5-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-β-D-arabinofuranosyl]thymine (937028-16-5)

Conditions	Yield
Multi-step reaction with 2 steps 1: 93 percent / pyridine / 20 h / 22 - 25 °C 2: 50 percent / pyridine / Heating View Scheme

thymine arabinoside (605-23-2) → 1-(2-O-octanoyl-β-D-arabinofuranosyl)thymine

Conditions	Yield
Multi-step reaction with 3 steps 1: 93 percent / pyridine / 20 h / 22 - 25 °C 2: 50 percent / pyridine / Heating 3: 50 percent / ammonium fluoride; Dowex(R) H(+) form resin / methanol / 22 - 25 °C View Scheme

thymine arabinoside (605-23-2) → 1-(2-O-pentanoyl-β-D-arabinofuranosyl)thymine

Conditions	Yield
Multi-step reaction with 3 steps 1: 93 percent / pyridine / 20 h / 22 - 25 °C 2: 68 percent / pyridine / Heating 3: 60 percent / ammonium fluoride; Dowex(R) H(+) form resin / methanol / 22 - 25 °C View Scheme
Multi-step reaction with 3 steps 1: pyridine / 20 °C 2: pyridine / Heating 3: NH4F; Dowex H+ form 50x2-100 / methanol / 20 °C View Scheme

thymine arabinoside (605-23-2) → 1-(2-O-decanoyl-β-D-arabinofuranosyl)thymine

Conditions	Yield
Multi-step reaction with 3 steps 1: 93 percent / pyridine / 20 h / 22 - 25 °C 2: 58 percent / pyridine / Heating 3: 42 percent / ammonium fluoride; Dowex(R) H(+) form resin / methanol / 22 - 25 °C View Scheme
Multi-step reaction with 3 steps 1: pyridine / 20 °C 2: pyridine / Heating 3: NH4F; Dowex H+ form 50x2-100 / methanol / 20 °C View Scheme

thymine arabinoside (605-23-2) → 1-(2-O-dodecanoyl-β-D-arabinofuranosyl)thymine

Conditions	Yield
Multi-step reaction with 3 steps 1: 93 percent / pyridine / 20 h / 22 - 25 °C 2: 95 percent / pyridine / Heating 3: 50 percent / ammonium fluoride; Dowex(R) H(+) form resin / methanol / 22 - 25 °C View Scheme
Multi-step reaction with 3 steps 1: pyridine / 20 °C 2: pyridine / Heating 3: NH4F; Dowex H+ form 50x2-100 / methanol / 20 °C View Scheme

thymine arabinoside (605-23-2) → 1-[2-O-pentanoyl-3,5-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-β-D-arabinofuranosyl]thymine (351523-13-2)

Conditions	Yield
Multi-step reaction with 2 steps 1: 93 percent / pyridine / 20 h / 22 - 25 °C 2: 68 percent / pyridine / Heating View Scheme
Multi-step reaction with 2 steps 1: pyridine / 20 °C 2: pyridine / Heating View Scheme

thymine arabinoside (605-23-2) → 1-[2-O-decanoyl-3,5-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-β-D-arabinofuranosyl]thymine (351523-05-2)

Conditions	Yield
Multi-step reaction with 2 steps 1: 93 percent / pyridine / 20 h / 22 - 25 °C 2: 58 percent / pyridine / Heating View Scheme
Multi-step reaction with 2 steps 1: pyridine / 20 °C 2: pyridine / Heating View Scheme

thymine arabinoside (605-23-2) → 1-[2-O-dodecanoyl-3,5-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-β-D-arabinofuranosyl]thymine (351523-14-3)

Conditions	Yield
Multi-step reaction with 2 steps 1: 93 percent / pyridine / 20 h / 22 - 25 °C 2: 95 percent / pyridine / Heating View Scheme
Multi-step reaction with 2 steps 1: pyridine / 20 °C 2: pyridine / Heating View Scheme

Upstream product

• 75-24-1 trimethylaluminum 
• 111582-87-7 1-((2R,3S,4R,5R)-3,4-Bis-trimethylsilanyloxy-5-trimethylsilanyloxymethyl-tetrahydro-furan-2-yl)-5-bromo-4-trimethylsilanyloxy-1H-pyrimidin-2-one 
• 111582-88-8 1-((2R,3S,4R,5R)-3,4-Bis-trimethylsilanyloxy-5-trimethylsilanyloxymethyl-tetrahydro-furan-2-yl)-5-iodo-4-trimethylsilanyloxy-1H-pyrimidin-2-one 
• 1463-10-1 5-Methyluridine 
• 7288-28-0 2,4-bis(trimethylsiloxy)-5-methylpyrimidine 
• 65-71-4 thymin 
• 3180-76-5 2',3',5'-tri-O-benzoyluridine 
• 6974-32-9 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose 
• 18646-11-2 α-D-ribofuranosyl-1-phosphate 
• 58-63-9 Inosine 
• 88054-41-5 1-((2R,3S,4S,5R)-3,4-Dihydroxy-5-hydroxymethyl-tetrahydro-furan-2-yl)-5-pyrrolidin-1-ylmethyl-1H-pyrimidine-2,4-dione 
• 3083-77-0 araU 
• 27963-98-0 2-amino-β-D-arabinofurano[1',2':4,5]-oxazoline 
• 25545-03-3 β-D-arabinofuranose 

Downstream Products

• 21052-26-6 Phosphoric acid mono-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-2-ylmethyl] ester 
• 22423-27-4 1-(Tri-O-acetyl-β-D-arabinofuranosyl)-thymin 
• 117626-85-4 Sodium; {[(2R,3S,4S,5R)-3,4-dihydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-2-ylmethoxy]-hydroxy-phosphoryl}-acetate 

Relevant articles and documents

Crystal Structure and Anti Herpes Simplex Virus Activity of 2,2'-Anhydro-1-β-D-arabinofuranosylthymine

1-β-D-Arabinofuranosylthymine (aThy; ara-T) is a potent selective anti herpes simplex virus drug.Its anhydro analogue, 2,2'-anhydro-aThy, was shown to be 9-fold less active and at least 3-fold less toxic than aThy.This compound was relatively stable at physiological pH and in strong acid but was rapidly hydrolyzed in base with a half-life of 18.3 min.The three-dimensional crystal structure of 2,2'-anhydro-aThy revealed a rigid structure with the arabinose ring in the unusual O1' endo, pucker, conformation.The trans-gauche conformation.The trans-gauche conformation along the C4'-C5' bond permits only intermolecular hydrogen bonding of the 5'-hydroxy and O3'.

Convenient synthesis of oligodeoxyribonucleotides bearing arabinofuranosyl pyrimidine derivatives and its duplex formation with complementary DNA

The oligodeoxyribonucleotides bearing 2,2′-anhydro-β-D-arabinofuranosyluracil derivatives were synthesized and the modified residue was converted to β-D-arabinofuranosyluracil derivatives or β-D-arabinofuranosylisocytosine derivatives by post-synthetic modification method. The melting profiles of their ODNs with complementary DNA were studied.

2',3'-O-phosphonoalkylidene derivatives of ribonucleosides: Synthesis and reactivity

A novel type of nucleotide analogues, the 2',3'-O-(1- diethylphosphono)alkylidene derivatives of ribonucleosides was prepared by redox reaction of diethyl chlorophosphite with various nucleoside orthoesters. Some of these compounds undergo interesting rearrangements when treated with nucleophiles. The configuration of the title compounds was determined by 2D-ROESY experiments. Biological activity of partially protected nucleotide analogues is also discussed.