N⁴-benzoyl-5-[(benzyloxy)methyl]-2'-deoxycytidine | 304849-84-1

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 嘧啶核苷
• 英文名称: N⁴-benzoyl-5-[(benzyloxy)methyl]-2'-deoxycytidine
• 英文别名: N-[1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-oxo-5-(phenylmethoxymethyl)pyrimidin-4-yl]benzamide
• CAS: 304849-84-1
• 化学式: C₂₄H₂₅N₃O₆
• 分子量: 451.479
• InChiKey: NGCXKNBFBMFMLJ-PWRODBHTSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  1.8
• 重原子数：
  33
• 可旋转键数：
  8
• 环数：
  4.0
• sp3杂化的碳原子比例：
  0.29
• 拓扑面积：
  121
• 氢给体数：
  3
• 氢受体数：
  6

反应信息

• 作为反应物：
  描述：

  N⁴-benzoyl-5-[(benzyloxy)methyl]-2'-deoxycytidine 在 4-二甲氨基吡啶 、 N,N-二异丙基乙胺 作用下， 以 四氢呋喃 、 吡啶 为溶剂， 反应 4.0h， 生成 N⁴-benzoyl-5-[(benzyloxy)methyl]-2'-deoxy-5'-O-(4,4'-dimethoxytrityl)cytidine 3'-(2-cyanoethyl diisopropylphosphoramidite)
  参考文献：
  名称：

  Aromaticvs. Carbohydrate Residues in the Major Groove: Synthesis of 5-[(Benzyloxy)methyl]pyrimidine Nucleosides and Their Incorporation into Oligonucleotides

  摘要：

  The synthesis of 5-[(benzyloxy)methyl]-substituted pyrimidine 2'-deoxynucleosides 14 and 15 starting from the uracil derivative 6 and tetra-O-acetyl-D-ribose is described (Schemes 1-3). These nucleosides were converted to the corresponding cyanoethyl phosphoramidites 18 and 19, respectively, and incorporated into oligodeoxynucleotide decamers. The 5-[(benzyloxy)methyl]-nucleoside building blocks T-bo(d) and C-bom(d) (bo = benzyloxy, bom = (benzyloxy)methyl) - shape analogs of the naturally occurring glucosylated nucleosides 1 and 2 (see Fig. 1) - lead to weaker binding affinities of oligodeoxynucleotides pairing to DNA as well as RNA complements. The modification is more destabilizing in the case of T-bo(d) than C-bom(d). Analysis of the thermodynamics of duplex formation shows that T-bo(d) and C-bom(d), incorporation leads to a smaller entropy change in duplex formation that is, however, overcompensated by a less Favorable enthalpy term. Molecular-modeling studies suggest that the benzyl groups reside in the major groove which would explain the improved pairing entropy as a result of the exclusion of ordered H2O.

  DOI：

  10.1002/1522-2675(20000809)83:8<1962::aid-hlca1962>3.0.co;2-8
• 作为产物：
  描述：

  四乙酰核糖 在 1H-1,2,4-三唑 、 4-二甲氨基吡啶 、 sodium hydroxide 、 N,O-双三甲硅基乙酰胺 、 偶氮二异丁腈 、 三氟甲磺酸三甲基硅酯 、 四丁基氟化铵 、 三正丁基氢锡 、 三乙胺 、 三氯氧磷 作用下， 以 四氢呋喃 、 吡啶 、 甲醇 、 水 、 甲苯 、 乙腈 为溶剂， 反应 76.75h， 生成 N⁴-benzoyl-5-[(benzyloxy)methyl]-2'-deoxycytidine
  参考文献：
  名称：

  Aromaticvs. Carbohydrate Residues in the Major Groove: Synthesis of 5-[(Benzyloxy)methyl]pyrimidine Nucleosides and Their Incorporation into Oligonucleotides

  摘要：

  The synthesis of 5-[(benzyloxy)methyl]-substituted pyrimidine 2'-deoxynucleosides 14 and 15 starting from the uracil derivative 6 and tetra-O-acetyl-D-ribose is described (Schemes 1-3). These nucleosides were converted to the corresponding cyanoethyl phosphoramidites 18 and 19, respectively, and incorporated into oligodeoxynucleotide decamers. The 5-[(benzyloxy)methyl]-nucleoside building blocks T-bo(d) and C-bom(d) (bo = benzyloxy, bom = (benzyloxy)methyl) - shape analogs of the naturally occurring glucosylated nucleosides 1 and 2 (see Fig. 1) - lead to weaker binding affinities of oligodeoxynucleotides pairing to DNA as well as RNA complements. The modification is more destabilizing in the case of T-bo(d) than C-bom(d). Analysis of the thermodynamics of duplex formation shows that T-bo(d) and C-bom(d), incorporation leads to a smaller entropy change in duplex formation that is, however, overcompensated by a less Favorable enthalpy term. Molecular-modeling studies suggest that the benzyl groups reside in the major groove which would explain the improved pairing entropy as a result of the exclusion of ordered H2O.

  DOI：

  10.1002/1522-2675(20000809)83:8<1962::aid-hlca1962>3.0.co;2-8

文献信息

• Aromaticvs. Carbohydrate Residues in the Major Groove: Synthesis of 5-[(Benzyloxy)methyl]pyrimidine Nucleosides and Their Incorporation into Oligonucleotides
  作者：Reto Bertolini、Jürg Hunziker

  DOI：10.1002/1522-2675(20000809)83:8<1962::aid-hlca1962>3.0.co;2-8

  日期：2000.8.9

  The synthesis of 5-[(benzyloxy)methyl]-substituted pyrimidine 2'-deoxynucleosides 14 and 15 starting from the uracil derivative 6 and tetra-O-acetyl-D-ribose is described (Schemes 1-3). These nucleosides were converted to the corresponding cyanoethyl phosphoramidites 18 and 19, respectively, and incorporated into oligodeoxynucleotide decamers. The 5-[(benzyloxy)methyl]-nucleoside building blocks T-bo(d) and C-bom(d) (bo = benzyloxy, bom = (benzyloxy)methyl) - shape analogs of the naturally occurring glucosylated nucleosides 1 and 2 (see Fig. 1) - lead to weaker binding affinities of oligodeoxynucleotides pairing to DNA as well as RNA complements. The modification is more destabilizing in the case of T-bo(d) than C-bom(d). Analysis of the thermodynamics of duplex formation shows that T-bo(d) and C-bom(d), incorporation leads to a smaller entropy change in duplex formation that is, however, overcompensated by a less Favorable enthalpy term. Molecular-modeling studies suggest that the benzyl groups reside in the major groove which would explain the improved pairing entropy as a result of the exclusion of ordered H2O.