N-[2-hydroxy-5-(9-phenylxanthen-9-yloxy)cyclopentyl]-2-(thymin-1-yl)acetamide | 611183-05-2

• 分子结构分类: 有机化合物 - 有机杂环化合物 - 苯并吡喃
• 英文名称: N-[2-hydroxy-5-(9-phenylxanthen-9-yloxy)cyclopentyl]-2-(thymin-1-yl)acetamide
• 英文别名: N-[(1R,2R,5R)-2-hydroxy-5-(9-phenylxanthen-9-yl)oxycyclopentyl]-2-(5-methyl-2,4-dioxopyrimidin-1-yl)acetamide
• CAS: 611183-05-2
• 化学式: C₃₁H₂₉N₃O₆
• 分子量: 539.588
• InChiKey: VWOUNVBUAAWIPF-KODFZCBSSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  3.1
• 重原子数：
  40
• 可旋转键数：
  6
• 环数：
  6.0
• sp3杂化的碳原子比例：
  0.26
• 拓扑面积：
  117
• 氢给体数：
  3
• 氢受体数：
  6

反应信息

• 作为反应物：
  描述：

  2-氰乙基N,N-二异丙基氯亚磷酰胺 、 N-[2-hydroxy-5-(9-phenylxanthen-9-yloxy)cyclopentyl]-2-(thymin-1-yl)acetamide 在 N,N-二异丙基乙胺 作用下， 以 四氢呋喃 为溶剂， 反应 1.0h， 以59%的产率得到(2-cyanoethyl)[1'-(2-(thymin-1-yl)acetylamino)-3'-(9-phenylxanthen-9-yloxy)cyclopent-2'-yl]-N,N-diisopropylphosphoramidite
  参考文献：
  名称：

  Synthesis of Cyclopentane Amide DNA (cpa-DNA) and Its Pairing Properties

  摘要：

  We recently reported on the synthesis and pairing properties of the DNA analogue bicyclo[3.2.1]-amide DNA (bca-DNA). In this analogue the nucleobases are attached via a linear, 4-bond amide-linker to a structurally preorganized sugar-phosphate backbone unit. To define the importance of the degree of structural rigidity of the bca-backbone unit on the pairing properties, we designed the structurally simpler cyclopentane amide DNA (cpa-DNA), in which the bicyclo[3.2.1]-scaffold was reduced to a cyclopentane unit while the base-linker was left unchanged. Here we present a synthetic route to the enantiomerically pure cpa-DNA monomers and the corresponding phosphoramidites containing the bases A and T, starting from a known, achiral precursor in 9 and 12 steps, respectively. Fully modified oligodeoxynucleotides were synthesized by standard solid-phase oligonucleotide chemistry, and their base-pairing properties with complementary oligonucleotides of the DNA-, RNA-, bca-DNA-, and cpa-DNA-backbones were assessed by UV melting curves and CD-spectroscopic methods. We found that cpa-oligoadenylates form duplexes with complementary DNA that are less stable by -2.7 degreesC/mod. compared to DNA. The corresponding cpa-oligothymidylates do not participate in complementary base-pairing with any of the investigated backbone systems except with its own (homo-duplex). As its congener bca-DNA, cpa-DNA seems to prefer left-handed helical duplex structures with DNA or with itself as indicated by the CD spectra.

  DOI：

  10.1021/jo034143q
• 作为产物：
  描述：

  2-aminocyclopentane-1,3-diol 在 吡啶 、 咪唑 、 四丁基氟化铵 、 1-(3-二甲基氨基丙基)-3-乙基碳二亚胺 作用下， 以 四氢呋喃 、 二甲基亚砜 、 N,N-二甲基甲酰胺 为溶剂， 反应 23.0h， 生成 N-[2-hydroxy-5-(9-phenylxanthen-9-yloxy)cyclopentyl]-2-(thymin-1-yl)acetamide
  参考文献：
  名称：

  Synthesis of Cyclopentane Amide DNA (cpa-DNA) and Its Pairing Properties

  摘要：

  We recently reported on the synthesis and pairing properties of the DNA analogue bicyclo[3.2.1]-amide DNA (bca-DNA). In this analogue the nucleobases are attached via a linear, 4-bond amide-linker to a structurally preorganized sugar-phosphate backbone unit. To define the importance of the degree of structural rigidity of the bca-backbone unit on the pairing properties, we designed the structurally simpler cyclopentane amide DNA (cpa-DNA), in which the bicyclo[3.2.1]-scaffold was reduced to a cyclopentane unit while the base-linker was left unchanged. Here we present a synthetic route to the enantiomerically pure cpa-DNA monomers and the corresponding phosphoramidites containing the bases A and T, starting from a known, achiral precursor in 9 and 12 steps, respectively. Fully modified oligodeoxynucleotides were synthesized by standard solid-phase oligonucleotide chemistry, and their base-pairing properties with complementary oligonucleotides of the DNA-, RNA-, bca-DNA-, and cpa-DNA-backbones were assessed by UV melting curves and CD-spectroscopic methods. We found that cpa-oligoadenylates form duplexes with complementary DNA that are less stable by -2.7 degreesC/mod. compared to DNA. The corresponding cpa-oligothymidylates do not participate in complementary base-pairing with any of the investigated backbone systems except with its own (homo-duplex). As its congener bca-DNA, cpa-DNA seems to prefer left-handed helical duplex structures with DNA or with itself as indicated by the CD spectra.

  DOI：

  10.1021/jo034143q