N-(2,5-dihydroxycyclopentyl)-2-(thymin-1-yl)acetamide | 611183-01-8

• 分子结构分类: 有机化合物 - 有机杂环化合物 - 二嗪类
• 英文名称: N-(2,5-dihydroxycyclopentyl)-2-(thymin-1-yl)acetamide
• 英文别名: N-[(2R,5R)-2,5-dihydroxycyclopentyl]-2-(5-methyl-2,4-dioxopyrimidin-1-yl)acetamide
• CAS: 611183-01-8
• 化学式: C₁₂H₁₇N₃O₅
• 分子量: 283.284
• InChiKey: NAGJCHNFVVQXIS-HTQZYQBOSA-N

物化性质

• 熔点：
  >210 °C (decomp)
• 密度：
  1.47±0.1 g/cm3(Predicted)

计算性质

• 辛醇/水分配系数(LogP)：
  -1.8
• 重原子数：
  20
• 可旋转键数：
  3
• 环数：
  2.0
• sp3杂化的碳原子比例：
  0.58
• 拓扑面积：
  119
• 氢给体数：
  4
• 氢受体数：
  5

反应信息

• 作为反应物：
  描述：

  N-(2,5-dihydroxycyclopentyl)-2-(thymin-1-yl)acetamide 在 吡啶 、 四丁基氟化铵 作用下， 以 四氢呋喃 、 二甲基亚砜 为溶剂， 生成 N-[(1S,2R,5R)-2-hydroxy-5-(9-phenylxanthen-9-yl)oxycyclopentyl]-2-(5-methyl-2,4-dioxopyrimidin-1-yl)acetamide
  参考文献：
  名称：

  Synthesis of a Cyclopentane Amide DNA Analogue and Its Base Pairing Properties

  摘要：

  cpa-DNA monomers containing the bases adenine and thymine have been synthesized starting from the known compound 1 in 12 steps. Partially and fully modified cpa-thymidine and cpa-adenosine containing oligodcoxynucleotides were synthesized by standard oligonucleotide chemistry. Fully modified homo-cpa-A sequences lead to duplex destabilization by -1.4degreesC/mod. relative to DNA. As its congener bca-DNA, cpa-DNA prefers left-handed duplex formation where possible.

  DOI：

  10.1081/ncn-120022837
• 作为产物：
  描述：

  (1α,2β,5α)-2-(tert-butyldimethylsilyloxy)-6-oxabicyclo<3.1.0>hexane 在 palladium on activated charcoal 吡啶 、 4-二甲氨基吡啶 、 氢氧化钾 、 phosphate buffer 、 pig liver esterase 、 四丁基氟化铵 、 氢气 、 sodium hydride 、 1-(3-二甲基氨基丙基)-3-乙基碳二亚胺 作用下， 以 四氢呋喃 、 乙醇 、 水 、 N,N-二甲基甲酰胺 、 甲苯 为溶剂， 20.0~95.0 ℃ 、1.01 MPa 条件下， 反应 29.0h， 生成 N-(2,5-dihydroxycyclopentyl)-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