5'-O-(tert-Butyldimethylsilyl)thymine 3'-O-(allyl-N,N-diisopropylphosphoramidite) | 183905-76-2

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 核苷和核苷酸类似物
• 英文名称: 5'-O-(tert-Butyldimethylsilyl)thymine 3'-O-(allyl-N,N-diisopropylphosphoramidite)
• 英文别名: 1-[(2R,4S,5R)-5-[[tert-butyl(dimethyl)silyl]oxymethyl]-4-[[di(propan-2-yl)amino]-prop-2-enoxyphosphanyl]oxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione
• CAS: 183905-76-2
• 化学式: C₂₅H₄₆N₃O₆PSi
• 分子量: 543.716
• InChiKey: KRIBXLJMMYOBMA-OSJMCWGYSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  5.09
• 重原子数：
  36
• 可旋转键数：
  13
• 环数：
  2.0
• sp3杂化的碳原子比例：
  0.76
• 拓扑面积：
  89.6
• 氢给体数：
  1
• 氢受体数：
  7

反应信息

• 作为反应物：
  描述：

  5'-O-(tert-Butyldimethylsilyl)thymine 3'-O-(allyl-N,N-diisopropylphosphoramidite) 在 RuCl2(1,3-dimesityl-imidazolidin-2-yl)(PCy3)(=CHPh) 、 四氮唑 、 叔丁基过氧化氢 作用下， 以 二氯甲烷 、 甲苯 、 乙腈 为溶剂， 反应 9.0h， 生成 1(R_P)-(2(R)-(tert-butyldimethylsilyl)oxymethyl-5(R)-(thymin-1-yl)tetrahydrofuran-3(S)-oxyl)-3(S)-(3(S)-(tert-butyldimethylsilyl)oxy-5(R)-(thymin-1-yl)tetrahydrofuran-2(S)-yl)-1-oxo-3,6-dihydro-2,7-dioxaphosphepine
  参考文献：
  名称：

  构象受限的环状磷酸三酯键合二核苷酸的合成及NMR研究

  摘要：

  合成了其中磷酸二酯键在环状磷酸三酯结构中构象受限的四个非对映异构二核苷酸。来自差向异构体5'- C-乙烯基胸苷衍生物，包含两个末端烯基部分的二核苷酸，是通过标准亚磷酰胺化学方法构建的，并用作闭环复分解（RCM）反应的底物。从而，获得并分离了在核苷间键中具有七个成员磷酸环的四个非对映异构二核苷酸，并通过先进的NMR研究结合受限的分子动力学（rMD）模拟阐明了它们的构型。发现七个成员环在天然核酸主链中提供一定程度的构象限制，并且发现四个二核苷酸之一有利于两个相邻的胸腺嘧啶部分之间的堆叠。

  DOI：

  10.1016/s0040-4020(01)01047-x
• 作为产物：
  描述：

  N,N,N',N'-四(1-甲基乙基)-二氨基亚磷酸 2-丙烯-1-基酯 、 5’-O-(叔丁基二甲基甲硅烷基)胸苷 在 四氮唑 、 二异丙胺 作用下， 以 乙腈 为溶剂， 反应 1.5h， 以95%的产率得到5'-O-(tert-Butyldimethylsilyl)thymine 3'-O-(allyl-N,N-diisopropylphosphoramidite)
  参考文献：
  名称：

  Deoxyadenosine and Thymidine Bases Held Proximal and Distal by Means of a Covalently-Linked Dimensional Analogue of dA·dT: Intramolecular vs Intermolecular Hydrogen Bonding¹

  摘要：

  Deoxyadenylic acid and deoxythymidilic acid have been attached to a covalently-linked cross section, (sic), on the same side (proximal) and on opposite sides (distal) by synthetic sequences involving various combined protection/deprotection steps. The structures in aqueous solution buffered at pH 7.0 have been examined by 2D-NOESY NMR spectroscopy. The covalently-linked cross section provides a template that stabilizes dA . dT base pairing in the proximal isomer at 2 degrees C. In the distal isomer, it contributes to favorable conformations for intermolecular association.

  DOI：

  10.1021/ja9618255

文献信息

• Covalently Cross-Linked Watson-Crick Base Pair Models
  作者：Xiaoxin Qiao、Yoshito Kishi

  DOI：10.1002/(sici)1521-3773(19990401)38:7<928::aid-anie928>3.0.co;2-o

  日期：1999.4.1

  Structural characteristics of Watson-Crick hydrogen-bonded base pairs are displayed by methylene-bridged base pairs of type A. The shown superposition of the X-ray structure obtained for the base pair A (Rib1 =Et; Rib2 =Me) over that of a C-G base pair illustrates that A occupies an area similar to that occupied by a traditional Watson-Crick hydrogen-bonded base pair. Temperature-dependent 1 H NMR studies indicate that the energy barrier for rotation along its CH2 bridge is about 10 kcal mol-1 , and that it exists predominantly in one conformer at -70°C.
• Borsting, Philip; Sorensen, Anders M.; Nielsen, Poul, Synthesis, 2002, # 6, p. 797 - 801
  作者：Borsting, Philip、Sorensen, Anders M.、Nielsen, Poul

  DOI：——

  日期：——
• Synthesis of Conformationally Restricted Dinucleotides by Ring-Closing Metathesis
  作者：Anders M. Sørensen、Poul Nielsen

  DOI：10.1021/ol0067639

  日期：2000.12.1

  [GRAPHICS]The ring closing metathesis reaction has been used in the synthesis of conformationally restricted dinucleotides as well as a 3'-nucleotide analogue. From bis-allylic nucleoside phosphates obtained from simple nucleoside precursors, the synthesis of unsaturated cyclophosphates has been accomplished using either Grubbs' catalyst or an improved analogue. Hereby, the conformational freedom of the nucleic acid phosphordiester linkage has been efficiently constrained.
• Dinucleotides containing two allyl groups by combinations of allyl phosphotriesters, 5-allyl-, 2′-O-allyl- and 2′-arabino-O-allyl uridine derivatives as substrates for ring-closing metathesis
  作者：Philip Børsting、Morten Freitag、Poul Nielsen

  DOI：10.1016/j.tet.2004.09.023

  日期：2004.11

  Five different dinucleotides, each containing two allyl groups in various positions, were prepared and studied as substrates for ring-closing metathesis reactions. These dinucleotides were designed from appropriate nucleoside building blocks combining four different positions for the allyl group; the allyl phosphotriester linkage, 5-allyl-2' -deoxyuridine, and ribo- as well as arabino-configured 2'-O-allyluridine. Thus, convenient procedures for these building blocks were developed. From the dinucleotides, two new cyclic nucleotide structures were obtained; one connecting two adjacent nucleobase moieties and the other forming an unsaturated four-carbon linkage between the phosphate moiety and the adjacent pyrimidine nucleobase. The latter cyclic dinucleotide was also prepared with a saturated four-carbon linkage using a tandem ring-closing metathesis-hydrogenation procedure. This compound was found to be significantly more stable towards a nucleophilic ring-opening than its unsaturated counterpart. (C) 2004 Elsevier Ltd. All rights reserved.
• Methodology for the Synthesis of Dinucleoside Monophosphates Containing A 2′-Deoxy-3-Isoadenosine Unit: 3-iso-dApT and Tp(3-iso-dA)
  作者：Nelson J. Leonard †、Neelima

  DOI：10.1080/07328319608002437

  日期：1996.7

  2'-Deoxy-3-isoadenylyl(3'-5')thymidine and thymidylyl-(3'-5')-2'-deoxy-3-isoadenosine have been synthesized by mild protection/deprotection methodology that circumvents facile N3-Cl' hydrolytic cleavage of the 2'-deoxy-3-isoadenosine moiety.