Cytidin

• 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: Cytidin
• 英文别名: N⁴,N⁴,O^2'_,O3'_,O5'-pentadeuterio-cytidine；N-deuterio-2-deuteriooxy-1-[(2R,3R,4S,5R)-3,4-dideuteriooxy-5-(deuteriooxymethyl)oxolan-2-yl]pyrimidin-4-imine
• 化学式: C₉H₁₃N₃O₅
• 分子量: 248.18
• InChiKey: UHDGCWIWMRVCDJ-ROGKNSEASA-N

计算性质

• 辛醇/水分配系数(LogP)：
  -1.4
• 重原子数：
  17
• 可旋转键数：
  2
• 环数：
  2.0
• sp3杂化的碳原子比例：
  0.56
• 拓扑面积：
  130
• 氢给体数：
  5
• 氢受体数：
  6

反应信息

• 作为产物：
  描述：

  胞苷 在 重水 作用下， 以 氘代甲醇-d 为溶剂， 生成 Cytidin
  参考文献：
  名称：

  嘧啶核苷及其盐类晶体中6CH⋯O5′之间短分子内非键接触性质的新观点

  摘要：

  摘要 在一些天然嘧啶核苷及其衍生物的结构描述中，6CH 基团与O5'氧之间的短分子内接触早已被提出。然而，这些相互作用的特征并没有完全解决。根据 X 射线研究，假设这些接触具有氢键的特征。然而，一段时间以来，人们对这种意见的有效性的怀疑越来越多。因此，我们已经开始详细调查以阐明这个问题。对胞苷 (Cyd)、乙炔胞苷 (ϵCyd) 及其盐酸盐、硝酸盐和磷酸二氢盐的研究基于 X 射线分析、红外光谱和通过 CNDO/2 方法计算的电子密度。对 8 种选定核苷的 IR 光谱进行详细比较检查，其中 4 种表明存在这种短接触的证据，证明相关接触不能具有分子内氢键的特征，而是具有排斥性。这一结论得到了参与短分子内接触的 6CH 伸缩振动吸收带的低色位移以及碳原子 6C 上电子密度的正值的支持。在所有研究化合物的晶体结构的相同投影的计算机图表的基础上，我们还试图找到导致短分子内排斥接触存在或不存在的因素，

  DOI：

  10.1016/0022-2860(92)80193-l

文献信息

• A new outlook on the nature of short intramolecular non-bonded contacts between 6CH⋯O5′ in the crystals of pyrimidine nucleosides and their salts
  作者：M.Danuta Bratek-Wiewiórowska、Magdalena Alejska、Joanna Sarzyńska、Karol Surma、Marek Figlerowicz、Maciej Wiewiórowski

  DOI：10.1016/0022-2860(92)80193-l

  日期：1992.12

  participating in short intramolecular contacts, as well as by the positive value of electron density on the carbon atom 6C. On the basis of computer diagrams of the same projectiobs for the crystal structures of all studied compounds, we also tried to find the factors responsible for the existence or absence of the short intramolecular repulsive contact, and to predict the effect of such a contact on the conformational

  摘要 在一些天然嘧啶核苷及其衍生物的结构描述中，6CH 基团与O5'氧之间的短分子内接触早已被提出。然而，这些相互作用的特征并没有完全解决。根据 X 射线研究，假设这些接触具有氢键的特征。然而，一段时间以来，人们对这种意见的有效性的怀疑越来越多。因此，我们已经开始详细调查以阐明这个问题。对胞苷 (Cyd)、乙炔胞苷 (ϵCyd) 及其盐酸盐、硝酸盐和磷酸二氢盐的研究基于 X 射线分析、红外光谱和通过 CNDO/2 方法计算的电子密度。对 8 种选定核苷的 IR 光谱进行详细比较检查，其中 4 种表明存在这种短接触的证据，证明相关接触不能具有分子内氢键的特征，而是具有排斥性。这一结论得到了参与短分子内接触的 6CH 伸缩振动吸收带的低色位移以及碳原子 6C 上电子密度的正值的支持。在所有研究化合物的晶体结构的相同投影的计算机图表的基础上，我们还试图找到导致短分子内排斥接触存在或不存在的因素，
• Ground State Properties of the Nucleic Acid Constituents Studied by Density Functional Calculations. 2. Comparison between Calculated and Experimental Vibrational Spectra of Uridine and Cytidine
  作者：Nicolas Leulliot、Mahmoud Ghomi、Hervé Jobic、Othman Bouloussa、Vladimir Baumruk、Christian Coulombeau

  DOI：10.1021/jp9921147

  日期：1999.12.1

  Vibrational spectra of two ribonucleosides containing pyrimidine bases, i.e., uridine and cytidine, were analyzed in the solid state at low temperature by neutron inelastic scattering (NIS) and in an aqueous solution at room temperature by Raman scattering and Fourier transform infrared absorption (FT-IR). Analysis of all these experimental spectra, measured on both native and deuterated (on labile hydrogens) species, allows a complete set of information on the vibrational modes arising from the base residues and ribose to be obtained. To interpret the vibrational spectra, a harmonic force field has been estimated for isolated ribonucleosides at the Hartree-Fock (HF) and density functional theory (DFT) levels. All these calculations have been performed by means of the Becke-Lee-Yang-Parr (B3LYP) local exchange and correlation functional (for DFT calculations) and the split valence basis sets, 631G(()*()), including nonstandard polarization functions on heavy atoms (for DFT and HF calculations). The lowest energy conformers of these ribonucleosides, i.e., C3'-endo/ anti and C2'-endo/anti have been used in the vibrational mode calculations, where C3'-endo and C2'-endo refer to the N-type and S-type ribose puckering, respectively, and anti designates the orientation of base with respect to the sugar. The absence of any imaginary frequencies in the vibrational calculations confirms that the optimized geometry of the ribonucleosides well corresponds to their local mimima. The addition of the zero-point vibrational energy (ZPVE) to the electronic energy does not, however, change the energy order of the conformers. In both ribonucleosides, the C3'-endo/anti conformer has a lower energy than the C2'-endo/ anti one. It has been shown that NIS intensities calculated at the DFT/B3LYP/631G(()*()) level account more accurately for the characteristics of the experimental spectra. Therefore, the assignment of the observed vibrational modes has been extensively discussed in this paper on the basis of the results calculated by means of the DFT method. On the other hand, comparison between observed and calculated NIS spectra of native and deuterated species can give insight on the effect of intermolecular hydrogen bonding in the solid phase. Finally, the calculated results seem to be able to interpret the Raman marker shifts observed upon the A-Z helix transitions of poly- and oligonucleotides (C3'-endo/anti to C2/-endo/anti conformational transition of the cytosine residue), as well as those related to the UUCG tetraloop hairpin, involving C2'-endo/anti uridine and cytidine residues found in the middle positions of this highly stable tetraloop.