Plavec J, Fabre-Buet V, Uteza V, Grouiller A, Chattopadhyaya J
Department of Bioorganic Chemistry, University of Uppsala, Sweden.
J Biochem Biophys Methods. 1993 Jul;26(4):317-34. doi: 10.1016/0165-022x(93)90033-k.
Solution structures of 1-(beta-D-psicofuranosyl)thymine (HMT) (5) and 1-(1'-cyano-beta-D-ribofuranosyl)-thymine (CNT) (6) based on 3JH,H coupling constants (1H-NMR at 500 MHz) and nOe enhancement studies were further refined by molecular mechanics calculations using the AMBER force field. These complementary NMR-molecular mechanics studies helped us to define the torsion angles inside the NMR-defined conformational hyperspace. Atom-centered monopole charges were derived for molecular mechanics calculations by fitting the molecular electrostatic potential on freely optimized geometries of 5 and 6 using HF/3-21G level of theory by GAUSSIAN 92 program. The conformation of 5 and 6 can be summarized as follows: (i) the pseudorotational analyses showed that the North conformer is predominant in both 5 (> 70%) and 6 (97%). While the molecular mechanics could correctly predict the energetic preference of North over South type puckered sugar moiety for 5 and 6 it could not provide any clue to the fact that the 1'-CN group in CNT (6) drives the pseudorotational equilibrium more effectively towards North than 1'-CH2OH in HMT (5). (ii). The NMR-observed preference of anti over syn conformation across the glycosyl bond in 5 and 6 was correctly shown by the energetic preference of anti conformers by approx. 10 kJ/mol. (iii) The populations of the staggered rotamers across C4'-C5' (gamma +, gamma t and gamma -) calculated from 3J4'5' and 3J4'5" coupling constants from NMR spectroscopy show that gamma + and gamma t rotamers are preferred. Molecular mechanics calculations are also in an excellent agreement here with the results of solution studies: in 5 gamma + and gamma t rotamers are equally populated and a small energy difference in potential energy is established, while in 6 the larger energy difference in potential energy is found which reflects a higher preference for gamma + rotamer in solution. The energetic preferences found among the lowest energy conformers of 5 (North-gamma +/gamma t-anti-epsilon t1) and 6 (North-gamma +/gamma t-anti) in molecular mechanics calculations are in an excellent agreement with the preferences of the major conformers found by NMR spectroscopy in solution.
基于3JH，H耦合常数（500 MHz下的1H-NMR）和nOe增强研究，1-（β-D-呋喃伪果糖基）胸腺嘧啶（HMT）（5）和1-（1'-氰基-β-D-呋喃核糖基）胸腺嘧啶（CNT）（6）的溶液结构通过使用AMBER力场的分子力学计算进一步优化。这些互补的NMR-分子力学研究帮助我们确定了NMR定义的构象超空间内的扭转角。通过使用GAUSSIAN 92程序在HF/3-21G理论水平上拟合5和6的自由优化几何结构上的分子静电势，得出用于分子力学计算的以原子为中心的单极电荷。5和6的构象可总结如下：（i）假旋转分析表明，在5（>70%）和6（97%）中，北构象异构体均占主导。虽然分子力学可以正确预测5和6中北型褶皱糖部分相对于南型在能量上的偏好，但它无法解释CNT（6）中的1'-CN基团比HMT（5）中的1'-CH2OH更有效地将假旋转平衡推向北这一事实。（ii）。5和6中通过NMR观察到的糖基键上反式构象优于顺式构象的偏好，在能量上反式构象异构体约10 kJ/mol的偏好中得到了正确体现。（iii）根据NMR光谱中的3J4'5'和3J4'5"耦合常数计算出的C4'-C5'（γ+、γt和γ-）上交错旋转异构体的丰度表明，γ+和γt旋转异构体更受青睐。分子力学计算在此处也与溶液研究结果非常吻合：在5中，γ+和γt旋转异构体的丰度相等，且势能存在小的能量差异，而在6中发现势能存在更大的能量差异，这反映出溶液中对γ+旋转异构体有更高的偏好。在分子力学计算中，5（北-γ+/γt-反式-εt1）和6（北-γ+/γt-反式）最低能量构象异构体之间发现的能量偏好与NMR光谱在溶液中发现的主要构象异构体的偏好非常吻合。
