Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho Str, 03680, Kyiv, Ukraine.
J Mol Model. 2013 Oct;19(10):4223-37. doi: 10.1007/s00894-013-1880-2. Epub 2013 May 29.
Combining quantum-mechanical (QM) calculations with quantum theory of atoms in molecules (QTAIM) and using the methodology of sweeps of the energetic, electron-topological, geometric and polar parameters, which describe the course of the tautomerization along the intrinsic reaction coordinate (IRC), we showed for the first time that the biologically important A∙A base pair (Cs symmetry) formed by the amino and imino tautomers of adenine (A) tautomerizes via asynchronous concerted double proton transfer (DPT) through a transition state (TS), which is the A(+)∙A(-) zwitterion with the separated charge, with Cs symmetry. The nine key points, which can be considered as electron-topological "fingerprints" of the asynchronous concerted A∙A ↔A ∙A tautomerization process via the DPT, were detected and completely investigated along the IRC of the A∙A*↔A*∙A tautomerization. Based on the sweeps of the H-bond energies, it was found that intermolecular antiparallel N6Н⋯N6 (7.01 kcal mol(-1)) and N1H⋯N1 (6.88 kcal mol(-1)) H-bonds are significantly cooperative and mutually reinforce each other. It was shown for the first time that the A∙A ↔A ∙A tautomerization is assisted by the third C2H⋯HC2 dihydrogen bond (DHB), which, in contrast to the two others N6H⋯N6 and N1H⋯N1 H-bonds, exists within the IRC range from -2.92 to 2.92 Å. The DHB cooperatively strengthens, reaching its maximum energy 0.42 kcal mol(-1) at IRC = -0.52 Å and minimum energy 0.25 kcal mol(-1) at IRC = -2.92 Å, and is accompanied by strengthening of the two other aforementioned classical H-bonds. We established that the C2H⋯HC2 DHB completely satisfies the electron-topological criteria for H-bonding, in particular Bader's and all eight "two-molecule" Koch and Popelier's criteria. The positive value of the Grunenberg's compliance constant (5.203 Å/mdyn) at the TSA∙A ↔A ∙A proves that the C2H⋯HC2 DHB is a stabilizing interaction. NBO analysis predicts transfer of charge from σ(C2-H) bonding orbital to σ (H-C2) anti-bonding orbital; at this point, the stabilization energy E((2)) is equal to 0.19 kcal mol(-1) at the TSA∙A ↔A ∙A.
我们首次结合量子力学（QM）计算和原子在分子中的量子理论（QTAIM），并使用描述沿着内在反应坐标（IRC）的互变异构化过程的能量、电子拓扑、几何和极性参数的扫掠方法，表明由腺嘌呤（A）的氨基和亚氨基互变异构体形成的具有生物学重要意义的 A·A 碱基对（Cs 对称性）通过过渡态（TS）通过异步协同双质子转移（DPT）互变异构化，该过渡态是带分离电荷的 A(+)·A(-)两性离子，具有 Cs 对称性。沿着 A·A*↔A*·A 互变异构化的 IRC，检测到并完全研究了可以被认为是异步协同 A·A↔A·A 互变异构化过程的电子拓扑“指纹”的九个关键点。基于氢键能量的扫掠，发现分子间反平行 N6H···N6（7.01 kcal mol-1）和 N1H···N1（6.88 kcal mol-1）氢键具有显著的协同性，并相互加强。首次表明，A·A↔A·A 互变异构化是由第三个 C2H··HC2 氢键（DHB）辅助的，与另外两个 N6H···N6 和 N1H···N1 H 键不同，它存在于 IRC 范围内 -2.92 至 2.92 Å。DHB 协同增强，在 IRC = -0.52 Å 时达到最大能量 0.42 kcal mol-1，在 IRC = -2.92 Å 时达到最小能量 0.25 kcal mol-1，并伴随着另外两个上述经典氢键的增强。我们确定 C2H··HC2 DHB 完全满足氢键的电子拓扑标准，特别是 Bader 的和 Koch 和 Popelier 的所有八个“双分子”标准。在 TSA·A↔A·A 处，Grunenberg 顺应常数的正值（5.203 Å/mdyn）证明了 C2H··HC2 DHB 是一种稳定的相互作用。NBO 分析预测电荷从 σ(C2-H)成键轨道转移到 σ(H-C2)反键轨道；此时，在 TSA·A↔A·A 处，稳定能 E((2))等于 0.19 kcal mol-1。
