Przybylski Jennifer L, Wetmore Stacey D
Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge Alberta T1K 3M4 Canada.
J Phys Chem B. 2009 May 7;113(18):6533-42. doi: 10.1021/jp810472q.
This study uses a variety of computational models and detailed, systematic potential energy surface scans to examine the hydrolysis of 2'-deoxyuridine. First, the unimolecular cleavage was studied using a model that only includes the nucleoside. Although comparison of experimental and (PCM-B3LYP/6-31+G(d)) calculated (Gibbs energy) barriers confirms that hydrolysis occurs via a fully dissociative (S(N)1) mechanism with a rate-limiting step of glycosidic bond dissociation, this model does not provide a complete picture of the hydrolysis mechanism. When the model is expanded to include one explicit water nucleophile, gas-phase optimizations are unable to model charge separation in the reaction intermediate, while optimizations that implicitly incorporate the effects of bulk solvent do not accurately model the second reaction step (nucleophilic attack following dissociation) due to insufficient (water) nucleophile activation and (uracil anion) leaving group stabilization. Further expansion of the model to include three explicit water molecules allows for discrete proton transfer from the water nucleophile to the uracil anion, and thereby generates smooth reaction surfaces for both the dissociative (S(N)1) and concerted (S(N)2) pathways. Furthermore, for the first time, this computational model for the uncatalyzed hydrolysis of the N-glycosidic bond in a nucleoside predicts that the dissociative mechanism is more favorable than the concerted pathway, which supports experimental findings. It is also found that although (implicit) solvent-phase single-point calculations on gas-phase geometries can yield similar energies to solvent-phase optimizations, the geometries can be very different and not all potential reaction routes can be fully characterized. Therefore, care must be taken when interpreting mechanistic information obtained from gas-phase structures. This work provides a template for generating other nucleoside or nucleotide hydrolysis models including those relevant to both uncatalyzed and enzyme-catalyzed reactions.
本研究使用了多种计算模型以及详细、系统的势能面扫描来研究2'-脱氧尿苷的水解反应。首先，使用仅包含核苷的模型研究了单分子裂解反应。尽管实验和（PCM-B3LYP/6-31+G(d)）计算的（吉布斯自由能）势垒比较证实水解反应通过完全解离（S(N)1）机制发生，且限速步骤为糖苷键解离，但该模型并未完整呈现水解机制。当模型扩展到包含一个明确的水亲核试剂时，气相优化无法模拟反应中间体中的电荷分离，而隐含纳入本体溶剂效应的优化由于（水）亲核试剂活化不足和（尿嘧啶阴离子）离去基团稳定性不够，无法准确模拟第二个反应步骤（解离后的亲核攻击）。将模型进一步扩展到包含三个明确的水分子时，允许水亲核试剂向尿嘧啶阴离子进行离散质子转移，从而为解离（S(N)1）和协同（S(N)2）途径生成平滑的反应表面。此外，该核苷中N-糖苷键无催化水解的计算模型首次预测解离机制比协同途径更有利，这与实验结果相符。研究还发现，尽管对气相几何结构进行（隐含）溶剂相单点计算可得到与溶剂相优化相似的能量，但几何结构可能差异很大，并非所有潜在反应途径都能得到充分表征。因此，在解释从气相结构获得的机理信息时必须谨慎。这项工作为生成其他核苷或核苷酸水解模型提供了模板，包括那些与无催化和酶催化反应相关的模型。
